>> I WOULD LIKE TO WELCOME
EVERYBODY BACK FOR DAY 2 OF OUR
NIH COMMON FUND SYMPOSIUM.
GLYCO INFORMATICS AT THE
INTERFACE OF DISEASE AND DATA.
WE HAVE STWO SESSIONS TODAY.
THE MORNING SESSION WILL BE
HOSTED BY MICHAEL PIERCE AND
GENERALLY ORGANIZED AROUND
CANCER GLYCO BIOLOGY WITH OTHER
IMPORTANT TOPICS THROWN IN AND
THEN THE SECOND SESSION THIS
AFTERNOON, CHAIRED BY NANCY
DAHMs, ON RARE DISEASES AND
INFORMATICS ASSOCIATED WITH
UNDERSTANDING RARE DISEASES.
I'M GOING TO TURN IT OVER TO
MICHAEL PIERCE TO INTRODUCE OUR
SPEAKERS FOR THE FIRST SESSION.
THANKS, MICHAEL.
>> THANKS, MIKE.
YEAH, SO I'M MICHAEL PIERCE,
UNIVERSITY OF GEORGIA AND IT'S
MY PLEASURE TO INTRODUCE OUR
FIRST SPEAKER IN OUR CANCER
GLYCO BIOLOGY SESSION, DR. AVERY
POSEY WHO WILL TELL US ABOUT
EXPLOITING TRUNCATED
O-GLYCOSYLATION IN TUMORS FOR
IMMUNOTHERAPY.
>> THANK YOU.
I WOULD LIKE TO THANK THE
ORGANIZERS FOR THE INVITATION TO
SPEAK HERE TODAY.
THE BULK OF MY LAB'S WORK
FOCUSES ON A SYNTHETIC IMMUNO
GLOBUE LYNN MOLECULE THAT
IS--IT'S AN ARTIFICIAL T-CELL
RECEPTOR AND IT UTILIZES
COMPONENTS OF 2 DIFFERENT
ADAPTIVE IMMUNE RELATED
MOLECULES OF T-CELL RECEPTOR, OR
PORTIONS OF THE T-CELL RECEPTOR
THAT ARE IMPORTANT FOR
ACTIVATING A T-CELL AND
VERITABLE DOMAINS FROM
MONOCLONAL ANTIBODIES AND THESE
WHEN COMBINED IN A KHIHIGH
MERRIC MOLECULE CAN REDIRECT
T-CELL ACTIVATION AND
SPECIFICITY TOWARDS THE ANTIGEN
THAT IS THE TARGET OF THAT
MONOCLONAL ANTIBODY THAT THE
EXTRA CELLULAR DOMAIN IS DERIVED
FROM.
IN THE FIRST GENERATIONS OF
THESE MOLECULES THIS WAS THE
FORMAT OF THOSE KHIHIGH MERRIC
ANTIGEN RECEPTORS AND THEY HAVE
THE BENEFIT OF BEING NONMHC
RESTRICTED AND SO THESE
MOLECULES CAN NOW BE TRANSFERRED
INTO T-CELLS REGARDLESS OF AN
INDIVIDUAL'S HLA AND IN ADDITION
THEY CAN OPERATE IN CD4 AND CD8
T-CELLS SIMILARLY REGARDLESS OF
WHAT THE COAL O RECEPTOR IS, CD4
OR CD8.
ANOTHER BENEFIT THAT I ALWAYS
LIKE TO POINT OUT TO MY CAR
T-CELL PEOPLE IS THAT ANTIBODIES
HAVE A BROADER REPERTOIRE OF THE
MOLECULES THEY CAN TARGET BEYOND
WHAT A T-CELL RECEPTOR CAN
TARGET, SO THESE CAN TARGET
PEPTIDES AND NUCLEIC ACIDS,
LIPIDS, CARBOHYDRATES,
PHOSPHORALATED TARGETS AS WELL
AS OTHER CHEMICALS.
MULTIPLE GENERATIONS OF THESE
MOLECULES HAVE NOW BEEN
DEVELOPED, EVOLVED OVER THE LAST
30 YEARS, INCLUDING THE
INCLUSION OF A CO-STIMLATTORY
DOMAIN INSISTS IN THIS MOLECULE
OR MULTIPLE STIMLATTORY DOMAINS
AND INCLUSION OF THESE MOLECULES
HAVE BEEN SHOWN TO ENHANCE THE
SURVIVAL OF CAR T-CELLS AND
PROLIFERATION AND AUGMENT
EFFECTOR FUNCTIONS.
WE GENERATE THESE NOW
COMMERCIALLY BUT ALSO
PRECLINICALLY USING VIRAL
VECTORS.
THESE T-CELLS, PROJECTION
NEURONS OR PIONS O CLONAL
T-CELLS FROM THE PATIENTS OR
NORMAL DONORS ARE TRANSDUCED AND
CODING IF THIS NEW MOLECULE
THAT'S BEEN EXPRESSED ON THE
SURFACE OF THOSE T-CELLS AND
DEPENDING ON THE SPECIFICITY OF
THE MONOCLONAL ANTIBODY FROM
WHICH THE SCFB WAS DERIVED, THE
T-CELLS ARE DIRECTED TOWARDS A
NEW TARGET AND IN THIS CASE, THE
SCHEMATIC CD19 AND USING
ANTICD19 CAR CONSTRUCT AND THAT
ILLICITS ACTIVATION OF THE
T-CELLS AND LEADS TO EFFECTOR
FUNCTIONS SUCH AS SIGNIFY
TOLL-LIKE RECEPTOR SIS AND
KILLING OF THE CD19 POSITIVE
CELLS, THERE ARE NOW 6 FDA
APPROVED CAR T-CELL THERAPY FIST
ARE THE TARGET CD19 AND 2 THAT
TARGET BCMA FOR THE TREATMENT OF
MULTIPLE MYELOMA.
THE FIRST PATIENT WHO WAS
TREATED WITH THESE TYPES OF
THERAPEUTICS, HIS DATA IS
PRESENTED BEFORE YOU ON THIS
SCREEN, 1 DAY BEFORE INFUSION,
LARGE NUMBER OF CIRCULATING CD19
POSITIVE B-CELLS IN THIS
INDIVIDUAL LEUKEMIC B-CELLS
MOSTLY, 1 MONTH AFTER INFUSION
OF THEIR T-CELLS, COMPLETE
ABLATION SHOWING THE POTENCY OF
THESE THERAPEUTICS, HOWEVER
THOSE DO COME WITH SOME RISK, SO
THERE'S AN INCREASE RISK OF
INFECTION OF PATIENTS WHO HAVE
EXPERIENCED B-CELL PLASSIA DUE
TO TREATMENT WITH THESE KINDS OF
CAR T-CELLS INCLUDING VIRAL
INFECTION, SOME OF WHICH CAN BE
SEVERE, LIFE THREATENING OR EVEN
FATAL.
IN ADDITION WE KNOW THAT WHILE
THESE T-CELLS MAY PERSIST FOR A
LONG TIME IN INDIVIDUALS LESS
SHOWN IN THE RED AND BLUE
TRIANGLES AND BLUE CIRCLES AND
CAN LEAD TO COMPLETE LOSS OF
B-CELLS SHOWN WITH THE BLUE
SQUARES OVER A DECADE, THIS WAS
REPORTED IN THE FIRST 2
INDIVIDUALS TREATED WHO ACHIEVED
A COMPLETE RESPONSE, OUR FIRST
PATIENT DID DIE OF COVID-19 LAST
YEAR AND I THINK THAT ALSO
POINTS TO A VULNERABILITY OF
TARGETING A MOLECULE THAT'S NOT
TUMOR SPECIFIC AND LASTLY, MY
LAB RECENTLY SHOWED THAT THERE'S
THE PRESENCE OF CD19 TRANSCRIPTS
AND PROTEIN O A SUBSET OF BRAIN
PERISIGHTS THAT MAY BE A
CONTRIBUTOR TO NEUROTOXICITY
RELATED TO THESE THERAPEUTICS
AND SO ALL OF THAT TAKEN INTO
CONSIDERATION, TELLS US THAT WE
STILL NEED TUMOR SPECIFIC
TARGETS FOR B-SELMA LIGNANCYS
FOR OTHER LEUKEMIAS AND WE KNOW
THAT WE NEED THESE 4 GLEEL CELLS
O BLASTOMA AND OTHER SOLID
TUMORS SO THAT TAKES ME TO THE
CRUX OF THIS PRESENTATION WHICH
IS HOW DO WE GET TOWARDS A TUMOR
SPECIFIC TARGET.
FIRST WE WERE INTERESTED IN HOW
TO GET TOWARDS A SOLID TUMOR
SPECIFIC TARGET BUT REALLY WE
STILL NEED THESE FOR HEME OOT O
POETIC MALLIGNANCYS AS WELL, SO
MY LAB IS INTERESTED IN THESE
WAYS SO WE CAN EXPLORE THE
DIFFERENTIATED GLYCOSYLATION
THAT OCCURS IN TUMORS IN THE
CONTEXT OF TUMOR ASSOCIATED
PROTEINS OR REALLY FAVORABLE
IMMUNOTHERAPY TARGETS FOR
TARGETING MORE SPECIFICALLY A
MALIGNANT CELL WHILE SPARING
NORMAL CELLS, SO WE FOCUS ON THE
GLYCANS, REALLY BECAUSE FOR US
THIS IS VERY SIMPLE, SO IT'S A
SIMPLE MONODISCIPLINARY
SACCHARIDE THAT WE KNOW THERE
ARE ANTIBODIES THAT CAN
ACCOMMODATE THE CARBOHYDRATE AS
WELL AS PROTEIN BACKBONE LEADING
TO MORE SPECIFIC TARGETING OF
THESE MOLECULES.
SO THE FIRST STORY I WANT TO
TELL YOU ABOUT IS WORK THAT
WE'VE DONE TO TRY TO UNDERSTAND
HOW THIS CHANGE IN GLYCOSYLATION
AFFECTS TUMOR GROWTH AS WELL AS
THE CONTRIBUTION OF THE IMMUNE
MICROENVIRONMENT AND THIS IS
WORK BY A NEW POST DOC IN MY LAB
DR. SHAWNA BROOKENS.
SO WE KNOW THIS IS EXPRESSED IN
MEAN EPITHELIAL TUMORS THAT IT
CAN BE QUITE UBIQUITOUS IN
EXPRESSION IN SOME TUMORS AND
NOT FOUND IN HEALTHY TUMORS.
WE ALSO KNOW THAT THE SUGARS
THAT I JUST POINTED OUT, THESE
TRUNCATED DPLI KAN--KANAS ARE
THE--GLYCANS ARE THE LIGANDS FOR
THE SUGAR BINDING RECEPTORS LIKE
THE SIGLECs, AND THESE ARE
PRESENT ON INNATE IMMUNE SEISS,
SOME ARE ON ADAPTIVE IMMUNE
CELLS, SOME LEAD AS LEPTIN LIKE
MACROPHAGE, AND LEPTIN WHICH
BINDS TO THE TN-ANTIGEN AND
BINDING OF THE TN-ANTIGEN BY
EXPRESSING NGL CAN LEAD TO'MUNE
O SUPPRESSIVE FUNCTION SO
SKEWING OF T-CELLS TO IL10
PRODUCING T-CELLS, MORE
IMMUNOSUPPRESSIVE, AS WELL AS
THIS HAS ALSO BEEN SHOWN FOR AN
IMPORTANT IRPT ACTION FOR GLYCO
PEPTIDES BY DENDRITIC CELLS AND
THIS IS ALSO THOUGHT TO BE
IMMUNOSUPPRESSIVE BECAUSE THE
DENDRITIC CELLS THAT EXPRESS NGL
ARE THOUGHT TO BE IMMATURE OR
TOLL-LIKE RECEPTORRER GENIC, SO
PRESENTATION OF THESE PEPTIDES
CAN LEAD TO A TOLL-LIKE RECEPTOR
RAISING IMMUNE RESPONSE WHICH IS
NOT WHAT WE WANT FOR ANTITUMOR
RESPONSE.
AND SO I ACTUALLY WILL SKIP THIS
SLIDE IN THE INTEREST OF TIME
BECAUSE I THINK THAT THIS CROWD
APPRECIATES HOW O-GLUE MARIOUS
COSCALCULATIONS CAN BE DISRUPTED
THROUGH COSMIC OR T-CELL SIPGHT
ACE ASK THAT CAN LEAD TO THE TN
ANTIGEN ORSILATION OF THAT FORM
[INDISCERNIBLE].
WE DO KNOW THAT LOSS OF COSMIC
DUE TO SILENCING IS A MAJOR
CONTRIBUTOR TO THE PRESENTATION
OF THE TN-ANTIGENOT CELL SURFACE
OR SIL-TN-AND THIS IS SHOWN BY A
GROUP IN COPENHAGEN, OF PATIENTS
WITH PANCREATIC CANCERS AND THIS
CAN BE A CONTRIBUTE TO DECREASED
EXPRESSION WITH BOTH THE
CHAPERON FOR THE SYNTHASE AND
THE T-SYNTHASE, ASK TNF ALPHA,
IL17 AND IL4 OR TGF BETA OR LPS
OR SEVERAL MICRORNAs HAVE BEEN
DEMONSTRATED TO DECREASE
EXPRESSION OF COSMIC AS WELL AS
T-SYNTHASE AND SO WE THINK THAT
AN EARLY INSULT, EARLY
INFLAMMATION CAN LEAD TO CHANGE
IN OGLYCOSYLATION THAT MAY BE
RELEVANT TO WOUND HEALING THAT
MACROPHAGES AND DENDRITIC CELLS
EXPRESSING NGL CAN COME INTO AN
INFLAMED TISSUE AND THAT LEADS
TO RESOLUTION OF THAT
INFLAMMATION BUT IN A TUMOR WITH
ONCO GENIC MUTATIONS AND
INCREASED PROLIFERATION, THIS
IMMUNE SUPPRESSION IS ACTUALLY
COULD YOU WANTER TO AN ANTITUMOR
RESPONSE AND WE DO KNOW THAT
FROM WORK FROM OTHERS IN THE
FIELD THAT IN DPLEEL BLASTOMA
AND LUIS LUNG CARCINOMA AND
COLORECTAL CANCER MODELS THAT
THE INVASION OF MGL POSITIVE
INNATE IMMUNE CELLS HAPPEN IN
TUMORS THAT EXPRESS THE
TN-ANTIGEN AND IF YOU DEPLETE
THOSE CELLS BOTH THE DENDRITIC
CELLS AND MACROPHAGESSA THE SAME
TIME IN THIS MODEL YOU DO
REDUCED TUMOR GROWTH WHEREAS
TN-POSITIVE DEPLETE TUMOR
GROWTH, IF YOU DEPLETE THE TN2
POSITIVE CELLS CAN YOU RESTORE
WILD TYPE GROWTH IN THOSE
TUMORS.
SO FOR OUR WORK, WE UTILIZED THE
KPC MODEL AND A PANCREATIC MODEL
THAT DEVELOPED SPONSPONTANEOUS
TUMOR.
THESE TUMORS HAVE BEEN SINGLE
CELL CLONED AND LIMITING
SOLUTION TO IDENTIFY TUMORS THAT
REPRODUCIBLY ROUGH ATOM DUCE A
T-CELL LOW OR T-CELL HIGH
MICROENVIRONMENT AND WE'VE
UTILIZED SOME OF THESE SINGLE
CELL CLONE LINES TO INVESTIGATE
HOW THE TN ANTIGEN PRESENT IN
THESE TYPES OF TUMORS MIGHT
CHANGE THE MICROENVIRONMENT BOTH
IN A T-CELL HIGH AND A T-CELL
LOW ENVIRONMENT.
SO MY POST DOC HAS KNOCKED OUT
COSMIC USING CRISPR/CAS 9, AND
LOOKING FOR THE TN ANTIGEN AND
THEN WE'VE DONE SOME EVALUATION
OF THEIR GROWTH.
INSHALLLY THE GROWTH DIFFERENCE
BECAME APPARENT THROUGH CHANGE
IN THE COLOR OF THE FEIGNILE RED
IN THE MEDIA A FEW CELLS, WHERE
THOSE CELLS THAT ARE TN POSITIVE
THAT ARE NOT COSMIC SEEM TO HAVE
INCREASED GLYCOLYTIC ACTIVITY,
THE IMMEDIATE COLLAR CHANGE IS
FASTEST, AND WE PLATE THE CELLS
AND MEASURED THEIR ADHERENCE
OVER TIME SO OVERALL STRATEGY 3
DAYS WE CAN SEE THERE'S AN
INCREASE PROLIFERATION INCREASED
GROWTH, OF THE CELLS THAT HAVE
COSMIC KNOCK OUT AND TNANTIGEN
EXPRESSION AND WE ALSO MEASURED
THIS IN AN WOUND HEALING ASSAY
WHERE WE DO A SCRATCH TO A
CONFLUENT PLATE AND WATCH THOSE
CELLS MIGRATE BACK TO FILL THAT
SCRATCH AND THOSE THAT HAVE A
KNOCK OUT OF COSMIC OF INCREASED
PROLIFERATION, INCREASED
MIGRATION, WE SEE THAT BOTH FOR
THE T-CELL LOW LINE AS WELLsA
T-CELL HIGH LINES, IT'S MORE
EXAGGERATED FOR THE T-CELL LOW
LINES AND WE'VE TAKEN THESE
PARENTAL AND COSMIC KNOCK OUT
CELL LINES OF WHICH WE HAVE 4
DIFFERENT CELL LINES THAT ARE
PARENTAL OR COSMIC KNOCK OUT AND
WE ARE CURRENTLY VALIDATING
THESE RESULTS WITH SOME OF THE
GENES THAT WERE OF INTEREST TO
US ARE INVOLVED IN MONOCYTE
RECRUITMENT AND DIFFERENTIATION,
LIKE IL34 AND LIFT ARE INVOLVED
IN EMT LIKE SNIWE 2 AND EMT, ARE
INVOLVED, WE ALSO SEE CHANGES IN
RESPONSE TO HYPOXIA, TNF ALPHA
SIGNALING WHICH WE THINK MIGHT
BE MODELING OR MIMICKING AN
INFLAMED ENVIRONMENT, BECAUSE WE
KNOCKED OUT COSMIC HE WE LOOKED
WHAT INFLAMMATION MIGHT BE
CONTRIBUTED TO THESE CELLS.
WE SEE CHANGES IN THE PPEAEVER
PATHWAY AND ALSO CHANGES IN
CHECK POINT DECREASED CHECK
POINT EXPRESSION SO THESE CELLS
ARE PROLIFERATING MORE AS WELL
AS CHANGES IN THE UNFOLDED
PROTEIN RESPONSE.
WE'VE INJECTED THESE TUMORS
INVIVO AND BLACK 6 MICE AND SEEN
THAT THERE'S INCREASED GROWTH OF
THE TN POSITIVE TUMORS BOTH BY
VOLUME AND WEIGHT.
IN ADDITION, WHEN WE EXTRACT THE
CD45 CELLS FROM A TUMOR, WE SEE
THERE ARE DIFFERENCES IN BOTH
THE T-CELLS THAT ACTUALLY
EFFECTOR AND MEMORY CD8 T-CELLS
AS WELL AS IN THE MYELOID CELLS
SO WE SEE THERE'S A DIFFERENCE
IN MONOSITTIC MDSCs, WE
REPRODUCIBLY SEE THIS IN
MULTIPLE TUMOR MODELS, WE ALSO
SEE A DIFFERENCE IN Foxp3
EXPRESSION SO TREGULATORY CELLS
AS WELL AS SOME DENDRITIC CELL
RETINAL LOCATIONIC CELLS, SO
WE'RE NOW MOVING TOWARD RNA
SINGLE CELL SEQUENCING TO
PROVIDE A SYNTHESIS OF WHAT ARE
CELL POPULATIONS PRESCRIBINGENT
WHO ARE THE INNATE IMMUNE CELLS
THAT ARE RESPONDING TO THIS
CHANGE IN GLYCOSYLATION, AND
THEN WITH HOPES WE COULD TARGET
THOSE CELLS ARE RESOLUTION OF
INCREASED TUMOR GROWTH.
SO THOSE, WHAT I JUDGE UTV
EXPLAINED TO YOU ARE APPROACHES
HERE THAT WE PLAN TO TAKE NEXT
STEPS.
AND THEN ON THE OTHER SIDE OF
THE STORY WE WORKED ON DIFFERENT
THERAPEUTICS THAT TARGETED TUMOR
ASSOCIATED ANTIGENS OR IMMUNE OR
THERAPY TARGETS USING
CAR-T-CELLS BUT I WON'T DISCUSS
THAT BUT IT WAS TARGETING TNF 1
AND WE DEMONSTRATE THAD A
SIGNALING DIFFERENCE IN THOSE
KHIHIGH MERRIC RECEPTORS COULD
ENHANCE THE CO STIMULATION OF
THESE CAR T-CELLS AND LEAD TO
ENHANCED PERSISTENCE AND WE MOVE
THIS TO A CLINICAL TRIAL.
OUR SECOND VERSION OF THIS
TARGETS FIBER NECTIN AND THIS
WAS VERY NOSTALGIC FOR US
BECAUSE WE WERE INTERESTED IN
ANTIBODIES THAT TARGET THE TN
ANTIGEN OF GLYCO PROTEINS, THE
FIRST KNOWN ANTIBODY OF THIS
CLASS IS CALLED FDC6 IT WAS
DEVELOPED IN THE 80S AT FRED
HUTCH AND [INDISCERNIBLE] AND IT
WAS SHOWN TO BE TUMOR SPECIFIC
THAT IT COULD RECOGNIZE A
SPECIFIC GLYCO FORM OF FIBER
NECTIN, NOT PRESENT IN NORMAL
PLASMA FIBER NECTIN AND ADULT
SKIN, CONNECTED TISSUE, LARGE
INTESTINE AND COULD BE
IDENTIFIED IN FIBER BLASTS AS
WELL AS IN TUMOR CELL LINES THAT
THIS ANTIBODY COULD RECOGNIZE
ORAL CARCINOMAS BUT NOT NORMAL
ORAL MUCOSAL OR EVEN
PREMALIGNANT LESIONS AND WHEN
ISOLATED FROM NORMAL FIBER
NECTIN THAT ONLY THIS FIBER
NECTIN WAS SHOWN TO ENHANCE THE
ENT PHENOTYPES OF TUMOR CELLS
LIKE A549 LUNG CANCER CELLS THAT
ONLY THE ONCO-FIBER NECTIN COULD
DECREASE IN CADHERREN AND
INCREASE [INDISCERNIBLE] WHEREAS
NORMAL FIBER NECTIN COULD NOT
SUGGESTING THIS IS A RELEVANT
MOLECULE FOR TARGETING AND
INHIBITING TO DECREASE
METASTASIS, SO WE GENERATED CAR
T-CELL UTILIZING SCFB, WE ALSO
GENERATED CAR T-CELLS FOR A
FIBER NECTIN, A DEFICIENTLY
SPLICED DOMAIN BUT NOT A COSTLY
DOMAIN.
THEE SHOW THAT THESE CAR T-CELLS
COULD SECRETE INTERFERON GAMMA,
QUITE A LOT OF INTERFERON GAMMA
AGAINST PLOOF THATE CANCER TUMOR
CELLS AS WELL AS KILL THESE
CELLS ENVITROW, IF WE TESTED
THESE CAR T-CELLS AGAINST NORMAL
PROSTATE T-CELLS THEY HAVE NO
REACTIVITY, IF WE IMK OUT THE
AXON THAT HAS THE BGHPTY
EPITAUPE THAT IS RECOGNIZED BOO
I THIS ANTIBODY, THERE IS NO
SECRETION BY KILLING AS IF AS IF
WE KNOCKED OUT GALIN T6 AND THIS
IS SHOWN TO BE IMPORTANT FOR
MODIFYING THE BTHPGY EPITOPE.
INVIVO WE SEE THE SIMILARITY
TREND WHERE THESE T-CELLS ARE
QUITE POTENT AT REDUCING TUMOR
BURDEN IN MICE.
THE 5 D 5 CAR T-CELLS ARE JUST
AS GOOD, WE SEE A REBOWBD OF
TUMORS THAT WE'RE TARGETED BY
FIBER NECTIN TARGETING CAR
T-CELLS AND WE HAVE WO, TO DO TO
UNDERSTAND WHAT ARE THOSE
MECHANISMS OF ESCAPE.
WE SEE QUITE A LOT OF
INFILTRATION OF CAR T-CELLS
TARGETING FIBER NECTIN AS WELL
AS A CHANGE TO WHAT WE JUST
GENERALLY ARE CONSIDERING THE
CHANGE IN TUMOR TO MATE RICK
COMCISION, WE'RE INTERESTED IN
HOW CAR T-CELLS TARGETING FIBER
NECTIN MIGHT BE AFFAIRS TEAM
LEADERRERRING THE MATRIX, WE
KNOW FROM VALERIE WEAVERS WORK
AND OTHER WORK THAT COLLAGEN AND
FIBERS ARE DIFFERENTIALLY
ALIGNED IN TUMORS COMPARED TO
NORMAL TISSUE, WE'RE INTERESTED
IN WHETHER TARGETING FIBER
NECTIN, WE COULD POTENTIALLY
RESOLVE THOSE CHANGES IN THE
STROMA.
AND THEN LASTLY, WE WERE
INTERESTED IN HOW CAR T-CELLS
TARGETING EXTRA CELLULAR MATRIX
PROTEIN KILL 1 OF THOSE
MECHANISMS OF DEATH, THIS IS
DIFFERENT THAN HOW T-CELLS
NORMALLY TARGET THROUGH CELL
SURFACE MECHANISM, AND WE CAN
GET THAT THROUGH FAST
INTERACTIONS AND INTERFERON
GAMMA SIGNALING AND THESE ARE
PREVIOUSLY BEEN DEMONSTRATED TO
BE IMPORTANT FOR LOSS, IMPORTANT
MECHANISMS OF HOW CAR T-CELLS
HAD FOUND THAT IF YOU COMPLETELY
LOSE THE SENSITIVITY TO
INTERFERON GAMMA IN A TUMOR SO
LOSS OF INTERFERON GAMMA
RECEPTOR THAT OUR CAR T-CELLS
COULD NO LONGER KILL THEM AND SO
THIS WAS ACTUALLY RECENTLY
REPORTED BY 3 SEPARATE GROUPS,
SCIENCE IMMUNOLOGY, NATURE
COMMUNICATIONS AND THEN MOST
RECENTLY IN NATURE, WE ALSO
FOUND THAT IF YOU ADD A TLR 2 OR
TLR 6, TLR 26 OR 4 AGANIST, TO
THESE CO-CULTURES THAT YOU COULD
ACTUALLY SYNERGIZE AND OVERCOME
THIS DEFICIENCY IN KILLING SO
OUR WORK NOW IS TRYING TO
UNDERSTAND HOW WE CAN ENHANCE
THE KILLING OF CAR T-CELLS BY
INCORPORATING THESE SIGNALING
MECHANISMS INTO THE CAR OR INTO
THE T-CELL THEMSELVES WITHOUT
HAVING TO USE A TLR 4 AGANIST
WHICH IN WHICH CASE IS LPS WHICH
WE CANNOT USE IN PATIENTS.
AND SO, OUR SUMMARY IS THAT
WE'VE SHOWN THAT TRUNCATED
OGLYCOSYLATION CONTRIBUTES TO
ENHANCE TUMOR GROWTH IN T-CELLS
BUT THE GLOS COSALATION DOES
CHANGE THE MIKE O ENVIRONMENT
AND BY TARGETING THE T-CELLS WE
MAY BE ABLE TO NORMALIZE THE
IMMUNE MICROENVIRONMENT AND
DECREASE IMMUNO SUPPRESSION.
WE'VE ALSO SHOWN THE CAR T-CELLS
CAN TARGET EXTRA CELLULAR MATRIX
PROTEINS AND HERE WE'VE SHOWN AN
EXTRA CELLULAR MATRIX PROTEIN
THAT,A PEERS TO BE IMPORTANT FOR
EMT, THAT THESE CELLS ARE LYTIC,
THEY CAN KILL TUMOR CELLS
INVITRO AND INVIVO AND THEN, I
JUST WANT TO HARKEN BACK TO MY
FIRST INTRO AND TOP THAT TUMOR
SPECIFIC AGENTS ARENY NEEDED FOR
B-SELMA LIGNANCIES AND ALL OTHER
TUMORS THAT ARE USED IF ARE
IMMUNO THR ACTIVITIES AND
PROJECTSY LIKE BY SPECIFIC
ANTIBODIES IN CAR T-CELLS AND
WITH THAT I WILL SAY THANK YOU
TO MY LAB, COLLABORATORS AND
FUNDING.
I WILL TAKE ANY QUESTIONS YOU
MIGHT HAVE.
>> OKAY, WELL, THANK YOU AVERY,
THAT WAS REALLY FANTASTIC.
I THINK WE WILL HOLD QUESTIONS
UNTIL AFTER THE NEXT TALK.
DR. STACIE MALAKER, WAS
ORIGINALLY SCHEDULED FOR 10:40
AND SHE CAN'T BE WITH US TODAY
UNEXPECTEDLY.
SO WE WILL TAKE QUESTIONS
DR. PAPPROXIMATE OSEY IS
DR. HAENDALL, AFTER
DR. HAENDAL'S TALK, SO IF HAVE
YOU SPECIFIC QUESTIONS PLEASE
PUT THEM IN THE SEND LIVE
FEEDBACK AREA, IF YOU CLICK ON
THAT, YOU CAN TYPE IN YOUR
QUESTION AND THAT WILL BE
TRANSFERRED TO OUR CHAT AND WE
WILL BE LOOKING AT THOSE AFTER
DR. HAENDAL'S TALK, SO THANK YOU
AND I'M SURE THERE WILL BE VERY
INTERESTING QUESTIONS IN JUST A
FEW MINUTES.
SO DR. HAENDEL.
>> GOOD MORNING.
>> THERE YOU ARE, WELCOME.
SO THIS IS DR. MELISSA HAENDA
LUNIVERSITY OF COLORADO SCHOOL
OF MEDICINE SPEAKING ON WHY WE
NEED ALL THE ORGANISMS,
HARMONIZING PHENOTYPES AND GENO
TYPES AND DISEASES.
SO TAKE IT AWAY, THANK YOU.
ALL RIGHT TODAY I WILL TALK
ABOUT WHY WE NEED ALL THE
ORGANISMS, WHY WE NEED GENO
TYPES, PHENOTYPES AND DISEASES,
THIS IS WORK THAT'S LED BY THE
INTERNATIONAL CONSORTIUM AND
WE'RE DELIGHTED TO PRESENT THIS
WORK TO YOU TODAY.
SO FIRST OF ALL I JUDGE UTV
WANTED TO TALK ABOUT SOME
FOUNDATIONAL IDEAS THAT WILL
KIND OF BE A THEME THROUGHOUT
THE TALK.
SO THERE ARE A LOT OF YOU KNOW
NEEDS TO KIND OF COAALATE
KNOWLEDGE FROM AROUND THE WORLD
FROM DIFFERENT SOURCES, FROM
DIFFERENT ORGANISMS, FROM
DIFFERENT DOMAINS AND WE LIVE IN
THIS WORLD OF DISTRIBUTED DATA
ON THE LEFT SO IF WE'RE PUTTING
TOGETHER A PUZZLE, A BIOLOGY
KNOWLEDGE PUZZLE WE CAN HAVE
THIS ANALOGY OF PUTTING TOGETHER
THIS PUZZLE THAT IS THE BRIDGE
OF THE SAN FRANCISCO BAY.
AND WE CAN HAVE DIFFERENT RICH
HIGH QUALITY DATA ABOUT EACH
INDIVIDUAL ELEMENT SUCH AS
SPECIES SPECIFIC OR DID THEA
TYPE SPECIFIC RESOURCES.
WE CAN AGGREGATE THESE DATA AND
ESSENTIALLY IT'S EQUIVALENT TO
PUTTING THOSE PUZZLE PIECES ALL
IN A BOX.
AND THAT'S REALLY GREAT FOR A
LARGE SCALE INDEXING SO FOR
EXAMPLE, THE WAY IN WHICH GOOGLE
SEARCH WORKS, WE CAN SEARCH
BASED ON STRINGS AND FREQUENCY
OF SEARCHES AND SEARCH CO
OCCURRENCE AND THESE TYPES OF
THINGS, BUT THAT'S VERY
DIFFERENT THAN HAVING A FULLY
INTEGRATED DAILY BASIS THEA
ECOSYSTEM WHERE WE CAN ACTUALLY
PUT ALL THE PUZZLES DISPGHT BY
CAREFUL ALIGNMENT OF THESE
DIFFERENT DISTRIBUTED DAT
ARESOURCES, USING CONCEPTUAL
FRAMEWORKS AND CONSISTENT
IDENTIFIERS, WE CAN COME UP WITH
A BIG PICTURE VIEW, UNDERSTAND
WHERE THE GAPS ARE AND HAVE
CROSS DOMAIN INSIGHT BY BOTH
HUMANS AND MACHINES.
AND SO, FUNDAMENTALLY WHAT THE
MONARCH INITIATIVE AIMS TO DO IS
THAT LATTER, IS TAKE ALL THE
DIFFERENT KNOWLEDGE RESOURCES WE
HAVE AND BRING THEM TOGETHER
INTO A UNIFIED MANNER THAT WILL
ALLOW US TO GAIN NEW INSIGHTS.
SO SO MY EXAMPLE FOR TODAY IS A
LITTLE BIT OF HOW DO WE USE THE
DIAGNOSTIC FOR DATA.
SO MONARCH WAS FOUNDATION IF HOW
WE UNDERSTAND HOW WE USE
PHENOTYPIC INFORMATION TO
IMPROVE DIAGNOSTICS AND
PREVAILING CLINICAL DIAGNOSTIC
PIPELINES LEVERAGE ON ONLY A
TINY FRACTION OF THE POTENTIAL
DATA ABOUT AN INDIVIDUAL
PATIENT, AS WELL AS ITS
RELATIONSHIP TO POPULATION AND
COHORT LEVEL INFORMATION.
SO THAT INCLUDES PHENOTYPING,
BUT ALSO MANY OMICS, PHENOTYPES,
SOCIAL DETERMINANTS OF HEALTH,
ENVIRONMENTAL HEALTH AND
EXPOSURE, DISEASE SURVEILLANCE,
SURVEY INSTRUMENTS AND MANY
OTHER THINGS THAT WOULD HELP US
BETTER CREATE A PICTURE OF THE
INDIVIDUAL PATIENT AND IT'S
RELATIONSHIP TO THE POPULATION
OR COHORT WHICH IS REALLY
FUNDAMENTALLY THE GOAL OF
PRECISION MEDICINE.
SO THE MONARCH INITIATIVE
DEVELOPED A PHENOTYPE ONTOLOGY,
ABOUT 12 YEARS AGO.
IT'S NOW OVER 14,000 TERMS, THIS
ONTOLOGY IS REPRESENTED AS A
GRAPH.
AND THIS GRAPH HAS TERMS SUCH AS
HIPOSMIA OR DEEPLY SET EYES THAT
CAN BE EXPRESSED IN TERMS OF
LOGICAL INTERPRETATION IN
RELATION TO OTHER ONTOLOGYS, SO
FOR EXAMPLE, THE TERM HIPOSMA IS
REPRESENTED AS A LACK OFERER
ACCEPTION OF CELL USING THE
GENOME ONTOLOGY TERM WHICH AT
THE TIME I DID THIS QUERY HAD 34
ANNOTATIONS AND 22 SPECIES.
SO CREATING THIS
INTEROPERABILITY ACROSS
DIFFERENT CONTEXTS, SO THE HUMAN
PHENOTYPE IS USED TO DESCRIBE
THE ABNORMAL GENE FUNCTION
WHEREAS THE GENE ONTOLOGY IS
USED TO DESCRIBE THIS ABILITY
BUT WE HAVE THE ABILITY TO
EPITHELIAL GREAT DATA ACROSS
MANY DIFFERENT SPECIES
POTENTIALLY FOR HELP IN
DIAGNOSTICS AND MECH INFORM
DISCOVERY AND THE HPO IS NOW THE
DEFACTOR STANDARD FOR DESCRIBING
RARE DISEASE PATIENTS PHENOTYPES
FOR DIAGNOSTIC PURPOSES.
SO HERE'S AN EXAMPLE OF THAT, SO
THIS IS 2 CHILDREN WHO CAME INTO
THE SAME CLINIC WITHIN A FEW
WEEKS OF EACH OTHER, 1 WAS A 3
YEAR-OLD GIRL AND A 14 YEAR-OLD
BOY ON THE RIGHT.
AND IT'S IMPORTANT TO UNDERSTAND
HOW THIS WORKS AS AN EXAMPLE
EVEN THOUGH IT'S NOT GLYCO
BIOLOGY BUT I WILL GET TO THAT
IN A MINUTE.
THIS THESE THIS CASE, THOO 2
PATIENTS WERE NOT DIAGNOSEABLE
BASED ON THE WHOLE EXOME
SEQUENCING THAT WAS PERFORMED
AND IT WAS UNTIL THE CLINICAL
GENETICIST WENT THROUGH AND
CAPTURED THE CLINICAL GENOTYPE
IN GREEN ON THE LEFT AND
YELLOWOT RIGHT THEY WERE ABLE TO
DIAGNOSE THESE PATIENTS WITH
DIFFERENT VALID AND RELIABLE
YABTS IN THE SAME GENE, WHICH
TURNS OUT TO BE CAUSAL FOR
STIENER SYNDROME AND IT'S
INTERESTING TO NOTE THAT THESE
MATCHES ARE NOT EXACT.
SO WE'RE USING A GRAPH MECHANISM
THAT LOOKS TO FIND ALMOST OVER
8000 DISEASE PROTILES SHOWN IN
THE MIDDLE, WE LOOK FOR THE 1
THAT'S MOST SIMILAR TO THE
PHENOTYPIC FEATURES THAT ARE
DESCRIBED ABOUT THE PATIENT.
SO FOR EXAMPLE, THE LITTLE GIRL
HAS CONE SHAPED SYNTHESIS OF THE
FELL ANGIES OF THE HAND AND HAS
A SHORTER MAX TO THE FINGER NOW
A HUMAN CAN SEE THAT BUT WE NEED
TO MAKE THAT MORE FOR THE
MACHINE.
NOW CLINICALLY THAT'S NOT
ASSOCIATED AS MUCH AS YOU MIGHT
THINK BUT IN THE GRAPH, IT'S
ACTUALLY THESE ARE 2 SIBLING
TERMS IN THE GRAPH SO THEY'RE
QUITE CLOSELY RELATED BUT NOT
EXACT.
SO USING THIS ALGORITHM WE CAN
THEN, DENTIFY THE MOST SIMILAR
SET OF PHENOTYPIC FEATURES THAT
A DIFFERENT PATIENT HAS TO OUR
GOLD STANDARD PROFILES SUCH AS
WIDER AND STIENER SYNDROME SHOWN
IN THE MIDDLE.
SO THIS AN EXAMPLE OF HOW WE CAN
ACTUALLY IMPROVE DISEASE
DIAGNOSTICS WITH THE MOLECULAR
GLYCO PHENOTYPES.
SO THAL CASE WE'RE LOOKING AT
HOW USEFUL IS IT TO INCLUDE
GLYCO PHENOTYPES, WE TOOK 18 OF
THE MOST FREQUENTLY ASSOCIATED
PHENOTYPES WITH FUCOSIDOSIS, AND
THESE ARE COMPOSED OF A
SELECTION OF 16 OF THESE
PHENOTYPES.
AND THEN ESSENTIALLY THESE ARE
SHOWN AT THE BOTTOM, SO THOSE
ORANGE 1S ON THE LEFT.
SO WE BASICALLY LOOKED TO SEE
WHAT WAS THE SORT OF PERCENTAGE
OF A THOUSAND SIMULATED PROFILES
WHICH FUCOSIDOSIS IS CORRECTLY
MATCHED THAT IS RANKED NUMBER 1
IN THE PROFILE SIMILARITY
MATCHING ALGORITHM THAT I SHOWED
YOU ON THE PRIOR--ON THE PRIOR
SCREEN AND YOU CAN SEE THAT JUST
THE INCLUSION OF THOSE 2 GLYCO
PHENOTYPES REALLY GREATLY
IMPROVED THE DIAGNOSTIC
EFFICIENCY, SO THIS IS JUST A
VALIDATION OF WHAT WE ALREADY
KNEW THAT ESSENTIALLY BECAUSE
GLYCO PHENOTYPES ARE VERY
SPECIFIC AND NOT COMMONLY SEEN
ACROSS MANY DISEASES AT THAT
LEVEL OF GRANULARITY, THAT IS
DEEP IN THE GRAPH, THEY CAN BE
EXTRAORDINARILY HELPFUL IN A
DIAGNOSTIC SETTING.
SO I WANT TO TALK A LITTLE BIT
ABOUT WHAT IS THE MOST
CLINICALLY USEFUL WAY TO DEFINE
A GROUP OF DISEASES AND THE WORK
TO DEVELOP THE MONDO ONTOLOGY
WHICH IS A DISEASE ONTOLOGY THAT
UNITES A VARIETY OF DIFFERENT
DISEASE ONTOLOGY RESOURCES FOR
COMPLEX DISEASES, CANCER,
INFECTIOUS DISEASES, RARE
DISEASES, MENDELIAN DISEASES AND
WE REALLY NEEDED A SYSTEMATIC
WAY OF RELATING THESE IN ORDER
TO BE THE HANDLE FOR THOSE HPO
PROFILES I SHOWED EARLIER ACROSS
DIFFERENT SOURCES SO WHY NOT
JUST USE MAPPINGS ACROSS
SOURCES.
MANY PEOPLE MAP ACROSS
TERMINOLOGIES AND THE PROBLEM IS
THAT THOSE, THOSE MAPPINGS AND
TERMINOLOGIES ARE OFTEN MUTUALLY
INCONSISTENT, THEY CAN BE IN THE
SQUARED SET OF MAPPINGS, 1 TO 1
EQUIVALENCE AND FURTHER MORE
THEY'RE VERY OFTEN LACKS
PROVIDENCE IN DEFINING WHAT WAS
TRULY EQUIVALENT AND WHAT THOSE
CURATION RULES FOR THE MAPPINGS
REALLY WERE.
FURTHER MODEL CITIZENNER WHEN
YOU THINK ABOUT DISEASE ENDITYS
AS HANDLES, THEY'RE REALLY
HANDLES FOR ANNOTATIONS AGAINST
FOR DIFFERENT RELATIONSHIPS, AT
DIFFERENT LEVELS OF GRANULARITY
AND DIFFERENT CONTEXTS, USING
DIFFERENT VOCABULARIES, SO THIS
IS JUST A SMATTERING OF THE FEW
OF THE RESOURCES THAT WE
INTEGRATE WHEN WE THINK ABOUT
DISEASE, SUCH AS WEIDERMAN
STIENER SYNDROME, DIFFERENT
VARIANTS, DIFFERENT DISEASES TO
GENES TYPE, VARIANTS AND VAIRMT
ENVIRONMENTAL FACTORS SUCH AS
THOSE SHOWN ON THE RIGHT,
ANNOTATE BAR DISEASES TO
VARIANTS WHERE AS ONEM ANNOTATES
DECS TO GENES AND FENNISTERATION
O TYPES AND THEN THE COMPARATIVE
TOXIC O GENOMICS TO DISEASES TO
GENES AND ENVIRONMENTS.
SO EACH OF THESE DIFFERENT
RESOURCES CONTRIBUTES TO A
DIFFERENT ASPECT OF THE MODEL IN
THESE DISEASES SUCH AS WEIDERMAN
STIENER ISIN DROAM SO WE TRY TO
COAALATE ALL THOSE INTO A MODEL
TO INTEGRATE THESE DATA FOR
MECHANISTIC DISCOVERY AND
DIAGNOSTIC PURPOSES.
SO THIS IS JUST AN EXAMPLE OF
HOW THIS WORKS FOR FOR A GLYCO
PHENOTYPE.
I WAS TRYING TO FIND MY NOTES
HERE.
SO THIS IS A GRAPH
REPRESENTATION OF THE
DYSFUNCTIONAL COSMIC GENE WE
JUST HEARD ABOUT AND A MOLECULAR
CHAPERON FOR GLYCO TRANSFER ACE
AND WHAT WE CAN SEE IS THAT OVER
THERE ON THE LEFT, WE HAVE A
VARIETY OF DIFFERENT PHENOTYPES,
THAT ARE ASSOCIATED WITH A
VARIETY OF DIFFERENT DISEASES AS
INDICATED IN THE GREEN IN THE
SECOND FROM THE LEFT THAT MAY
HAVE IMPLICATIONS FOR GLYCO
TRANSFER ACE.
THERE'S THAT 1 DYSFUNCTIONAL
GENE IN ORANGE.
WE HAVE EPIGENETIC FAGHTORS SUCH
AS HYPER METHYLATION AND
FUNDAMENTALLY THAT GLYCO
PHENOTYPE IS AN ABNORMALITY OF
OGLYCANS WHICH ARE THE AFFECTED
BIOLOGICAL ENTITIES WHICH WE
ALSO KNOW MAY AFFECT GUT
MICROBIOME AND SO THIS KIND OF
SHOWS YOU JUST SORT OF HOW WE
WOULD NAVIGATE THE GRAPH THAT
WAS PUT TOGETHER IN TERMS OF
MODELING ON THE PRIOR SLIDE.
AND SO, WE CREATED MONDO TO
BASICALLY BRING TOGETHER ALL
THESE DIFFERENT DISEASE
RESOURCES SUCH AS OMICS AND CIT,
GUARD FOR RARE DISEASES, ET
CETERA USING AN ALGORITHM CALLED
KBOOM AND THIS WAS TO INITIALLY
SEE THE ONTOLOGY AND IT
BASICALLY USES A VARIETY OF
LOGICAL AND PROBABLISTIC
INFERENCE TO DETERMINE
EQUIVALENCES ACROSS THESE
DIFFERENT RESOURCES AND THEN A
CURATOR, YOU KNOW WE HAVE A
NUMBER OF CURATORS WHO GO
THROUGH THE LOW PROBABILITY OF
EQUIVALENCE, TO UNDERSTAND WHICH
ARE EQUIV LEAPT AND WHICH ARE
NOT.
SO WHAT WE FOUND IS THAT
ESSENTIALLY THERE'S A LOT OF
ERRORS IN RECONCILING THESE
DIFFERENT DISEASE RESOURCES
UMPIRES STREAM AND WE WORK WITH
EACH SOURCE TO TRY TO FRO
PROVIDE FEEDBACK TO EACH SOURCE
SO FOR EXAMPLE, WITH MESH WE
HAPPEN TO FIND THAT THERE WERE 2
BRANCHES OF MESH, 1 THAT WERE
EQUIVALENT BUT WERE DUPLICATED,
1 HAD ALPHANUMERIC NUMBERING
SYSTEM AND 1 HAD A ROMAN
NIEWMERAL MEMBERS, AND IT WAS
FED BACK TO MESH AND THEY
CORRECTED IT AND THOSE TERMS
HAVE BEEN MERGED IN MESH AND IN
MONDO.
AND SO THIS IS JUST AN EXAMPLE
OF HOWAN OITATIONS CAN WORK IN
CONTEXT.
SO THIS IS BASED ON GLUE MARIOUS
O BIOLOGY OR KEVI, SO THIS CAN
BE BOUND TO MOLECULES AND THE
FREE 1S CAN BE SACCHARIDES OR
DERIVATIVES AND SO HERE WE SHOW
12 DISEASES WITH NAMES ALONG
WITH THE MUTATED GENES AND THE
MONDO ID AND WHETHER THE
ACTIVITY IS INCREASED OR
DECREASE.
SO YOU CAN SEE JUST
UNDERSTANDING ALL THE DIFFERENT
DISEASE ENTITIES THAT ARE
ALIGNED OR ANNOTATED HERE WITH
DIFFERENT TYPES OF GLYCO
BIOLOGY, SO FOR EXAMPLE, HERE WE
HAVE GLYCO PROTEINS TO WORK WITH
THE RATHER FAMOUS
[INDISCERNIBLE] WHICH IS A
DECREASE IN N-DPLE 1 DEFICIENCY
AND YOU CAN SEE THE MONDO TERM
FOR THAT.
SIMILARLY HERE WE HAVE
NUCLEOTIDE SUGARS WHERE WE HAVE
HER EDUCATIONALITARY MYOPATHY
AND THAT'S AN INCREASE AND SO,
WE HAVE KIND OF A WAY OF SORT OF
VISUALIZING INCREASES IN GLYCAN
BY O SYNTHESIS AND DECREASES IN
GLYCAN DEGRADATION AND PROBLEMS
WITH GLYCAN TRANSPORTAN OITATED
ACROSS THIS GRAPH OF GLYCO
BIOLOGY SO WE CAN ALSO CAPTURE
THIS INFORMATION FROM VARIOUS
LAB TECHNIQUES SO FOR EXAMPLE,
WE HAVE DIFFERENT SAMPLES
COLLECTED FROM DIFFERENT
ANATOMICAL STRUCTURES SUCH AS
BLOOD, URINE, CEREBRAL
SPINAL--OR GLYCAN ANALYSIS, MASS
SPEC, GLYCO TRANSFER ACE,
ASSAYS, ET CETERA, AND THESE CAN
INFER THEN, GLYCO PHENOTYPES
SUCH AS REDUCED BLOOD, HEP A RIN
SULFATE CONITRATION, AND I
GLYCANS THESE ARE THE PHENOTYPES
WE WOULD USE FOR DESCRIBING
DISEASES THAT ARE ASSOCIATED
SUCH AS HEREDITARY OFTWOE
CONDROAMAS, AND SO CAN YOU KIND
OF SEE HOW WE RELATE THE
OUTCOMES OF GLYCO BIOLOGY ASSAYS
IN SPECIFIC ANATOMICAL CONTEXTS
TO THE GLYCO PHENOTYPES THAT ARE
THEN ASSOCIATED WITH THOSE MONDO
DISEASE.
SO KIND OF PUTTING TOGETHER THAT
WHOLE DISEASE MODEL THAT I
SHOWED EARLIER.
AND SO WHEN WE TRY TO DO THIS,
ACROSS THE MANY SOURCES OF
INFORMATION, SHOWN OVER ON THE
LEFT ARE MANY DIFFERENT SOURCES,
PUBLICATIONS, KEY HAVE KEVI, WE
HAVE GLYCO 2 KAN--KANA, WE HAVE
K, WE HAVE REACT OHM, WE HAVE
GLY CONNECT AND A VARIETY OF
OTHER SOURCES, WE CAN INTEGRATE
THOSE GLYKAN--KANA KNOWLEDGE
RELATED SOURCES USING SOME OF
THE MODELING TECHNIQUES I SHOWED
EARLIER, SUCH AS UNDERSTANDING
WHAT DPLI KAN--KANAS EXIST AND
THEIR DERIVATIVES AND WHAT
GLYCAN BINDINGS EXIST, WHAT
PRODUCTS ARE THERE AND HOW ARE
THESE ASSOCIATED TO DISEASES.
THOSE ARE ASSOCIATED VIA
SPECIFIC ONTOLOGYS AND
REPOSITORIES SUFFER FROM AS THE
GENE ONTOLOGY AND GLY-2
KAN--KANA, AND --CAN, AND THEN WE CAN
INTEGRATE ALL THIS IN DISEASE
DIAGNOSTICS AS I SHOWED EARLIER.
SO I WANT TO TALK ABOUT THE
CROSS SPECIES ASPECTS OF THIS,
SO AS YOU ALL KNOW, GLYCO
GIVING--YOUOLOGY AND WELL
CONSERVED ACROSS THE TREE OF
LIFE.
AND OTHER SPECIES AREN'T JUST
RELEVANT, EACH 1 HAS VERY UNIQUE
PHENOTYPES SO FOR EXAMPLE, NAKED
MOLE RATS DON'T GET CANCER,
ARMADILLOS ARE THE NATURAL HOST
OF LEPROSY, A MICROBACTERIUM
WHICH IS THE ONLY OTHER ORGANISM
THAT GETS LEPROSY BESIDES
HUMANS, AND TREE SHREWS ARE MORE
SIMILAR THAN MOUSE MODELS.
SO THIS IS DIFFERENT BIOLOGY
THAT WE MAY USE TO UNDERSTAND
THE DISEASE BETTER.
SO MODEL ORGANISMS MATTER TO
PATIENTS.
SO OVER HERE ON THE LEFT, WE
HAVE 19,201 CODING GENES IN THE
HUMAN GENOME AND APPROXIMATELILY
21% OF THOSE ARE ASSOCIATED WITH
A CAUSAL VARIATION THAT LEADS TO
A PHENOTYPIC OUTCOME.
IF WE TAKE THE ORTHOLOGS OF
THESE 19,201 GENES AND WE LOOK
AT THE 5 MOST COMMONLY UTILIZED
MODEL ORGANISMS SUCH AS YEEOF
THE, MOUSE, ELGANNAS, ZEBRA FISH
AND DROSOPHILA, AND WE LOOK AT
THE CURATED PHENOTYPES THAT IS
ABNORMAL TRAITS THAT BEEN
ATTRIBUTED TO THESE 19,201
ORTHOLOGS IN THESE SPECIES WE
HAVE 83% COVERAGE OF THE HUMAN
CODING GENOME AND IF WE COMBINE
THESE WE HAVE 84% OF THE HUMAN
COVERAGE CODING GENOME ANDEE
IT'S QUITE A LOT OF DATA THAT WE
MIGHT LEVERAGE GIVEN THE
CONSERVATION OF GLYCO BIOLOGY
ACROSS THE FIELD FUNCTIONS
LODGENY IF YOU LIKE.
SO THE INCLUSION OF JUST 5
SPECIES AND WE HAVE MANY, MANY
MORE IN THE RESOURCE BOOSTS
PHENOTYPIC COVERAGE OF GENES BY
63%.
SO THIS IS THE MONARCH KNOWLEDGE
GRAPH AND FOR THOSE WHO ARE MORE
TECHNICAL IN THE AUDIENCE, I
WANT TO PROVIDE THIS AS A
RESOURCE SO WE COLLECT DIFFERENT
INFORMATION ABOUT GENES
VARIANTS, MORPHOLOGY, MODEL
ORGANISMS, DISEASES, PHENOTYPES,
GENE FUNCTION, PROTEIN
INTERACTIONS AND EXPRESSION DATA
AND PATHWAYS FROM A VARIETY OF
DIFFERENT SOURCES SHOWN IN THE
MIDDLE SHOWING A VARIETY OF
DIFFERENT ONTOLOGIES AND
STANDARDS THAT CAN THEN ALL BE
LOADED INTO OUR KNOWLEDGE GRAPH
WHICH IS THE FUNDAMENTAL
RESOURCE THAT DRIVES OUR WEBSITE
AND OUR API SHOWN AT THE BOTTOM
FOR CROSS SPECIES QUERYING AND
INFERENCE AS WELL AS FOR
DIAGNOSTIC TOOLS.
THE GRAPH HAS 818,000 GENE
PHENOTYPE ASSOCIATIONS WITH OVER
9000 GENE-DISEASE ASSOCIATIONS
AND 30,000 NONCAUSAL
GENE-DISEASE ASSOCIATIONS FOR
MORE THAN 70 SPECSYS.
SO I WANTED TO JUST TO CLOSE OUR
CONVERSATION OFF TODAY TO BOLDLY
WHERE NO MAN, NO HUMAN, NO
ORGANISM HAS GONE BEFORE.
GLYCOBIOLOGY IS REALLY SOMETHING
THAT NEEDS TO BE THOUGHT ABOUT
IN A CROSS SPECIES MANNER AND WE
NEED TO LEVERAGE THE KNOWLEDGE
WE GAME FOR ALL THE ORGANISMS TO
HELP AND FOR OUR UNDERSTANDING
OF HUMAN DISEASE BIOLOGY, SIM
ABTIC DISEASE MORPHOLOGY IS 1
APPROACH AND 1 THING FROM A
TRANSLATIONAL CONTEXT IS IT
CONSIDERS THE PATIENT AS A
BIOLOGICAL SUBJECT THAT CAN BE
COMPARED TO THE DIFFERENT
ORGANISMSES THAT ARE'S DIFFERENT
THAN MOST CLINICAL SETTINGS
WHERE, YOU KNOW THE ELECTRONIC
HEALTH RECORD IS REALLY
GENERALLY VERY FOCUSED ON
CAPTURING FILLING AND CAPTURING
QUALITY OF CARE ISSUES AND NOT
NECESSARILY THE DATA WITH THE
GOAL OF THINKING ABOUT THE
PATIENT AS AN ORGANIZATIONS
ORGANISM.
PHENOTYPING ALL THE
ORGANIZATIONS INFORMS REALLY CAN
LEVERAGE THE DIVERSITY OF GENO
TYPE, PHENOTYPE OUTCOMES IN THE
DIFFERENT ORGANISMS FOR AGAIN
FOR INFERENCE IN OUR BEDDING OF
FLIEK O BIOLOGY, AND DATA
INTEGRATION ACROSS SOWSHESS AND
SPECIES IS ABSOLUTELY CRITICAL
FOR UNDERSTANDING FLIEK O
BIOLOGY GIVEN ITS CONSERVATION
ACROSS THE TREE OF LIFE.
I WANTED TO THANK A NUMBER OF
DIFFERENT PEOPLE, PETER
ROBINSON, CHRIS MUNGAL IN
PARTICULAR FOR THEIR PARTNERSHIP
OVER MANY YEARS IN CREATING THE
MONARCH INITIATIVE, I WOULD
ESPECIALLY LIKE TO THANK JB
GOURDINE, WHO LED THE LAB FOR
THE GLYCO BIOLOGY AND THE MONDO
ONTOLOGY.
I WANT TO THANK ALL OF THE MANY,
MANY RESOURCES THAT WE WELCOMER
WITH TO INTEGRATE THEIR DATA
THEY HAVE BEEN ABSOLUTELY
FUNDAMENTAL PARTNERS IN CREATING
THIS INTEGRATED RESOURCE AND
FINALLY OUR 3 MAJOR FUNDING
SOURCES FROM THE OFFICE OF THE
DIRECTOR AND NHGRI OR CENTER FOR
EXCELLENCE AND GENOME SCIENCES
IN OUR U24 FOR THE HUMAN
PHENOTYPE ONTOLOGY GRANT.
AND THANK YOU VERY MUCH.
>> OKAY, THANK YOU SO MUCH, MESS
MELISSA, THAT WAS REALLY
FASCINATING LET ME MENTION TO
EVERYONE, AGAIN, PLEASE SUBMIT
QUESTIONS USING THE LITTLE ICON
THAT SAYS SEND LIVE FEEDBACK AND
THOSE WILL COME UP IN OUR CHAT
AND I WILL LOOK AT THEM AS I
MENTIONED EARLIER IN CASE YOU
JOINED US A BIT LATE,
DR. MALAKER WILL NOT BE SPEAKING
THIS MORNING, WE WILL TAKE THE
OPPORTUNITY OF HER TIME TO ASK
QUESTIONS ABOUT THE FIRST 2
TALKS FROM DR. HAENDALL AND
DR. POSEY AND GO AHEAD AND SEND
QUESTIONS IN AND I WILL START
WITH THE FIRST QUESTION FROM
[INDISCERNIBLE].
FOR DR. POSEY, GREAT TALK.
IS IT KNOWN IF TN ANTIGEN
MODIFIED FIBER NECTIN HAS
ALTERED SENSITIVITY TO VARIOUS
MMPs?
>> THAT'S A GREAT QUESTION.
I ACTUALLY JUST SPENT SOME TIME
LOOKING FOR THE ANSWER TO THAT
AND IT DOESN'T APPEAR THAT THAT
HAS IS KNOWN.
I THINK THAT THE--I THINK THAT
THE NEW--WELL THE ANTIBODY THAT
WAS DEVELOPED IN 2012 THAT
TARGETS NORMAL FIBER NECTIN, AND
CAN ALLOW ISOLATION OF THESE 2
DIFFERENT GLYCO FORMS WILL BE
REALLY IMPORTANT IN THAT WORK,
BUT THAT DOESN'T APPEAR TO BE
KNOWN.
>> OKAY, THANK YOU.
THE NEXT QUESTION FROM SIRIAM
[INDISCERNIBLE], THE ISSUE YOU
RAISED IS THAT TARGETING ALL
CD19 WILL DEPLETE B-CELLS AND
THUS THIS IS NOT, IDEAL
APPROACH, DO YOU SEE SIMILAR
LIMITATIONS WITH TN ANTIGEN
WHICH IS REDUCED IN A NUMBER OF
TUMOR TYPES THAT IS TO SAY NOT
COMPLETELY SPECIFIC AND PERHAPS
ALSO EXPRESSED ON SOME NORMAL
TISSUES, REGULATING GUT AND
MICROBIOTA AS SHOWN BY
DR. HAENDAL FOR EXAMPLE.
>> YES FOR SPECIFICITY OF CAR
T-CELLS IS AN ISSUE THAT WE TEND
TO OVERCOME BY UTILIZING THE TN
ANTIGEN IN COMBINATION OF TUMOR
ASSOCIATED IMMUNOTHERAPY
TARGETS.
TO GATE DATE WE HAVE NOT SEEN
OFF TARGET EFFECTS OF THESE
TYPES OF T-CELLS AND WE MEASURED
THAT IN OUR ANIMAL MODELS WHICH
EXPRESSES PROTEINS IN THE TN 18
GENT IN TN FIBER NECTIN BUT THEY
DO AS MENTIONED IN THE PREVIOUS
TALK, THE GLYCOSYLATION IS
CONSERVED AMONGST MANY OF THESE
ORGANISMS INCLUDING MICE AND SO
WE DON'T SEE TARGETING OF TN
ANTIGEN IN THE MOUSE MODEL AND
IN TERMS OF CONTRIBUTING TO
TOXICITY IN THE MOUSE MODEL, WE
ALSO MEASURED THIS INVITRO WITH
NORMAL HUMAN PRIMARY CELLS,
DON'T SEE INCREASED TOXICITY
AGAINST NORMAL HUMAN PRIMARY
CELLS ENCLUEDING THOSE FROM THE
KIDNEY AND COLON AND IN ADDITION
WE HAVE TREATED 18 PATIENTS NOW
IN A CLINICAL TRIAL TARGETING
TNF 1 AND DON'T SEE SEVERE
TOXICITY IN THESE PATIENTSA
WELL.
SOPHISTICATEDY WE THINK THAT WE
ARE ON THE PATH TOWARDS
DEVELOPING SPECIFIC REAGENTS,
HOWEVER, I THINK THAT MULTIPLE
OF THESE WILL BE NECESSARY
BECAUSE TUMOR SPECIFIC TARGETS
ARE HETEROGEANIOUS AND THAT'S
JUST THE NATURE OF THE TUMOR.
>> OKAY.
THANKS AVERY, I WILL SWITCH OVER
TO MELISSA NOW, THERE'S A
QUESTION, BASED ON YOUR
RESEARCH, DO YOU HAVE ANY
RECOMMENDATIONS AND WHAT TYPES
OF DATA FROM THE GLYCO
INFORMATICS SPACE WOULD HELP
FILL SOME OF THE GAPS THAT YOU
MENTIONED?
>> THAT'S A GREAT QUESTION, IT'S
BASICALLY HOW CAN WE ALL WORK
TOGETHER TO BE MORE
INTEROPERABLE.
I DO THINK AND THIS IS A FEW
YEARS AGO WHEN JP WROTE THE
SURVEY PAPER OF WHAT EXISTS AND
WHAT RESOURCES AND I CAN PUT THE
LINK INTO THE CHAT THAT SOME OF
THOSE GAPS STILL EXIST AND YOU
KNOW I THINK THE 1 SLIDE THAT I
THOUGHT WAS MOST IMPORTANT TO
SHOW IS REALLY THAT ASSAY SLIDE,
SO THE WAY IN WHICH WE DESCRIBE
GLYCO BIOLOGY ASSAYS IN THE
LITERATURE IS NOT DESCRIBING IN
SUCH A WAY THAT IT'S EASY TO
NECESSARILY CURATE INDIVIDUAL
PHENOTYPES WITH INDIVIDUAL
PATIENTS IN TERMS OF COHORTS AND
SO THERE'S KIND OF MULTIPLE
PROBLEMS THERE, 1 IS YOU KNOW
SORT OF HOW DO WE CREATE
COMPUTABLE PHENOTYPIC
INFORMATION IN THESE STUDIES MOW
MATTER WHICH ORGANISM IT COMES
FROM, WHEN WE PUBLISHED BUT THEN
ALSO HOW DO WE UNDERSTAND A
VARIATION ACROSS INDIVIDUALS AND
I DIDN'T TALK ABOUT IT TODAY BUT
WE'VE, IN THE GLOBAL ALLIANCE
FOR GENOMICS AND HEALTH WE
DEVELOPED A NEW STANDARD CALLED
PHENOPACKETS WHICH AIMS TO BE
INDIVIDUAL CASE LEVEL
INFORMATION AND SO, 1 OF THE BIG
CHALLENGES THAT WE HAVE WITH THE
GLYCO BIOLOGY IS THAT WE SEE
QUITE A LARGE SPECTRUM, EVEN IN
THE SAME DISEASE DIAGNOSIS THAT
THE GLYCO PHENOTYPES ARE
ACTUALLY QUITE HETEROGEANIOUS
DEPENDING ON WHICH TYPE OF
PHENOTYPE WE TALKING ABOUT AND
SO WE REALLY NEED THAT CASE
LEVEL INFORMATION ABOUT EACH
PATIENT SO WE CAN UNDERSTAND THE
SORT OF EXPRESSIVITY AND
PHENOTYPES AND PENETRANTS ON AN
INDIVIDUAL CASE LEVEL, AND THAT
RARELY GETS PUBLISHED IN
LITERATURE, IT'S USUALLY SUMMARY
TABLES LIKE THE AVERAGE WAS THIS
LEVEL OF SOME GLYCAN AND WANOT
SO THATIA WHERE THE BIGGEST GAP
IS AND HOW EACH INDIVIDUAL
RESOURCE THEN CURATES THAT
INFORMATION IS ALSO DIFFERENT
AND SO IT SORT OF PROMULGATES
THAT SAME PROBLEM AND SO WHEN WE
HARMONIZE THAT KNOWLEDGE, WE--IT
ENDS TO NOT HAVE THE FULL
PROMINENCE OF WHAT THAT SUMMARY
LEVEL INFORMATION WAS FROM THE
LITERATURE IN THE FIRST PLACE,
NEVER MINDING THE FACT THAT IT'S
NOT AT A CASE LEVEL, SO TO ME
THAT'S WHERE THE BIGGEST GAP IS
THAT SORT OF INDIVIDUAL ASSAY
RESULTS THE PIPELINE ALL THE WAY
TO KNOWLEDGE BASIS.
>> OKAY, GREAT.
>> MAYBE JAMBOREE OF
[INDISCERNIBLE] CURATION IN THE
NEXT GLUE MARIOUS O CURATION
MEETING.
>> I WOULD BE DELIGHTED.
>> ALL RIGHT, THERE YOU GO,
MIKE.
>> WE NEED TO ORGANIZE THAT.
>> IN ITALY, OKAY?
NYES, DEFINITELY IN ITALY WITH
WINE.
>> ALL RIGHT, SO,.
>> SO THAT'S THE PLAN.
>> OKAY, ANOTHER QUESTION FOR
MICHELLE,.
>> MICHAEL CAN I FOLLOW UP
QUICKLY WITH MELISSA?
>> SURE.
>> SO MELISSA I APPRECIATE THE
CROSS SPECIES DISCUSSION THAT
YOU PUT FORWARD, AND YOU KNOW
THE CORE FUNCTIONS OF DPLI
KAN--KANAS ARE CONSERVED ACROSS
SPECIES BUT THE STRUCTURE THAT
DOES SOMETHING IN 1 SPECIES
MIGHT BE DIFFERENT TO GLYCAN
STRUCTURE FOR INSTANCE, URONIC
ACIDS MIGHT SUBSTITUTE FOR
SIALIC ACIDS SO THE GENES MIGHT
NOT BE THE LENGTH TO LINK
TOGETHER GLYKAN--KANA SPECIES SO
IS THERE AN OBVIOUS WAY TO MAKE
GLYKAN--KANA STRUCTURES ACROSS,
AND NOT STRUCTURALLY HOMOLOGOUS
STRUCTURES.
>> YES, I SEE WHAT YOU MEAN AND
I THINK, YOU KNOW WE
FUNDAMENTALLY HAVE MADE A LOT OF
PROGRESS ON GENES AND VARIANTS
BUT BOTH FOR THE GLYCO BIOLOGY
BUT ALSO FOR GENOMICS IN GENERAL
HAVE BOTH THE SAME KINDS OF
ISSUES, YOU KNOW SAME THING WITH
LIPID OMICS AND OTHER FUNCTIONS
THAT REALLY, YOU KNOW WE NEED TO
BE TARGETING, YOU KNOW PROTEOMIC
AND LIPID OMIC AND
GLYCO-PROFILES NOT VARIANT AND
PROFILES.
AND SO I THINK YOU'RE ABSOLUTELY
RIGHT.
ONE THING THAT WE HAVE DONE A
LOT OF WORK ON THAT'S HELPFUL,
IS JUST THE FOCUS ON THE
PHENOTYPIC ASPECTS AND THE
ASSAYS BECAUSE THOSE ARE, YOU
KNOW REALLY INDEPENDENT AND ALSO
THAT ALLOWS US TO TAKE INTO THE
INFLUENCES OF THE ENVIRONMENT
AND I ALSO DIDN'T TALK ABOUT
THAT TODAY BUT WE HAVE AN
ONTOLOGY CALLED ECTO WHICH
FOCUSES ON ENVIRONMENTAL
CONDITIONS WHICH ARE INFLUENCERS
IN THIS CONTEXT AS WELL SO YOU
NEED THE BIG PICTURE OF WHAT ARE
ALL THE SORT OF PRESSURES ON AN
ORGANISM TO HAVE THAT CHANGED
GLYCO-BIOLOGY AND THEN HOW DO WE
MEASURE THAT GLYCO BIOLOGY.
SO 1 OF THE THINGS THAT HAVE
BEEN GOOD IS THAT SORT OF
REPRESENTATION GRAPH THAT I
SHOWED YOU OF THE GLYCAN BIOLOGY
CAN THE DISEASES WITH THOSE
DIFFERENTITYS, THAT DOES NOT
REQUIRE ANY GENE OR VARIANT
LEVEL INFORMATION TO MAKE THOSE
ASSOCIATIONS.
SO SO IT DOES HELP US AND THAT
GLIE O BIOLOGY REPRESENTATION
HAS HAD--YOU KNOW J. P. DID AN
INNORMOUS AMOUNT OF WORK WITH
[INDISCERNIBLE], AND SINCE KEVI
IS FOUNDATION FOR GENE ONTOLOGY
AT LEAST WE HAVE A BETTER
REPRESENTATION OF HOW THAT FLIEK
O BIOLOGY WORKS WHERE WE DO HAVE
CONSENSUS IN WHICH TAXA IT
APPLIES TO SO YOU KNOW THESE ARE
ALL THESE THINGS NEED
IMPROVEMENT BUT THERE ARE WAYS
TO CREATE THOSE STRUCTURAL
ASSOCIATIONS THAT DON'T RELY ON
THE GENETICS BUT WE HAVE NOT YET
CREATED GLYCO PROTILES FOR THE
DIAGNOSTICS.
THIS WORK WAS KIND OF EARLY IN
TERMS OF ASSESSING THE UTILITY
OF INCLUDING THE GLYCO PHENOTYPE
BUT I COMPLETELY AGREE WITH YOU,
I THINK AS THIS FIELD MOVES
FORWARD INTO PRECISION MEDICINE
THAT WE NEED TO GO BEYOND JUST
PHENOTYPIC MATCHING BUT ACTUALLY
LIKE GLUE MARIOUS COBIOLOGY
MATCHING IN TERMS OF THE
STRUCTURAL SIMILARITIES SO I
LOVE THAT IDEA.
>> YEAH, THANK YOU FOR REALLY
THOROUGH ANSWER THERE AND THANK
YOU FOR SEEING THE EXPERIENCE OF
GLYCO BIOLOGY PHENOTYPES.
SO RELATED TO THIS, MICHELLE
VAUGHN ASKS DO YOU HAVE DATA
THAT'S COLLECTED OR CATALOGED
THAT WOULD PROVE THE DATA
INTEGRATION YOU DESCRIBE?
NTHAT'S A GOOD QUESTION AND A
FOLLOW UP TO THE EARLIER 1 THAT
I TALKED ABOUT WITH PHENOPACKETS
ALREADY, I THINK ANOTHER THING,
SO WOE HAVE BEEN ALSO AGAIN I
DIDN'T TALK ABOUT IT TODAY BUT
WORKING ON A DATA MODELING
LANGUAGE CALLED [INDISCERNIBLE]
WHICH BASICALLY HELPS STRUCTURE
SCHEMAS IN SUCH A WAY THAT DATA
FROM KNOWLEDGE BASES CAN BE MADE
INTEROPERABLE, THIS WAS ORIGE
NAWILLLY DEVELOPED AS PART OF
THE NCATS BIOMEDICAL DATA
TRANSLATOR AND THE MONARCH
KNOWLEDGE GRAPH BUT IT'S USED
FOR A WIDE VARIETY OF DIFFERENT
RESOURCES, NOW EVERYTHING FROM
MICROBIOMES TO CANCER--SO WE
HAVE AA CANCER MODEL.
WE USE IT FOR LANGUAGE
TRANSLATIONS AND ALL KINDS OF
DIFFERENT THINGS AND IT'S
BASICALLY A MECHANISM TO KIND OF
HAVE A FOUNDATION OF HOW WE
ASSOCIATE--SO WE HAVE ONTOLOGYS
AND WE HAVE DATA MODELS, AND IT
SEEMS LIKE WHEN WE'RE
INTEGRATING DATA, WE REALLY
FUNDAMENTALLY ARE CHALLENGED BY
THE FACT THAT EVEN PEOPLE ARE
USING THE SAME ONTOLOGYS, THEY
ARE USING THEM IN VERY, VERY
DIFFERENT WAYS, DIFFERENT
COLLECTIONS OF ENUMERATIONS FOR
A GNCHT DATABASE FIELD.
IT'S VERY HARD TO MAP ACROSS
RESOURCES THAT USE VERY
DIFFERENT MODELING STRATEGIES,
AND IT'S REALLY NOT BEEN A
STANDARD FOR RESEARCH LIKE WE
MIGHT HAVE FOR EHR DATA FOR OMOP
FOR EXAMPLE SO THAT STARTING TO
HELP US CREATE MORE BOARN
INTEROPERABLE DATA BUT THEN
FUNDAMENTALLY IF COMES COME--IT COMES
BACK TO THE JOURNALS, THAT
AREN'T APLAYED TO THE LITERATURE
AND SO MUCH OF OUR DATA
REGARDLESS OF WHICH OF THOSE
REPOSITORIES WE'RE TALKING ABOUT
IS CURATED FROM THE LITERATURE
SO GETTING JOURNALS TO ADOPT ANY
OF THESE STANDARDS, I THINK AS A
COMMUNITY LEVEL CHALLENGE THAT
WOULD HELP EVERYBODY CURATE
THEIR PIECES OF THAT SORT OF
PIECE MEAL DATA MODEL THAT WE'RE
TRYING TO CORRELATE.
>> GREAT.
THANK WE HAVE ANOTHER COUPLE
QUESTIONS.
THIS 1'S FOR DR. POSEY, CAN YOU
PROVIDE MORE INFORMATION ABOUT
HOW TRUNCATED OGLUE MARIOUS CANS
AFFECT THE CELLULAR
PROLIFERATION.
>> SO WE'RE DIGGING INTO OUR
RNASEQ DATA TRYING TO VALIDATE
THE JEEP CHANGES THAT WE SEE
BEFORE GOING MORE INTO WHICH
PROCESSES MAY BE ENHANCING TUMOR
GROWTH AS WELL AS CHANGE IN
IMMUNE CONTRIBUTIONS, IMMUNE
PLIEK ROUGH ATOM ENVIRONMENT,
BUT OTHER VS DEMONSTRATE THAD A
LOSS OF COSMIC INCREASE IN
TN ANTIGEN EXPRESSION, INDUCES
INKREETIONED MAP KINASE
SIGNALING AND THIS IS
PRESIEWBLABLY CAUSED BY A CHANGE
IN RECEPTOR AGGREGATION, CELL
SURFACE SIGNALING.
YOU CAN IMAGINE THAT
CARBOHYDRATES DEFINITELY ARE
INVOLVED IN RECEPTOR
INTERACTIONS, AND THAT BY
CHANGING THAT YOU AFFAIRS TEAM
LEADERRER THE SIGNALING, WE--YOU
ALTER THE SIGNALING AND WE
DEFINITELY CHANGES IN LOSS OF
GENES WHEN WE CHANGE CELL
SURFACE ON THE THE GLYCANS.
>> ONE OTHER QUESTION FROM
[INDISCERNIBLE]: DO YOU OFTEN
USE IMMUNE DEFICIENT OR IMMUNE
COMPETENT MOUSE MODEL FIST YOUR
XENOGRAPH STUDIES AND HOW
VARIABLE IS TUMOR UPTAKE AND
GLYCOSYLATION BETWEEN THESE 2
DIFFERENT MODELS?
>> YEAH, SO WE USE BOTH IMMUNE
COMP TEBT AND IMMUNO DEFICIENT
MODELS IF ARE OUR IMMUNE COMTENT
MODELS WE'RE USING MOUSE TUMOR
LINES AND REALLY TRYING TO
UNDERSTAND THE CONTRIBUTIONS TO
THE TUMOR MICROENVIRONMENT,
IMMUNE MICROENVIRONMENT, FOR THE
XENO GRAPH STUDIES WE'RE USING
HUMAN CELL LINES AND WE TEST OUR
HUMAN CAR T-CELLS AND WE'RE
PROBING FOR EFFICACY AS WELL AS
SOME TOXICITY OR TOXICOLOGY FOR
THE ANIMALS.
VARIABILITY AND UPTAKE, WE DON'T
SEE A DIFFERENCE IN UPTAKE OF
THE TUMORS IF WE HAVE EITHER
WILD TYPE DPLI COSALATION OR
WE'VE KNOCKED OUT COSMIC.
AND IN TERMS OF ANTIGEN LOSS, SO
WE--WE HAVEN'T SEEN ANTIGEN LOSS
FOR THE TARGETS THAT I TOLD I
ABOUT, THE TNF 1 OR THE TN FIBER
NECTIN, ALTHOUGH THE TN FIBER
NECTIN STORY IS EVOLVING SO
WE'RE TRYING TO UNDERSTAND HOW
TUMORS ARE ESCAPING THERE, FOR
A--A RELATED MOLECULE
[INDISCERNIBLE] AS A TARGET FOR
CAR T-CELLS WE DEFINITELY SEE
LOSS OF MESOTHELIN AS WELL AS
CAR T-CELL EXHAUSTION BUT FOR
THE EXHAUSTION WE ARE INTERESTED
IN WAYS OF AFFAIRS TEAM
LEADERRER THE SIGNALING OF THE
MOLECULES TO ENHANCE PERSISTENCE
OF CELLS AND OVERCOME
EXHAUSTION.
I THINK IT IS AN INTERESTING
QUESTION OF HOW CHANGES IN TUMOR
GLYCOSYLATION CAN PROMOTE OR
OVERCOME T-CELL EXHAUSTION AS
WELL.
>> SO AVERY ANY OF THE CLEANS
THAT YOU IDENTIFIED FOR THE
PANCREATIC CANCER SINGLE CELL
CLONES, WOULD YOU CALL ANY OF
THOSE CANCER STEM CELLS OR
OTHER--CAR T STRATEGIES THAT ARE
TRYING TO TARGET CANCER STEM
CELLS.
THERE ARE SO CD133 IS THOUGHT TO
BE A GOOD TARGET FOR CANCER STEM
CELL, ALTHOUGH YOU KNOW IT'S A
GLYCO FORM OF CS D133 THAT'S
ONLY RECOGNIZED BY THE MULTANI
ANTIBODY, NOT ALL--NOT ANY OF
THE OTHER CD133 ANTIBODIES THAT
HAS BEEN ASSOCIATE WIDE CANCER
[INDISCERNIBLE].
ALTHOUGH MANY IN THE FIELD ARE
RUNNING WITH ANTICD133 TARGETING
FOR--TO TARGET CANCER STEM CELLS
AS WELL AS I THINK A FEW OTHER
TARGETS AS WELL.
>> THANKS AVERY.
>> OKAY, WELL, THANKS TO BOTH OF
OUR SPEAKERS AND WHEN WE FINISH
THE REST OF THE TALKS, IF YOU
HAVE OTHER QUESTIONS FOR AVERY,
I THINK MELISSA IS GOING TO HAVE
TO LEAVE BUT GO AHEAD AND PUT
THOSE IN THE CHAT BOX AND WE
WILL GET TO THOSE A LITTLE BIT
LATER.
BOY THIS WENT BY REALLY QUICKLY,
SO, I THINK WE'RE READY FOR OUR
NEXT SPEAKER DR. RADOSLAV GOLD
MAN FROM GEORGETOWN UNIVERSITY,
HEP A RAN 6-0 ENDOSULF FAT AS IN
HNSCC AND OTHER CANCERS.
>> THANKS FOR THE INTRO.
NICE TO SEE EVERYBODY.
WELCOME TO THE MEETING, I AM
DPLAD I DON'T HAVE TO TALK ABOUT
[INDISCERNIBLE] AFTER STACIE AND
I AM SORRY YOU CANNOT HEAR HER.
SHE HAS REALLY EXCITING STORIES
TO TELL HER AND AT THE BEGINNING
OF UNIAND THAT COULD BE A GOOD
OPPORTUNITY FOR YOU TO CONNECT
WITH HER STORY.
I WILL--I WILL TELL BUT OUR
STUDIES ON 6-0 ENDOSULFATES IN
HEAD AND NECK CANCERS AND OTHER
MALIGNANCIES AND I HOPE YOU CAN
SEE MY SLIDES.
SO THIS IS A STORY THAT IS QUITE
SIMPLE.
>> RAJA J--RADO WE CAN'T SEE YOUR
SLIDES.
>> OKAY.
>> ALL WE SEE IS YOU.
>> THAT'S NOT BAD BUT I WILL TRY
TO MAKE IT EVEN BETTER.
I WILL TRY TO MAKE THE CASE AND
THEN TALK ABOUT HOW THEY'RE
IMPORTANT IN MANY DIFFERENT
CANCERS.
THE PEOPLE THAT DO CANCER WILL
BE IMMEDIATELY SKEPTICAL BECAUSE
CONNECTING 1 ENSIEM TO THE
ENTIRE CANCER FIELD IS A HIGH
BAR, EVEN THE P53 THAT WE HEAR
ABOUT FOR THE LAST 50 YEARS IS
CONNECTED TO MAYBE 50% OF THEM
AND SO, HOW IS THIS SO
IMPORTANT?
MAYBE 1 THING TO SAY IS 2
ENZYMES SO MAYBE I HAVE A BETTER
CHANCE GIVEN THAT, BUT THE SULFA
TAIS INHIBITORS ARE EXISTING IN
HUMAN AND 2 FORMS, SO THE SULF 1
AND 2, AND THEY ARE A CLASSIC
MEMBER OF THE SULFUR BASED
FAMILY OF ENZYMES THEY SHARE THE
SITE WITH THE OTHERS AND THEY
ARE DISTINGUISHED BY BEING THE
ONLY NEUTRAL PH ENDOSULFA TAIS
INHIBITORS, THEIR ACTIVITIES
OPTIMAL AND NEUTRAL PH AND THEY
ARE SECRETED ENZYMES, AND THEY
ACT IN THE EXTRA CELLULAR
ENVIRONMENT AS OPPOSE TO
MAJORITY OF THE OTHER SULFA TAIS
INHIBITORS WHICH ARE IS THE
LYSOSOMA AND THEY PARTICIPATE IN
DEGRADATION OF THE SULFATED
TARGETS.
THE ENDOSULFA TAIS INHIBITORS
DON'T DEGREAT THE POLYMERS, THEY
JUSTENT'RE END THE PATTERN, AND
THE SULFATION IS IMPORTANT AND
PROTEINS WITH THE H EP A RAN
SULFATE THE RTK LIGANDS AND
THEIR RECEPTORS, MANY PROYAISS,
MANY IMMUNE REGULATING MOLECULES
ARE SEQUESTERED ON THE HEP A RAN
SULFATES AND THE DISTRIBUTION,
REGULATION OF THEIR DISTRIBUTION
IS QUITE IMPORTANT.
THESE 2 ENZYMES ARE 65%
IDENTICAL AND YOU KNOW IF YOU
LOOK AT IF YOU LOOK AT KNOCK OUT
STUDIES, DOUBLE KNOCK OUT OF THE
SULF 2 IN MICE IS EMBRYONIC
LETHAL, NOT EXACTLY SO SOME OF
THE MICE GET BORN BUT MOST OF
THEM DIE NEAR BIRTH FROM
INABILITY TO SWALLOW.
AND IT'S INTERESTING TO NOTE
THAT THIS TOWBL KNOCK OUT
BASICALLY PREVENTS INNOVATION OF
THE ESOPHAGUS AND THE MICE
CANNOT SWALLOW.
SINGLE KNOCK OUTS ARE OKAY, THE
MICE SURVIVE SO THERE IS SOME
KIND OF ASSUMPTION THAT THE
ENSWRIMS MIGHT BE REDUNDANT AND
DO SIMILAR STUFF, BUT I WILL
MAKE THE CASE THAT MAYBE NOT THE
ONLY STORY.
AND RECENT STUDIES ACTUALLY
QUITE STRONGLY SUPPORT THE
IMPORTANCE OF ENZYME SO FOR
EXAMPLE, A STUDY THAT USED THE
SIMPLE ANTIBODIES
[INDISCERNIBLE] TO TREAT
COLOANGEALL CANCER IN A MOUSE
MODEL, SO THEY ARE INTERESTING,
WE STUMBLED ON THEM IN THE HEAD
AND NECK AND ON THE STUDY IS THE
LEFT SIDE, THE IMMUNO
HISTOCHEMIST RADIOY WILL SHOW
THAT YOU THE TUMOR TISSUES HAVE
QUITE NICE UPREGULATION OF THE
SULF 2 ENZYME COMPARED TO
ADJACENT NORMAL AND THAT
CORRELATES WITH THE KI-INCREASE
67 AND THE SAME AREAS OF THE
TUMORS THEN WE TRY TO MAKE AN
ADDITIONAL SENSE OUT OF THE
UPREGULATION OF THE ENZYMES IN
HEAD AND NECK TUMOR BASED ON ECG
DATA AND LOOKED AT ALL THE
ENZYMES THAT SYNTHESIZE THE
HEPATITIS EAR AN SULFATE
POLYMERS AND CHANGES IN HEAD AND
COMEK AND THE 1S THAT ARE MOST
CONSISTENTLY UPREGULATED IN THAT
DISEASE.
TOGETHER WITH SOME OF THE
EXTENSION ENZYMES THAT BUILD
LONGER AND HEPATITIS EAR AN
SULFATE CHANGES AND WHAT IS
DEFINITELY NOT INCREASED ARE THE
SULFUR TRANSFER ACES SO 1 CAN
SORT OF ASSUME THAT IN THE
CONTEXT OF HEAD AND NECK, WE
WILL BE BUILDING LONGER,
UNDERSULFATED POLYMERS OF HEP A
RAN AND WE THINK THAT IMPACTS
THE DISEASE PROGRESSION.
THE UPREGULATION HAPPENS NOT
ONLY IN THE LEVEL IN THE TCG
DATA BUT ALSO IN THE RECENT
CP TEX STUDIES, IT'S VERY CLEAR
THAT ARE UPREGULATED AND IT'S
ALSO THE CASE THAT WHAT IS
IMPACTED IS NOT JUST THE
EXPRESSION OF THE ENZYMES BUT
ALSO SURVIVAL OF THE PATIENTS.
SO, IF WE DO JOINT ANALYSIS OF
THE SULF 1 AND 2 IN THE
SCWAIMOUS CELL CARCINOMAS, YOU
SEE THOSE ARE POOR OUTCOMES,
THOSE ARE THE RED BARS AND THE
LOW, LOW ARE ASSOCIATED WITH
MUCH BETTER OUTCOMES INVARIABLY
FOR BOTH OF THE OVERALL
SURVIVALS AND THE PROGRESSION
FOR INTERVAL, IF WE BUILD A
MULTIVARIANT MODEL OF THE
SURVIVAL.
INCLUDING TUMOR STAGE, RADIATION
THERAPY AND OTHER IMPORTANT
FACTORS, YOU WILL SEE THAT
SOMETHING LIKE TUMOR STAGE IS
SIGNIFICANTLY ASSOCIATED WITH
OUTCOMES BUT INDEPENDENT OF
THAT, SULF 2 REMAINS AN
IMPORTANT FACTOR IN HEAD AND
NECK SURVIVAL.
BUT SULF 1 BECOMES
INSIGNIFICANT.
THIS IS AN INTERESTING
OBSERVATION BUT WHEN WE FURTHER
STUDY THE DATA, AND BREAK OUT
THE STUDY SETS INTO THE TUMORS
WHICH ARE EARLY STAGE AND LATE
STAGE WE NOTICE AN INTERESTING
PATTERN THERE.
THE SULF 1 ENZYME I AM NOT PACTS
SURVIVAL IN EARLY STAGE TUMORS
AND SULF 2 DOES NOT IMPACT THE
SURVIVAL AT THAT STAGE.
YOU CAN SEE IT ON THE HAZARD
RATIOS IN THE TABLE AND ON THE
LEFT-HAND SIDE, THE ENZYME
BECOMES IMPORTANT IN LATER STAGE
AND IT IS ACTUALLY MORE
IMPACTFUL OVERALL, MOSTLY
BECAUSE MOST OF THE TUMORS
REPRESENTED IN THOSE STUDY SETS
ARE ACTUALLY ADVANCED TUMORS, SO
THEY ARE THE 3-1 RATIO OF THE
LATE STAGE WHERE COMPARED TO THE
EARLY STAGE TUMORS AND WHAT YOU
ALSO CAN SEE ON THE GRAPH ON THE
RIGHT HAND SIDE IS THAT THE SULF
1 IS UPREGULATED AT AN EARLY
STAGE OF THE DISEASE.
SO, CONSISTENT WITH THAT, IT
ALSO IMPACTS SURVIVAL AT AN
EARLY STAGE.
SO NOW I WILL TURN A BIT TO THE
ENZYMES THEMSELVES AND HOW THEY
FUNCTION AND THE FIRST SLIDE IS
INTENDED TO SHOW YOU THE
COMMONALITIES BETWEEN THE 2
ENZYMES.
THE SCHEMATIC AT THE BOTTOM
SHOWS THE ORGANIZATION OF THAT
ENZYME, IT HAS A INTERIM
CATALYTIC DOMAIN, A HYDROPHILIC
DOMAIN AND A C-TERMINAL DOMAIN
WHICH ALSO IS IMPORTANT FOR
CATALYST.
THIS ARCHITECTURE IS CONSERVED
WITH THE SULF 1 AND 2 THE
ENZYMES ARE BOTH PROCESSED, THEY
ARE HEAVILY N-GLYCOSYLATED BY
INTERFER KNOW FOR SUBUNITS AND
THOSE SUBCOMMUNITIES REMAIN
LINKED BY DISCIPLINARY SULFIDES
IN 1 PIECE.
SO WHEN WE WORKED OUT THE
OVEREXPRESSION OF THE ENZYMES
YOU CAN SEE ALL THOSE CHANNELS
ON TOP, THAT THE FULL LENGTH
PROTEIN MIGRATES AS SOMETHING
AROUND 150 KILODALTONS, AND CAN
BE PURIFIED BY LEATHAL AFFINITY
THAT IS QUITE ABOUT WITH PURITY,
THAT OVEREXPRESSION SYSTEM IS
ACTUALLY A BREAK THROUGH FOR US,
WE STRUGGLED FOR A LONG TIME
WITH LOW ABUNDANCE OF THE
ENZYMES, THEY ARE ALL ABUNDANT
IN MOST OF THE CONTEXT OF HUMAN
BIOLOGY AND THEY DON'T EXPRESS
VERY WELL, PROBABLY BECAUSE OF
ALL THE BTMs THAT THEY'RE
ASSOCIATED WITH THEM AND THEY
EXPRESS QUITEENTIOUS FICIENT AND
WE GET MILLIGRAMS FROM THEM FROM
A HEX 293 SYSTEM PENSION SYSTEM
WITHULENTY VIRAL CONSTRUCTS.
THE STRUCTURE ON THE RIGHT HAND
SIDE POINTS OUT THAT THAT THE
MOLDLES OF THESE ENZYMES BUILT
BY ALPHA FOLD ARE VERY SIMILAR,
THEY ARE NOT CRYSTAL STRUCTURES
BUT ALPHA FOLD PREDICTS QUITE
SIMILAR IN THE CATALYTIC END AND
THIS PIECE OVER HERE IS THAT
CONSERVED DPLI SEEN RESIDUE IN
THE ACTIVE SITE WHICH IS
ESSENTIALLY FOR CATTAL SIS.
SO, SO FAR THEY ARE QUITE
SIMILAR TO ENZYMES AND THEY
MIGHT BE REDUNDANT.
BUT THE RECENT STUDIES ALSO
POINT OUT THAT WHEN YOU LOOK AT
THE [INDISCERNIBLE] AND THE
EXPRESSED PROTEINS YOU WILL
NOTICE THAT THE SULF 2 IS
ACTUALLY DISTINCTLY HIGHER
MOLECULAR WEIGHT THAN THE SULF
1.
AND IF YOU TREAT THAT WITH CHOND
REORGANIZATION OF THE
INSTITUTEIN, THE ENZYME SHIFTS
BY 50 KILO DALTONS TO A MASS OF
THE SULF 1 ENZYME.
AND IT WAS SHOWN BY A FRENCH
GROUP IN A VERY NICE RECENT
PAPER THAT ACTUALLY THIS ENZYME
IS A CHONT REORGANIZATION OF THE
INSTITUTEIN SULFATED MOLECULE
AND THAT IS SOMETHING THAT TOOK
20 YEARS TO DISCOVER.
I THINK THAT THAT'S ALSO RELATED
TO THE FACT THAT THE EXPRESSION
OF THOSE ENSWROIMS IS QUITE
TRICKY AND SO NOBODY NOTICED FOR
A LONG TIME THAT ACTUALLY THE
HEP A RAN SULFATE PROCESSING
ENZYME IS ITSELF A CHOND
REORGANIZATION OF THE
INSTITUTEIN SULFATED MOLECULE
AND SO THAT POINTS OUT THE
DIFFERENCES BETWEEN THE 2
ENZYMES AND HERE ARE THE
MOLECULES IN THE ALPHA FOLD
MODEL AND THE SCHEMATICS SHOW
THAT THE TERMINAL AGENTS
DISPLAYED IN RED, TOGETHER WITH
THE VERY C-TERMINAL PART, FORM
THE CATALYTIC ACTIVE DOMAIN AND
IN ADDITION TO THAT, THAT IS
THIS LARGELY DISORDERED
HYDRAULIC DOMAIN WHICH
PARTICIPATES IN THE CATALYST AS
WELL.
THE DATA AVAILABLE FROM FROM
[INDISCERNIBLE] GROUP AND HIS
[INDISCERNIBLE] THE FRENCH GROUP
AS WELL, ROMAN [INDISCERNIBLE]
IS THE PI THERE, SHOWED THAT THE
ENZYMES ARE PROCESSIVE BECAUSE
THEY MAKE MULTIPLE COMPLEX WITH
THE HEP A RAN SULFATE POLYMERS
THANKS TO INTERACTIONS MEDIATED
BY THE CATALYTIC DOMAIN, AT THE
SAME TIME THE HYDROPHILIC DOMAIN
ISSUESS, THE HYDROPHILIC DOMAINS
ARE MORE DIVERGENT AND THE
HYDROPHILIC DOMAIN ARE ALSO THE
SUGMENTORSHIP SKILL OF THE
SULFATE 2 PROTEIN WHICH IS
DECORATED BY THE CHOND
REORGANIZATION OF THE
INSTITUTEIN SULFATE CHAIN.
SO THANKS TO DIFFERENCE IN THESE
SPECIES THERE IS QUITE A BIT OF
DIFFERENCE IN SUBSTRATES.
AND THAT'S SOMETHING UNDER
INTENSE INVESTIGATION IN MY LAB
AND OTHER LABS, AND IT IS AT
THIS POINT UNKNOWN SO USING
SMALL MOLECULES AS A SUBSTRATE,
THE DIFFERENCES BETWEEN
[INDISCERNIBLE] ARE SUBTLE BUT
USING OTHER SUBSTRATES WE HOPE
TO DISTINGUISH THEIR ACTIVITIES
IN VITROW.
IN FACT WHAT IS QUITE
INTERESTING IS THAT THE
CHONDROITIN SULFATE MODULES
ACTIVITY HEAVILY AND IF YOU
REMOVE THE CHOND REORGANIZATION
OF THE INSTITUTEIN SULFATE THE
ACTIVITY OF THE ENZYME
INCREASES, NEARLY DOUBLES AND
SOOOSE NOT ONLY INTERESTING WHEN
IT'S MODIFIED BUT IT ALSO
IMPACTS FUNCTION.
WHAT WE DID NEXT IS TO DETERMINE
THE GLYCO FORMS OF THE SULF 1
AND 2 ENZYMES IN THE
OVEREXPRESSION SYSTEM AND
BECAUSE THE ENZYMES ARE 65%
IDENTICAL, 1 EXPECTS THAT THE IN
GLYCOSYLATION WOULD BE SIMILAR
AND THAT'S THE CASE, THE ONLY
DIFFERENCE WE NOTICE IS THAT THE
SEQUENCE AT THE N-TERMINUS 1 OF
THEM IS ASSOCIATED ONLY WITH
SULF 2 AND THAT 1 IS DECORATED
BY THE C-TERMINUS, AND THE OTHER
WOKNOW IS ON THE SULF 1 AND IT
IS NOT OCCUPIED UNDER SULF 2
OTHERWISE ALL THE OTHER SITES
ARE OCCUPIED AND THEY ARE
OCCUPIED BY SIMILAR STRUCTURES
IN TERMS OF IF SULF 2 COMPLEX
GLYCANS WITH AT THAT SITE OR
HIGH [INDISCERNIBLE].
SO THERE IS QUITE A BIT OF
SIMILARITY IN THAT BPN AND
THAT'S SUMMARIZED IN THIS
SCHEMATIC, YOU CAN SEE THAT MOST
OF THE NGLUE MARIOUS CANS SIT ON
THE KACCT THEA LYTIC DOMAIN AND
THERE IS NO INFORMATION SOINAR
IN TERMS OF IMMEDIATIFYING
CATALYTIC ACTIVITY DIRECTLY BUT
YOU KNOW THAT REMAINS TO BE
STUDIED.
WELL, IT'S QUITE CLEAR FROM THIS
IS DEPENDING ON WHICH CELL WILL
BE EXPRESSING THESE ENZYMES,
THEY WILL BE QUITE DIFFERENT.
THE GLYCOSYLATION IS CELL
DEPENDENT SO WHAT IS QUITE
INTERESTING IS ALSO TO LOOK AT
THE DISTRIBUTION OF THE
PRODUCTION OF THESE ENZYMES, IN
SINGLE CELL RNA SEQ DATA, THIS
DATA SET THAT I AM SHOWING YOU
IS RELATED TO THE HEAD AND NECK
CANCER, AND THE AUTHORS SHOW
THAT THE SULF 1 ENZYME DERIVES
PRIMARILY FROM FIBRO BLASTS
WHEREAS THE SULF 2 ENZYME IS
USED BY THE CANCER CELLS, AND
SOME OTHER CANCER CELL TYPES
INCLUDING THE FIBRO BLASTS AS
WELL, BUT IT'S QUITE STRIKING AS
YOU CAN SEE ON THE GRAPH ON THE
RIGHT HAND SIDE, THAT THE SULF 1
DERIVES ALMOST EXCLUSIVELY FROM
THE FIBRO BLAST CELLS AND THE
SULF 2 IS DOMINANT IN THE TUMOR
CELLS.
THIS IS SOMETHING THAT WAS
ACTUALLY NEVER DESCRIBED AND
MOST OF THE STUDIES THAT ANALYZE
THE SULF IN TUMORS SHOWS IT
IMPACTS TUMOR CELLS BUT THEN
THERE IS SOMEWHAT CONFUSING
LITERATURE AT SULF 1 IMPACT ON
THE CANCER CELLS WHICH IS IN MY
OPINION AND WE NEED TO DO
STUDIES WITH THE FIBRO BLASTS
ARE INCLUDED IN THE PICTURE.
WE DID CONFIRM THAT OBSERVATION
ACTUALLY BY INSITUE
HYBRIDIZATION STUDIES AND THIS
IS A HEAD AND NECK TUMOR AND
WHAT YOU CAN SEE IN GREEN IS ON
TUMOR CELLS AND NORMAL
EPITEALIA, THE REST OF THE SLIDE
IS SOME KIND OF STROMA AND ON
THE RIGHT HAND SIDE OF THAT
SLIDE, IS TUMOR WITH TUMOR
STROMA, WHERE THE SULF ENZYME IS
RICH.
YOU CAN SEE IT IN THE PINK OR
WHATEVER COLOR AND ON THE
LEFT-HAND SIDE, THESE ARE
STRUCTURES OF NORMAL GLANDS AND
IN THAT--IN THAT PART OF THE
SLIDE, THE SULF 1 IS NOT PRESENT
SO THAT'S THE CANCER ASSOCIATED
STROMA THAT IS RICH IN THOSE
CELLS.
AND IF YOU ZOOM INTO THAT SLIDE,
YOU START SEEING THE SULF 2
EXPRESSION AND THAT'S AGAIN
INSIGHTUE HYBRIDIZATION ON TOP
OF THE IMMUNO HISTOIN YELLOW AND
YOU SEE THOSE YELLOW DOTS MOSTLY
ON THE TUMOR BUT ALSO IN THE
STROMA NEXT TO THE SULF 1.
FROM THAT POINT OF VIEW, IT'S
QUITE INTERESTING TO LOOK AT THE
CORRELATION OF OTHER GENES WITH
THE SULF.
IN THE IN THE EXPRESSION HAD BY
MRNA OR PROTEOMICS, THERE IS A
SET OF GENES WHICH ARE STRONGLY
CORRELATED WITH THE SULF 1
ENZYME AND MUCH MORE WITH THE
SULF 2 ENZYME, THE CORRELATION
CO EFFICIENTS, FOR EACH POINT
AND WHAT TURNS OUT TO BE TRUE IS
THAT MOST OF THOSE ADDITIONAL
PROTEINS ARE HIGHLY CORRELATED
WITH SULF 1 COME FROM THE CANCER
ASSOCIATED FIBRO BLASTS, ALL
THESE PROTEINS LISTED IN THE
TABLE COME FROM [INDISCERNIBLE]
AND MANY OF THEM ARE HEP A RAN
SULFATE BINDING PROTEINS.
THIS IS STATISTICALLY
SIGNIFICANCE DIFFERENCE WHEN YOU
BUILD THOSE HISTOGRAMS OF
CORRELATION COENTIOUS FICIENTS
IN THE CAF GENES VERSUS ANY
OTHER GENE, YOU SEE THE SHIFT TO
THE MUCH HIGHER CORRELATION, AND
AND WHEN YOU LOOK AT EXPRESSION
OF THE PROTEINS IN THE HEAD AND
NECK DATA SETS, THERE IS A GROUP
PROTEINS WHICH ARE HIGHLY
UPREGULATED SIGNIFICANTLY AND TO
A GREAT DEGREE THAT ARE ALL
HEPATITIS EAR AN SULFATE BINDING
PROTEINS THAT COULD BE BINDING
BY THE REAC IV THERAPY OF THE
SULFS.
IN FACT, SULF 1 IS 1 OF THEM.
SOPHISTICATEDY THERE'S A SET OF
PROTEINS WHICH ARE QUITE
COMMONLY DERIVED FROM CANCER
ASSOCIATED FIBRO BLASTS, THERE
ARE SUPPLIED TO THE TUMORS BY
THAT CELL TYPE AND THAT ARE
REGULATED IN QUITE IMPACTFUL
WAYS BY THAT SULF 1 ENZYME AND
BASED ON THAT WE BRO POSED THIS
MODEL IN WHAT HAPPENS IN THE
HEAD AND NECK TUMOR TISSUES
WHERE THE SULF 1 IS SUPPLIED BY
THE FIBRO BLAST, THAT'S ITS JOB,
THE SULF 2 THAT COMES FROM TUMOR
CELLS WILL BE MODIFIED
DIFFERENTLY AND WILL HAVE
SOMEWHAT DIFFERENT TARGET ANDS
ACTIVITIES AND JOINTLY THEY EDIT
THE EXTRA CELLULAR MATRIX IN
SUCH WAYS THAT PRACTICE PLOATS
TUMOR INVASION AND IS CONNECTED
TO MISREGULATED IMMUNE RESPONSES
IN THE TUMORS, TUMOR
ENVIRONMENT.
SO I SHOWED YOU THAT THE SULFS
ARE UPREGULATED QUITE COMMONLY
AND CONSISTENTLY IN THE HEAD AND
NECK TUMORS THAT THE SULF 1
COMES FROM THE CAFs AND THEY
REGULATE MANY PATHWAYS.
THAT AT THIS POINT, WE GET
INVARIABLY ASKED BY VIEWERS OR
COLLEAGUES, WHAT IS THE PATHWAY
THAT IS IMPORTANT IN THIS CASE.
AND I THINK THAT IT'S ACTUALLY,
YOU KNOW A LITTLE BIT OF AN
OVERLIMP LIAISONIFICATION OF
THAT PROBLEM, I DON'T THINK THAT
THOSE ROUGHLY 600 INTERACTIONS
REGULATED BY THESE INTERACTIONS
CAN BE TRANSLATED INTO 1 SINGLE
EVENT THAT IS IMPORTANT; WE HAVE
HERE INTERACTION OF MANY CELL
TYPES WITH MATRIX AND WITH THOSE
CELLS AND DEPENDING ON WHICH
STAGE OF THE PROGRESSION OF THE
TUMOR, WE ARE AT AND DEPENDING
ON THE SPECIFIC PATIENT CONTEXT,
THIS MAY DIFFER, BUT WHAT DOES
PROBABLY HAPPEN IS THAT THE
SULFs BECOME SORT OF A HELP OF
COMMON REGULATORY EVENTS THAT
TRANSLATE INTO THE SURVIVAL
[INDISCERNIBLE].
AND THERE WE NOW STARTED USING
TUMOR BIOLOGY MODELS TO CAPTURE
THIS COMPLEX SET OF INTERACTIONS
AND WE STARTED LOOKING ACTUALLY
AT WHOLE CULTURES OF THE TUMOR
CELLS WITH THE CANCER ASSOCIATED
FIBRO BLASTS IN [INDISCERNIBLE]
MODELS.
THOSE ARE NICE MODELS WHERE WE
MIX 6000 CANCER CELLS EMBEDDED
IN MATRIGEL AND LOOK AT THEIR
PROGRESSION OR INCREASE OVER 5
DAYS.
THE CELLS ARE FLUORESCENTLY
LABELINGED, THEY FORM THOSE
SPHEROID STRUCTURES AND IN THE
CULTURE OF THE SKC35 HEAD AND
NECK CELL CANCER LINE ALONE OVER
3 DAYS YOU CAN SEE THEY DON'T
INCREASE, THEY ACTUALLY SHRINK A
LITTLE BIT BECAUSE THE SPHEROID
IS SOMEWHAT LOOSE IN DAY 1 AND
IN THE CONTEXT OF CO-CULTURES
WHERE WE ADD 300 CANCER
ASSOCIATED FIBRO BLASTS AND 3000
TUMOR CELLS, THERE IS A QUITE
DISTINCT PROLIFERATION OF THAT
STRUCTURE, CO CULTURE, INCLUDING
INCLUSION INTO THE MATRIGEL, SO
CAN YOU SEE HOW DIFFERENT THE
FINE O TYPE IS WHEN YOU CULTURE
THE CELLS ISSUES THE CANCER
CELLS,A LONE OR ADD THE FIBRO
BLAST INTO THE PICTURE.
AND THIS THAT WE WANT TO EXPAND
S&P ACTUALLY THE FACT THAT WHEN
WE KNOCK OUT THE TOOLS IN THE
CANCER CELL AND WHEN WE KNOCK
OUT 1 IN THE CANCER ASSOCIATED
FIEB ON BLASTS IS INCREASED AS I
SHOWED BEFORE BUT THE KNOCK OUT
CELLS NO LONGER STIMULATE EACH
OTHER.
SO I DO FIND THAT REALLY
INTERESTING, IN CONTEXT OF OTHER
TUMORS IN ANALYSIS OF THE CELL
LINES OVERALL IN THE CANCER CELL
LINE ENCYCLOPEDIA THAT WAS QUITE
NICELY THAT SULF 1 AND SULF 2
STORAGE.
IF YOU LOOK ACROSS ALL THE
TUMORS THEY EXPRESS SULF 1 BUT
MUCH MORE THAN FIBRO BLASTS,
THEY STAND OUT AS SOMETHING AS
AN IMPORTANT SOURCE OF THAT
INZEME, IF YOU LOOK AT SULF 2,
THAT'S NOT THE CASELET SULF 2
FIBRO BLASTS SOURCE IS SOMEWHERE
HERE IN THIS LEGION EMPLOY
FRESES IN HEAD AND NECK AND CELL
LINES THAT THAT PROVIDE A
SOURCE.
>> RADO, WE ARE A BIT OVER TIME,
CAN YOU GO FOR THE END.
>> YEAH.
SO HERE'S THE LAST SLIDE AND
THAT TELLS YOU THAT WHEN WE LOOK
AT EXPRESSION AND SURVIVAL OF
THOSE AND IT SHOWS SURVIVAL IN
DIFFERENT CANCERS AND MAYBE
THAT'S SUPPLIED BY THE CANCER
ASSOCIATED FIBRO BLAST IS THE
COMMON DENOMINATOR THERE IN
CONTEXT OF THE SULF 1.
SO I WANT TO THANK THE PEOPLE IN
MY LAB WHO DID THE WORK ON THIS,
THEY CONTINUE TO DO THE CO
CULTURES AND EXPRESSIONS, SO IN
THESE HEX CELLS AND I WANT TO
THANK ALSO COLLABORATORS AND A
NUMBER OF FUNDING SOURCES AND
ORGANIZATIONS.
>> THANK YOU VERY MUCH RADO,
THAT WAS REALLY, REALLY
INTERESTING, WE HAVE SOME
QUESTIONS IF YOU HAVE OTHER
QUESTIONS FOR RADO, WE WILL TAKE
THOSE AFTER OUR NEXT 2 TALKS.
SO I WOULD LIKE TO INTRODUCE OUR
NEXT SPEAKER DR. SRIRAM,
NEELAMEGHAM, STATE OF UNIVERSITY
OF NEW YORK BUFFALO, A
PAN-CANCER ANALYSIS OF GLYCO
GENE DISREGULATION.
SRIRIAM, ARE YOU--
>> YOU CAN SEE MY SCREEN RIGHT?
>> WE CAN SEE YOU BUT NOT YOUR
SCREEN YET.
>> THAT'S YOU RUNNINGOT BEACH I
GUESS.
>> THAT'S ME WISHING I WAS
RUNNING ON THE BEACH ESPECIALLY
SINCE IT'S SNOWING HERE.
IS THIS GOOD FOR YOU.
>> THANK YOU VERY MUCH.
>> YEAH, WELL IT'S A PLEASURE TO
PRESENT.
I WANT TO THANK MIKE AND ROGER
FOR PUTTING THIS SYMPOSIUM
TOGETHER, I ENJOYED MANY OF THE
TALKS WHAT I WILL TALK ABOUT
TODAY IS A COUPLE THINGS WE'VE
BEEN WORKING ON IN THE GROUP.
ONE OF THEM IS ABOUT AN ONTOLOGY
TO DESCRIBE GLYCO ENZYMES
PARTICULARLY WITH FOCUS ON
HUMANS AND THE SECOND IS HOW
THIS CAN BE APPLIED TO LOOKING
AT TCB GATTA AND THE CANCER
GENOME IS SO THIS IS WORK DONE
LARGELY BY TED GROTH, AND COLLAB
IDENTITY ARES FROM THE ONTOLOGY
COMMUNITY THAT YOU HEARD FROM
TODAY AND THE COLLEAGUES OF
MINE.
THE WORK WE HAVE IS KINDLY
SUPPORTED BY NHLBI ASHES
CYSTANCE TECHNOLOGY PROGRAM
WHICH IS THE BREAD AND BUTTER
FOR THE LAB AND THE SUPPORT IS
APPRECIATED AND IT HELPS GET THE
ONTOLOGY WORK DONE AND SOME OF
THE CANCER WORK IS SUPPORTED BY
SUBCONTRACT AND FROM
[INDISCERNIBLE] AND IN TERMS OF
GLYCOSYLATION, IT'S A PROESES IS
BY WHICH YOU HAVE COMPLEX
CARBOHYDRATES AND THIS CAN TAKE
PLACE IN MULTIPLE SCAF OLDER
PEOPLE WOULDS ON AND LIPIDS
ONENDING GLUE MARIOUS CANS AND
ALL GLYCANS OF ALL TYPES AND
THESE ARE SORT OF
FUNCTIONALLIZED AND MADE BY
ENZYMES WHICH WE CALL GLYCO
ENZYMES AND THESE GLYCO ENZYMES
IN OUR DEFINITION DON'T JUST
INCLUDE THE ENZYMES THAT HAD THE
CAT LATTIC ACTIVITY BUT THEY
INCLUDE ENZYMES THAT ARE
METABOLT-ONTIC IN NATURE, HAVE
TRANSPORT PROCESSES, STRUCTURAL
RULES AND CO FACTOR FUNCTIONS
AND WHEN YOU STARTED LOOKING AT
YOU KNOW GLYCO GENE REGULATION,
WHAT WAS STRUCK WAS THERE WAS NO
ONTOLOGY ENZYMES IN A SYSTEMATIC
WAY IN A COMPLETE MANNER.
AND SO WE SET OUT TO SORT OF
START TO DEFINE WHAT THIS
ONTOLOGY IS AND WHAT WE DEFINED
SO FAR IS APPROXIMATE 286 HUGH
MAN GLIEM GLYCO ENZYMES THAT ARE
CURATE AND THESE ARE CLASSIFIED
INTO 134 MOLECULAR FUNCTIONS AND
134 BIOLOGICAL PROCESSES AND
MULTIPLE COMPARTMENTS, AND I
WILL SHOW YOU THIS IN A MINUTE.
THE REASON WE STARTED GET
INTERESTED IN THIS IS BECAUSE OF
THE LACK OF SYSTEMATIC
ORGANIZATION THAT WOULD HELP US
TO DO OVER PRESENTATION AND
ANALYSIS.
SOPHISTICATEDY MY LAB IS
INTERESTED IN CONNECTING THE
GENES IN THE CELL TO THE GLYCANS
THAT THEY WOULD PRODUCE AND FOR
THIS PARTICULAR PURPOSE WE AND
WE'RE WORKING WITH ROGER AND
MIKE IN GETTING THIS INTO THE
PROJECT PORTAL.
AND ALSO WE ARE USING THIS TO
SORT OF CREATE NETWORKS OF DPLI
COSALATION REACTION BECAUSE THIS
WOULD BE A NICE WAY IN WE COULD
OVERLAY EXPERIMENTAL DATA ON
TPHREU RACING COSALATION AND
STRUCTURE DATA ON TOP OF IT TO
GET MORE INSIGHT IN THE PROCESS.
AND THAT'S ARE CONNECTED TO
INFORMATION AVAILABLE AT UNIPROT
AND ENGL, SO ONCE IT'S CONNECTED
IT CONNECTED PRETTY MUCH
EVERYWHERE, SO WE ARE FOCUSED ON
PROCISELY WHAT THIS DOES IN
TERMS OF WHAT THEY REGULATE
BECAUSE IT WOULD BE A TERMINAL
GLYCOSYLATION AND GLYCOSYLATION
ADDITIONAL INFORMATION ABOUT
PATHWAYS TO ACT ON.
THIS IS RELATED TO THE GENE
ONTOLOGY SO NOW OUR GOAL
BASICALLY IN THE SHORT-TERM IS
TO SORT OF GET THIS ONTOLOGY
ACCEPTED AND SLOWLY MAKE OUR WAY
INTO THE GUEST INTEGRATED INTO
THE GENE ONTOLOGY, FOR EACH OF
THESE ENZYMES WE DEFINE ACTION
ROOTS WHICH WE WILL GO THROUGH
AND CONSTRAINTS, EVERYTHING IS
YELLOW IS OUR CONTRIBUTION AND
OUR GOAL IS NOT TO THE DUPLICATE
EFFORT BUT INTEGRATE INTO
EXISTING RESOURCES.
IF YOU WANT MORE INFORMATION, WE
HAVE A PAGE THAT DESCRIBES ALL
THESE IN DETAIL.
SO WE'VE TAKEN THESE GLYCO GENES
AND THESE ARE CLASSIFIED AND
OTHERS HAVE SYNTHESIS AND SOME
DO DEGRADATION OF OUR ENZYMES
AND IN TERMS OF PATHWAYS THAT I
HAVE DIVIDED THIS THAT CREATE
PATHWAYS ALONG ELONGATION AND
BRANCHING AND CAPPING AND THE
THESE ARE N-GLYCOSYLATION AND IN
THAT SUBCLASS OF SYNTHESIS AND
IN GLYCOSYLATION PROCESSING AND
ALL IN GLYCOSYLATION OF THE NECK
TYPE AND THE NECK TYPES BY
PATHWAYS.
AND AND THE SUGAR STRUCTURE IT
FOR THE SCAFFOLD AND FOLLOWING
THESE STRUCTURES WE INCLUDE
ENZYMES, DILACTENZYMES AND ALSO
AND THE CAPPING ENZYMES AND
SULFATIONS ARE A GOOD WHYED THAT
WE'VE TAKEN EVERY ENZYME AND
SAID WHICH PATHWAY DO THEY ACT
ON AND WHICH PART DO THEY ACT
ON?
I DON'T HAVE TIME TO GO THROUGH
THIS BUT WE'VE DONE A LOT OF THE
SAME THINGS AND OTHER TRANSFER
ACES, GLUE MARIOUS COSDACES
TRANSPORTS ET CETERA AND THE
NUMBERS HERE TELL YOU HOW MANY
OF THESE GENES HOW MANY ARE
MODIFYING ENZYMES, REGULATORS
AND, ET CETERA AND THE SAME
THING FOR COMPARTMENTS, THESE
HAVE BEEN CLASSIFIED IN THE ER,
GOLGY AND THE ADDITIONAL
COMPARTMENTS BASED ON SOME OF IT
AS MANUELLY CURATED ABOUT IA
LARGE PART OF IT AM CANS FROM
GENE ONTOLOGY.
SO AN IMPORTANT THING THAT WE
ARE TRYING TO GET DONE OVER HERE
IS SORT OF DEFINE, YOU KNOW HOW
DOES A GLOI COSALATION REACTION
AND WE'VE CREATED REACTION RULES
IN TERMS OF HOW TO DESCRIBE THIS
WHEN YOU HAVE GLYCOSYLATION
TAKING PLACE IN THE HUMAN
SYSTEM, THERE ARE ESSENTIALLY 5
TYPES OF REACTIONS THAT OCCUR.
IT CAN BE ADDITIONAL REACTIONS
WITH THE SALIC ACID IS ATTACHED
TO A GLUE MARIOUS COSMEAN CHAIN,
A BRACKET IS SHOWN BY THE A MARK
AND FLUICOSE IS MOVE FRIDAY THIS
CHAIN, A REVERSIBLE REACTION
WHERE YOU CAN HAVE GLUCOSE 1
PHOSPHATE AND GLUCOSE 6
PHOSPHATE AND CAN YOU HAVE A
SUBSIDIARY CONSTITUTION REACT
AND TO
HYULU RONNIC AND THOSE ENZYMES
DON'T GIST ACT ON 1 PARTICULAR
SUBSTRATE, THAT CAN ACT ON
MULTIPLE TYPES OF SUBSTRATE AND
THERE'S SUBSTRATE AMBIG WITY
WHICH IS USING THE QUESTION MARK
IF THE LINKAGE IS UNCERTAINTY,
IF ALL THE STRUCTURE CANS APPEAR
FOR EXAMPLE, AND THIS IS THE
CASE COULD BE A SUBSTRATE BUT
IT'S NOT NECESSARY THEN IF YOU
HAVE AN INTERNAL SITE, THEN WE
SEE THE SITE WHERE WE HAVE A
CHEMICAL REACTION AND THAT'S THE
3 DOT AND THERE'S A BRANCH IN
THE MIDDLE, THEY WILL PRODUCE
THE DOT LIKE THIS AND IF THE
REACTION TAKES PLACE IN THESE
PARTICULAR DOMAINS, THEN WE
BEDETECTION ANTIBODY THE TEXT.
SIMILAR TO THIS, THERE ARE
PRIMARY CLASSIFICATIONS OF OF
THOSE ENZYMES AND THESE ARE
BASED SO AN ENZYME MIGHT REQUIRE
THIS AND THIS WITH THE SUBSTRATE
IT'S REACTING WITH OR IT'S A
POSITION WHERE IT'S A 2-3, 6 AND
THE ENZYME DIDN'T CARE ABOUT IT
SO THESE RULES OF SUBSTRATE
AMBIG WIT SKPE BAKUGAN
DISCRIMINATION DESCRIBE LAWN
MOWER AN ENZYME SCRUTINIZED AND
I THINK IT HAS IMPLICATIONS NOT
ONLY FOR ENZYMATIC REACTION AND
DESCRIPTION OF ENZYMES BUT ALSO
DESCRIBING IN GENERAL HOW
MOLECULAR GENERATION OF PROTEINS
AND CARBOHYDRATES TAKE PLACE IN
THE CONTEXT OF LECTUREINS THAT
TAKE PLACE.
WHAT WE TRY TO DO IS ESSENTIA
WILY TAKE MANY OF THE RULES THAT
WERE PROAFIOUSLY DESCRIBED FOR
DESCRIBING THESE GLYCOSYLATIONY
ACTION IN TERMS OF SYMBOLS THAT
ARE USED BUT WE TEND THEM TO
LOOK AT IPAD INSTRUCTIONS YOU
DON'T NEED A COMPUTER AND IT'S
INTUITIVE ININATE AND YOU WE TRY
TO REDUCE THE NUMBER OF SIM BOOM
BOOM BOOM BOOMS TO THE BARE
MINIMUM, BUT IT SHOULD BE USEFUL
FOR LECTUREIN AND LOOKINGA THE
DPLI KAN--KANA AREAS AND OTHER
INFORMATION THAT BE RESORTED.
AND I THINK IF YOU CAN DECIDE ON
A COMMON FORMAT FOR DESCRIBING
THESE STRUCTURES, THEN IT CAN
MAKE SOFTWARES INTEROPERABLE
WHICH GOOD FOR US.
SO ONCE YOU JUST FIND THESE
PARTICULAR ENZYMES, IT'S
POSSIBLE TO LOOK AT WHAT THESE
ARE DOING IN A PATHWAY, IN THIS
PARTICULAR NATURE, AND YOU
CAN--STARTING WITH THE INITIAL
MOLECULE AND GIVEN CERTAIN
ENZYMES THE ONTOLOGY ALLOWS TO
YOU CREATE PATHWAYS AND SMALL
DESCRIPTION AS SHOWN OVER HERE.
MORE IMPORTANT WHAT WE REALLY
INTERESTED IN ONTOLOGY IS SORT
OF THE LINK GENE EXPRESSION DATA
TO GLYCAN STRUCTURE DATA SO THIS
IS AN EXAMPLE OF A BREAST CANCER
SYSTEM WHERE WE BASICALLY TAKEN
HER TBO FROM THE TCGA DATA SET
AND DOING OVERPRESENTATION
ANALYSIS, OVERPRESENTATION
ANALYSIS SAYS IF I HAVE THE
ENTIRE GENOME WITH ALL THE
JEERNS INSIDE IT, WHICH OF THESE
PATHWAYS OR WHICH OF THESE GLYCO
GENES ARE GOING UP IN THIS
PARTICULAR SYSTEM OR GOING DOWN
IN A PARTICULAR SYSTEM OR
DIFFERENTIALLY ALTERED AND WE
COMPARED THOSE ON TO THE CANNED
WHAT WITH THE GENE ONTOLOGY AND
REACT OHM AND WHAT I TRY TO
POINT OUT IS THAT THE GLYCO
ENZYME GIVES YOU A MUCH MORE
REFINED UNDERSTANDING OF
PATHWAYS THAT ARE DISREGULATED
DURING CANCER COMPARED TO THESE
OTHER ONTOLOGYS, FOR EXAMPLE IN
THIS CASE, WHAT'S GOING UP IS
NDPLI COSALATION PATHWAY AND
WHAT THIS TELLS YOU IS THAT THE
PATHWAY IS WHAT GOES UP AND NONE
OF THESE OTHER PATHWAYS ACTUALLY
CHANGE.
WE SHOULD PLOT THE ENZYME
CHANGES IN THE FULL CHANGES OF
BREAST CANCER VERSUS NORMAL,
WHAT YOU SEE IS THAT MOST OF
THESE ENZYMES THAT ARE SHOWN
HERE IN THE PATHWAY ARE ACTUALLY
INCREASED ALONG WITH SOME
[INDISCERNIBLE] THAT ARE STATIST
LIKE SIGNIFICANT INCREASED IF
YOU SEE THE AND SEE THIS
PARTICULARLY AND THIS IS A
SUBSTRATE FOR DPLI COSALATION
AND IF YOU GO AND TRIM DOWN AND
LOOK AT THE LIST OF DREAMS IN
THE GLYCOSYLATION PATHWAYS THEY
INCLUDE THINGS THAT ARE IN THE
CORE BY SYNTHETIC PATHWAY BUT
INCLUDE GENES LIKE AND
NECESSARILY FOR THE TYPE OF
UNDERSTANDING THAT AND WE NEED.
SO YOU CAN DO THIS AGAINST
ANTIGENOME OR CAN YOU DO IT FOR
SPECIFIC GLYCO JEERNS SO NOW
INSTEAD OF LOOKING AT THE WHOLE
GLUE MARIOUS COAND IN THE GENES
WHICH 1S ARE DISREG AUTOLOGY
WIDE RESPECT TO OTHER GLYCO
GENES IN THE SYSTEM AND WHAT
THIS PREDICTS IS THAT ALL
GLYCOSYLATION IS AFFAIRS TEAM
LEADERRERRED AND THE GENES
INVOLVED IN THE DECREASED OR
SCIENTIFIC INCREASE BECAUSE WE
GET MORE ANTIGENS AND THESE HAVE
[INDISCERNIBLE] TAKING PLACE AND
YOU HAVE CERTAIN [INDISCERNIBLE]
TAKING PLACE.
SO WHAT HAPPENS OVER HERE IS
ESSENTIALLY A NUANCE
UNDERSTANDING OF WHAT TPHREU
RACING COSALATION PATHWAYS ARE
ALTERED AND THIS IS PROVIEDMAN
BY SOME DEGREE BY K BUT IT'S NOT
JUST THE [INDISCERNIBLE], IT'S
ALSO THE SERIES AND THE SPECIFIC
GENES IN THE LACTOSERIES THAT
ARE REDUCED SO IT GIVES YOU A
BETTER UNDERSTANDING OF THE
GLYCOSYLATION PROCESS AND THE
GENES THAT ARE REGULATING.
SO WE WENT ON BEYOND THIS AND
SAYING WELL, YOU KNOW WE HAVE AN
ONTOLOGY NOW TO SORT OF LOOK AT
CLASSIFYING PATHWAYS, CAN WE
AMRI TO A MUCH LARGER DATA SET
SO WHAT TED'S DONE BASICALLY IS
TAKE AND THESE PATIENTS IN THE
RNA SEQ DATA THAT'S AVAILABLE AT
THE TCGA AND THESE ARE SORT OF
AND THE MOTIVATION FOR THIS IS
INVOLVED IN MANY DIFFERENT
PATHWAYS AND REGULATE THE
HALLMARKS OF CANCER AND IN
PARTICULAR, I WOULD LIKE TO
POINT OUT PROLIFERATION, IMMUNE
DESTRUCTION, AND INVASION AND
METASTASIS WHICH I THINK HAVE
BEEN DISCUSSED TODAY AND THESE
DATA SETS THAT ARE THERE FOR
THESE PATIENTS, EXIST FOR 33
DIFFERENT TYPES OF CANCERS.
NOW THE FIRST THING WE DID WAS
WE JUST SAID, LET'S PARSE OUT
THE GENES IN THESE CANCERS AND
THESE ALOAN CAN THEY ALONE
CLASSIFY TUMORS FROM COMING FROM
DIFFERENT AREAS.
SO WE TOOK THE DATA, PARSED OUT
GLYCO GENES AND PUT THEM ON THE
BLOT AND WHAT YOU SEE AMAZINGLY
IS THAT EVERY TOMB--EACH OF
THESE DOTS IS A PATIENT AND YOU
CAN SEE THAT THERE'S NICE
CLUSTERING OF THE TUMORS BASED
ON THE TYPE OF ORGANS THEY COME
IN, YOU KNOW THE BRACCA, ARE ALL
HERE, THE LUNGS ARE ALL OVER
HERE AND SO ON.
AND YOU LOOK AT THEM IN TERMS OF
JUST ORGAN SYSTEMS OVER HERE,
WHAT YOU CAN SEE IS THAT THESE
DIFFERENT ORGAN SYSTEMS SORT OF
CLASSIFY THEMSELVES TOGETHER.
FOR EXAMPLE, IF IF YOU HAVE C&
S, OVER HERE THERE'S DPLEE O
PLAOF THOMA AND LOWER GRADE
GLIOMAS, AND THEY CLUSTER
TOGETHER AND THESE THIS CANCER
FROM THE SKIN AND THE EYES, SORT
OF CLUSTERED TOGETHER FOR THE
LIVER, AND THE CARCINOMA AND THE
HEPATITIS EATIC CARCINOMA THEY
ARE BOTH CLUSTER TOGETHER.
SO INTERESTINGLY IT'S NOT JUST
THAT THE GENES AND THE FLIEK O
GENES DIFFERENTIATE DIFFERENT
TUMORS, ALSO ORGANS THAT HAVE
SIMILAR ORIGINS TEND TO CLUSTER
TOGETHER AND YOU CAN SEE THAT
FOR THESE 3 EXAMPLES, ARE
SOMETIMES YOU SEE DIFFERENCES
FOR EXAMPLES, IF YOU LOOK AT
LUNG CANCERS OF 2 TYPES THEY'RE
NOT QUITE OVERLAPPING EACH OTHER
AND SIMILARLY FOR--FOR JEEPS
THAT MIGHT BE INVOLVED IN OTHER
PATHWAYS FOR EXAMPLE, ENDOCRINE
PATHWAYS THAT ARE CLOSE TO EACH
OTHER AND THE SAME THING FOR
KIDNEY, 3 TYPES OF KIDNEY
CANCERS ARE CLOSE TO EACH OTHER
AND SOME CANCERS FOR EXAMPLE, IF
YOU LOOK AT BLOOD CANCERS LIKE
ACUTE MYELOID LEUKEMIA AND
THINGS THAT ARE INVOLVED IN
LEUKEMIA THESE ARE IN TERMS OF
GLYCO GENES AND SO THESE GLYCO
GENES IN THESE SYSTEMS DIFFERENT
AND YOU CAN CLASSIFY THEM BASED
ON MULTIOMICS FRAMEWORK USING
WHAT'S CALLED THE PAN-CANCER
CLASSIFICATION WHICH USES
PROTEOMICS GENOMICS AND
TRANSCRIPTOMICS AND YOU CAN SEE
THAT MANY OF THESE THINGS SORT
OF COME TOGETHER, ALL THE
GYNECOLOGICAL CANCERS BREAST
CANCER, OVARIAN CANCER, UTERINE
CANCER, CERVICAL CANCER IS OVER
HERE BECAUSE IT'S MORE OF A
SCWAIMOUS MORPHOLOGY AND YOU CAN
SEE THE GASTRO, RECTAL,
COLORECTAL, STOMACH ARE
TOGETHER, [INDISCERNIBLE] IS FAR
AWAY BECAUSE THAT'S MORE OF A
SCWAIMOUS MORPHOLOGY SO IT'S
REALLY INTERESTING YOU CAN CLASS
FLY TUMORS BASED ON JUST THE
FLIEK O GENES.
SO NOW, TD GLYCO GENES ARE
DIFFERENT IN DIFFERENT ORGANS SO
THAT MIGHT WELL EXPLAIN THESE
DIFFERENCES SO WE ASK THE
QUESTION, THIS IS INTERESTING,
BUT CAN YOU ACTUALLY CLASSIFY
DIFFERENT TUMOR TYPES AND
DIFFERENT MOLECULAR SUBTYPES,
BASED ON JUST THE FLIEK O JEEPS
SO WE PARSE OUT THE GLYCO GENES
AND THEN WE TOOK DIFFERENT TYPES
OF TUMORS AND TOOK MOLECULAR
CLASS UCHGS FOR EACH OF THEM AND
FOR EXAMPLE, THIS IS THE BREAST
CANCER TO EXPAND UPON IN A FEW
MINUTES AND THIS IS JUST SHOWING
THE PAN 50 CLASSIFICATION OF THE
GENES OVER HERE AND SHOWING THIS
IS THE NORMAL ALONG THE BASAL
AND LUMINAL A AND B AND THIS IS
A 2 D PLOT AND YOU CAN GET MORE
AS I WILL SHOW YOU IN A BIT.
IF YOU LOOK AT THE HISTOLOGY,
YOU WILL HAVE TO DESCRIBE WHAT'S
WITH THE TUMORS AND WHAT WILL DO
THIS THING AS WELL, IF YOU LOOK
AT BRAF MUTATION, YOU CAN SEE
THAT THE GLYCO GENES ALONE
WITHOUT ANYTHING ELSE CLASSIFY
DIFFERENTLY SO BRAF MUTATION
KAWS CANCER WHICH EXPRESS
PRESUMABLILY DIFFERENT
STRUCTURES ON THEM.
NOW WE'VE GONE AND THAT I CANNEN
ALL OF THESE TUMORS ABOUT 16 OF
THEM THAT HAVE SUFFICIENT
NORMALS AND DIFFERENTIAL
EXPRESSION ON ALL OF THEM AND
THIS IS AN EXAMPLE OF A HER 2
POSITIVE CANCER SHOWING SOME
GENES GO DOWN AND SOME GO UP
ANDA ABOUT A THIRD OF
DISREGULATED INVARIABLY IN A
CANCER WE'VE SEEN SO THEREYA A
PHENOMENAL CHANGE IN THE
STRUCTURES AND THE GLYCO ENZYMES
AND THEY AREN'T REALLY SPECIFIC
TO SPECIFIC GLYCAN TYPES THEY
JUST GENERALLY DISREGULATED IN
THESE CANCERS AND YOU CAN SEE
THAT FOR MULTILE CANCER TYPES
FOR ALL THE GENES THAT THEY'RE
LOOKING AT LONG WITH DIFFERENT
FAMILIES AND WHAT'S REALLY
INTERESTING ABOUT THIS IS THAT
TUMOR TYPES, SIMILAR TYPES ARE
CLUSTERED TOGETHER, THESE ARE
ALL NEUROLOGICAL CANCERS THAT
ARE CLOSE TO EACH OTHER.
IF YOU COMPARE THIS RECTAL AND
COLO CANCER THEY'RE ALL RED OVER
HERE, CAN YOU SEE THE RATE TO
EACH OTHER IF YOU TAKE THESE
FIGURES YOU CAN SEE ALL THESE
GENES ARE DOWN REGULATED IN
THESE PARTICULAR 2 TYPES OF SO
ON SO CAN YOU SEE
[INDISCERNIBLE] THAT SIMILAR
TUMORS BASED ON ORIGIN WILL HAVE
SIMILAR PATHWAY DISREGULATION
DURING CANCER WHICH I THOUGHT
WAS REALLY INTERESTING, I WON'T
GO INTO THIS IN MUCH DETAIL BUT
JUST THEY WE PULLED UP THE TOP
GENES IN EVERYONE 1 OF THESE
CLUSTERS AND KIDNEY AND GUIN
OICOLOGICAL AND THEY ARE CERTAIN
GENES THAT ARE GOING UP AND
GOING DOWN, AND THEY DON'T
BELONG TO ANY SPECIFIC PATHWAY,
THEY BELONG TO MULTIPLE PATHWAYS
IN THIS PARTICULAR SYSTEM, SO
THEY BELONG TO ALL SORTS OF
PATHWAYS THAT ARE ALTERED SO
THEN THE QUESTION AS YOU KNOW IS
WHICH PATHWAYS ARE ALTERED IN
THESE THINGS SO WE TOOK THE
GLYCO ENZYME MORPHOLOGY AND WE
USE THAT FOR THE EXPRESSION DAT
FAR ALL THESE PARTICULAR TUMORS
AND YOU LOOK AT ALL THE
DIFFERENT PATHWAYS WHAT ARE THE
PATHWAYS THAT ARE DISREGULATED
AND THESE ARE THE PATHWAYS THAT
ARE REDUCED, THESE ARE GOING UP
AND IT'S INTERESTING BECAUSE WE
HEARD A TALK ON OLD GIVING--YOU
COSALATION PATHWAYS, AND SOME OF
THE GENES ARE GOING DOWN AND
THAT'S CALLING TN ANTIGENS AND
THE OTHER PART WE HEARD ABOUT
AND EXTRA CELLULAR DEGRADATION,
SO THIS IS RADDA'S TALK TALKING
ABOUT DEGRADATION AND SULF 1 AND
2, THERE'S ALSO OTHER CHANGES
THAT TAKE PLACE IN THESE CANCERS
THAT ARE UNIFORM, FOR EXAMPLE,
[INDISCERNIBLE] IS GOING UP IN
MANY TYPES OF CANCERS AND
ADDITIONAL PATHWAYS THAT ARE
ALTERED AND YOU CAN FIND YOUR
FAVORITE GENE OVER HERE.
WE HAVE A WHOLE WEBSITE THAT
CURATES THAT IS PEOPLE CAN COME
IN AND CURE QUERY ALL THESE
THINGS IN THAT PARTICULAR
WEBSITE.
BUT WHAT'S REALLY INTERESTING IS
I THOUGHT THAT ALL THESE
DIFFERENT CANCERS THAT HAVE YOU
HAVE DIFFERENT PATHWAYS
DISREGULATED, SOME OF THEM ARE
READ HERE, PLURIBU IN OTHER
CANCERS AND SO ON, SO EVEN
THOUGH THE GLYCO GENES ARE
DISREGULATE INDEED MULTIPLE
CANCER TYPES, WHAT WE OBSERVING
OR WHAT WE THINK IS OBSERVING IS
THAT THE GENES, THE PATTERNS OF
CARBOHYDRATE STRUCTURES IS
ACTUALLY DIFFERENT BECAUSE
DIFFERENT PATHWAYS ARE
DISREGULATE INDEED DIFFERENT
KANGSER TYPES, YOU CAN ALSO SEE
CLOSE ASSOCIATION HERE FOR THE
RECTAL AND COLORECTAL OVER HERE,
CAN YOU SEE THAT THESE SORT OF
THINGS THAT ARE STOMACH AND
FIGURES ARE SIMILARLY
DIFFERENTIATED AND SO THE
PATHWAYS THAT SORT OF NEED
CHANGE OR ARE DOWN REGULATED OR
UPREGULATED ARE SIMILAR SO CAN
YOU SEE THAT HERE FOR THE KIDNEY
AND YOU SEE SIMILAR
DISREGULATION FOR CANCER TYPES
FOR THOSE BASED ON ORGAN SYSTEMS
BUT TOTALLY DIFFERENT PATTERNS
FOR EACH CANCER.
WE'VE GONE ON 1 STEP FURTHER AND
LOOKED AT LET'S SEE SO YOU CAN
STUDY 1 PARTICULAR CANCER IN
MOLECULAR CANCER AND BREAST
CANCER AND WE APLAYED MACHINE
LEARNING IN THESE THINGS TO
CLASSIFY 6 DIFFERENT TYPES OF
EXAMPLES THAT ARE EXISTING, THIS
IS BASAL, HER 2, LUMINAL,
LUMINAL AB AND YOU SAID, YES WE
HAVE 286 FLIEK O GENES BUT
MEASURED EXPRESSION IN THE
GENES, LET'S SEE WHAT IS A
MINIMUM NUMBER YOU NEED IN ORDER
TO EXPLAIN THE DIFFERENCES AMONG
THESE THINGS AND WE'VE DONE THIS
AND WE'VE SORT OF ABOUT 50 GLYCO
GENES IN ORDER TO EXPLAIN
DIFFERENCES IN ABOUT 85%
ACCURACY AND ALL THESE DIFFERENT
CANCERS THAT CAN YOU GET, AND
THESE ARE SOME OF THE GENES THAT
ARE INVOLVED IN THERE, APPEAR IN
THE GLYCO LIPID PATHWAY.
AND CANCER, WE CAN ALSO CREATE
THESE PROGRESSION MAPS WHERE YOU
CAN GO IN AND TAKE IT AND SAY
THIS IS THE CLUSTER OF PATTERNS
YOU'RE SEEING ON A PCA PLOT, AND
THIS IS A NORMAL TUMOR THAT
GOING INTO THE NIEWMOR TUMORS
BASAL OR LUMINAL A OR B AND YOU
CAN SEE DIFFERENT IF YOU TAKE
GLYCO GENE 50 AND YOU PLOT
PROGRESSION MAP, IT'S PRETTY
SIMILAR TO PAN 50, SO
GLYCOSYLATION HAS THE NEED TO
PLOT, NOT EXACTLY THE SAME
AMOUNT OF PAN 50 BUT COMPARABLE
LEVELS OF INFORMATION IS PAN 50
BECAUSE OF CLASSIFICATIONS WE
SEE OF USING GLYCO GENES ALONE
IN DIFFERENT TYPES OF CANCER
SUBTYPES IS QUITE COMPARABLE TO
WHAT WE SEE IN PAN 50.
CAN YOU USE IN INFORMATION TO
SORT OF LOOK AT PROGRESSION MAPS
HOW DO THESE STRUCTURES OR GLYCO
GENES CHANGE DURING CANCER AS IT
GOES FROM A NORMAL TO A TUMOR
USING BASAL FOR EXAMPLE, AND YOU
SEE THAT THESE GO UP FOR A
WHILE, THESE ARE IMPORTANT FOR
THE PATHWAY, YOU HAVE PATHWAYS
RELATED TO C& B CYTOTOLL-LIKE
RECEPTORIC ACIDS THAT GO UP AND
THESE GENES THAT ARE GOING UP
AND YOU CAN SEE THANKS TAKING
PLACE IN TRANSFER ACES OR
STRUCTURES, SOME GENES, LIKE
TRANSFERS 8 AND IN PARTICULAR
CASE, THE BASAL GOES UP FOR A
WHILE AND THEN GOES DOWN.
AND SO, THESE TUMOR
HETEROGENERATED AITYS THAT WE
TALKED ABOUT YESTERDAY THAT ARE
NOT ALL PATIENTS OF THE SAME ARE
REALLY BECAUSE WE CATCH SOME OF
THEM, AND WE CATCH OTHERS IN
THIS PARTICULAR STAGE AND SO THE
TUMORS HAVE A SORT OF SIGNATURE
OF TPHREU --GLYCAN STRUCTURE CHANGES AND
THESE COMMUNITIES COME TOGETHER
AND THE BIO-INFORMATICS COULD
CONTRIBUTE TO THIS.
SO I WILL JUST CLOSE OUT WITH
CONCLUSIONS WHAT WE'VE DONE IS
WE'VE GOT A GLYCO ENZYME
ONTOLOGY WHICH WHICH IN OUR
STUDIES ENHANCES IT IS GENE
ENRICHMENT ANALYSIS ACROSS
DPRIEK O BI--GLYCO BIOLOGICAL
PATHWAYS.
GEICO GENES CAN DIFFERENTIATE
TUMORS BUT THEY CAN DISTINGUISH
BETWEEN DIFFERENT MOLECULAR
TYPES, AND THEY SUGGEST THAT THE
EXPRESSION OF GENES IN DIFFERENT
CANCERS, THE DIFFERENCES IN THE
GLYCO GENES AND SPECIFIC CANCER
TYPES ALSO TRANSLATE IN
CHAIMPLES IN PATHWAYS TO
TENTIALLY IS LIGANDS IN
DIFFERENT CANCERS WHICH WILL BE
DIFFERENT BUT RELATED IN TERMS
OF ORGAN SYSTEMS AND ALSO
CREATED A SYSTEM IN A FRAMEWORK
IN WHICH WE CAN HAVE A
PROGRESSION MAP TO ELECTRIC AT
HOW DO GENES EVOLVE DURING
CANCER AND SO FAR TO THE EXTEND
THAT WE'VE DONE ANALYSIS THESE
GENES ARE SIMILAR AND POETIC
TEBTIAL TO DISTINGUISH DIFFERENT
CANCER TYPES AND TO LOOK AT
DIFFERENT MOLECULAR SUBTYPES
THAT COULD BE LOOK AT IT FROM A
SYSTEMS BIOLOGY PERSPECTIVE SO
THANK YOU IF ARE YOUR ATTENTION
AND WELCOME QUESTIONS AT THE
END.
>> THANK YOU SO MUCH, THAT'S
REALLY FASCINATING.
I'M SURE WE WILL HAVE QUESTIONS.
JUST PUT THOSE IN THE SEND LIVE
FEEDBACK LINK THERE AND SO WE'RE
BEHIND TIME SO LET'S MOVE
DIRECTLY TO OUR NEXT SPEAKER
DR. JOSHUA KLEIN, BOSTON
UNIVERSITY, REDUCING AMBIGUITY
IN GLYCO FORM ASSIGNMENT USING
RETENTION TIME MODELING AND
GLYCAN NETWORK SMOOTHING.
>> SO THAT I FIT IN TIME, I WILL
JUST TALK ABOUT REDUCING
AMBIGUITY THROUGH RETENTION TIME
MODELING.
SO THANK YOU EVERYONE FOR HAVING
THE PATIENCE TO SIT THROUGH MY
TALK TODAY AND THE ORGANIZERS
LETTING ME TALK TODAY AND MAY
YOU NOT REGRET IT.
SO KEY WORDS TO DEFINE A PREP SO
I WILL TALK EXCLUSIVELY ABOUT
LIQUID CHROMATOGRAPHY COUPLED
MASS SPECTROMETRY MASS
SPECTROMETRY, WE WILL TALK ABOUT
TYPES OF ADDUKS AND DPLIK O
PEPTIDE AND GLYCAN COMCISION
ASSIGNMENT USING RELATIVE
PRETENSION TRIEM PREDICTION.
ONE OF THE IMPORTANT THINGS TO
TALK ABOUT WHEN IDENTIFYING
FLIEK O PEPTIDES WITH MASS
SPECTROMETRY, HOW DO WE IDENTIFY
THEIR FRAGMENTS WE TAKE A
PEPTIDE PLUS 1 OR MORE LOCALIZED
GLYCANS SOMEWHERE IN THE
SEQUENCE AND WE GET A KIND OF
MASS SPECTRUM WITH MANY
DIFFERENT TYPES OF FRAGMENTS.
WHEN WE FRAGMENT THE DPLI
KAN--KANA, WE GET CHUNKS OF THE
GLYCAN SIS ASSOCIATED FROM THE
PEPTIDE AND THE REDUCING END OF
THE GLYCANS SILL ATTACHED TO THE
INTACT PEPTIDE.
WITH A BIT MORE ENERGY WE CAN
START TO SEE PEPTIDE BACKBONE
FRAG METROPOLITANS BEING Y-IONS
SOME OF THEM WILL HAVE A DPLI
KAN--KANA TO ATTACH AND THE MORE
ENERGY YOU PUT INTO THE
MOLECULE, THE DIFFERENT
PROPORTIONS OF THESE TYPES OF
PROTOTYPES YOU WILL GET.
SO THERE IS NOT 1 ENERGY TO USE
THAT WILL GIVE YOU PERFECT
FRAGMENT ANTICIPATION FOR ALL
PEPTIDES MEANING YOU WON'T GET
PERFECT FRAGMENTATION OF THE
DPLI KAN--KANAS AND YOU NOT
ACCURATELY SAVE WHAT IS ATTACHED
AND WHERE.
BUT WE CARE ABOUT ACCURATE
GLYCAN ASSIGNMENT, SAY WE HAVE
THIS DPLI KAN--KANA ON A
PEPTIDE,--DPLI CAN ON A PEPTIDE,
HOW WOULD WE IDENTIFY IT?
WE COULD LOOK AT THE TOTAL MASS
AND THE MASS SPECTROMETER CAN
TELL US WHAT THE INTACT MASS OF
THE PRECURSOR ION WAS.
IF WE'RE LUCKY WE CAN FRAGMENT
THE GLUE MARIOUS CAN AND
DETERMINE AND THE COMPOSITION BY
LOOKING AT PIECES THAT FALL
APART AND WHAT THEY ADDED UP TO
COME BACK TO TOGETHER BUT
THEY'RE ALSO LA BILE GROUP THAT
DON'T SHOW US THE BREAK DOWN
WHILE ATTACHED TO THE PEPTIDE.
SILIC ASITS AND AXONION IONS
DERIVED FROM ACID CONTAINING
IONS.
EVEN THOUGH THOSE AREN'T
ATTACHED TO THE PEPTIDE, WHEN WE
OBSERVE THEM, THEY CAN TELL US
THAT THE MONOSACCHARIDE FOR THE
WHOLE MONOSACCHARIDE ATTACHED TO
ANOTHER MONOSACCHARIDE 1, SAY WE
HAVE A AVE A GLYCAN THAT HAS--OR
IT COULD BE A GAL ALPHA GALL
WITH A DEOXYHEX OAZ ATTACHED
SOMEWHERE BUT FOR LACK OF A
BETTER PLACE TO DRAW IT WILL
SHOW IT ATTACHED TO THIS
TERMINAL.
THESE 2 BRANCHES ARE NEARLY THE
SAME PASS, THEY DIFFER BY ONLY
.11 DALTON WITHERSPOONERS, NOW
WE COULD SAY WHEN WE LOOK FOR
THE ION BUT THE REST OF OUR
STRUCTURE HAS SIALOGLYCANSIC
ACID ON THIS, SO IT'S NOT
INDICATIVE, SO SIMILARLY WE
CAN'T USE THE DEOXYHEXOSE AS THE
DISCRIMINATING FACTOR BECAUSE
THERE'S 1 ON THE ORIGINAL
STRUCTURE AND IF WE WERE TALKING
ABOUT MUSEUM MANS WE COULD SAY
WELL HUMANS DON'T DO ALPHA GAL
ALPHA GAL, WE DON'T CONSIDER
THIS BEING IN THE SEARCH SPACE
BUT MAYBE WE'RE NOT DEALING WITH
HUMAN DATA AND YOU COULD SAY
THAT MASS SPECTROMETRY ALL LOVED
TO TALK ABOUT HOW ACCURATE YOUR
INSTRUMENTS ARE, THEY CAN TELL
WHEN A PROTEIN SNEEZES, SURELY
THEY CAN TELL THE DIFFERENCE
BETWEEN .01 DALTONS AND MOST OF
THE TIME THEY CAN BUT UNLESS
THINGS ARE WORKING PERFECTLY,
THIS CAN STILL HAPPEN WITH THAT
EXPERIMENT.
WHAT'S MORE IS THIS IS NOT THE
ONLY SITUATION WHERE WE WOULD
OBSERVATION THIS AMBIGUITY,
THERE ARE MANY, MANY SITUATIONS
WHERE THIS CAN OCCUR, A COMMON 1
IS WHEN WE ACTUALLY HAVE AN
ERROR IN SELECTING MONOISOTOPIC
MASS AND WE SUBSTITUTE ASILIC
ACID FOR 2 DEOXYHEXODACES.
WE CAN ALSO HAVE MUCH LARGER
AMBIGUITYS WHEN WE HAVE LARGE
SUBSTITUTION EVENTS AND WE ARE
LOOKING AT BIGGER MASS ACCURACY
TOLERANCE WHERE WE TAKE THIS
HUGE CHUNK OF GLYCAN COMPOSITION
AND SUBSTITUTE IT FOR HOMOGENOUS
HEXES, BUT YOU COULD SAY THIS IS
UNCOMMON AND YOU WOULDN'T EXPECT
SUBSTITUTION COMPLEMENT HERE TO
BE PRESENT IN YOUR GLYCAN
DATABASE AND IF YOU'RE WORKING
WITH A REASONABLE CONSERVATIVE
DATABASE THAT'S PROBABLY TRUE,
ABOUT YOU AS WE SEE THE RISE OF
DATABASE FREE RADICALS
APPROACHES, THIS BECOMES MORE OF
A CONCERN.
WE MIGHT ALSO BE LOOKING FOR
THOSE INTERESTING MODIFICATIONS
LIKE SULFATION OR FOSTER NURSED
FARALATION AND SIGNATURE IONS TO
DISCRIMINATE THEM BUT THEY HAVE
DIFFERENT FEATURES THAT WE MIGHT
USE WHEN WE CAN'T RELY ON THOSE.
ALTERNATIVELY, YOU CAN HAVE A
SUBSTITUTION OF SULFATE PLUS 2
HEX ACTS AND REPLACE THAT WITH 3
HEXOSES AND WITH A RELATIVELY
NEAR THE SAME, COMPOSITION AT
THE ROOT OF THE GLYCAN.
AT A LARGE ENOUGH TOTAL DPLI
KAN--KANA MASS, THIS IS TOTALLY
FINE FOR--GLYCAN MASS THIS IS
TOTALLY FIEP FOR A MISMATCH
BECAUSE WE'RE UNRELIABLE TO
IDENTIFY SODIUM AS AN ION AND IF
YOU DON'T KNOW YOU'RE LOOKING AT
SOMETHING WITH SULFATION ON IT
YOU MIGHT VERY WELL ACCEPT THE
IDENTIFICATION OF THOSE 3 HEXES.
IT'S JUST THE FACT THAT
SULFATION IS NOT PART OF A
COMMON SEARCH SPACE COMPONENTS.
THE SAME THING WILL APPLY FOR
PHOSPHORYLATION, TOO, IF YOU'RE
DEALING WITH MAMMALIAN GLYCANS
YOU HAVE SO MANY MORE
OPPORTUNITIES TO MAKE MISTAKES
AS UGC AND UAC ARE DIRECT
SUBSTITUTIONS WITH HEXOSE, OR
DEOXYHEXOSE TO BE PAIRED WITH SO
ALL THE PROBLEMS WE HAVE WITH
SALIC ACID WE WILL HAVE WITH
UGC.
NOW IF WE WERE TO LOOK AT A
PROSTATE CANCER SERUM DATA SET,
TAKEN FROM THIS PUBLISHED DATA
SET, THANK TO YOU THE AUTHORS
WHO PROVIDED THIS DAT TO BE
FREELY AVAILABLE, YOU SEE THIS
BIMODAL CHROMEATOGRAPHIC PEAK
FOR THIS GRID SERVICES KAN--KANA
AND ANOTHER PEAK PRIMATES MORDAL
DPLI KAN--KANA, AND ANOTHER PEAK
BUT IT'S GAINED A HEXOSE AND A
FUCOSIDOSIS.
THEY HAVE ADENTICAL PEAK APEXS
EVEN FOR THE 2 DIFFERENT MODES
COULD THIS BE AN AMMONIUM
DEDUCTION FOLLOWED BY
SUBSTITUTION BECAUSE THIS WAS IN
OUR DATABASE?
HOW COULD WE DISTINGUISH THESE 2
STRUCTURES IF WE CAN'T SEE
RELIABLE FRAGMENTATION OF THE
GLYCAN.
WELL, MAYBE THAT'S A FLUKE BUT
WHAT IF WE WERE TO LOOK AT IT IN
THE CONTEXT OF THE ENTIRE
CHROMEATOGRAPHIC DISTRACTION
WITH ALL THE DPLI KAN--KANAS
ATTACHED TO IT.
WE THIS CLUSTER HERE OF
DISCIPLINARYSILATED FORMS AND
TRISILATED FORMS MUCH LATER AND
MONOSILATED FORMS MUCH EARLIER
BUT THAT MONOSILATED FORM WE
WERE JUST TALKING ABOUT AS
AMBIGUOUS SHOWS UP IN THE
DISCIPLINARYSILATED CLUSTER, IT
BE BE MISS PLACED OUR
CHROMATOGRAPHY IS WISHY WASHY WE
CAN'T TRUST IT ALL THE TIME.
WHAT IF WE LOOKED AT ANOTHER
DATA SET.
DO WE SEE THE SIMILAR PATTERN
THAT MAYBE WE COULD STRUOF THE
THIS FURTHER?
BUT WE HAVE THE SAME BUNDLING OF
TRI THAT WILLATED FORMS AND
DISCIPLINARY THAT WILLATED FORMS
BUT WE SEE THERE ARE FORMS IN
THE TRI THAT WILLATED CLUSTER
AND EVEN MONOCYTE FORMS IN THE
DISCIPLINARY THAT WILLATED
CLUSTER, DIFFERENT BACKBONE,
DIFFERENT DATA SETS ISSUES
DIFFERENT CANCER TYPES BUT STILL
WE SEE THE SAME THING.
CAN WE EXPLAIN THESE OVERLAPS.
WELL, WE CAN LOOK FOR SIGNATURE
IONS PERHAPS, WELL, HERE AT THE
2 TANDEM MASS SPECTRA, I
APOLOGIZE IN ADVANCE, THIS IS
GOING TO BE A COUPLE OF TEND
RAIN THIS TALK, SO THEY LOOK
SIMILAR, THERE'S MINOR VARIATION
IN THE IONS BUT FUNDAMENTALLY
ENOUGH, THERE ARE SALIC ACID TO
HEX NAC, TO THE IRON RATIO THAT
WERE CLOSE, SO IF THERE WERE A
WHOLE UNIT DIFFERENCE THERE
WOULD BE MORE PERCEPTIBLE
DIFFERENCE IN THE RATIO OF THOSE
2 IONS ABUNDANCES.
SOME CREDENCE THAT COULD BE
AMMONIA SUBSTITUTION, WHAT IF WE
LOOK AT ANOTHER PAIR OF GLYCO
FORMS FOR THIS SAME PEPTIDE
BACKBONE?
WELL, WE SEE PRETTY MUCH THE
SAME SITUATION, THERE'S NO FUCOS
E CONTAINING IONS AND THE RATIO,
AND THE SODIUM RATIO LOOKS
PRETTY SIMILAR.
IS THIS ENOUGH EVIDENCE TO CLAIM
THAT THIS IS THAT PESKY AMMONIUM
SUBSIDIARY TUITION AGAIN?
I WOULD ARGUE YES AND I HOPE TO
CONVINCE EVERYONE OF THAT SOON
BUT THE CONSEQUENCES OF NOT
CORRECTING THESE THINGS COULD
MEAN THAT YOUR QUANTIFICATION OF
GLYCO FORMS COULD BE OFF BY AS
MUCH AS 50%.
THE ASHES BUNKEDDANCE FROM THAT
CLAIM ADDUCT INCREASES THE
ABUNDANCE OVERALL FOR THE WHOLE
FLIEK O FORM CONSIDERABLY.
SO NOW I NEED TO CONVINCE YOU
THIS IS REAL.
SO FROM THE EARLIER DATA SET, WE
NEED TO SAY IF YOU WERE TO TAKE
2 PEPTIDES WITH GLYCANS THAT
DIFFER BY A SINGLE
MONOSACCHARIDE AND LOOK AT THEIR
DIFFERENCES IN RETENTION TIME,
WE OBSERVE A SYSTEMATIC OR
REGULAR RETENTION TIME CHANGE
ASSOCIATE WIDE THAT
MONOSACCHARIDE, HEX NAC AND
HEXOSE BOTH SHIFT A BIT EARLIER
AND FUCOSE HAS SLIGHTLY MORE
VARIATION EARLIER ON LATER,
HOWEVER SALIC ACID ALMOST CAN
ALWAYS SHIFT LATER BY A LARGE
AMOUNT.
BUT IT'S A PRETTY WIDE
DISTRIBUTION EMPLOY THAT WOULD
BE CONCERNING BECAUSE YOU WOULD
NOT WANT TO SEE ANY SUCH
VARIABILITY ANY TOOL YOU USE TO
CLASSIFY AN IDENTIFICATION.
BUT WE CAN EXPLAIN THAT BECAUSE
THE CHANGE IN RETENTION TIME FOR
A MONOSACCHARIDE VARIES OVER
TIME MUCH EARLY IN THE
EXPERIMENT, THE CHROMEATOGRAPHIC
RADIANT, THE RATIO OF THE ALPHA
COMPONENT IS AT SOME LEVEL BUT
LATER IN THE EXPERIMENT IT'S AT
ANOTHER LEVEL LEADING TO A
DRASTIC DIFFERENCE IN THE
CONDITIONS ON THE COLUMN,
LEADING TO THINGS FLOWING OUT A
DIFFERENT RATE.
WE CAN ALSO ENCOUNTER PROBLEMS
WHERE MANY DIFFERENT
MONOSACCHARIDES ARE DIFFERENT
AND MAYBE DIFFICULT TO
DISAMBIGUATE OR MAYBE THERE'S
NOT ENOUGH CONTRAST IN OUR DATA
TO ACCURATELY SOLVE 1 FROM THE
OTHER.
HOWEVER, THIS REGRESSION MODEL
THAT I'M SHOWING HERE EXPLAINS
95% OF THE VARIATION BETWEEN
PREDICTED AND OBSERVED
CHROMEATOGRAPHIC APEX TIMES.
SHOWN ANOTHER WAY, IF IF OUR
MODEL WERE PERFECT, EVERY DOT
HERE WOULD BE ALONG THIS MIDDLE
BEND OF THIS RESIDUAL PLOT BUT
WHAT WE'RE SEE SUGGEST THAT
WITHIN THESE CONFIDENCE
INTERVALS 95% OF THE VARIANCE IS
EXPLAINED.
WE HAVE A SMALL POPULATION OF
POINTS THAT ARE OUTSIDE OF OUR
PREDICTED INTERVAL, IT WAS MAYBE
MISIDEBTIFICATIONS, THEY MAY BE
CHROMEATOGRAPHIC ARTIFACTS,
REQUIRES FURTHER STUDY.
LET ME NOW DEFINE THE MODEL THAT
I'M USING, I WILL TALK ABOUT THE
APEX TIME OF A GLYCO PEPTIDE FOR
THE FUNCTION OF THE DPLI
--GLYCAN AND
THE FUNCTION IT'S ATTACHED TO.
EVERY PEPTIDE WILL HAVE ITS OWN
STARTING EVOLUTION TIME, THIS IS
THE SAME SORT OF STARTING POINT
YOU WOULD GET FROM 1 OF THOSE
NEW FANGLED DEEP LEARNING BASED
PEPTIDE RETENTION TIME
PREDICTERS THAT EVERYONE IS
USING IN NORMAL PROTEOMICS, BUT
FOR THE PURPOSES THE STARTING
POINT FOR THE EVOLUTION ORDER FF
ALL THE GLYCO FORMS OF THAT
PEPTIDE AS WELL, WE THEN ADD
SOME SHIFT, SPECIFIC TO
EACH,AMOUNT OF SACCHARIDE
COMPONENT IN THE DPLI KAN--KANA
COMPOSITION THAT IS MULTILIE
PLIED BY THE NUMBER OF TIME WEES
HAVE THAT MONOSACCHARIDE
COMPONENT PLUS AN ERROR.
BECAUSE THIS CHANGES OVER TIME,
WE NEED TO HAVE THE MODEL ALSO
CHANGE OVER TIME AND WHILE WE
COULD FIT A MODEL THAT USES
PRIOR INFORMATION SEQUENTIALLY
THAT RUNS THE RISK OF ABSORBING
ERRORS ON 1 END BUT NOT THE
OTHER END SO, FROM EARLIER BUT
NOT LATER.
ADDITIONALLY WE NEED A WAY TO
MAKE SURE THOSE AMENIUM ADDUCTS
DON'T CUE THE WAY THAT THE MODEL
LEARNS, SO WE NEED TO START BY
FITTING THE MODEL ON THE FLIEK O
PEPTIDES THAT ARE IDENTIFIED
BOTH AMMONIA OR ADDUCTED IF WE
DON'T SEARCH FOR AMMONIUM ADDUCT
WE CAN'T RULINNATED ANTIGENS
THEM OUT BUT WE EXPECT THE MODEL
TO BE ROBUST.
THAT ITERATIVELY FIT THE MODEL
THAT INCREASINGLY LESS CONFIDENT
OBSERVATIONS IN EACH OF THESE
TIME BUCKETS BY SAYING WELL,
THESE GLYCO FORMS WERE INCLUDED
IN THE LAST FIT SO WE BELIEVE
THE MODEL WILL BE BETTER AT
PREDICTING THE CORRECT
IDENTIFICATION FOR THIS NEW
GLYCO PEPTIDE THAT WE'RE NOT YET
CONFIDENT IN ANDA ADD THAT
INFORMATION TO THE NEXT MODEL
CAN TRAIN ON.
ADDITIONALLY WE CAN CORRECT GLUE
MARIOUS CAN IDENTIFICATIONS ON
EACH GLYCO PEPTIDE AS THE MODEL
RUNS PERFORMS INCREMENTAL
REVISION SO THAT WE CAN CORRECT
FOR ERRORS BEFORE WE LET THEM
PROPAGATE THROUGH THE MODEL.
SO SAY WE HAVE THAT SITUATION I
DESCRIBED EARLIER WHERE WE CAN'T
TELL THE DIFFERENCE BETWEEN THIS
ANTENNA AND THAT ANTENNA AND WE
HAVE RESERVED ATTENTION TIME FOR
THAT GLYCO PEPTIDE SO WE FIND
OUT WHICH CANDIDATE IS BEST, BUT
THIS MODEL IS SPECIFIED A AS
LINEAR MODEL SO WE CAN DEFINE
SOME SCORE AS A FUNCTION OF THE
PREDICTION INTERVAL SO JUST A
CONFIDENCE INTERVAL AROUND WHEN
THE EARLIEST POINT IS THAT IS
OBSERVED AND WHEN IT WOULD END,
OR WHEN WE WOULD NOT EXPECT IT
TO BE OBSERVED LATER.
IF WE WERE TO USE 1 GLYCAN WE
WILL GET A PREDICTION GIVEN IT'S
STARTING AT A CERTAIN TIME
SELECT THE MODEL AT 23 MINUTES
AND ANOTHER OF THE OTHER GLYCO
FORM AT 29 MINUTES WHICH GIVES
US THIS NEW TIME WHICH SUGGEST
THIS IS IS THE CORRECT
ADDITIONAL ANTENNA.
WE CAN DEFINE THE SCORE IN TERMS
OF THE PREDECLARATION INTERVAL
HERE, BUT THE SPECIFICS AREN'T
IMPORTANT.
TO AVOID LETTING THIS REVISION
PROCESS RUN RAM PANT, WE CAN
INCLUDE A CONSTRAINT THAT WE
CAN'T REDUCE THE AMOUNT OF
SIGNAL EXPLAIN BY MORE THAN 5%
SO WE CAN'T GET RID OF A SODIUM
IEKSON THAT'S ABUNDANT OR A
PEPTIDE PLUS 1 ION LIKE A
DPLUICOSE ATTACHMENT THAT WOULD
UNDERMINE THE CORRECT
IDENTIFICATION EVEN IF THE MODEL
IS REALLY CONFIDENT BECAUSE IT'S
NOT LEARNED THE RIGHT ANSWERS
YET.
SO IF WE HAVE THIS IN THE
ADDITIONAL CHANGE IN THE
RADIATION BECAUSE THE AUTHORS
DECIDED AT 180 MINUTES TO REALLY
SPEED UP THE CHANGE IN BETA TO
ALPHA WE CAN OBSERVE THE MODEL
PICKS THAT UP AND UPDATES
PRIMERS ACCORDINGLY.
IT DOES HOWEVER HAVE A POINT
WHERE, IT IS USHED DETERMINED TO
DIFFERENTIATE HEX NAT FROM
HEXOSE SO TD 2 PARAMETERS WORK
WELL TOGETHER AND THIS EXPLAINS
98% OF THE OPERATION OBSERVED.
SO LOOKING AT THOSE PLOTS WE CAN
SEE THE SAME TRENDS FOR FUCOSE
AND HEX NAC ARE PRESENT AND
DON'T CHANGE BY THAT MUCH BUT WE
CAN SEE THAT SALIC ACID DELTAS
ACTUALLY FORM ASKEWED
DISTRIBUTION INSTEAD OF A NORMAL
DISTRIBUTION WHICH WE SAW
EARLIER WHICH REFLECTS THAT
SHARP CHANGE IN ITS BEHAVIOR
WHEN THE GRADEIENT CHANGED NOW
WHAT ARE THE CONSEQUENCES IF YOU
USE THIS FOR IDENTIFICATION
PURPOSES.
IF YOU WERE TO RUN A DATABASE
SEARCH WITHOUT AMMONIUM ADDUCTS
OR RETENTION TIME CORRECTION,
YOU WOULD IDENTIFY OVER 580
DISTINCT GLYCO PEPTIDES AND YOU
LIKE THAT NUMBER BECAUSE IT'S
BIG.
BUT IT YOU WERE TO SEARCH FOR
AMMON CRUM ADDUCTS THAT NUMBER
WOULD FALL DOWN TO 474 BECAUSE
YOU TAKE GLYCANS LIKE THIS, AND
MERGE THEM INTO OTHER DPLI
KAN--KANAS LIKE THIS.
REDUCING THE TOTAL NUMBER OF
DISTINCT GLYCO FORMS THAT YOU
IDENTIFIED BUT HAVING A SMALLER
MORE CORRECT SUBSET.
AND ALSO IMPROVE YOUR
QUANTIFICATION ACCURACY.
LIKE I SAID BEFORE, YOU CAN SEE
UP TO A 50% INCREASE IN
ABUNDANCE OF RILE GLYCO FORMS
WHEN YOU CORRECT FOR ADDUCTS.
IF YOU FURTHER USE RETENTION
TIME MODELING, AND NOT JUST
EXACT OVERLAP TO CORRECT FOR
ADDUCTION, YOU CAN SEE A SET OF
38 ADDITIONAL CORRECTIONS
COMPARED TO WHAT YOU GET FROM
TOTAL INTERSECTION AND EVEN A
FEW MORE IDENTIFICATIONS GET
CORRECTED BY THE ABILITY TO
CORRECT THOSE OTHER AMBIGUITYS
LIKE MONOCISE O TOPIC PEAK
ERRORRORS OR THOSE LARGE
SUBSTITUTION SO CAN YOU SEE A
HUGE DIFFERENCE IN THE RESULTS
YOU GET, BUT YOU KNOW I CAN
CLAIM WHATEVER I LIKE IF I CAN'T
SHOW THAT THERE'S AN UNCERTAINTY
ESTIMATE THAT'S ASSOCIATED WITH
THE CORRECTIONS, IT DOESN'T
MATTER, HOWEVER, I CAN TAKE THE
PREDICTIONS THAT I'VE MADE AND
SHUFFLE THE ASSOCIATED LABELS
AND SHOW THAT THE MODEL STILL
PROVIDES USEFUL RESULTS EVEN AT
A RELATIVELY LARGE DISTANCE FROM
THE TRUSTEES, AND THE PREDICTION
INTERVAL.
HOWEVER, THE PREDICTION INTERVAL
IS ONLY A FEW MINUTES WIDE, SO
THIS ISN'T ENOUGH TO DRASTICALLY
DISIEW IDENTIFICATIONS.
TO BACK UP THAT CLAIM, THE
PREDICTION IS DRAWN HERE,
PREDICTION FROM THE CENTER OUT
TO THESE ORSWRONTAL LINES, IT'S
ONLY ABOUT 4 MINUTES AND WE CAN
SEE THERE ARE VERY FEW
ASSIGNMENTS THAT FALL OUTSIDE
THAT RANGE.
IF YOU DON'T USE RETENTION TIME
MODELING WITH THIS DATA SET YOU
COULD END UP MISSING FLIEK O
FORMS ENTIRELY BECAUSE ERRORS
LEAD TO THEM NOT BEING
ASSIGNABLE AT ALL.
THIS WOULD BE COMPLETELY
MISASSIGNED BECAUSE IT DOESN'T
HAVE SUFFICIENT EVIDENT IN THE
FRAGMENTATION ALONE TO CONVINCE
YOU OF THIS LARGE GLYCO FORM
EVEN THOUGH THE RETENTION TIME
FITS.
SIMILARLY, IT CAN HELP TO
SUPPORT THE PRESENCE OF OTHER
LOW QUALITY FRAGMENTATION EVENTS
ON OTHER GLYCO PEPTIDES, AGAIN
WE DON'T HAVE SUFFICIENT
EVIDENCE TO ASSIGN EXACTLY THIS
GLYCAN COMPOSITION.
BUT RETENTION TIME AND SUPPORT
EVIDENCE FROM OVERLAPPING FLIEK
O FORMS HIT, AND FINALLY NO
PRESENTATION IS COMPLETE WITHOUT
MENTIONING SARS-COV-2, GLYCO
PROTEOMICS HERE IS A SAMPLE FROM
1 OF TD ORGANIZERS VERY OWN DATA
SETS, THANK YOU VERY MUCH FOR
PROVIDING THIS SLIDE TO ME, WE
CAN SEE THAT IT PRODUCED LARGE
RETENTION TIME DELTASENTIOUS
SPECIALLY FOR THIS LONG RADIANT
OF OVER 400 MINUTE THIS IS MODEL
EXPLAINS 90% OF THE VARIABLE
ITSELF, AND PART OF THIS HAS TO
DO WITH JUST THE MAGNITUDE OF
THE DELTAS THAT WE SEE.
HERE'S THAT SAME RERIDDUAL PLOT
WHERE WE SEE THAT MOST OF THE
PREDICTIONS FOR THOSE
IDENTIFICATIONS FALL WITHIN THE
PREDICTION WITH APPROXIMATELY 10
MINUTES EVEN THOUGH WE HAVE A
HUGE SPREAD OF ADDITIONAL DIERKS
DENTIFICATIONS.
BECAUSE OF THE DEPTH OF COVERAGE
ON THIS DATA SET IT'S MUCH
EASIER FOR ANY SEARCH ENGINE TO
INCORRECTLY ACCEPT TOO MANY
IDs BECAUSE WE DON'T HAVE A
VERY STABLE FALSE DORPHY RATE
ESTIMATION PROCEDURE FOR GLYCO
PEPTIDES, HOWEVER, WE CAN USE
THIS ADDITIONAL COMPLIMENTARY
INFORMATION TOOL TO RILE OUT
SOME OF THESE REALLY WILD
OFFBASE IDENTIFICATIONS THAT IF
WE CHOOSE TO.
WE CAN ALSO USE IT TO SUPPORT
SULFATED GLYCO PEPTIDE
IDENTIFICATION, HERE WE CAN SEE
WE HAVE ENTIRELY NEUTRAL GLYCO
FORMS THIS PUNNEDLE CONTAINS
MONOSILLATED GLYCO FORMS AND
MONOSULFATED GLYCO FORMS AND
THEN WE HAVE A BUNDLE OF TBLIEK
O FORMS COMING OUT MUCH LATER
SULFATION DOESN'T REALLY HAVE A
GOOD RELIABLE SIGNATURE ION LIKE
HEXON NAC SULFATE BUT BASED ON
RETENTION TIME AND THIS TINY
LITTLE PEAK WE CAN SAY THIS IS
CORRECT DPLI KAN--KANA
ASSIGNMENT SO IN CONCLUSION,
RETENTION TIME IS ANOTHER
IMPORTANT DIMENSION FOR
CONTROLLING THE ACCURACY OF YOUR
GLYCO PEPTIDE ESTIMATION AND
IDENT IIVES, COMMON DPLI
KAN--KANA MODIFICATIONS MAY BE
CONCEALED BY NEARLY ISOBARIC
MASSES IF YOU DON'T LOOK FOR
DELTA RETENTION TIMES AND
UNKREKED ADDUCTS CAN CORRUPT OR
CONSEE SEAL QUANTITATIVE
MEASUREMENTS OF GLYCO FORM
ABUNDANCES, THANK YOU ALL FOR
YOUR PATIENCE IN SITTING THROUGH
THE TALK.
I WOULD LIKE TO THANK THE
RESEARCH GROUP AT BOSTON
UNIVERSITY, MY Ph.D. ADVISORS,
[INDISCERNIBLE] AND THE PEOPLE
WHO GENEROUSLY MADE THEIR
THEY'RE VALUABLE DATA PUB LIEBLY
AVAILABLE.
ALL THE SOFTWARE SHOWN HERE IS
FREE AND OPEN SOURCED, YOU CAN
GET THE SOURCE CODE AT THIS URL
AND PREBUILT GRAPHICALLY
INTERFACE AT THIS URL.
THANK YOU AGAIN FOR YOUR TIME
AND THANK YOU TO THE PRESENTERS
FOR NOT KICKING ME OFF.
>> THANK YOU JOSHUA, THAT WAS
REALLY A MAGNIFICENT AND I'M
GOING TO HAVE TO MOVE ON IT SEE
IF WE CAN PUT IN SOME QUESTIONS
HERE FOR THE MANLE MEMBERS FOR
JUST A FEW MINUTES.
THERE'S A QUESTION HERE FOR
SRIRIAM, CAN YOU VALIDATE THIS
FOR A SET OF GRIEK O GENES BY
OBSERVING A GEICO CHANGE IN THE
GLUE MARIOUS CONE?
HOW IS THIS DONE EXPERIMENTAL,
SRIRAM CAN YOU GIVE US INSIGHT
INTO THAT?
>> I THINK THE QUESTION IS
BASICALLY THE CORRELATION
BETWEEN GENE EXPRESSION AND THE
GLYCAN AND I THINK THIS IS THE
SORT OF, I THINK IF YOU JUST
MEASURE THE TRANSCRIPT LEVELS
AND YOU LOOK AT THE GLYCAN, THE
RELATIONSHIP IS HIGHLY
NONLYNNIAN IN TERMS OF HOW IT'S
TONE.
AND THAT'S NOT BECAUSE THERE'S
NO RERELATIONSHIP.
THE RELATIONSHIP EXISTS IN MY
OPINION, JUST NOT KNOWN WHAT THE
RELATIONSHIP EXACTLY IS.
I THINK YOU NEED TO CONSIDER
ADDITIONAL FACTORS LIKE
TRANSCRIPTION FACTOR
PARTICULARLY AND SORT OF SORT OF
REGULATION OF THAT PARTICULAR
GENE AND OTHER FACTORS THAT
REGULATE HOW DOES THAT GO IN
THIS THE CONTEXT OF THE PATHWAYS
THAT ARE THERE AND SO ON?
SO, YES, SO THE SHORT ANSWER IS
EVIDENCE THAT WE'VE SEEN IN THE
GLYCO GENE CHANGES DO RETURN OF
RESULTSALATE WITH EXPERIMENTAL
PROVIDED DATA FOR THE DPLI
KAN--KANA IN MANY, MANY, MANY
INSTANCES AND THE PEOPLE THAT
PAPER WE FINALLY WRITE WILL HAVE
A WHOLE TABLE SHOWING CASE WHERE
IS THEY HAVE HAD AGREEMENT WITH
IT BUT THERE'S A LOT MORE TO BE
DONE IN TERMS OF GENE EXPRESSION
REGULATION AND HOW IT'S
REGULATED AND JUST GETTING
FUNDAMENTAL AND UNDERSTANDING OF
THAT PROCESS WHICH WE CURRENTLY
DON'T HAVE BUT WE'RE WORKING
TOWARDS IT.
>> CAN I ADD SOMETHING, I'M
GUILTY OF THIS, MY LAB GENERATED
ALL KINDS OF GLYCAN PROFILES AND
YOU CAN SEE AND TRY TO CORRELATE
THEM IF GENE EXPRESSION PROFILES
AND YOU CAN MIC PICK OUT THINGS
THAT MAKE SENSE AND THINGS THAT
DON'T MAKE SENSE AND I'M
WONDERING THIS IS A CHALLENGE
FOR THE FIELD IF THERE'S A WAY
TO REPRESENT THE GLYCAN PROFILE
NOT AS A COLLECTION OF AIR BARS
OF DIFFERENT--THE ASHES
BUNKEDDANCE OF DIFFERENT GLYCAN
STRUCTURES BUT SOME KIND OF
VECTOR THAT SUMMARIZES ALL THE
RATIVE ABANDANCE OF ALL THE GLUE
MARIOUS CANS AND I DON'T KNOW
WHAT THIS IS BUT WE NEED SOME
UNIFYING QUANTITATIVE MEASURE
THAT,A LOWS US TO MORE ROBUSTLY
DO CORRELATIONS I THINK.
>> I THINK THAT'S MORE OF A
COMMENT THAN A QUESTION, MIKE, I
BELIEVE?
>> [LAUGHTER]
SORRY.
>> WELL THERE IS A QUESTION HERE
THAT'S RELATED AND THAT IS HOW
WOULD 1 GO ABOUT ACCESSING THE
GENES AND GENE ANNOTATIONS FROM
GLYCO ENDS ONCO ISA IT A
PUBLICLY AVAILABLE RESOURCE?
>> IF YOU SEND ME AN E-MAIL I
CAN SEND YOU THE LINK IT'S ON
THE GITHUB PAGE, IT'S OPEN
SOURCED SO IT'S NELL-NEB, YOU GO
TO THE LAB YOU WILL SEE THAT THE
ONTOLOGY IS ALREADY DEPOSITED,
IT'S BEEN FORMATTED IN THIS
MOMENT OF TIME, IT'S IN FINAL
REFINEMENT BEFORE SUBSITTING IF
TO OBR ONTOLOGY AND IT'S JUST
MORE COSMET I CHANGES BEING DONE
TO MAKE IT LOOK PRETTIER THAN
FUNCTIONAL INFORMATION THAT'S
CHANGED BUT IT'S FREELY
AVAILABLE AND OPEN SOURCED WE DO
IT ALL ON GITHUB AND YOU CAN SEE
IT WHEN IT COMES UP.
>> GREAT.
AND 1 MORE QUESTION HERE:
SRIRAM, DO THE GLYCOSYLATION
PATTERNS WITHIN ORGAN SYSTEMS
OVERLAP FOR DIFFERENT CANCER
SUBTYPES, FOR EXAMPLE,
EPITHELIAL VERSUS MESSENTERY ENK
MALVERSUS ENDOKRIEN AND CAN YOU
SHED LIGHT ON OVERLAPS OR
DEFENSES BETWEEN MALIGNANT AND
PRECURSOR LESIONS THAT DO EXIST?
>> YEAH, SO I DON'T THINK I HAVE
THE--I DON'T THINK I HAVE--
>> ANOTHER SEMINAR I GUESS.
>> WHAT'S THAT?
>> IT'S ANOTHER SEMINAR.
>> I GUESS IT'S A REALLY THOUGHT
PROVOKING PROCESS, I THINK IT'S
CRITICAL FOR PATIENT CARE,
PEOPLE WANT TO KNOW ARE
THEY--WHAT'S THE STATUS WHEN YOU
GO DOWN AND DO THESE
MEASUREMENTS ARE THEY GOING TO
GET SOMETHING THAT'S GOING TO BE
LIFE THREATENING OR JUST
SOMETHING REALLY BENIGN OR
SOMETHING THAT'S NOT REALLY
CANCEROUS IN NATURE AND I DON'T
KNOW THAT I HAVE THE EXACT
ANSWER BUT I CAN GO DOWN TO
SAYING WE STILL HAVE TO DO THIS
THING IN TERMS OF WHETHER
PROGRESSION MAPS CIBOL UP THE
STAGE SPECIFIC INFORMATION ON
THEM AND THAT'S SOMETHING WE ARE
WORKING ON, DO THESE PUBLISHING
MAPS AND THE GLYCO GENE PICK THE
SPECIFIC THING UP.
MANY OF THE CANCERS ARE LOOKING
AT HERE IN A PARTICULAR NATURE
PARTICULARLY FOR THE BREAST
CANCER SO I'M NOT SURE CAN YOU
ANSWER YOUR QUESTION ON
ENDOCRINE AND DIFFERENT TYPES
BUT, I GUESS I'M DOING A BAD JOB
OF ANSWER THIS QUESTION EXCEPT
TO SAY THAT I REALLY DON'T KNOW.
YOU KNOW THERE ARE SOME
OVERLAPS, THERE ARE SOME
DISTINCTIONS BUT YOU HAVE TO
REALLY FOCUS ON FINDING OUT
WHETHER DIFFERENT CELL TYPES IN
THE SAME ORGAN GIVE RISE TO
DIFFERENT SIGNATURES AND WE
HAVEN'T LOOKEDDA THE IT, THE
BREAST CANCER WORK WE'VE DONE IS
BASICALLY HORMONE RELATED IN
TERMS OF HER 2 AND DIFFERENT EGF
RECEPTOR FAMILIES.
THERE ARE NO MEASURE OF SAYING,
YOU KNOW ARE WE GOING TO BE ABLE
TO PICK UP EARLY PEOPLE IN THIS
LATE STAGE OF THE GAME.
>> I HAVE A QUESTION FOR RADO, I
REALLY APPRECIATED YOUR COMMENT
ABOUT HOW GAG STRUCTURE AND
SULFATION PATTERNS ARE GOING TO
INFLUENCE A HUGE ARRAY OF
DIFFERENT SIGNALING PATHWAYS,
IT'S NOT 1 THING, - IT IS MANY,
THINGS.
SO THE QUESTION, I GUESS IS
THERE I'M ASSUME THRG ARE A LOT
OF BIOINFORMATIC RESOURCES OUT
THERE THAT PARSE OUT SIGNALING
PATHWAYS, HOW WELL DO THEY
OVERLAY THE INFLUENCE OF
MODULATORS LIKE GLYCOGRID
SERVICES KAN--KANAS AFTER
ACTIVATION OF SIGNALING
PATHWAYS.
ARE THERE INFORMATIC TOOLS TO
HELP MODEL THAT.
>> I DON'T KNOW.
SO WHEN WE LOOK AT THAT, WE JUST
BASICALLY DO SOME KIND OF
LITERATURE SEARCHES AND TRY TO
BUILD SOME KIND OF MAPS OF
INFLUENCE BUT, IT ACTUALLY--THE
STUDENTS STRUGGLE THROUGH IT AND
I DON'T KNOW ABOUT RESOURCES
THAT I WOULD POINT OUT.
>> SO THEREYA A HOLE THERE.
>> YEAH.
>> OKAY, MIKE.
ANY OTHER QUESTIONS?
>> ONE LAST QUESTION FOR JOSH.
SO CAN YOU TELL US HOW WE'RE
DOING AS A COMMUNITY?
ARE WE MISSING A LOT OF STUFF?
ARE WE OVERANALYZING?
YOU GAVE US NICE CASE STUDIES
BUT HAVE YOU FELT MORE BROADLY
TO SEE HOW MUCH WE'RE FOOLING
OURSELVES?
>> THERE'S A SIGNIFICANT
FRACTION OF THE DPLI KAN--KANA
COMPOSITIONS REPORTED IN DPLI
KAN--KANA AND I FORGET THE NAME
OF THE DATABASE MAINTAINED IN
AUSTRALIA THAT SHOW COMPOSITIONS
THEY'VE TAKEN FROM PAPERS THAT
WERE NOT AWARE OF THIS
PHENOMENON.
THERE ARE SEVERAL NEW TOOLS THAT
ARE COMING OUT IN THE LAST 2 OR
3 YEARS THAT ARE STARTING TO
INCLUDE OMONIA REDUCTION IN PART
OF THEIR SEARCH STRATEGY AND THE
FURTHER GLYCO FEE AND DECIPHER
TO NAME JUST 3 THAT CAME OUT
RECENTLY HOWEVER, THESE AREN'T
REALLY GOOD AT EXPLAINING ALL OF
THE DIFFERENT TYPES OF
AMBIGUITIES THAT YOU WOULD
OBSERVE, ADDITIONALLY, IF YOU
WERE TO USE AN OFF THE SHELF
TOOL LIKE BIONIC THAT IS
DESIGNED FOR THIS TYPE OF WORK,
YOU WON'T GET ANY SORT OF
CORRECTIONS FOR THESE.
THE REAL THREAT OF COURSE IS
THAT YOUR GLYCO--YOUR GLUE
GLYCON IS
TOO SMALL AND YOU'RE MISSING OUT
ON NICHE CASES BUT WE ONLY
EXPECT WHAT WE EXPECT TO FIND.
IN--I HAVE A 3 OR 4 CANCER DATA
SETS THAT I'VE LOOKED AT, AND IN
AT LEAST 2 OF THEM, THE ACTUAL
CLAIMS OF DIFFERENTIAL ABUNDANCE
OF TBLIEK O FORMS AT A SPECIFIC
SITE IS CORRUPTED BY THIS TYPE
OF ERROR WHERE THEY OBSERVED
THAT AMMONIUM ADDUCTED ISOBERNEA
DEETIC FORM IS THE THING THAT IS
DIFFERENTIALLY EXPRESSED WHEN
IT'S REALLY JUST THE FRACTION OF
OMANYIA REDUCTION WHICH IS
INTRODUCED DURING SAMPLE PREP
THAT'S DIFFERING.
SO IT'S ACTUALLY A BATCH EFFECT
MAKING IT VERY DIFFICULT TO GIVE
YOU A HARD NUMBER ABOUT HOW BAD
IT IS.
>> SO MAYBE JUST A FOLLOW UP, SO
PEOPLE TRY TO ANCHOR THE GLYCO
PROTEIN COMPLEXEMIC ANALYSIS BY
DOING GLUE MARIOUS KOAMIC
ANALYSIS TOO TO DEFINE WHAT'S
ACTUALLY THERE IN AN ORTHOGONAL
WAY ARE THOSE BETTER ON MAYBE
THERE AREN'T ENOUGH DATA SETS
OUT THERE TO JUDGE IT YET?
>> THERE AREN'T MANY DATA SETS
TO DO THAT.
IT DOES TURN OUT TO BE BETTER
BECAUSE YOU CAN BE VERY
PERMISSIVE ON THE GLYCAN SEARCH
AND USE THAT TO GIVE YOU AN
UPFRONT PROFILE.
OBVIOUSLY THERE ARE LIMITS TO
DEPTH ESPECIALLY IF YOU WANT TO
THEN DRILL DEEPER WITH MASS
SPECTROMETRYOT GLYCANS WHICH
INVOLVES MORE SAMPLE HANDLING.
GLYCONNECT AND COMPOSER BOTH
GIVE US A WAY TO--GO GET THOSE
SAMPLE SPECIFIC GL YKOAMS IF WE
KNOW THEY'RE AVAILABLE TO US AND
THE ORGANISM OF INTEREST IS
INCLUDED THERE, HOWEVER, THOSE
NET WORKS WILL BE NECESSARY PLEA
INCOMPLETE.
AND SO, THESE EXPLORATORY
EXPANDED SYRUP SPACES WILL STILL
BE NECESSARY ANCHORING THINGS IN
EVERYTHING IN THE KNOWN SET
FIRST AND THEN THE SPECULATIVE
STUFF FURTHER OUT IS IMPORTANT.
I WANT TO TALK ABOUT ANOTHER
TECHNIQUE THAT I DEVELOPED
CALLED GLYCAN NETWORK SMOOTHING
WHICH DOES THAT BUT THAT THERE'S
ONLY TIME FOR 1 TALK.
>> MICHAEL, DOUG HAS 1 LAST
QUESTION, MAYBE TO CLOSE OUT THE
SESSION?
YOU WANT TO READ IT.
>> SURE.
I SEE IT.
DOUG SAYS HOW WOULD YOU RATE THE
USABILITY OF THE APPROACH THAT
YOU DESCRIBE?
HOW CAN ITS ADOPTION BE
PROMOTED?
I'M THINKING ABOUT THE GAP
BETWEEN SOFTWARE DEVELOPED AS
PART OF A RESEARCH PROPONENT
ECTOMYOSIN VERSUS A TOOL THAT BE
MADE AVAILABLE TO THE BROADER
COMMUNITY?
>> IT'S A GOOD QUESTION.
SO THE APPROACH I DESCRIBED IS
INTEGRATED TO THAT GLYCOPEPTIDE
SEARCH ENGINE THAT I WROTE.
OBVIOUSLY I USE IT AND A SMALL
MEMBER OF PEOPLE USE IT WHILE
THE OTHER TOOLS I MENTIONED
EARLIER HAVE REALLY LARGE REACH
IN THE COMMUNITY ESPECIALLY
BIONIC.
MY METHOD CAN COULD BE APPLIED
TO THAT SAME TYPE OF DATA I
DON'T NEED TO HAVE SPECIAL NSKS
ABOUT HOW THE SEARCH WAS DONE,
HOWEVER, WE DON'T HAVE A GOOD
WAY TO GET THE OUTPUT FROM 1
CLIEK O PROTEOMIC SEARCH TOOL TO
LOOK THE SAME AS EVERY OTHER
TOOL BECAUSE WE LACK
STANDARDIZATION IN HOW WE REPORT
GLYCO PEPTIDE IDs, IT'S A WORK
IN PROGRESS GIVEN ALL THE
DIFFERENT WAYS WE DO IDENTIFY
GLYCO PEPTIDES.
AS TO HOW RELIABLE THE TECHNIQUE
IS, IT IS SENSITIVE TO THE TYPE
OF DATA THAT YOU GIVE IT IF YOU
HAVE A VERY LARGE DATA SET AND
RELAXED FDR CONSTRAINTS, IT CAN
LEARN THE WRONG THINGS SO THE
PROCEDURE FOR AUTOMATICALLY
FITTING SUCH A MODEL, MAY BE
MORE DELICATE THAN I THINK IT IS
JUST BECAUSE I HAVE NOT SEEN IT
IN THE WILD.
[LAUGHTER]
>> OKAY.
THANK YOU FOR THE ANSWER JOSHUA
AND SRIRAM HAS I QUICK FOLLOW
UP, JUST BRIEFLY.
>> LIKE YOU WHAT SAID, MY
CONCERN IS ADDING MORE ADDUCTS
INCREASES DAILY BASIS THEA BASE
SIZE PARTICULARLY FOR LARGE
SAMPLE SYSTEMS WHERE YOU HAVE
SAY THE HUMAN PROTEIN COMPLEX I
DON'T MEAN THAT YOU'RE LOOKING
AT AND I'M JUST WONDERING
WHETHER ADDING VARIABLES CAUSES
MORE FALSE DISCOVERY UNLESS THE
PROGRAMS BUILT ARE REALLY,
REALLY, REALLY TIGHT AND I THAT
I SEE AS A CHALLENGE BECAUSE YOU
COULD ENTER IT 1 BY 1 AND POINT
THE DIFFERENCE OUT FROM A LARGER
SCALE THIS COULD BE A PROBLEM.
IN, THAT IS TRUE.
HOWEVER, WITH A COUPLE OF
CONSTRAINTS CAN YOU GREATLY
DIMINISH THAT.
FOR EXAMPLE, IF YOU ARE GOING TO
BE KEPTICAL OF ADDUKS ISSUES CAN
YOU LIMIT YOURSELF TO ONLY
ACCEPTING AN IDEPTICTION THAT IS
IESHES DENTIFIED BOTH UNADDUCTED
AND UNSUPPORTED ADDUBBED AND
THAT IS THE DEFAULT MODE FOR MY
TOOL THAT WILL LEAD TO
SITUATIONS WHERE YOU ONLY
FRAGMENT AND IDENTIFY THE
PRACTICING MENTORSHIP SKILLED
FORM YOU GET IT WRONG BUT
RETENTION TIME MODELING HELPS
YOU CORRECT THOSE SITUATIONS.
THERE IN AMMONIA ADDUKS THERE'S
NO SIGNATURE ION BECAUSE IT
FALLS APART AND LOOKS LIKE A
PROTEIN TANDEM INSPECTION BUT
OTHER TYPES LIKE METALLIC CAT
ION PRODUCTS ARE REALLY
DETEBILITYIBLE IN THE PEPTIDE
POLICE Y-AXONS THEY STRONGLY
BIND AND SHIFT EVERYTHING.
SO THOSE SHOULD NOT BE A HUGE
CONCERN FOR BALLOANING SEARCH
SPACE.
OBVIOUSLY, IMPROVEMENTS IN FDR
ARE ALWAYS NEEDED, GLYCO PEPTIDE
FDR TOOK A HUGE STEP FORWARD IN
2017 OR SO, BUT EACH THAT
TECHNIQUE HAS LIMITS.
>> OKAY, THANK YOU.
OKAY, THANK YOU JOSHUA AND ALL
OF OUR SPEAKERS TODAY WE ARE
GOING TO HAVE TO END THIS.
WE HAD A REALLY WONDERFUL
SESSION, GREAT QUESTIONS, AND
SO, MIKE, EVERYONE COMES BACK AT
1:00 O'CLOCK, IS THAT CORRECT?
>> 1:00 O'CLOCK.
YES.
>> OKAY, THANK YOU ALL AGAIN.
>> THANK EVERYBODY.
>> HELLO EVERYONE, WE HAVE 6
SPEAKERS AND THANK YOU TO THEIR
PARTIC PATHWAY GIVESITION AND AT
THE END OF THIS AFTERNOON'S
SESSION, WE WILL HAVE A PANEL
DISCUSSION WITH THE SPEAKERS
WILL BE AVAILABLE TO ANSWER THE
QUESTIONS.
AND SO I'M HAPPY TO INTRODUCE
OUR FIRST SPEAKER, HUGO BELLEN
FROM BAYLOR COLLEGE OF MEDICINE.
TAKE IT AWAY.
>> ALL RIGHT, SO I WILL TALK
ABOUT GLUCOSILL CERAMIDES ARE
GENERATED BY NEURONAL ACTIVITY
AND TRANSPORTED TO THE GLUE
MARIOUSA VIA EXOSTUDIES OF
MULTIPLE ENDOCRINES FOR
DEGRADATION UPON RELEASE OF THE
GLIAL TGF AND BMP FROM NEWT
FLIES.
THIS WORK WAS DONE BY A POST DOC
IN THE LAB.
SO CERAMIDE IS REALLY IMPORTANT
IN LIPID METABOLISM AND PLAYS A
REALLY IMPORTANT ROLE IN MANY
DISEASES BECAUSE WHEN THERE IS
LITTLE OR TOO MUCH, THERE ARE
PROBLEMS AND MANY TIMES THERE
ARE PROBLEMS WITH ALL KINDS OF
ISSUES, MEMBRANE FLUIDITY,
SIGNALING BETWEEN CELLS BUT ANY
NUMBER OF DISEASES AS SHOWN
SHEER, CAN YOU SEE IN THE
CERAMIDE IT'S SHOWN HERE, AND
WHEN THE PROCESS OF DEGRADATION
OF THE BACK TO CERAMIDE IS
IMPAIRED YOU GET GAWSHIER'S
DISEASE, AND THIS WILL BE THE
TOPIC OF THE TALK TODAY.
NOT ONLY FOR A MODIFIED BY SUGAR
AND [INDISCERNIBLE] AND GAL ACT
O SILL CERAMIDE PLAYS AN
IMPORTANT ROLE IN IMPAIRING THE
DEGRADATION OF [INDISCERNIBLE]
CAUSES A MORE DEBILITATING
DISEASE CALLED DEAD WHAT.
SO YOU CAN SEE THAT CERAMIDE IS
AT THE CENTER OF REALLY ONSET
DISEASES THAT ARE QUITE
SIGNIFICANT, MOST OF THEM IN
CHILDHOOD, AND WHEN WE LOOK AT
FINGER LIPID METABOLISM IT'S
QUITE COMPLICATED BECAUSE THE
SERIES POINTS MID IS PRODUCED
FIRST IN THE ER, WHEN SERIES
POINTSINE ARE BROUGHT TOGETHER
TO FORM INTERMEDIATES THAT ARE
EVENTUALLY IN THE ER AND END UP
IN CERAMIDE.
AND SERIES POINTS MID IS THEN
TRANSFERRED TO THE GOLGI AND IN
THE GOLGI, THERE ARE LOT EVER OF
CHANGES THAT CAN OCCUR TO
CERAMIDE AND YOU CAN MAKE
CERAMIDE AS ALREADY MENTIONED,
OR GLUE COCERAMIDE TO BUILD UP
ON THESE TO MAKE ALL OF THESE
DIFFERENT SERIES POINTS MIDS.
AND IT'S REALLY NOT WELL
UNDERSTOOD WHAT THEY'RE ALL
DOING BUT THEY ALL SEEM TO BE TO
SOME EXTENT IMPORTANT BECAUSE
DISRUPTION OF THE ENZYMES THAT
ARE PLAYING A ROLE IN THIS
PATHWAY CAN LEAD TO PRETTY
SEVERE PHENOTYPES.
SERIES POINTSA MINE IS EMBEDDED
IN THE PLASMA MEMBRANE AND
RETURN IN THE SPHLINGOSINE, AND
THIS CAN BE MODIFIED AS I SAID
AND THESE MODIFICATIONS ARE ALSO
TRANSFERRED FROM THE GOLGY TO
THE PLASMA MEMBRANE AND MAY PLAY
A ROLE IN THE VARIETY OF
PROCESSES.
NOW GBA WHICH IS GAWCHIER'S
DISEASE, WHICH IS AN ENZYME
THAT'S INVOLVED IN THE
HYDROLYSIS OF SUGAR FROM
CERAMIDE AND WHEN THAT ENZYME IS
IMPAIRED IT CAN LEAD TO A
VARIETY OF DISEASES FROM
CHILDHOOD TO ADULTHOOD IN ALL
CASES THE DISEASE IS RECESSIVE
AND I SHOULD NOTE THAT THE
PATIENTS OF KIDS WHO HAVE THESE
RECESSIVE DISEASE ARE OFTEN MORE
LIKELY TO GET PARKINSON'S
DISEASE, AND A FEW ARE LIKELY IN
STORAGE DISEASE BECAUSE THIS IS
A LYSOSOMAL STORAGE DISEASE WILL
HAVE ASSOCIATIONS WITH
PARKINSON'S DISEASE AND THE WAY
I THINK ABOUT IT IS THESE CASES
ARE VERY SEVERE CASES BECAUSE
BOTH COPIES OF THE PROTEINS
ENCODED BY THE GENES ARE
AFFECTED BUT ONLY 1 COPY IS
AFFECTED, IT MAY BE A MUCH MORE
INSIDIOUS AND SLOW PROCESS AND A
SIGNIFICANT PORTION OF THESE
PARENTS THAT CARRY THESE DISEASE
CAN GET PARKINSON'S DISEASE.
SO WHEN YOU APPROACH THIS, WHEN
WE START STUDYING DISEASES,
TYPICALLY TO FIRST TRY TO CREATE
SEVERE LOSS OF FUNCTION
MUTATIONS AND WE DEVELOP THIS
TECHNOLOGY BASED ORIGINALLY ON
MIMIC INSERTIONS, TRANSPOSABLE
ELEMENT INSERTIONS THAT WE COULD
CONVERT THROUGH WHAT IS SHOWN
HERE.
WE DO THIS WITH CRISPR
TECHNOLOGY AND WHAT WE DOE IS WE
INSERT INTO AN INTRON, HERE IS
THE GBA 1 B IN FRUIT FLY, AND
SPLICE IT ON TO GAL4, AND THAT
TRUNCATES TRANSCRIPTION BECAUSE
OF THE PRESENCE OF THE
[INDISCERNIBLE] AND THEN THE
GAL4 IS PRODUCED BY THIS
TRUNCATED TRANSCRIPT WHEN
TRANSLATED AND THE GAL4 CAN BE
USED FOR A VARIETY OF PURPOSES.
VERY OFTEN WE USE THIS TO
HUMANIZE THE FLY AND DRIVE AUAS
WITH A HUMAN CDNA BUT WE CAN
ALSO OBVIOUSLY USE THIS TO
LOCALIZE WHERE THE GENE IS
EXPRESSED AND WE DID THIS FOR A
GBA TO OUR SURPRISE, THE GENE
WAS ONLY EXPRESSED IN GLUE
MARIOUSA SO IN THE TOP, YOU SEE
IN GREEN THE NEURONS IN RED THE
GLIA AND IN THE RIGHT YOU SLEEP
APNEA AND OBESITYY A BLOW UP AND
YOU SEE THERE IS ABSOLUTELY NO
OVERLAP BETWEEN THE GREEN AND
THE RED.
BUT WHEN YOU LABEL FOR A GLIALL
MARKER, THERE IS NEARLY A
PERFECT OVERLAP BETWEEN THE 2
AND WE'VE DONE THIS WE'VE TRACED
THIS ASK WE NEVER SAW THERE WAS
IN NEURONS SO THIS BEGS THE
QUESTIONS, WHAT HAPPENS WITH
NEURONS PRODUCE THE DPLIEWK O
CERAMIDE AND MOW DID --HOW DOES IT
END UP IN GLIA AND FIRST WE
ASSAYED A WHOLE HOST OF
PHENOTYPES THAT WERE ASSOCIATED
WITH GBA BECAUSE THIS INSERTION
ALLOWS TO YOU LOOK AT THE
EXPRESSION PATTERN THAT IS A
SEVERE LOSS OF FUNCTION
MUTATION.
AND THE TAKE HOME MEASESSAGE
HERE IS THAT THE SYMPTOMS
TYPICALLY STORT SHOWING UP AT
DAY 15, 18, THE FLIES ARE SHORT
LIVED, THE GENERATEDITTIC SYSTEM
CLEAN, CAN YOU RESCUE THIS BY
EXPRESSION OF THE HUMAN CDNA AND
DIVIDE CDNA OR A GENOMIC RESCUE
CONTRUCT IN ALL CASES YOU HAVE
RESCUE.
THEY DON'T CLIMB VERY WELL BUT
THE KEY HERE IS TO FOCUS ON THE
MECHANISM BY WHICH THE CERAMIDE
IS TRANSFERRED FROM NEURONS TO
GLIA.
SO THIS ALLOWS SOME REALLY NICE
EXPERIMENTS IF YOU LOOK AT THESE
IN THE I THESE CELLS HERE THAT
ARE GLIA AND IT TURNS OUT THESE
CELLS THAT ARE LABELED IN GREEN
HERE EXPRESS GBA AND THE CELLS
THAT ARE LABELED IN GRAY DO NOT,
THOSE ARE THE PHOTO RECEPTORS,
THE NICE THING TO WORK WITH THE
EYE IS THAT YOU CAN REDUCE
ACTIVITY BY REDUCING PHOTO
RECEPTORS THROUGH LIGHT AND SEE
WHAT HAPPENS AND WHAT WE'RE
DOING HERE AND WE'RE MONITOR--WE
ARE MONITORING THE DPLIEWK O
CERAMIDE WITH AN ANTIBODY AS CAN
YOU SEE THE GLUCOCERAMIDE IS
ACCUMULATED IN THESE GREEN CELLS
THESE GLIAL CELLS.
NOW IF THE FLIES ARE RAISED IN
THE DARK, THERE ARE BARELY ANY
DPLEEL CERAMIDE THAT SURROUNDS
THE PHOTO RECEPTORS THAT ARE
LABELED IN RED HERE, YOU CAN SEE
THESE IN GREEN.
IF YOU LOOK AT GBA AND KEEP THE
GBA MUTANT IN THE DARK, YOU SEE
THERE IS ESSENT YELLLY NO
DIFFERENCE BETWEEN THE FLIES IN
THE DARK THAT ARE WILD TYPE
VERSUS THE FLIES THAT ARE GBA
RAISED IN THE DARK.
HOWEVER, WHEN YOU PUT THEM FOR
12 HOURS AND EXPOSE THEM TO
LIGHT, YOU START SEEING THAT
THERE IS A DPLIEWK O CERAMIDE
ACCUMULATION IN THE PHOTO
RECEPTORS AND THE GLUE MARIOUSA
START REALLY PILING UP HIGH
LEVELS OF DPLIEWK O CERAMIDE AND
THE GLUE MARIOUSA CLEARLY BECOME
SICK, THEY KIND OF BECOME
VACCULATED.
AND IF YOU DO THIS FOR AN EXTRA
DAY, CAN YOU SEE THAT THE PHOTO
RECEPTORS START REALLY SUFFERING
AND EVEN THOUGH AFTER YOU KNOW
THIS EXPOSURE FROM THE ABSENCE
OF GBA, THE DPLEEL CELLS KEEP ON
PILING UP THE GLUCOCERAMIDE,
THEY FAIL TO DEGRADE IT AND
THERE IS A VERY SEVERE DEMISE OF
THE PHOTO RECEPTORS AND THE
GLIAL CELLS.
AND THIS IS NICELY SHOWN WHEN
YOU LOOK AT TRANSMISSION
ELECTROMICROSCOPY, AND WHEN YOU
SEE THAT WHEN YOU LOOK IN THE
YELLOW WHITE BACKGROUND IF YOU
SEE THE BACKGROUND HERE YOU CAN
SEE THE BLUE CELLS HERE WHICH
ARE THE GLIAL CELLS AND NOTE O
RECEPTORS THEY FORM A NICELY
THIN SLIVER BUT IN THE MUTANTS
THEY BECOME EXPANDED AND THEY
BECOME LOADED WITH THESE HOLES,
THESE VACCULES.
AND IF WE NOW PRESENT YET
ANOTHER 12 HOURS OF LIGHT TO THE
YELLOW WHITE CELLS THAT HAVE TBA
AND WE LABEL FOR A LYSOSOMA
MARKER, CTSL, WE SEE THAT THERE
IS A MILD ACCUMULATION OF CTSL
AND IF THERE'S AN INCREASE IN
THE LYSOSTUDIES OF MULTIPLE
ENDOCRINES BUT WHEN YOU LOOK IN
THE GBA MUTANTS YOU SEE A
DRAMATIC INCREASE IN THE
LYSOSOME AND YOU CAN SEE THAT
THE CERAMIDE IS NOT CONFINED TO
THE LYSOSOMES BUT EXPANDS TRUE
OUT THE CELL, AND THAT THE PHOTO
RECEPTORS ARE REALLY HAMMERED,
SO THE LONGER YOU KEEP THEM
EXPOSED TO LIGHT, THE MORE
ACTIVE THEY ARE, THE MORE
DPLIEWK O CERAMIDE THEY FORM,
THE GLUCOCELL SERIES POINTS MID
CANNOT BE DEGRADED IN THE GLUE
MARIOUSA AND JUST PILES UP IN
THE DPLIA AND EVENTUALLY PILES
UP IN THE NEURONS.
IF YOU WAIT A FEW MORE DAYS YOU
GET A MASSIVE DEMISE OF THE
PHOTO RECEPTORS AND THE FLEEL
CELLS AS IS SHOWN HERE AND YOU
CAN SEE THAT THERE IS A MASSIVE
NEURY DEGENERATIVE PHENOTYPE IN
THE PHOTO RECEPTORS THAT ARE
INDUCED IN AFTER A FEW DAYS.
SO THE IN ACCIDENT QUESTION THEN
IS, IS ACTIVITY REALLY AT THE
ROOT OF THIS PHENOTYPE BECAUSE
WITH THE PHOTO RECEPTORS YOU
HAVE AN SAIRKS, WE CAN JUST
STIMULATE WITH LIGHT AND YOU CAN
SAY WELL, THAT'S IN THE PHOTO
RECEPTORS, WHAT ABOUT THE REST
OF THE BRAIN.
SO WE CAN EXPRESS WITH IN THE
NEURONS TRIP A WHICH IS A
TEMPERATURE SENSITIVE CHANNEL
THAT WHEN YOU KEEP THE FLIES AT
18, WILL NOT BE USED AND YOU CAN
SEE THAT THERE'S VERY LITTLE
DPLIEWK O CERAMIDE IN THE BRAIN
THAT IS SHOWN HERE AND WHEN
YOU--WE USE THE WORD HEAT SHOCK
BUT IT'S NOT REALLY WE JUST
TRANSFER THE FLIES FROM 18 TO 29
AND INDUCE THE ACTIVITY OF THIS
TRIP A CHANNEL SO THAT IT NOW
STARTS GAINING IONS AND WHEN YOU
SEE IS AGAIN, THROUGHOUT THE
BRAIN YOU CAN NOW SEE THE
DPLIEWK O CERAMIDE IS
ACCUMULATING SO IT'S CLEAR THAT
NEURONAL ACTIVITY PLAYS AN
IMPORTANT ROLE HERE.
ALL RIGHT, SO ARE THE NEURONS
PRODUCING THE GRIEWK O CERAMIDE
OR WHERE IS THAT GLUCOCERAMIDE
PRODUCED IF IT'S NOT IN NEURONS
SO THE FIRST THING THAT THEY DID
WAS TO KNOCK ON THE ENZYME THAT
IS IN THE GLUCOSILV TRANSFER ACE
AND SO THE IDEA IS NOW, LET'S DO
AN RNAI JUST IN THE PHOTO
RECEPTORS, THIS IS SHOWN HERE,
AND CHECK WHAT HAPPENS WITH
GLUCOCERAMIDE ACCUMULATION AND
HE OR SHE BOOSTED THE SIGNAL A
LITTLE BIT AND YOU CAN SEE THAT
THERE IS SOME GLUCOCERAMIDE IN
THE PHOTO RECEPTORS, THERE A LOT
OF DPLIEWK O CERAMIDE IN THE
CONTROLS BUT WHEN SHE KNOCKS
DOWN IN THE PHOTO RECEPTORS AND
THE ENZYME THAT MAKES DPLIEWK O
CERAMIDE OBVIOUSLY, YOU KNOW
VERY LITTLE DPLIEWK O CERAMIDE
IN THE PHOTO RECEPTOR, ALSO VERY
LITTLE GROUP OF CERAMIDE IN THE
GLUE MARIOUSA.
AND IN THE GLUE MARIOUSA THEY
ARRIVE THERE FROM THESE PHOTO
RECEPTORS.
IF SHE KNOCKS DOWN THE DPLIEWK O
SILL CERAMIDE AND TRANSFERAISE
IN THE GLIA, THERE IS NO EFFECT,
SO THAT ARGUES THAT WHATEVER IS
IN THE GLIA IS DERIVED FROM THE
PHOTO RECEPTORS AND INDEED
TRANSFER UP ON NEURONAL
ACTIVITY, THE GLUCOCERAMIDE TO
THE GLIA AND THAT THE ENZYME
THAT IS EXPRESSED SPECIFICALLY
IN THERE AND ABLE TO DEGRADE
THESE, GLUCOCERAMIDE BACK TO
SERUM, SO THIS RAISED THE
QUESTION AS TO HOW DOES--WHAT IS
THE MECHANISM BY WHICH GLC CER
IS TRANSFER FRIDAY NEURON TO
GLUE MARIOUSA UPON ACTIVITY SO
FOR THIS WE TURN TO VERTEBRATE
CELLS AND WHAT [INDISCERNIBLE]
DID IS SHE COLLECTED VERTEBRATE
CELLS, NEURONS IN GLIA AND
LOOKED AT THE EXPRESSION OF GBA
IN HUMAN CELLS IN THE GLIA AND
NEURONS AND NOTE THAT
IMMEDIATELY THAT IN GLIA THE
HUMAN GBA IS EXPRESSED MUCH MORE
ABUNDANTLY THAN IN NEURONS.
SHE THEN TOOK NBD, DPLIEWK O
CERAMIDE WHICH IS A
FLUORESCENTLY LABELED CERAMIDE,
TOOK THE NEURONS AND EXPOSED
THEM TO THIS MBD CERAMIDE FOR 30
MINUTES FOR 4-DEGREES CELSIUS
AND YOU CAN SEE NICELY THIS MBD
CERAMIDE WILL LABEL THESE
MEMBRANES AND IF YOU SHIFT THEM
TO 30-DEGREES CELSIUS FOR 30
MINUTES SOME OF IT IS
INTERNALIZED AND THAT IS WHAT IS
SHOWN HERE.
SO THIS IS VERY SIMPLE ASSAY.
NEXT, WHAT SHE DID IS SHE TOOK A
COVER SLIP, UNDERCOVER SLIP
CULTURED NEURONS AND SO, LET'S
MAKE SURE THOO THESE NEURONS ON
THE TOP CANNOT TOUCH THE NEURONS
THAT ARE AT THE BOTTOM.
SO THE NEURONS AT THE BOTTOM ARE
LABELED WITH GLC NBD AND THEY
AFTER 30 MINUTES TAKE UP IN GLC
CERAMIDE, THERE IS NO GLC SERIES
POINTS MID THAT TRANSFERRED FROM
THESE NEURONS THAT THE BOTTOM TO
THE NEURONS AT THE TOP.
HOWEVER, WHEN YOU CHANGE THAT
AND INSTEAD OF PUTTING NEURONS
AT THE TOP, YOU PUT GLIA AT THE
TOP, YOU SEE AGAIN NO LABEL OF
THE GLIA BUT YOU SEE A PRETTY
DIG 95 CANT DECREASE OF THE
GLUCOCERAMIDE THAT IS PRESENT IN
THE NEURON.
SO SOMEHOW, THE GLUCOSERIES
POINTSA MIDHERE IS RELEASED AND
IT'S NOT SHOWING UP IN GLIA,
HOWEVER, TO KNOCK DOWN GBA IN
GLIA AND WHEN YOU DO THAT YOU
SEE THAT THE GLIA START LABELING
PRETTY STRONGLY AS NBD GLC
CERAMIDE SO THIS ARGUES THAT IN
CELL CULTURE THE NEURONS WITH
THE CERAMIDE, THE NEURONS TAKE
IT UP, AND IF YOU KNOCK DOWN GBA
IN THE GLIA, THEN THE GLIA TAKE
IT UP AND IF YOU KNOCK DOWN GBA,
GLIA COULD BE THE PROCESS THE
GLUCOCERAMIDE AND THEREFORE PILE
UP THE GLUCOCERAMIDE.
THE NEXT QUESTION IS HOW IS THIS
TRANSFER OCCURRING FROM NEURONS
TO GLIA, WHAT ARE THE NECKANISMS
THAT UNDERLIE THIS.
AND SO, [INDISCERNIBLE] WAS
USING DIFFERENT MEDIA IS THIS
WAS A MEDIA THAT JUST CONSISTS
OF SUGARS AND SALTS.
ONE DAY WHEN SHE USED TGF BETA
AND SHE LOOKED AT THESE NEURONS,
SHE SAW THAT THERE WAS NO LABEL
AT ALL.
THAT ALL GLUCOCERAMIDE WAS
TRANSFERRED.
SO THIS WAS A SERENDIPITOUS
DISCOVERY SO SHE CULTURED THE
NEURONS IN ACSF AND THEN ADDED
50 NANO MOLARS OF TGF BETA AND
WHAT YOU THEN DO, IS YOU IMMUNO
PRECIPITATE WITH AN ANTIBODY
AGAINST CD63 WHICH RECOGNIZES
EXOSTUDIES STUDIES OF MULTIPLE
ENDOCRINES AND THE FIRST THING
YOU CAN SEE IS THAT WHEN YOU PUT
IN TGF BETA THERE IS A VERY
STRONG INDUCTION OF THE
PRODUCTION OF EXOSTUDIES OF
MULTIPLE ENDOCRINES AND SHE THEN
LOOKED THE EXOSTUDIES OF
MULTIPLE ENDOCRINES IN THE
ABSENCE OF TGF BETA AT THE MBD
CERAMIDE AND THERE WAS A VERY
OBVIOUS SIGNIFICANT INCREASE IN
THE MBD LEUCOSERUM.
SO WHAT ABOUT THE ENDOGENOUS
GLUCOCERAMIDE?
SO SHE CULTURED THE NEURONS, SHE
IN ACSF, WHICH DOESN'T CONTAIN
ANY PROTEIN JUST SALT AND SUGAR,
AND THEN PUT IN TGF BETA AND
THEN TOOK THE SUPERINATENT AND
THE CELLS AND MEASURED THROUGH
LIPID OMICS, THE LEVELS OF
CERAMIDE IN THE SUPERINATENT IN
THE LEVEL OF FLUKE O CERAMIDE IN
THE SUPERINATENT, AND YOU CAN
SEE THAT THE SUPERINATENT, IS
NOT MUCH ENRICHED IN CERAMIDE IN
GLUCOCERAMIDE.
THE IT HAS A MINOR DECREASE IN
THE CERAMIDE BUT IT'S NOT
STATISTIC LOAMACYY SIGNIFICANT
BUT IT CLEARLY ARGUES THAT THE
CELLS SECRETE THESE CERAMIDES IN
GLUCOCERAMIDE UP UPON EXPOSURE
OF THE TGF BETA SO I WOULD LIKE
TO END WITH THE MODEL HERE AND
SAY THAT UPON NEURONAL ACTIVITY
NEURONS PRODUCE GLIEWRK O
CERAMIDE IS VERY TOXIC IF IT
PILES UP.
THE GLIAL CELLS SECRETE SIGNAL
WHICH IS TGFBETTA AND IN FLY
THIS IS IS BPPAND ALL OF THIS TO
HOM O LOLLINGS TO TGF BETA AND
THAT IS RECEIVED BY THE NEURONS
THAT INDUCES THE FORMATION OF
THESE EXOSTUDIES OF MULTIPLE
ENDOCRINES, AND THESE EXOSTUDIES
OF MULTIPLE ENDOCRINES ARE
PRODUCED BY MULTICANNED WHAT
BODIES SO THE CERAMIDE FROM THE
MEMBRANE OF THE NEURONS TRAVELS
TO LYSOSOME BUT AT AN
INTERMEDIATE STEP AT THE
MULTI[INDISCERNIBLE] BODY STEP,
THE CERAMIDE, THE
MULTI[INDISCERNIBLE] BODIES
REDUCE THE MEMBRANE UNDER THE
FORM OF EXOSTUDIES OF MULTIPLE
ENDOCRINES, THESE EXOSTUDIES OF
MULTIPLE ENDOCRINES ARE THEN
TAKEN UP BY THE LYSOSOMES AND
THE LYSOSOMES--BY THE GLIAL
CELLS AND TRAFFIC IN A VERY
PRECISE WAY THAT WE HAVEN'T
REALLY FIGURED OUT IN ENOUGH
DETAIL TO TALK ABOUT RIGHT NOW,
BUT THEY END UP IN THE LYSOSOME
AND IN THE LYSOSOME THE SERIES
POINTS MID IT'S DEGRADED BA
BEING TO CERAMIDE.
AND IF THIS PROCESS DOES NOT
OCCUR IN GIA, THE IT PILES UP IN
GLUE MARIOUSA, THIS PILES UP IN
NEURON, AND EVENTUALLY LEADS TO
THE NEURONAL DEMISE.
AND SO I WILL END UP HERE AND
GIVE CREDIT, [INDISCERNIBLE] WAS
80% OF THE WORK AND WE HAVE
ELECTRON MICROSUPONY AND WE GOT
HELP FROM THE MAYO CLINIC FOR
METABOLOMICS.
THANK YOU.
>> GREAT.
THANK YOU SO MUCH HUGO, THAT WAS
A FASCINATING STORY AND AGAIN
FOR THE AUDIENCE, PLEASE CLICK
ON SEND LIVE FEEDBACK ICON TO
SUBMIT YOUR QUESTIONS AND THEN
AT THE END OF THIS AFTERNOON'S
SESSION, THE SPEAKERS WILL BE
AVAILABLE TO ANSWER THE
QUESTIONS.
OKAY?
SO MOVING ON OUR NEXT SPEAKER IS
LYNN SCHRIML, WHY THE UNIVERSITY
OF MARYLAND SCHOOL OF MEDICINE.
AND THE SHE WILL BE TELLING US
ABOUT MODELING AND INTEGRATING
RARE DISEASE DATA WITH THE HUMAN
DISEASE ONTOLOGY.
TAKE IT AWAY LYNN.
>> THANK YOU FOR INVITING ME TO
THIS MEETING, LOOKING FORWARD TO
TALKING TO BUT THE HUMAN DISEASE
ONTOLOGY AND SPECIFICALLY ABOUT
HOW WE MODEL AND INTEGRATE RARE
DISEASE DATA WITHIN THE THIS
ONTOLOGY.
IT'S QUITE A PROCESS AS YOU CAN
IMAGINE EXTENDING OVER SEVERAL
YEARS BUT BUT I'M GOING TO GIVE
YOU INSIGHTS IN HOW WE MAKE
THESE DECISIONS ABOUT MODELING
AND HOW WE INTEGRATE THIS DATA.
I WANT TO START OFF WITH LOOKING
AT HOW WE DEVELOP STANDARD AND
REALLY WALK YOU THROUGH THIS
KIND OF TIMELINE THAT ALL THE
VARIOUS STANDARDS OF PRODUCTS
I'VE BEEN INVOLVED WITH FOR THE
LAST 20 YEARS WITH THE
BIOMEDICAL ONTOLOGYS AND
METAGENOMIC STANDARDS REALLY GO
THROUGH THE SAME SORT OF STEPS.
AS CAN YOU SEE FROM THIS FIGURE,
A LONG PROCESS, NOT JUST A YEAR
FOR A SINGLE PROJECT OR A GRANT
CYCLE BUT CAN INVOLVE SEVERAL
DECADES OF WORK.
THE 4 KEY THINGS I WANT TO TALK
ABOUT ARE IN THE CIRCLES HERE,
SO IDENTIFYING A COMMON NEED.
WHEN YOU'RE WORKING ON THESE
TYPES OF PROJECTS REALLY
BRINGING A COMMUNITY TOGETHER TO
ADDRESS A COMMON NEED,
IDENTIFYING WHO IN THAT
COMMUNITY CAN WORK AS PARTNERS,
LOOKING AT HOW YOU CAN ORGANIZE
THAT INFORMATION, BUT NOT JUST
FOR YOUR PROJECT BUT HOW DO YOU
CONNECT IT TO OTHER DATA THAT'S
OUT THERE, HOW DO YOU MAKE IT
INTEROPERABLE.
AND THEN AGAIN, HOW YOU EVOLVE
THAT PROJECT OVER TIME TO HAVE
NEW IMPLEMENTATIONS, HOW TO
IDENTIFY NEEDS IN THE COMMUNITY
AND HOW TO BRING THOSE BACK
WITHIN OUR SYSTEM HERE SO YOU'RE
ALWAYS CONTINUALLY EVOLVING,
WORKING WITH THE COMMUNITY TO
BRING THAT INFORMATION TOGETHER
AND REALLY THE END GOAL ON THE
FAR RIGHT IS INTEROPERABLE
KNOWLEDGE RESOURCES.
THIS IS FOR NOT JUST THE
ONTOLOGY BUT FOR THE PARPTENERS
YOU WORK WITH AND FOR THE
COMMUNITY AT LARGE.
AS YOU CAN SEE ON THE SLIDE, THE
DISEASE ONTOLOGY OR THE DOH AS
WE LIKE TO CALL IT STARTED
HUMBLY WITH JUST A SMALL NUMBER
OF CLINICALLY AUTHORITATIVE
RESOURCES AND THEN WE'VE GROWN
FROM THERE AND THAT'S WHEY WILL
TAKEN--THEYUC ABOUT TODAY.
I WANTED TO TOUCH BASE AGAIN
ABOUT THESE INTERROPERABILITY
KNOWLEDGE RESOURCES.
THIS SLIDE IS SHOWING THE
DISEASE ONTOLOGY AND HOW WE
CONNECT THROUGH LENS OF DISEASE
TO ALL THESE DIFFERENT TYPES OF
DATA AND THEN THERE'S SOME
EXAMPLES AROUND THE OUTSIDE OF
THE SLIDE OF RESOURCES THAT ARE
PARTICULARLY I THINK IMPORTANT
FOR A GLYCO BIOLOGY AND YOU SEE
GLYGEN AND UNIPROBE AND MANY
OTHERS WE THROIRCHG OVER 300
SUCH RESOURCES BUT I REALLY WANT
TO CONTRAIT ON THE BLUE BOXES ON
THIS SLIDE, LOOKINGA THE
DIFFERENT TYPES OF DATA AND THE
REASON THESE TYPES OF DATA ARE
HIGHLIGHTED AND I THINK IT'S
IMPORTANT TO CONSIDER HOW TO
CONNECT INFORMATION ACROSS THESE
SYSTEMS.
WE DON'T WORK EVER IN JUST 1
SYSTEM, AND REALLY THINKING
ABOUT HOW ONTOLOGY CAN HAVE THAT
ROLE TO WORK WITH THE DIFFERENT
RESOURCES TO ENABLE THEM TO KNOW
WHEN THEY'RE TALKING ABOUT 1
PARTICULAR DISEASE, THEY ARE
REALLY TALKING ABOUT THE SAME
DISEASE, NOT A NAME VARIATION
NOT AN OLDER NAME, BUT TO THE
CONNECT THAT DATA AND THEN THEY
CAN EXCHANGE DATA OF THIS
INTEROPERABILITY THAT EXAMPLE IS
THE COMMON FUNDED EQUO SYSTEM OR
GENOME RESOURCES BUT THERE ARE
MANY, WHERE PLAY WORK TOGETHER
TO INTEGRATE MANY DIFFERENT DATA
TYPES AND THEN DISEASE IS JUST 1
OF THOSE ASPECTS THAT WE GET TO
WORK WITH.
ALLOCATES ITS HEART THE HUMAN
ONTOLOGY IS THE BASES OF DISEASE
AND WE WANT TO LOOK AT THE CAUSE
OF DISEASE.
SO WE STARTED ON THIS IN 2003
AND AS WE MOVE FORWARD WE WANT
TO UNDERSTAND THE DEEPER ASPECT
OF DISEASE.
HOW COULD WE TAKE THESE LONG
LISTS OF DISEASES, YOU KNOW THE
ICDs, THE MESHES, THE NCI
SOURCES WHICH ARE FANTASTIC
RESOURCES BUT HOW COULD WE
REORGANIZE THEM SO WE'RE LOOK AT
THEM AS A CLINICAL POINT OF VIEW
AND THAT'S THE IMAGE OF THE
MIDDLE OF THE SLIDE I AM SHOWING
YOU, THIS IS OUR OBO SLIDE, THIS
CLASSIFIES DISEASES INTO THEIR
MOST APPROPRIATE CATEGORY SO WE
CAN HAVE FURTHER INFORMATION
ABOUT THEM BUT ALSO BRING
RELATED DISEASES TOGETHER, WE
LOOK AT CLINICS SIGNIFICANT
FEATURES AND I LISTED THOSE ON
THE SIDE OF THE SLIDE, AND
THAT'S HOW IT REALLY STARTED,
HOW DO WE BEND THIS INFORMATION,
HOW DO WE GET FURTHER KNOWLEDGE
ABOUT IT BUT ON THE OTHER SIDE
I'LL SHOWING YOU OUR OWL TREE,
SO THIS IS OUR PROGRESSION OVER
TIME AND THIS IS INCLUDING
ONTOLOGYS THAT LOOK THEA OTHER
FEATURES AND MECHANISMS OF
DISEASE TO GIVE US FURTHER MORE
TAILED INFORMATION ABOUT THE
DISEASES THEMSELVES AND THEIR
MECHANISMS AND IF YOU WANT TO
LEARN MORE ABOUT THE PROJECT OR
OUR LATEST PAPER, I PUT A LINK
HERE IS IN THE NUCLEIC DATABASES
RESEARCH ISSUE THAT CAME OUT
LAST JANUARY.
CAN YOU ALSO GO TO OUR WEBSITE
WHERE WE DO GIVE YOU LINKS TO
ALL THE CITATIONS WE'VE
IDENTIFIED, A LINKING TO THE
DISEASE ONTOLOGY AND WE'RE AT A
LITTLE OVER 1500 AT THIS POINT.
SO PLEASE TAKE A LOOK AND YOU
CAN SEE ALL THESE VARIOUS USE
CASES AND MAYBE IDENTIFY OTHER
WAYS THAT WOULD BE ALIGNED TO
YOUR WORK.
BEFORE I MOVE ON I WANT TO TALK
ABOUT RARE DISEASE DATA
INTEGRATION ITSELF, JUST TO
REALLY HIGHLIGHT THESE STEPS, AS
CAN YOU IMAGINE THERE'S A LOST
RESOURCES OUT THERE FOR ANY TYPE
OF DISEASE, BUT FOR RARE
DISEASE, WE DATA FROM ALL THESE
RESOURCES BUT WHAT'S IMPORTANT
ABOUT THEM ARE THEY ARE
AUTHORITATIVE RESOURCES, WE'RE
CAREFUL WHERE WE JAR OR DATA
FROM AND HOW WE BRING IT
TOGETHER BECAUSE A BIG ASPECT OF
WHAT WE'RE DOING IS LOOKING AT
THIS VARIOUS DISEASE
REPRESENTATIONS AND AS YOU CAN
IMAGINE, ANY DATABASE HAS UPDATE
AS THE DEFINITE TIMES, DIFFERENT
CYCLES AND WE LOOK AT THAT
INFORMATION AND WE COMPILE IT
WITH THE CURRENT LITERATURE AND
WE REALLY BRING THE INFORMATION
TOGETHER IN OUR SYSTEM BUT WE
ALSO WANT TO LOOK AT HOW WE
CONNECT THAT DATA TO OTHER
VOCABULARIES SO THERE ARE A
NUMBER OF CLINICAL VOCABULARIES
OUT THERE OVER TIME, 1 THING WE
DO SPECIFICALLY IS WE DO MAP TO
EACH OF THEM AND THIS IS A
CURATED TASK AND A CONTINUAL
BASIS, WE ARE ABLE TO THEN
DISTINCTLY IDENTIFY THESE 1 TO 1
MAPPINGS AND THESE 2 TERMS ARE
EXACTLY RIGHT IN THESE CASES ARE
CONNECTED AND 1 RESOURCE SPLITS
OR ANOTHER PUTS THEM TOGETHER,
AS LIKE ALL THE SUBTEXT GOES
INTO 1.
THESE ARE CALLED SCOS MAPPINGS
AND WE'RE ABLE TO DISTINCTLY
DEFINE THESE 1 TO 1 WHEN THERE'S
BROADER OR NARROWER MATCHES SO
THAT ALLOWS TO DO A LOT OF
INTERESTING CONNECTIONS WITH THE
DISEASES.
THE LAST THING ON THE SLIDE I
WANT TO POINT OUT IS THAT NOW
THE CURRENT COULD YOU WANT IN
THE SLIDE, IN IS JUST UNDER
11,000, SO IT'S HYMN HALF OF
WHAT WE REPRESENT ARE CLASSIFIED
AS RARE DISEASES IN 1 OF THESE
SYSTEMS, SO AS I'M GOING
FORWARD, YOU WILL SEE THAT THE
THINGS WE'RE DOING FOR ALL OF
THE DISEASES IS SOMETHING VERY
MUCH DOING FOR RARE DISEASES.
WE REALLY HAVE MORE OF A
WHOLISTIC APPROACH FOR DECS AND
WE DO RECORD THAT THEY'RE RARE,
AND WHAT THE ASSPEBTS OF THEM
ARE RARE, BUT ALL OF THIS IS
BRINGING YOU TO SHOW US OUR
COMPLEX DISEASE MODELING WORK
THAT WE'VE BEEN WORKING ON FOR
THE NEXT 5 YEARS ACTUALLY.
SO WE HAVE A CLINICIAN TEAM AND
I WILL SHOW YOU AT THE VERY END
OF THE PRESENTATION.
BUT THEY'VE BEEN ASSESSING HOW
WE USE THE WORDS, WE USE TO
DESCRIBE DISEASES AND THIS SLIDE
IS MEANT TO SHOW YOU HOW WE
RECOGNIZE THE VERY FUZZINESS IN
THE WORK THAT WE'RE DOING SO IN
SOME TYPES OF RESOURCES HERE WE
LOOK AT THE HUMAN PHENOTYPE
ONTOLOGY, IN OTHERS WE LOOK AT
THE CLEFT LIP PAL MEAT MIGHT BE
A FEATURE OF A DISEASE WHEREAS
IN THE HUMAN DISEASE AND
ONTOLOGY WE HAVE DISTINCT
DISEASES REPRESENTED.
I THINK UNDERSTANDING WHAT TYPE
OF DATA YOU'RE WORKING WITH
APPROXIMATE ANY RESOURCE WHETHER
THEY'RE DESCRIBING A PHENOTYPE
OR PHENOTYPIC FEATURES OF A
DISEASE OR A DISEASE ITSELF IS
IMPORTANT AND THAT I THINK IS
THE COMMUNITIES MOVE IT A LOT IN
THE LAST NUMBER OF YEARS TO
REALLY DO THIS AND WE WORK WITH
HPO AGAIN AND OTHER GROUPS TO
MAKE SURE, YOU KNOW HOW WE'RE
DOING THIS AND THAT WE'RE
UNDERSTANDING EACH OTHER'S
REPRESENTATIONS.
AND I WANT TO GIVE YOU AN
EXAMPLE HERE OF DISEASE
NOMENCLATURE AND WHY IT'S
IMPORTANT.
DISEASES NAME CHANGE QUITE A BIT
OVER TIME AND YOU MAY HAVE
NOTICED THIS YOURS, I'M SHOWING
YOU AN EXAMPLE HERE OF JUST SOME
DISEASES THAT ARE PERINENT TO
OUR CONVERSATION TODAY, BUT THE
IMPORTANT PART HERE IS THAT AS
THESE TERM NAMES CHANGE, THERE
NEEDS TO BE A WAY TO KEEP TRACK
OF THEM AND THAT 1 OF THE ROLES
THAT WE PLAY WITHIN THE DOH.
SO AGAIN, THIS IS IMPORTANT
BECAUSE PEOPLE USE DIFFERENT
NAMES FOR DISEASES.
AT TIMES YOU WILL SEE IN THE
MIDDLE OF THE SLIDE, I THINK
YEAH, PGM 1 AS WE REFER TO AS A
DISEASE NAME IN THIS CASE, BUT
ACTUALLY THE PROPER DEC NAME IS
GENERAL DISORDER GLYCOSYLATION 1
T.
SO IT'S GOOD TO RECOGNIZE THAT
WE HAVE THESE NAMES AND TO
INTEGRATE THESE SYNONYMS WITH
THE PROPER NOMENCLATURE AND
UPDISTRICT ATTORNEY THESE AND
THIS IS SOMETHING WE DO A
REGULAR BASIS, WE GO THROUGH
DRNT AREAS OF THE ONTOLOGY AND
UPDATE THEM, REVIEW THEM WITH
WHAT THE COMMUNITY IS DOING SO
THAT WHEN DAT IS ASSOCIATED, 1
DATABASE WITH 1 NAME, BUT THE
NOMENCLATURE HAS CHANGED, WE CAN
STILL CONTINUALLY TRACK THAT AND
THEN ALL OF OUR USERS CAN AS
WELL.
NOW TALKING ABOUT THE DISEASE,
HOW WE MODEL THE DATEDDA IS WITH
THE ONTOLOGY AND THEN OUR
RESOURCES CAN ANNOTATE SO THAT'S
STEPS OF WHAT WE WANT TO YOU
THINK ABOUT MOVING FORWARD, SO
I'M SHOWING YOU ON THE LEFT A
NUMBER OF CLINICAL VOCABULARIES,
ACTUALLY THE ONTOLOGY FROM THE
BOUNDARY THAT ENCODE THESE
DIFFERENT TYPES OF INFORMATION
THAT WE WANT TO INCLUDE.
I AM HIGHLIGHTING ON THE ORANGE
ARROWS, THAT RECENTLY BEEN
ADDING, WHAT THESE ALLOW US TO
DO IS TO HAVE A VERY STRUCTURED
DESCRIPTION OF WHAT THESE
DISEASE TO DISEASE RELATIONSHIPS
ARE, USING ONTOLOGYS, WE USE
THEIR TERMS AND IDs SO IT'S
INTEROPERABLE METHOD FOR
CONTINUING TO EXPAND OUR
DESCRIPTION OF DISEASES
THEMSELVES.
HERE I'M SHOWING YOU AN EXAMPLE
OF THE VARIOUS MODELING FEATURES
AND MECHANISMS AND I'M
HIGHLIGHTING CHILDHOOD ONSET SO
WORKING WITH CLINGEN AND CIVIC,
WE DIFFERENTIATE THE DIFFERENT
AGES OF ONSET FOR THESE
CONDITIONS AS PEOPLE ARE AND OUR
GROUP IS ANNOTATING THE CLINICAL
DPROWPS IN CIVIC AND THAT IS
GOING INTO CLINGEN AS WELL, SO
WE WORKED WITH THE HUMAN
ONTOLOGY TO DO THIS, THIS IS
SHOWING THE PROCESS OF DOING
THAT WHERE WE IDENTIFY THE
TOMORROWS AND BRING IN THE ONSET
ONTOLOGY AS PART OF THE HPO AND
THEN WE ANNOTATE THAT
INFORMATION ACROSS ALL THE
DISEASES WHERE WE DO
DEFINITIVELY KNOW THE AGE OF
ONSET OF A DISEASE AND I'M
SHOWING YOU ON THE RIGHT SIDE AN
EXAMPLE OF A DISEASE ONTOLOGY
PAGE WHERE WE HAVE THE
DEFINITIONS THAT ARE DEFINED BY
OUR CURATORS AND THEY FOLLOW
VERY SPECIFIC GUIDELINES TO DO
THIS, SO THE BOTTOM RIGHT I'M
SHOWING YOU IS HOW WE DEFINE
THIS ONSET RELATIONSHIP, NOW IS
PART OF ONTOLOGY WORK WHERE WE
DEFINE WHAT ARE COWLED SUBCLASS
LOGICAL AXIOMS AND IN THIS CASE,
WE USE A RELATIONSHIP TERM
CALLED EXISTENCE STARTS DURING,
THAT'S 1 PHRASE AND THEN IN
CHILDHOOD ONSET IS THE HPO TERM,
THIS ALLOWS US TO HAVE THIS
PHRASE ASSOCIATED WITH WITH
CHILDHOOD ONSET AND THEN TO
INTEGRATE THAT INTO OTHER
DISEASE TERMS SO THEN WE CAN
SAY, AH, THIS TERM IS ALSO A
CHILDHOOD ONSET DISEASE AND WE
DO THIS THROUGHOUT ALL OF THE
DATA TYPES I WAS SHOWING ON THE
LAST SLIDE, ASHES NAT ME, CELL
TYPES WE STARTED WITH THOSE
ANDONATOLOGYS SO WE HAVE A MORE
ROBUST DESCRIPTION OF DISEASE.
NOW I WANT TO GIVE YOU ANOTHER
EXAMPLE HOW BRINGING THIS
INFORMATION TOGETHER GIVES YOU A
MORE EXTENDED VIEW OF DISEASE.
THIS IS WORK WE DID WITH THE
DATABASE, THE LAST NUMBER OF
YEARS, IS TO REALLY DESCRIBE FOR
ANY DISEASE THAT HAS AN IMMUNE
ASPECT TO IT TO BRING THAT
INFORMATION TOGETHER, SO THAT
YOU SEE ON THE LEFT SIDE OF YOUR
SLIDE, WHERE ALL THESE DIFFERENT
TYPES OF IMMUNE SYSTEM RELATED
DISEASES ARE THEN BROUGHT UNDER
THE AUTOIMMUNE DEC BRANCH AND
THEN AGAIN WE LOOK AT COMMON
MECHANISM BY DOING THIS.
OVERALL THOSE ONTOLOGYS I'VE
BEEN TALKING ABOUT THAT WE'VE
BEEN INCLUDING IN THIS, WE HAVE
ALMOST LENCH THOUSAND OF THESE
ASSOCIATIONS BEEN CURATED BY OUR
TEAM.
AND THAT WILL BRING--AND THEY
ALLOWS US TO HAVE AN ENRICHED
EXPLANATION OF DISEASES BUT
AGAIN TO HAVE DIFFERENT LENSES
LOOKING AT ANATOMY LENS AND
THESE LENSES TO GIVE DIFFERENT
VIEWS OF ONTOLOGY AND THE DATA.
NOW THIS SLIDE IS REALLY JUST
GOING INTO THE MODELING, A
LITTLE BUILT MORE, SO AS WE WERE
DOING ALL THIS WORK OVER THE
LAST 5 YEARS WE WANT TO THINK
ABOUT--SO THIS AN EARLY MODEL WE
PUT TOGETHER LOOKING AT BREAST
CARCINOMA SO WE HAVE A VIEW IN
OUR MIND OR EVEN WRITING IT UP
ON THE BOARD AS WE'RE WORKING ON
IT, HOW DO WE HAVE THESE
DIFFERENT DESCRIPTIONS WHAT HAVE
A DISEASE COULD BE AND HOW BEING
WE PUT THAT INTO THE ONTOLOGY.
YOU KNOW FIRST YOU HAVE THE
IDEA, AND THEN THE ONTOLOGY
MODELING HAS TO OCCUR AND SO
THIS IS REALLY WHAT'S THAT'S
DESCRIBING.
OUR CLINICAL GROUP, WE ALSO WENT
THROUGH A NUMBER OF EXERCISES,
MANY, MANY MONTHS OF THINKING
ABOUT WHAT ARE ALL THE ODORSITS
OF DISEASE, DISEASE IS NOT
CLEAN, IT'S A MESSY SYSTEM,
THERE'S LOTS OF EXPRESSIONS TO
THE RULES, SO WHAT I'M SHOWING
YOU HERE TO THE VARIOUS
EXCEPTIONS TO THE RULE OR
ODORSITS THAT WE HAVE TO DEAL
WITH SO WE HAVE THE SAME DISEASE
BUT DIFFERENT FACTORS INVOLVED
AND HOW DO YOU INCLUDE THAT, HOW
DO YOU MODEL IT, THEN ON THE
OPPOSITE SIDE, YOU HAVE
DIFFERENT DISEASES, THAT GD HAVE
THE SAME OR OVERLAPPING FACTORS,
SO AGAIN, VARIOUS TYPES OF
SITUATIONS AND THESE ARE THE
VARIOUS SITUATIONS WE WORKED ON
TO DEVELOP OUR MODEL TO BE ABLE
TO CHARACTERIZE DATA ABOUT
DISEASES.
AS YOU CAN WELL IMAGINE AND GIVE
OUT DISEASES, THERE'S ALWAYS
DIFFERENT ASPECTS INVOLVE WIDE
DISEASE AND WHAT WE'RE SHOWING
YOU HERE IS THIS IS REALLY A
SPECTRUM.
VERY FEW DISEASES FALL ON THE 2
ENDS.
MANY THINGS FALL IN THE MIDDLE
OF THIS SPECTRUM.
IT MAKE ITS VERY COMPLICATED TO
CHARACTERIZE BUT VERY
CHALLENGING AND ACTUALLY REALLY
INTRIGUING TO WORK ON IT, THESE
VERY MULTIFACTORIAL ASPECTS OF
HUMAN DISEASE AND THAT'S WHERE
YOU HAVE BEEN WORKING FOR THE
LAST NUMBER OF YEARS TO GET THE
ONTOLOGY SO WE COULD ENCODE ALL
THIS INFORMATION WITH ALL THOSE
LISTS OF ONTOLOGYS I SHOWED YOU.
ONE OF THE LISTS WE PUT TOGETHER
TO START TO THINK ABOUT WHAT IS
THAT CONTINUUM, THINGS LIKE WIDE
WHAT DOESN'T HAVE ENVIRONMENTAL
TRIGGERS BUT MANY GENES OR MANY
GENETIC COMPONENTS TO THE VERY
BOTTOM OF THE SLIDE, SOMETHING
LIKE RISIN POISONING AND SO
AGAIN, THIS IS THE HELPED US
DEVELOP THE MODEL. THIS IS THE
MODEL WE ARE PUTTING TOGETHER
AND WE ARE PUTTING IN FOR A
PUBLITIONICATION THIS MONTH.
WHAT I WANT YOU TO WALK AROUND
IN A CIRCLE AND YOU'RE LOOKING
AT A LITTLE BIT, THINK ABOUT ALL
THE VARIOUS THINGS THAT CAN COME
INTO PLAY FOR A HUMAN DEC TO
OCCUR.
WHAT AFFECTS IT, WHAT IMPACTS
IT.
SO THAT WAS OUR TASK, REALLY TO
THINK ABOUT AND TO DO DEEP, DEEP
DIVING AND LITERATURE, AND WHAT
WAS GOING TO IMPACT THESE, HOW
CAN WE MODEL AND THEN IF WE
DEVISE THE MODEL COULD WE THEN
IMPROVE THE ONTOLOGY, COULD WE
THEN TEST IT AND ASSESS HOW WELL
THE MODEL DID, BUT ALSO THE GOAL
OF ALL THIS ALSO IS TO HAVE A
MORE ENRICHED UNDERSTANDING OF
DISEASE.
ONE OR SLIDE ABOUT THE MODELING;
WELL, ACTUALLY 2 MORE.
I THINK.
SO 1 ASPECT OF THIS IS LOOKING
AT DISEASE DRIVERS BECAUSE
THAT'S THE CURRENT FOCUSES OF
OUR WORK AND WE WORKED WITH A
NUMBER OF OTHER FOUNDRY GROUPS
TO REALLY COME UP WITH THE BEST
WAY TO WHAT THESE DRIVERS ARE SO
WE COULD CATEGORIZE THEM,
CONNECT THEM TO OTHER ANATOLOGYS
BUT ALSO REALLY TO JUST BE ABLE
TO UNDERSTAND HOW THESE
MECHANISMS WORKING AND DESCRIBE
THEM IN THE ONTOLOGY.
THIS IS OUR DESCRIPTION OF HOW
THIS PROCESS WORKS SO WE HAVE
THIS MODEL, WE WANT TO TEST THE
MODEL SO WE HAVE DISEASES IN THE
ONTOLOGY, WE LOOK AT THE
ENVIRONMENT AMILLIO FACTORS, WE
HAVE THIS ENVIRONMENTAL FACTOR
ONTOLOGY, AND THEN IF THERE ARE
NEW TERMS THAT NEED TO BE ADDED
WE DO AND THEN WE'RE ABLE TO
ANNOTATEOT LEFT SIDE, THE
CLASSIFICATION OF THE DISEASES
THEMSELVES.
FETAL ALCOHOL SYNDROME IS A GOOD
EXAMPLE OF THE FIRST 1 WE PUT IN
TO REALLY LOOK AT ALL THE
VARIOUS FACTORS AND BUT AGAIN
WE'RE USING THIS PAST DISEASE
DRIVER AND ALCOHOL IS THE DRIVER
FOR THE DISEASE.
BUT WE HAVE A MODEL THAT'S
GREAT, WE HAVE NEED TO TEST IT
TO MAKE SURE OUR KNOWLEDGE OF
CURRENT DISEASES AND THE
CONDITIONS DIDN'T BREAK IT OR
DID IT BREAK IT AND WHAT DO WE
NEED TO CHANGE.
SO I WILL SHOW YOU 2 SLIDES OF
DISEASES THAT WERE THE RESULT OF
THIS.
SO WE WORKED FIRST ON DIABETES
COLLITEIS AND PART --MELLITUS AND THIS
IS THE TEAM BRINGING IN THEIR
KNOWLEDGE ABOUT HOW DIABETES
SHOULD BE DESCRIBED IN THE
CLINICAL SETTING AS WELL AS
LITERATE AND YOU ARE THIS
RESULTED IN A CHANGE OF OUR TREE
ITSELF, AN UPDATED VERSION OF IT
AND THEN ALSO BECAUSE DIABETES,
THE WORD IS OFTEN USED FOR
DIABETES MELLITUS AS WELL, SO WE
REVIEWED THAT AREA OF ONTOLOGY
AND UPDATED AND INTEGRATE ALL
THIS INFORMATION.
SO THIS IS SOMETHING WE PUT A
LOT OF TIME IN, LOTS OF DISEASES
WE DO THIS WORK WITH, SO THAT WE
CAN IMPROVE THOSE
CLASSIFICATIONS.
NOW THE LAST SLIDE HERE, IS
TALKING ABOUT ASTHMA, THIS IS
DEFINITELY A MORE COMPLEX ASPECT
OF WHAT WE ARE DOING AND YOU CAN
SEE THE TREE AS CHANGED 82IT A
LOT BUT THIS IS THE FIRST
INSTANCE WE LOOKED AT ENDOTYPES
AND THESE ARE IN REPORT QUITE A
LOT IN LITERATURE FOR COMPLEX
DISEASES, THESE PATHOPHYSIOLOGY,
TYPE COMBINATIONS AND I CLICKED
THE DEFINITION OF T-2 ASTHMA
THEA THE BOTTOM TO GIVE YOU
REFERENCE BUT THERE ARE A NEW
WAY TO LOOK AT GROUPS OF
PATIENTS AND WHAT ARE THE
ASSPEBTS OF THERE DISEASE AND
THIS IS ALL REVISED IN THE
ONTOLOGY BUT THIS IS A
CLINICALLY RELEVANT WAY OF
LOOKING AT COMPLEX DISEASE BUT
IT BRINGS IN A LOT OF NEW
ASPECTS WE THEN--WE THEN ARE
ABLE TO IMPROVE OUR DATA
CONNECTIONS.
AND LASTLY I WANT TO SHOW YOU MY
TEAM, THERE'S A CLINICAL TEAM UP
AT THE TOP AT THE CANNED WHAT
SCHOOL OF MEDICINE AND WE HAVE A
NUMBER OF CURATORS AND
INFORMATICS AVAILABLE AS WELL IN
THE TEAM AND BRINGING THIS DATA
TOGETHER.
THANK YOU AND IT WILL CLICK INTO
THE LAST COUPLE SLIDES, THIS IS
JUST ALL THE GROUPS WE WORK WITH
AND IT'S TOO MUCH FOR 1 SLIDE,
BUT JUST WANT TO MAKE SURE IT
GOT MENTIONED, THANK YOU IF ARE
YOUR TIME.
>> GREAT.
THANK YOU LYNN FOR A FANTASTIC
PRESENTATION, AGAIN EVERYONE
PLEASE USE THE SEND LIVE
FEEDBACK LINK TO SUBDMIT YOUR
QUESTIONS, WE WILL ASSEMBLE ALL
THOSE QUESTIONS IN THE CHAT AND
THEN THE END OF THE SESSION THIS
AFTERNOON, THE SPEAKERS WILL BE
AVAILABLE TO ANSWER THE
QUESTIONS, OKAY?
SO MOVING ON TO OUR NEXT SPEAKER
OUR NEXT SPEAKER IS EVGENIA,
SHISHKO VA WHY THE UNIVERSITY OF
WISCONSIN AND THE TIELTS OF HER
TALK IS DEFINING MITOCHONDRIAL
PROTEIN FUNCTION AND DISEASE
PATHOLOGY THROUGH MULTI-OMIC
PROFILING.
OKAY,A TAKE IT AWAY EVGENIA.
>> THANK YOU TO THE ORGANIZERS
AND THANKS VERY HAVING ME.
CAN YOU SEE MY--WE CAN SEE YOUR
SLIDE.
[INDISCERNIBLE] MOUSE?
LET ME--I SEE YOUR POINTER.
OKAY, SO VERY EXCITED TO TALK TO
YOU ABOUT THIS PROJECT THAT I'VE
BEEN WORKING ON FOR WIGHT A
WHILE IN THE NEXT 20 MINUTES I
WILL TALK A LOT ABOUT PROTEOMICS
AND BIO-INFORMATICS AND REAR
DISEASES I WON'T TALK ABOUT ANY
ASSPEBTS OF GLYCO BIOLOGY
HOWEVER, WHICH MAY BE A BIT OF A
CHANGE OF BASE [INDISCERNIBLE]
FOR OTHER PRESENTATIONS TODAY.
SO, BEFORE WE DIVE INTO SCIENCE,
I WOULD LIKE TO POINT OUT THAT
THIS PROJECT HAS BEEN VERY LONG
IN MAKING, THE INITIAL FUNDING
FOR IT WAS OBTAINED IN 20 FEIGN
BY MY BOSS JOSH COON AND THE
DAVE P A GLIARINI, THEY SPENT
SEVERAL YEARS COLLECTING CELLS
AND DATA COLLECTION AND THEN WE
SPENT YEARS COLLECTING DATA
SHARINGA, AND DRAFTING
MANUSCRIPT AND THEN WITH THE
LAST YEAR THE MANUSCRIPT IS IN
REVIEW AND RECENTLY ACCEPTED FOR
US AND SHOULD APPEAR IN PRINT
SOON.
ALONG WITH THE COURSE OF THE
PROJECT NEARLY 30 PEOPLE HAVE
CONTRIBUTED TO IT.
TOO MANY TO NAME RIGHT NOW, BUT
WE ALSO PICKED UP SEVERAL
COLLABORATORS FROM ALL OVER THE
WORLD INCLUDING THE UK AND
TURKEY.
SO IT'S JUST REALLY BEEN QUITE A
GLOBAL EFFORT FOR THIS PROJECT.
MORE OFTEN THAN NOT, IT IS QUITE
TYPICAL THAT THE LAB MAY LOOK AT
RNA OR RNASEQ OR PERHAPS
PROTEINS USING SPECIFICALLY
PROTEOMICS AND THAL TENDENCY TO
LOOK AT BIOMOLECULES TO LOOK IN
SPECIFIC SUBSECTION SYSTEM
ACTUALLY SOMEWHAT LIMITING
BECAUSE THE TRUTH IS THAT INSIDE
THE CELLS THEY DON'T EXIST IF
ISOLATION AND THEY TEND TO
INTERACT WITH EACH OTHER AND
WORK TOGETHER QUITE A BITE.
THE EXAMPLE SHOWN HERE IS THE
DEPICTION OF LIPID SYNTHESIS
PATHWAYS AND AS YOU CAN SEE HERE
IT HERE AND LIPIDS PROTEINS AND
METABOLITES AND SHOWN IN COLORS
REALLY WORK TOGETHER TO CARRY
OUT THIS VARIOUS PROCESSES, AND
IF WE WERE TO MEASURE PROTEINS
ALONE, IT WOULD GET A VERY
DIFFERENT AND MOST LIKELY
INCOMPLETE FUNCTION OF THIS
[INDISCERNIBLE] PATHWAYS.
AND THE NEED FOR THIS PULTY OMIC
STUDY THAT INTERROGATE SEVERAL
KINDS OF BI MOLECULES IS REALLY
APPEARANCE IN STUDIES OF
METABOLISM AND KIND OF OVERALL
METABOLOMICS BASIS FOR MANY
INTERROGATIONS OF MANY
BIOLOGICAL SYSTEMS.
THESE ORGANLES ARE PARTICULARLY
IMPORTANT TO THE STUDIES BECAUSE
OF THE METABOLIC PATHWAYS THAT
OCCUR IN THEM.
THERE ARE SOME BI CHEMICAL
PROCESSES THAT TAKE PLACE IN
MITOCHONDRIA THAT ARE TEXTBOOK
MATERIALS SUCH ASOXIDATIVE
PHOSPHORYLATION OR OTCA CYCLE
AND THERE ARE SOME LESS THAN
WELL KNOWN PROCESSES LIKE STRESS
SIGNALING, OR LIPID
MODIFICATION.
GIVEN HOW MANY PROCESSES OCCUR,
IT COMES AS NO SURPRISE THAT
THERE ARE VARIOUS HUMAN DISEASES
THAT ARE ASSOCIATED WITH
MITOCHONDRIAL DYSFUNCTION AND
THIS ORDER IS IN THE INDIVIDUAL
EFFECT AND THIS IS ASSOCIATED
WITH SINGLE MUTATIONS IN THE
SINGY GENE, AND SOME OF THEM
QUITE PROMINENT IS
CARDIOMYOPATHY OF PARKINSON'S
DISEASE, IT'S VERY SIGNIFICANT
IMPORTANT ORGANLES OF PROTEIN
COMPLEX I DON'T MEAN OF
MITOCHONDRIA IS NOT SUPERWELL
ANNOTATED, [INDISCERNIBLE] IS
THE PROTEINS TO LOCALIZE IN 2
MITOCHONDRIA IN HUMAN CELLS AND
ABOUT 25% OF THESE PROTEINS ARE
ACTUALLY LACKING FUNCTIONAL
MUTATION.
SO THE GOAL OF OUR PROJECT HERE
WAS TO TRY TO PROVIDE THESE
PROTEINS WITH SOME KIND OF
FUNCTIONAL DESCRIPTION THROUGH
GENERATING A LARGE COLLECTION OF
KNOCK OUT CELL LINES.
SO WE BEGIN BY INSTRUCTING THE
LIST OF PROTEINS FROM
[INDISCERNIBLE] WHERE WE THEN
FILTERED THAT LIST AGAINST A
LIST OF PROTEINS THAT ARE
NONESSENTIAL EXPRESS INDEED CELL
LINE AND IF MADE THE KNOCK OUT
CELL LINES FOR US SO IF WE LOOK
AT THE LIST OF CHARACTERIZED
PROTEINS WE WANT TO FOCUS ON THE
1S THAT LACKED ESTABLISHED
FUNCTIONAL LIMITATIONS SO WE
REALLY WANTED TO LOOK AT THOSE
THAT ARE JUST--WE REALLY DON'T
KNOW ANYTHING ABOUT THEM,
CHROMOSOME 5 [INDISCERNIBLE]
THIS TYPE OF PROTEINS ALSO
WANTED TO FOCUS ON THE 1S THAT
HAD NO HOMOLOGY WITH YEAST
BECAUSE OTHERWISE YOU SHOULD
DISCOVER THOSE IN YEAST, FOR THE
CHARACTERIZED PROTEINS, WE TRY
TO COMPOSE THE LIST IN SUCH A
WAY THAT IT WOULD INCLUDE
SEVERAL MEMBERS OF EACH CORE
METAON CHONDRIAL PATHWAY, AND
SORT OF THE PATH THAT I SHOWED
YOU EARLIER, THE TCGA CYCLE
SIGNALING MITOCHONDRIAL DNA
STABILITY MAKING ALL OF THOSE
PATHWAYS ARE COVERED BY OUR LIST
OF CHARACTERIZED ON PROTEINS
MOST ARE FOCUSED ON THE 1S IN
PRIORITIZED PROTEINS THAT
ENCLOUDED THAT CONTAIN THE KNOWN
DISEASE ASSOCIATIONS.
AS DOCUMENTED ON THE DATABASE.
ONCE WE WENT THROUGH STEPS OR
FILTERING WE END UP WITH A LIST
OF GENE TARGETS, 6 OF WHICH WERE
THE SENTINAL TARGETS SO THAT THE
PROTEINS AND 50 WERE THE
UNCHARACTERRIZED 1S THAT WE WERE
HOPING TO ANNOTATE IN THE
PROCESS OF STUDY.
WE PASS THIS ON TO HORIZON WHERE
THE USE CRISPR CAS TECHNOLOGY TO
GENERATE THE KNOCK OUTS FOR US.
ONCE IN POSSESSION OF THE KNOCK
OUT WE GREW THE CELL LINES IN 3
TO 4 REPLICATES AND I ALSO NEED
TO MENTION THAT FOR THE CELL
LINES WOULD HAVE DUPLICATE
CLONES MEANING THE SAME KNOCK
OUT WAS CREATED USING 2
DIFFERENT GUIDE RNAs SO IT WAS
200 DIFFERENT KNOCK OUT CELL
LINES THAT WERE THEN--THEN
ANALYZED USING 3 DIFFERENT
DISCOVERY MASS SPEC ROMETRY
PLATFORMS SO IF WE ANALYZE THE
PROTEINS USING SINGLE SHOT
PROTEOMICS AND LABELED
PREQUANTITATION, WE ALSO
PERFORMS A DISCOVERY LIPID OMICS
ASSAY USING CMS, AND TARGETED
METABOLOMICS USING UGCMS, AND WE
ALSO HAD MITOCHONDRIAL
DNSEQUENCING AND CELL GROWTH
PHENOTYPING.
AS A RESULT OF THIS EFFORT WE
ENDED UP WITH OVER 1000
MOLECULAR MEASUREMENTS PER EACH
CELL LINE THAT WE PROFILED.
AND MAJORITY OF THOSE
MEASUREMENTS WERE PROTEIN
MEASUREMENTS, IN FACT WE MEASURE
IT NEARLY 1000 MITOCHONDRIA
PROTEINS WHICH KOYOKO SPONDY
LIGHTISSED TO 81% OF THE
PROTEINS REPORTED TO BE IN
[INDISCERNIBLE].
WE ALSO HAD OVER 50 DIFFERENT
CLASSES AND METABOLITES
REPRESENTING SEVERAL SMALL
MOLECULE CLASSES.
AS YOU MENTIONED ONCE YOU WORK
WITH SUCH AMOUNT OF DATAY SO
IT'S 4000 MEASUREMENTS TIMES THE
NUMBER OF CELL LINES THAT WE
GREW, YOU END WITH ABSURDLY
LARGE DATA SET.
SO WE HAD OVER 8 MILLION
MOLECULAR MEASUREMENTS THAT WE
GENERATED IN THE COURSE OF THE
STUDY AND BY THE WAY WE PULLED
THIS STUDY MITOMICS WHICH STANDS
FOR MITOCHONDRIAL ORPHAN PROTEIN
MULTIOMIC CRISPR SCREEN SO IT'S
THE NAME OF THE APPROACH AS WELL
AS THE NAME OF THE DATA SET WE
GENERATED OPERATED AND AS YOU
MENTIONED, SHARING A DATA SET
THAT LARGE AND EXPLORING THAT
DATA BECOMES VERY CHALLENGING
QUICKLY SO THROUGHOUT THE COURSE
OF THE STUDY, WE USE THE CUSTOM
WEBSITE APPROACH TO SHARE THE
DATA AMONGST DIFFERENT
COLLABORATING GROUPS AND NOW,
THIS WEBSITE COULD BE FOUND OUT
UNDER THE MAIN MITOMICS APP.
AND IT WAS USED IN THE LAB
PREVIOUSLY CALLED AGER NOT, I
WILL NOT GO INTO TOO MUCH DETAIL
ABOUT THIS TOOL, AND YOU CAN
READ ALL ABOUT IT IN THIS
APPLICATION FROM 2020.
BUT BRIEFLY, THEY WILL USE THIS
WITH THE CONTROLS AND THE
GENERATE A DATABASE TAKEN--THEY
CAN BE USED TO CREATE THIS
CUSTOM WEBSITE AND WHILE WE USE
THIS INTERACT WITH THE WEBSITE,
THEY CAN GENERATE ONDEMAND
VISUALIZATIONS AND EXPLORE THE
DATA THROUGH THE VARIETY OF
COMMONLY USED [INDISCERNIBLE],
RELATION ANALYSIS AND SUCH.
AND SINSZ THIS EXISTS AS A
WEBSITE, IT'S VERY EASY TO SHARE
THIS DATA TO CURATE THE DAILY
BASIS AT AND IT'S ALSO PASSWORD
PROTECTED SO SPECIFIC
INDIVIDUALS NEED TO BE INVITED
TO VIEW THE DATA SO IT'S QUITE
SAFE.
SORRY, I'M HAVING AN ISSUE
CLICKING THE SLIDES.
ONE SECOND.
HERE WE GO SO WHEN YOU FIRST
GENERATE A LARGE DATA SET LIKE
THAT, YOU TYPICALLY WOULD DO
SOME KIND OF SPOT CHECKING OF
THE DAILY BASIS THEA AND THAT'S
WHAT WE DID, AS YOU KNOW WE HAD
MANY PROTEINS OF NEW FUNCTION,
SO WE LOOK TO SEE HOW THE LOSS
OF THOSE PROTEINS AFFECTS THE
PHENOTYPES OF THE CELLS.
ONE OF THE CELL LINES WORK WITH
THE CONTAIN THE DELETION OF THE
ENZYME CALLED [INDISCERNIBLE],
PULSATIVITY 2 AND THIS ENZYME
TURNS INTO KARNITTINE AND IN THE
LIPID OMICS DATA FOR THE CELL
LINE VERY QUICKLY IDENTIFIED
THAT THERE WAS AN ACCUMULATION
OF THE THE KARNITTINE SPECIES
THERE WAS A SPECIFIC LOSS OF
FUNCTION WITH THIS PROTEIN.
SIMILARLY, WE OBSERVED CHANGES
IN METABOLOMICS DATA FOR
EXAMPLE, IN THE CELL LINE THAT
LACKED THE PROTEIN CALLED SLC 25
A 1, WE NOTICED THAT THERE WAS A
PRONOUNCED ACCUMULATION OF
METABOLITE OF 2 HYDROXIC ACID
AND THIS IS CONSISTENT WITH THE
FUNCTIONAL PROTEIN BECAUSE AS OF
CTLA21 WAS A TRANSPORTER IN IT'S
ABSENCE IT ACCUMULATES AND GETS
CONVERTED INTO THE
[INDISCERNIBLE] ACID WHICH IS
WHAT WE'RE OBSERVE IN THE
METABOLOMICS DATA AND THIS IS
THE HALLMARK OF THE DISEASE
CALLED [INDISCERNIBLE] AND IT
AND CAPITULATE AND THOSE TYPES.
--AND THERE'S KIND OF GLOBS OF
METABOLITES THROUGHOUT THIS.
PLOT IT'S HARD TO TELL WHAT THIS
IS FOR THE BEHAVIOR, WE'RE
OBSERVING BOTH, YOU KNOW THERE
COULD BE TECHNICAL EXPLANATIONS
BAZ IF YOU REMEMBER WE USE THE
DIFFERENT PLATFORMS AND USE
SEPARATE PAL ATS IF ARE THIS
ANALYSIS, THIS COULD BE A
REFLECTION OF THE DATABASE
ITSELF AND PERHAPS FUNCTIONAL
CONNECTION IF THE LIPIDS AMONGST
TRITE TO TYPE IT IN AND
CONNECTION BETWEEN LIPIDS AND
THE VARIOUS PROTEINS.
MANY ASPECTS OF [INDISCERNIBLE]
RANDOM BUT NO MATTER HOW WE
CHANGE THE PARAMETERS AND WE
ALWAYS END UP WITH THIS CLUSTER
HERE AND THIS VERY TIGHT CLUSTER
ACTUALLY, IS ZOOMED IN HERE AND
YOU COULD ACTUALLY SEE IT
CONSISTS WITH A LOT OF AND
CORRELATION AND MICRO STUDIES OF
MULTIPLE ENDOCRINAL PROTEINS SO
IT WAS ENCOURAGING TO SEE SUCH
TYPE CONNECTIONS AND WE ALSO
NOTICE THAT THERE'S SEVERAL
SMALL METABOLITES SUCH AS
[INDISCERNIBLE] ACID AND SID
RICK ACID AND
PROPIONYLKARNITTINEITINE AND
THEY'VE BEEN KNOWN TO HAVE VERY
SIGNIFICANT FUNCTIONS IN MIGHT
MITOCHONDRIA.
SO ALL IN ALL THIS IS
ENCOURAGING BUT THE DATA
MAINTAINS RELATIONSHIPS AND
PERHAPS AGAIN LOOKING FOR NOVEL
RELATIONSHIPS, AND USING THIS
DATA SET.
SO 1 OF THE MOLECULAR PATHWAYS
WAS BY SYNTHESIS OF CO
FACTOR--COQ10 IT'S A MOLECULE
THAT PLAYS A ROLE IN OXIDATIVE
MOLECULARRIZATION.
SO WE SAW THE DEPLETES OF THE
FINAL LEVELS OF THIS MODEL AND
THIS WAS SUPER HAPPY TO SEE THAT
ONCE WE LOOKED ACROSS VARIOUS
CELL LINES OF THE PROFILE, IN
OUR STUDY, WE NOTICED THERE WAS
A KNOCK OUT APPEARED THAT HAD
THE PHENOTYPE VERY SIMILAR TO
THE 1S THAT AND PROTEINS MISSING
OBSERVED IN THE CELL LINES THAT
WERE MISS NOTHING VARIOUS
ENZYMES THIS IS QUITE CURIOUS
AND WE HAVE MORE INFORMATION
ABOUT THE POSSIBLE FUNCTION
HERE.
SO THIS IS A CHANGE OF VARIOUS
PROTEINS IN THE CELL LINES HERE,
AND YOU CAN SEE THE PEER ITSELF
IS INCREASING THE METHOD BUT
ALSO OBSERVE THERE ARE SEVERAL
MEMBERS OF THE THIS PATHWAY
DEPICTED HERE AND INTERESTINGLY,
WE ARE ALSO SEVERAL COMPONENTS
OF A COMPLEX MODULE AS WELL AS
FACTORS SHOWN HERE IN GREEN AND
BLUE, THAT WERE ALSO DECREASED
AND YOU CAN SEE THAT THE COMPLEX
1 OR COQ ARE RELATED TO EACH
OTHER SO THERE NEEDS TO BE SOME
SORT OF COORDINATION BETWEEN THE
2 BUT THE MOMENT UPON WHEN WE
MADE IN OBSERVATION HAS BEEN
NOTHING KNOWN ABOUT HOW THOSE 2
MAY BE TALKING TO EACH OTHER AND
HOW THOSE LEVELS MIGHT BE
COORDINATED AND AN INTERESTING
PIECE CAME FROM NEW CASTLE
UNIVERSITY IN HIS LAB AND IN
FACT, THE COLLABORATORS CLINICAL
GENETICIST AND THEY HAVE COME
ACROSS A FAMILY WHERE APPEARANCE
HARVARD MUTATION IN APPEARED
GENE IN 1 OF THE CHILDREN HAPPEN
TO BE HOMOZYGOUS FOR THIS
MUTATION, WHICH CAUSE FATAL
SYNDROME THAT INVOLVED COMPLEX
LIST OF SYMPTOMS SHOWN OVER HERE
AND INTERESTINGLY THESE SYMPTOMS
ARE QUITE CONSISTENT WITH THE
LOSS OF POINTS AND CUE
FUNCTIONALITIES AS WELLs 1, SO
THIS WAS ANOTHER POINTING THAT
HOW IT WAS INVOLVED SO IN THE
INTEREST OF TIME I WILL SKIP THE
DESCRIPTIONS OF SOME OF THIS
OTHER BIOCHEMICAL DATA, BUT
BASICALLY FOR EVER A SERIES OF
RISKS WE DEMONSTRATED HERE CAN
INTERACT WITH VARIOUS ASSEMBLY
FACTORS OF COMPLEX 1 AND IT'S
FACT OF THE LOSS OF THOSE ON
CELLULAROXIDATIVE COMSUMPTION
RATE IS ALSO CONSISTENT WITH
THIS ROLE IN COQ AS WELL AS
FUNCTIONALITY COMPLEX 1.
BASED ON THE INITIAL MASS SPEC
DAILY BASIS IT ISA AND FURTHER
BIOCHEMICAL EXPERIMENTS, SORT OF
PROPOSED THIS MODEL OF THE PEER
OF FUNCTION WHERE IT SLIDES ON
THE INTERPHASE OF COMPLEX 1 AND
BIOSYNTHESIS, SORT OF ACHIEVING
EXPRESSION OF [INDISCERNIBLE]
AND TYING THE 2 PATHWAYS
TOGETHER.
AND ACTUALLY WE NAMED PYURF,
NDUFAFQ, WHICH IS INVOLVE WIDE
THIS PROCESS.
ANOTHER STORY WE HAD ABOUT KNOCK
OUT OF THE PROTEIN CALLED
RABIF5, IT'S ALSO KNOWN AS C20
ORF24, AND NOW COLLABORATING IN
THE LAB, [INDISCERNIBLE] MADE AN
OBSERVATION SHOWING THAT THE
DOES HE LESION WAS A VERY
SPECIFIC LOSS AND DECREASE IN
ABUNDANCE OF THE PROTEIN OF CO1
AND AS YOU CAN SEE WE HAVE 2
CELL LINES WITH THE LACKING OF
RABIF5, SO IT WAS A VERY STRONG
OBSERVATION.
AND THIS WAS VERY INTERESTING
BECAUSE TMCO1 IS A VERY
IMPORTANT POINT ITSELF, IT'S A
PROTEIN THAT'S ENDOPLAZ MIDSIC
RETIC LUMRELATED TO PROTEIN, AND
IT MAY HAVE A FUNCTION IN
CALCIUM TRANSFERAISE.
SO THIS WAS CURIOUS TO US
BECAUSE AS YOU KNOW RABIF5 IS A
MITOCHONDRIA PROTEIN AND WE
WONDERED IF THE 2 TYPES WERE
TOGETHER AND MAYBE INVOLVED IN
THE CROSS TALK WITHIN THESE 2
TYPES OF ORGANLES.
SO WE VALIDATED THIS OBSERVATION
THROUGH WESTERN BLOT AND THIS IS
ALSO WHICH IS SHOWN OVER HERE
AND WE ALSO SHOWED USING SMALL
INTERFERON RNAs THAT THE LOSS
OF RABIF5 IS THE LOSS OF 1 AND
THE OTHER WAY AROUND DELETION OF
TEAM CO1 WITH THE LOSS OF RABIF5
SO THIS IS ACTUALLY NEUTRAL.
WE ALSO GOT A VERY INTERESTING
PIECE OF INFORMATION FROM OUR
COLLABORATORS AND THE LAB AT THE
UNIVERSITY IN TURKEY AND HAD IS
ALL GENETICIST AND THEY'VE BEEN
WORKING WITH SEVERAL FAMILIES
IMPACTED BY A RARE DISEASE OLD
SUPERFICIAL THORACIC DISPLASSIA,
CFTD, AND MOST KNOWN CASES OF
THE DISEASE ARE RELATED TO
MUTATIONS IN GENE 1501 HOWEVER,
THERE ARE SOME CASES OF THE
DISEASE THAT HAVE NOT BEEN
EXPLAINED BY ANY MUTATIONS IN
TMC01.
THE LAB WAS ACTUALLY ABLE TO
FIND A MUTATION IN THE GENE
ENCODING IN RABIF5 THAT CAUSED A
LOSS OF PROTEIN THAT'S A SINGLE
ACID
ACID LIMITATION THAT DOESN'T
APPEAR IN THE SICKNESS OF THE
GENE AND THERE WAS THIS FAMILY
SHOWN OVER HERE, THE GENO GRAM
OF THIS HERE, THAT ACTUALLY HAD
SEVERAL INDIVIDUALS AIVETTED BY
THIS DISEASE, SO HERE AT THE
SPECIFIC MUTATION AND RAPIDLY 5.
WE WERE ACTUALLY ABLE TO OBTAIN
THE FIBRO PLAOF THES FROM AN
EFFECTIVE INDIVIDUAL SHOWN HERE
AND BY SOME MIRACLE THE CELLS
WERE SHIPPED FROM THIS AND CAME
FROM THIS INDIVIDUAL AND SHIPPED
FROM TURKEY ARRIVED TO ST. LOUIS
AND THERE OUR COLLABORATOR WAS
ABLE TO INSPECT THEM AND NOT
WILD TYPE SEQUENCE OF RAB5 IF
AND CAUSED INCREASE OF THE TMCO1
AND THIS LED TO THE
[INDISCERNIBLE].
IN THE INTEREST OF TIME WE WILL
HAVE TO SKIP THE OTHER STORIES
WE OBSERVED BUT THERE WAS
ANOTHER PUBLICATION THAT
DESCRIBES THE PATHOLOGY THAT WAS
LINKED TO A RARE FATAL
AUTOINFLAMMATORY SYNDROME THAT
IS DEMONSTRATED AND WITH STORAGE
ISSUES WITH THE LOSS OF C2
ORFSCAIN AND THE RESULT OF THIS
PROJECT WE MANAGED TO PROPOSE
SOME POSSIBLE FUNCTIONAL
LIMITATIONS FOR ANOTHER FEIGN OR
CHARACTERIZE PROTEINS AND ALL OF
THESE OBSERVATIONS APPEAR IN THE
MANUSCRIPT AND THEY'RE READY
APPROXIMATE FOR FUTURE
BIOLOGICAL STUDIES.
SO IN CONCLUSION, I WOULD LIKE
TO REMIND YOU WE WORKED ON THE
PROJECT CALLED MIRROR IMAGE
TOPICS WHICH IS A LARGE
MULTIOMIC RESOURCE FOR THE
MITOCHONDRIA HAL BIOLOGIC
IMMUNITY THAT CHARACTERIZES OVER
200 VARIOUS IMK OUT CELL LINES
IN LOOKING TO ESTABLISH
CONNECTION MITOCHONDRIA PROTEINS
OF KNOWN AND KNOWN FUNCTIONS AND
DM THE COURSE OF THE PROJECT WE
WERE ABLE TO PROVIDE FUNCTIONAL
MUTATIONS FOR SEVERAL PROTEINS
AND PINPOINT THEIR ROLES IN
VARIOUS RARE DISEASES AND IN
GENERAL THE MOST IMPORTANTLY
MITOTIC SYSTEM HYPOTHESIS
GENERATING RESOURCE, WE'RE
HOPING THAT IT WILL REALLY JUMP
IN IT AND FOLLOW UP ON THE LEADS
FOR THE RIGHT DISCOVERY IN THIS
RESOURCE.
I'D LIKE TO THANK NUMEROUS
MEMBERS OF THE LAB THAT WORKED
ON THIS PROJECT OVER THE YEARS
ALSO OUR COLLABORATORS IN LABS
FROM ALL AROUND THE WORLD AND
OUR FUNDING RESOURCES AND OF
COURSE ALL OF YOU, THANKS A LOT.
>> GREAT, THANK YOU SO MUCH,
EVGENIA, GREAT TALK.
AS A REMINDER PLEASE USE THE
LINK: SEND LIVE FEEDBACK, TO
SUBCOMMIT YOUR QUESTIONS AND
AGAIN AT THE END OF OUR
AFTERNOON SESSION IN ABOUT AN
HOUR AND ALL THE SPEAKERS WILL
AVAILABLE TO ANSWER THOSE
QUESTIONS.
SO NOW TO MOVE ON, OUR NEXT
SPEAKER IS DANIEL GRAHAM AT THE
BROAD INTUITY AND THE TIELT OF
HIS TALK IS CLUES FROM HUMAN
GENETICS IMPLICATE GLYCO BIOLOGY
AND INTESTINAL BARRIER INTEGRITY
AND INFLAMMATION.
OKAY, CAN YOU TAKE IT AWAY,
DANIEL?
>> OKAY, THANKS.
IT'S REALLY NICE TO BE WITH YOU
THIS AFTERNOON AND I'VE REALLY
ENJOYED ALL THE TALKS SO FAR.
AND IT'S A PLEASURE TO BE ABLE
TO TELL YOU A BIT ABOUT OUR WORK
IN HUMAN GENETICS AND AND OUR
JOURNEY FROM GOING FROM LEADS
FROM HUMAN GENETICS TO DISEASE
MECHANISMS THAT LED US TO FLIEK
O BIOLOGY AND THEN UNEXPECTED
WAY TAUGHT US A LOT ABOUT THE
MECHANISTIC BASIS OF HUMAN
DISEASE AND OUR STRATEGIC PLAN
EDGE CEREALLY FOCUSED ON THIS
IDEA THAT THERE'S TREMENDOUS
GENETIC DIVERSITY AROUND THE
GLOBE AND IN POPULATIONS AND
THIS HAS BEEN ENRICHED OVER THE
YEARS THROUGH EVOLUTION AND THE
TASK OF EVOLUTION HAS REALLY
BEEN IN THE'MUNE SYSTEM TO
BALANCE THE RISK OF AUTOIMMUNITY
WITH PROTECTIVE DEFENSE AGAINST
PATHOGENS AND IN THAT CONTEXT,
PATHOGENS ARE REALLY STRONG
SELECTIVE PRESSURE FOR
EVOLUTION.
SO, AS A RESULT OF THAT, THERE
ARE GENES THAT ARE GENETIC
VARIANTS THAT ARE ASSOCIATE WIDE
ROBUST PROTECTION AGAINST
PATHOGENS BUT THEY COME AT THE
RISK OF AUTOIMMUNITY.
AND THE REVERSE IS TRUE AS WELL,
THERE ARE VARIANTS THAT ARE
ASSOCIATED WITH PROTECTION FROM
IMMUNO DEFICIENT PATHOGENS OR
AUTOIMMUNITY BUT SUSCEPTIBILITY
TO INFECTION THROUGH THE COURSE
OF IMMUNO DEFICIENCY.
AND THIS RICH SOURCE OF GENETIC
DIVERSITY HAS BEEN KIND OF AN
ENGINEER OF DISCOVERY FOR
UNDERSTANDING HOW THE IMMUNE
SYSTEM WORKS AND HOW AUTOIMMUNE
IMMUNE
DISEASES PROGRESS IN GENERAL AND
THERE ARE A COUPLE OF DIFFERENT
GENETIC STRATEGIES THAT HAVE
BEEN REALLY FRUITFUL IN THIS
REGARD SO GWAS STUDY VS BEEN
GOOD AT FINDING COMMON VARIANTS
THAT ARE ASSOCIATED WITH DISEASE
OUTCOMES AND THEY TEND TO HAVE A
SMALL EFFECT SIZE BECAUSE THEY
AFFECT--THEY FALL IN NONCODING
REGIONS OF THE GENOME, AND THEY
AFFECT GENE EXPRESSION AND
SUBTLE WAYS BUT NEVERTHELESS,
THEY POINT TO IMPORTANT GENES
THAT HAVE STATISTICAL
ASSOCIATIONS WITH DISEASE
PHENOTYPES AND MORE RECENTLY AS
THE COST OF THE SEQUENCING HAS
GONE DOWN, WE'VE SEEN MORE AND
MORE EXOME SEQUENCING STUDIES
THAT ARE REALLY VERY WELL
POWERED TO FIND CODING VARIANTS
IN GENES THAT ARE MORE RARE BUT
HAVE A LARGER EFFECT SIZE
BECAUSE THEY AFFECT PROTEIN
FUNCTION AND IF YOU CAN FIGURE
OUT HOW THEY AFFECT PROTEIN
FUNCTION, IT LEADS YOU DIRECTLY
TO MECHANISMS IN SOME CASES.
SO OUR STRATEGY HAS BEEN TO
LEVERAGE ADVANCES FROM GWAS AND
EXOME SEQUENCING TO MAP RISK
GENES AND VARIANTS TO CELLULAR
FUNCTION AND TO DO THAT WE'VE
EMPLOYED A NUMBER OF CRISPR
SCREENS USING MANY DIFFERENT
READ OUTS AND IMMUNE PATHWAYS
AND FROM THERE FOLLOW UP WITH
MULTIOMICS STRATEGIES TO TRY TO
FIND MOLECULAR MECHANISMS FOR
THESE GENESS AND VARIANTS AND
THEN BUILDING OUT TOWARDS THE
MORE PHYSIOLOGICAL UNDERSTANDING
OF HOW THESE VARIANTS WORK IN
ANIMAL MODELS AND BY STUDYING
PATIENT SAMPLES.
AND THE GOAL OF ALL OF THIS IS
TO AGAINERATE NEW INSIGHTS
SPECIFIC DETAILS ON DISEASE THAT
ARE SUFFICIENTLY DEEP TO FORMUTE
NEW THERAPEUTIC HYPOTHESIS.
AND IF YOU TURN THE CRANE, CAN
YOU DO THIS PROCESS OVER AND
OVER AND CAN YOU MAP GENES TO
PATHWAYS AND FIND NOW
CONNECTIONS BETWEEN GENETIC
VARIANCE AND BIOLOGICAL
PROCESSES.
WE'VE DONE A LOT OF WORK IN
INFLAMMATORY BOWEL DISEASE,
CHRONS AND ULCRATIVE COLITIS AND
MAP WAYS TO ADAPTIVE IMMUNITY
AND HANDLING MICROBIAL PATHOGENS
AS WELL AS MICROBIOME ENTITIES
BUT WHAT IS PERHAPS MORE
SURPRISING IS THE CONNECTION THE
GENETIC CONNECTION BETWEEN IBD
AND EPITHELIAL BARRIER FUNCTION
AND IN THIS CONTEXT, THE BARRIER
ACTIVITY IN THE COLON IS
CONFERRED BY 3 DIFFERENT LAYERS,
SO THE FIRST LAYER IS THE
EPITHELIAL CELL LAYER AND THIS
FORMS A BARRIER THROUGH THE
FORMATION OF JUNCTIONAL
COMPLEXES THAT FUSE THE CELLS
TOGETHER AND IT'S--IT'S
ESSENTIALLY IMPERMEABLE TO
MICROBES.
AND THEN AT THE VERY SURFACE OF
THE EPITHELIAL CELLS AND THE
GLYCOICAL EXPECTATIONS LAYER,
THESE DENSE GLYCO PROTEINS THAT
AGAIN PERFORMANCE AN IMPORTANT
BARRIER FUNCTION AND THEN BEYOND
THAT, IS THE MUCUS, AND THE
MUCUS IS OBVIOUSLY THE WELL
CHARACTERIZED BLIEK O PROTEIN
THAT HAS UNIQUE VISITINGICAL
ELASTIC PROPERTIES THAT FORM A
BEAR WRER TO PENETRATION THROUGH
MIKE ROBES IN THE MICROBIOME AND
TOGETHER THESE 3 ELEMENTS REALLY
PROTECT THE IMMUNE SYSTEM FROM
INVASION OF FOREIGN ENTITIES,
AND ALSO LIMIT INFLAMMATION, AND
SO, THIS IS THE MAJOR LINK TO
FLIEK O BIOLOGIES IN THIS
BARRIER INTEGRITY FUNCTION.
SO THE MUCUS IS SECRETED BY
GOBLET CELLS IN THE MUCOSA.
AND SECRETING THAT LARGE VOLUME
OF MUCUS PUTS QUITE A BURDEN ON
THE ENDOPLASMIC RETIC LUMOF
THESE CELLS.
--CAN BE OBSERVED AT THE SINGLE
CELL LEVEL IN TRANSCREPT OHMICS
AND IN HEALTHY SUBJECTS YOU SEE
STRONG STRESS SIGNATURE AND
CELLS, AND THAT'S REAL LE A
FUNCTION OF THE FACT THAT THEY
HAVE TO MAKE SO MUCH LIKE O
PROTEIN MUCINs, AND DURING THE
COURSE OF PROTEIN TRANSLATION
AND GLYCOSYLATION IN THE ER, IT
WAS GLYCOSYLATION SIGNALS SERVE
AS SORTING SIGNALS TO TRAFFIC,
PROTEINS THROUGH ER TO THE GOLGI
AND SECRETED INTO THE LUMEN OF
THE GUT AND UNDER STRESS OR
UNDER DURESS, CAN YOU SEE AN
ACCUMULATION OF UNFOLDED
PROTEINS IN THE ER, AND CELLS
HAVE DEVELOPED MANY SENSOR ARMS
THAT CAN DETECT UNFOLDED
PROTEINS AND THEN ILLICIT AN
ADAPTIVE RESPONSE TO THE
UNFOLDED PROTEIN RESPONSE TO
UPREGULATE ALL OF THE SECRETION
MACHINERY INCLUDING
GLYCOSYLATION MACHINERY TO TRY
TO RESOLVE THE STRESS OF THE
CELLS CAN DO THEIR JOB AND MAKE
THE MUCIN BARRIER.
SO THERE ARE 3 SENSOR PATHWAYS
THAT DETECT ER STRESS AND THEY
CONVERGE ON 3 TRANSCRIPTION
FACTORS XBP1 ATF6 AND ATF4, AND
SO WE DEVELOPED CRISPR SCREENING
STRATEGY TO TRY TO IDENTIFY NEW
IBD RISK GENES THAT AFFECT ER
STRESS RESPONSES.
SO WE SET UP 3 REPORTER SYSTEMS,
THE FIRST IS AN ER STRESS TEST
WHERE WE BLOCK GLYCOSYLATION
WITH [INDISCERNIBLE] AND MEASURE
LIFE OR DEATH OUTCOME OF THE
CELLS.
THE XEKD SCREENING IS LOOKING AT
ACTIVATION OF XBP1 THROUGH A
SPLICING EVENT THAT TURNS ON
UNFOLDED PROTEIN RESPONSE AND
THE THIRD SCREENING SYSTEM IS
LOOKING AT ER HOMEOSTASIS
ESSENTIALLY MEASURING THE RATIO
OF SECRETORY OUTPUT TO CHAPERON
OCCUPANCY.
AND IN 1 OF IN THE XBP SLICING
AND WHEN WE KNOCK IT OUT, IT'S
THE XBP1 REPORTER IT TURNS OUT
TMEM258 IS LOCATED IN A RISK
LOCATED FOR CHRONS DISEASE AND
THIS GENE IS NOT VERY WELL
CHARACTERIZED AND IT HAS 2
TRANSMEMBRANE DOMAINS AND THAT'S
IT, THERE'S REALLY NOTHING
RECOGNIZABLE OUT IN THAT GENE IS
HENCE IT WAS OVERLOOKED IN THE
GWAS STUDIES BECAUSE THERE'S NO
KNOWN FUNCTION AND THERE'S
OTHERS IN THE NEIGHBORHOOD SO WE
EMBAKERRED ON A SERIES OF
STUDIES TO FIGURE OUT WHAT
TMEM258 DOES, IT LOCALIZED
EXCLUSIVE TO THE ER WITH CHAPPER
OWNS LIKE KALNECKSIN AND WE YOU
KNOCK IT OUT IT BLOCKS PATHWAYS
WITH [INDISCERNIBLE].
AND AND THEN WE DID PROTEOMIC
EXPERIMENTS THAT OPENED THE
DOORS FOR US IN GLYCO BIOLOGY.
IT TURNS OUT TMEM 258 WAS AN
UNKNOWN SUBUNIT OF THE OST
COMPLEX, SO THIS IS THE
OLIGOSACCHARIDE TRANSFERAISE
COMPLEX, HIGHLY CONSERVED ACROSS
THE TREE OF LIFE AND PERFORMS
THE FIRST STEP IN TPHREU RACING
COSALATION OF MASON PROTEINS.
AND A COUPLE YEARS AFTER WE MADE
THIS DISCOVERY THERE'S A
BEAUTIFUL CRYOEM STRUCTURE
PUBLISHED OF THE OST COMPLEX AND
YOU CAN SEE TMEM258 NESTLED INTO
THE TRANSMEMBRANE REGION HERE.
SO IT WAS EASY TO MISS BUT
NEVERTHELESS IT IS A REQUIRED
COMPONENT OF THIS COMPLEX.
SO WE MADE A XOK OUT MOUSE AND
IT'S EMBRYONIC LETHAL BUT THE
HEXES SURVIVE AND WE'RE ABLE TO
TAKE HETEROZYGOUS COLONIC STEM
CELLS AND MAKE ORGANOID CULTURES
AND YOU CAN SEE THESE SPHEROID
ORGANLES WE WERE ABLE TO
GENERATE AND USE CRISPR TO KNOCK
OUT THE OTHER 258 AND WHEN WE DO
SO THE CELLS UNDER GO ER STRESS
AND THE BARRIER DISSOLVES SO
THIS REALLY HIGHLIGHTS THE
IMPORTANCE OF GLYCOSYLATION AND
MAINTAINING ER HOMEIO STASE AND
I SAY HOW IMPORTANT THAT IS FOR
CELLS IN EPITHELIAL LAYER TO
FORM THE BARRIER AND TO CRETE
MUSEINS AND HOST SYSTEM FROM
INVASION BY MICROBES.
SO THIS A SCHEMATIC THAT I'M
SURE IS VERY FAMILIAR TO MOST OF
THE AUDIENCE HERE, LOOKING AT
NGLYCOSYLATION IN THE EM TR AND
THE 258 IS THE OST ACTS HERE
EARLY, AND AND STEP OF
GLYCOSYLATION BUT OUR SCREENING
CAMPAIGN IDENTIFIED A WHOLE LOT
OF OTHER IBD RISK GENES THAT ARE
ACTING WITH THE SAME PATHWAY
WHICH IS SOMEWHAT SURPRISING
INCLUDING RFT 1 AND ANOTHER GENE
I WILL TALK ABOUT A BIT,
SLCTHREEN 8A, THIS TRANSPORTER
GENE TRANSPORTS MAN GANNA EASE
AND ZINC AND IT'S AN IMPORTANT
FACTOR FOR THESE TRANSFER ACE
INSWROAMS THAT ELABORATE TPHREU
RACING KAN--KANAS LOOK THE GOLGY
SECRETATTORY PATHWAY.
THESE HAD BEEN IN DISORDS OF
GLYCOSYLATION SO THERE WERE
HYPER FOREVERRIC MUTATIONS THAT
LEAD TO NULL PROTEIN AND HAVE
VERY SEVERE OUTCOMES ASSOCIATE
TD WITH DEVELOPMENTAL DEFECTS
AND SO FORTH.
SO THESE ARE VERY SEVERE
MUTATIONS AND THE MUTATIONS WE
SEE IN IBD ARE MORE SUBTLE, SO,
THEY'RE MORE COMMON AND THEY
HAVE EFFECTS THAT ARE NOT QUITE
AS PENETRANT OF DISORDERS OF
GLYCOSYLATION BUT NEVERTHELESS,
ASSOCIATED 39 A IS A POSTER
CHILD OF A MRI O TROAPIC VARIANT
AND THE REASON IS THAT THIS ALLY
91 T SUBSIDIARY CONSTITUTION IS
ASSOCIATED WITH RISK OF IBD, BUT
ALSO BLOOD LIPID LEVELS,
CARDIOVASCULAR DISEASE,
SCHIZOPHRENIA, PARKINSONS, AND
MANY OTHER PHENOTYPES.
AND THAT'S PROBABLY A REFLECTION
OF HOW IMPORTANT MAN GANNA EASE
IS IN FOR MANY BIOLOGICAL
SYSTEMS BUT ALSO THE IMPORTANCE
OF GLYCOSYLATION IN MANY
DIFFERENT ORGAN SYSTEMS AND
DISEASES.
SO WE MADE A KNOCK-IN MOUSE
WHERE WE INTRODUCED THIS RISK
VARIANT A391 T TO THE ENDOGENOUS
39 A 8 LOCUST AND WE MEASURED IF
THE BLOOD MAN GANNAIES AND WE
SEE REDUCED MANGANESE IN THESE
MICE IN THE BLOOD, LIVER AND
COAL AN AND LEVELS OF ZINC WERE
NORMAL AND WE HYPOTHESIZED THAT
THE VARIANT AND THE LACK OF
MANGANESE WOULD AFFECT THESE
STRUCTURALLY ARES AND I'M
SHOWING CERTAINLY--CERTAINLY
LECTURE ROUGH ATOM MICROGRAPH OF
A SINGLE EPITHELIAL CELL AND AT
THE TIP OF THE EPITHELIAL CELL,
YOU SEE THESE FINGER LIKE
PROJECTIONS OF MICROVILLI AND AT
THE VERY END OF THE THE VILLI,
SEE THE SHADOWY LAYER, THAT'S
THE GLYCO KALYX AND THE A3192,
THE FLIEK O FELIX HAS BEEN IN
PATCH, SUGGESTING THAT THE
DEFECT RESULTS IN VARIED DEFECTS
AND ANOTHER WAY TO LOOK AT THIS
ABOVE THE GLYCO CALYX, AND YOU
CAN STAIN THE MUCUS LAYER WITH P
A S AND WILD TYPE YOU SEE NICE
PALE PLURIBU DENSE MUCUS LAYER
ABOVE THE EPITHELIUM AND IN THE
VARIANT MICE THIS MUCUS LAYER IS
THINNER.
AND MORE VISCUS.
THIS MUCUS LAYER PREVENTS A
BARRIER BY MICROBES WHICH YOU
CAN DEFECT IN FISH ON THE GREEN
PROBE ON THE RIGHT HERE AND YOU
CAN SEE IN THE VALID AND
RELIABLE YABT THERE'S MORE
BACTERIA CLOSER TO THE
EPITHELIAL LAYER APPROXIMATE AND
IN FACT, SOME CASES PENETRATING
SUGGESTING THAT THERE'S EXPOSURE
TO THE IMMUNE SYSTEM AND CHRONIC
LOW GRADE INFLAMMATION.
SO AS A RESULT OF THESE COMPLEX
BARRIER, WE SEE IN THESE MICE A
LEAKY GUT SO WHEN WE FEED THEM A
DYE ORALLY, YOU CAN SEE IT
TRANSLATEICATES INTO THE BLOOD
MUCH MORE RAPID LOAMACYY THAN
THE VARIANT AND THIS LEAKY
BARRIER SENSITIZES MICE TO CO
LITIS, AND SO WHEN WE TRIGGER BY
DSS, WHICH IS THE EPITHELIAL
IRRITANT, THE VARIANT MICE DROP
WEIGHT VERY RAPID LOAMACYY AND
DEVELOP 69S SIGNS OF
INFLAMMATION, SEVERE
INFLAMMATION IN THE COLON THAT
CAN BE VISUALIZED HERE.
THIS IS I THINK A REALLY
INTERESTING EXAMPLE OF A GENETIC
VARIANT THAT AFFECTS
GLYCOSYLATION AND THE OUTCOME IS
VERY DIVERSE ACROSS DECEASES.
SO EVEN THIS COMMON A391 T
VARIANT IS ASSOCIATED WITH MANY
DECEASES INCLUDING IBD BUT NOT
EVERYBODY WHO CARRY THIS IS
VARIANT GETS ANY DISEASE AND
SOME PEOPLE GET IBD, SOME PEOPLE
GET SCHIZOPHRENIA AND OTHER
DISEASES WHICH SUGGEST THERE ARE
MANY OTHER ADDITIONAL EXTRANSIC
VARIABLES THAT INTERACT WITH THE
VARIANT TO CAUSE DISEASE SO THAT
COULD BE OTHER GENERATEDITTIC
VARIABLES THAT THAT PUSH THE
PATHWAY TOWARDS 1 DISEASE OR THE
OTHER BUT ALSO VIERNLTAL
VARIABLES FOR EXAMPLE, MANGANESE
IN THE DIET OR INSULT TO THE
MICROBIOME THAT MIGHT RESULT
FROM INFECTION BUT THE FACT THAT
THE OUTCOME OF A GENERATED
THETIC SUGGESTS THAT THERAPEUTIC
INTERVENTIONS CAN TIP THE
DALLASCOWBOYS.COM BANS AND THERE
MAY BE OPPORTUNITIES TO RESTORE
MAIN GANNA EASE OR EFFICIENT OF
A GLYCOSYLATION TO TREAT MANY OF
THESE COMMON AUTOIMMUNE
DISEASES.
SO I'LL PAUSE HERE BECAUSE WE'RE
A LITTLE SHORT ON TIME.
I WANT TO ACKNOWLEDGE MY LONG
TIME COLLABORATORS WHOSE BUYER
CHAMPIONS OF GENETICS AND
FUNCTIONAL GENOMICS, I ALSO WANT
TO ACKNOWLEDGE 2 POST DOCS WHO
WORKED ON THIS, AND FUNDING BEST
WORK AND AND I'LL PAUSE HERE,
THANK YOU.
THANK YOU SO MUCH DANIEL, THAT'S
A FASCINATING STORY.
AND AGAIN, FOR EVERYONE IF HAVE
YOU QUESTIONS FOR DANIEL OR
OTHER SPEAKERS PLEASE US THE
SEND LIKE LIVE FEEDBACK LINK TO
SUBMIT IME ANDS AGAIN AT THE END
OF OUR AFTERNOON EGZ ISS IN
ABOUT 40 MINUTES WE GALLON
THROUGH THOSE QUESTIONS.
SO OUR NEXT SPEAKER IS CHIARA
MANCIN- I FROM
RUTGERIATRICKIZATIONS ROBERT
WOODS JOHNSON MEDICAL SCHOOL AND
HER TALK IS DEVELOPING ZEBRA
FISH MODELS OF DISTROGLY
KAN--KANA OPEN MEETINGATHY.
SO THANK YOU VERY MUCH FOR
HAVING ME, AND TO BE ABLE TO
TELL YOU SOME OF THE LATEST
RESEARCH WE'VE BEEN DOING IN MY
LABORATORY AT RUTGERS AND THE
CHILD HEALTH INTUITY SO I'VE
BEEN INTERESTED IN THE KINETICS
OF DYSTROGLYCANOP A THY FOR A
NUMBER OF YEARS SO THIS IS
BITTER IN THE MUSCLE IN THE EYES
AND IN THE BRAIN.
THESE KIDS WILL HAVE VERY SEVERE
AND MULTITELETYPES OF OCULAR
DEFECTS BOTH IN THE RETINA,
RETINA DISPLACIA BUT ALSO IN THE
ANTERIOR CHAMBER SO THAT WOULD
BE YOUR LENS OR YOUR CORN RA.
THIS IS DISREPRESENTED IN THE
CEREBELLUM AND BRAIN STEM ARE
SEVERELY DISRUPTED THIS IS THE
MOST SEVERE FORM THAT'S AND THIS
IS WWS AND THESE CHILDREN IN
GENERAL WILL SURVIVE 3 TO 6
YEARS OF LIFE.
AND YOU MIGHT HAVE HEARD OF THIS
GENE THAT'S IN DUCHENNEAND THIS
THE GLYCANS CAUSES SOME TYPE OF
MUSCLE DISEASE THESE ARE COMPOSE
OF OF 2 SUBUNITS FROM THE SAME
GENE THAT JUST CLEAVED TO HAVE
DATA IN THE MEMBRANE AND ALPHA
GLYCAN OUTSIDE OF THE CELLULAR
SPACE IN THE INTRA CELLULAR MATE
EXCITATORY HERE IT SHOWS 1 OF
THE INTERACTORS WHICH IS LAM NIN
2 ALSO MUTATIONS IN LAM NIN
MUSCULAR DISORDER, THIS
INTERACTION IS MEDIATED THROUGH
1 OF THESE DISORDERS IS THAT
THEY'RE CLINICALLY AND SOWED YOU
THIS HERE THE FLUID IN THE BRAIN
WHITE INSTEAD OF BEING BLACK,
IT'S A DIFFERENT MRI BUT YOU CAN
APPRECIATE HOW DISRUPTIVE THIS
BRAIN IS AND IF YOU GO DOWN THE
SPECTRUM THERE ARE 18 GENES THAT
HAVE BEEN IDENTIFIED THIS FAR
THAT CAN EXPLAIN UP TO 70% OF
CASES OF THIS, DEPENDING ON THE
COHORT THAT YOU WORK WITH AND
MUTATIONS IN THE SAME CAN CAUSE
A RANGE OF PHENOTYPES FROM THE
VERY AND SLIGHTLY LESS FEVER TO
PATIENTS HAVING NO BRAIN
PHENOTYPE AND ONLY MUSCULAR
DYSTROPHY WITH VARYING SEVERITY
AND SOMETIMES SHOWING UP LATER
IN LIFE OR IN SOME LIMITED CASES
AUTISM AND INTELLECTUAL
DISABILITY, THERE IS NO CLEAR
GENO TYPE CORRELATION EVEN
THOUGH THERE ARE CLASSES OF THIS
THAT WE WILL DISCUSS.
IN A SECOND.
THIS HAS HAPPENED THROUGH
DECADES NOW STARTING FROM LARGE
FAMILIES WITH TRADITIONAL
LINKAGE ANALYSIS APPROXIMATE
WITH THE ADVENT OF SEQUENCING
NOW 32 WITH THE GENES AND
SPORADIC CASES AND IT WAS REALLY
MAIRKSZING WHEN THE SEQUENCING
CAME INTO LINE BECAUSE IT TOOK
10 YEARS TO TO IDENTIFY THE
FIRST GROUP OF GENES WITH THIS
LARGE FAMILY STUDIES AND THEN IN
THE NEXT 3 YEARS AND TRY TO GIVE
INFORMATION ON GENETIC DIAGNOSIS
AND THESE GENESS ARE IESHES
DEBTIFIED APPROXIMATE WE GAME
INVESTED IN THE DEVELOPING ZEBRA
FISH MODEL THAT COULD HELP VERY
QUICKLY FIGURE OUT WHETHER THE
GENE FTION OBTAINED THROUGH THE
SEQUENCING THE CAUSATIVE GENE
AND FIGURE OUT WHAT THE
PHENOTYPE OF THIS RETINAL
LOCATIONIN OPEN MEETINGATHY WAS
IN THE ZEB WRA FISH.
SINCE I'M NOT PROSEPTORSING ANY
BIOINFORMATIC, MY CONTRIBUTION
TO THE SYMPOSIUM IS TO LET YOU
KNOW ABOUT SOME OF THE SHARING
SITES THAT ARE AVAILABLE FOR
GENETICS, MATCH MAKER EXCHANGE
AND GENE MATCHER INTO THESE
SYSTEMS AND I ALWAYS WANT TO
MAKE SURE THAT IT'S NOT JUST
NECESSARILY FOR THE GENETICIST,
IF THERE'S A GENE OF INTEREST
AND YOU WOULD LIKE TO STUDY
SPECIFIC VARIANTS THAT MAY
CHARGE THE FUNCTION OFIOURE
PROACTIVE TEEN YOU CAN PUT THE
GENE OF INTEREST INTO THE
DATABASES WHICH IS SOMETHING
THAT WE'RE DOING IN PARTICULAR
FOR SOME OTHER PROJECT IN THE
LAB TO TRY TO IDENTIFY SPECIFIC
DOMAINS THAT HAVE CLINICAL
RELEVANCE.
SO THIS HAS REALLY INFORMED ALSO
THE GLYCO BIOLOGY BECAUSE AS
THESE GENES WERE IDENTIFIED
THERE HAS BEEN WORK FROM
MULTIPLE LABS TO TRY TO FIGURE
OUT WHAT YOU WERE DOING AND THIS
HAS AX ALLOWED TO US TO IDENTIFY
ALL OF COMPOSITION--SORRY, THE
COMPOSITION OF THE GLYKAN--KANAS
THAT ARE BOUND TO AND THAT ARE
DISRUPTED IN THESE DISORDERS.
THIS HAS BEEN REALLY COMPLICATED
EFFORT, FOR EXAMPLE, I WAS
INVOLVED IN THE IESHES
DENTIFICATION THAT WAS WITH AND
THEN WE FINALLY FIGURED OUT THAT
IT'S NECESSARY TO ADD THE
[INDISCERNIBLE] TO THESE MAN OS
THESE ARE ALL GLYCANS, SO IT'S
DIFFERENT FROM END.
AND WE FIGURED OUT WHAT ALL
THESE TRANSFERAISES DO WHICH
TOOK A LONG TIME AND THIS ALSO
HELPED CHANGE A CLASSIFICATION
OF THE DISEASE SO AS THEY WERE
SAYING BEFORE, SOMETIMES THAT
HAVE MUTATIONS IN THESE WHICH
ARE VERY, VERY RARE AND
SECONDARY THESE THAT HAVE
MUTATIONS IN THE TRANSFER ACES
THAT GLUE MARIOUS COSALATE FOR
THE GLYCAN AND THEN THERE IS A
GROUP OF THAT AIVET THE
GENERATION OF THE DONEARS FOR
THE MANO AND THE RIBITOL THAT
WILL THEN BE FED TO THE TRANSFER
ACES TO GENERATE THESE GLYCANS.
WE STILL HAVE 30% OF CASES THAT
DO NOT HAVE A GENETIC DIAGNOSIS
AT THIS TIME.
AND I WOULD LIKE TO REMIND YOU
THAT SOPHISTICATED RIGHT NOW
WELL IS A BIG EFFORT TO IDENTIFY
NONCODING OF REGULATORY
MUTATIONS WITH THE IDEA THAT
SOME OF THESE MAY BE IN THE
KNOWN GENES BECAUSE THEY'VE BEEN
DISCOVERED FOR A WHILE NOW AND
WE CAN IESHES DENTIFY ALL THESE
MUTATIONS IN GROUPS TO IDENTIFY
THERAPEUTIC INTERVENTION.
AND HERE I WANT TO TELL YOU
ABOUT OUR OWN CONTRIBUTION IN
TRYING TO DO THIS WHICH IS
TRYING TO DEVELOP ZEBRA FISH
MODELS OF THE DJSTROGLYCACIN, OP
A THIES, AND SO MOST OF THE
MOUSE MODEL ARES WHERE THE JEEPS
ARE REMOVED IN SPECIFIC TISSUES
AT DIFFERENT TYPES BUT THERE
ISN'T A GENETIC MODEL WHERE YOU
MODEL THE ENTIRE DEVELOPMENT,
THE ENTIRE DEVELOPMENT AND
DISRUPTION OF THE ENTIRE IN THE
WHOLE BODY, THE ZEBRA FISH IS A
GREAT MODAND HE WILL I CAME TO
IT AS I STARTED DOING EXOME
SEQUENCING BECAUSE IT'S FAST,
YOU CAN ACTUALLY LOOK AT AN
EMBRYO IS SEE THE DEVELOPMENT OF
THE EYES OF THE BRAIN AND OF THE
MUSCLE WITHIN 24 HOURS, OF
FERTILIZATION, AND THE MOM WILL
HAVE HUNDREDS OF BABIES THAT ARE
EXTERNALLY FERTILIZED WHICH ALSO
GIVES YOU ACCESS TO THE VERY
FIRST FERTILIZED CELL AND YOU
CAN PERFORM GENETIC
MODIFICATIONS AND INTERVENTION
IN THE 1 CELL EMBRYO.
HERE SHOWING [INDISCERNIBLE] AND
NUCLEOTIDE BUT NOW WE CAN ALSO
DO CRISPR CAS 9 WHICH I WILL
TELL YOU ABOUT IN A SECOND.
THIS IS AN OLD EXAMPLE BUT I
REALLY LIKE THIS PARTICULAR FISH
MODEL BECAUSE MULTIPLE FISH
MODELS ENDED UP SHOWING EXACTLY
THE SAME PHENOTYPE, THIS WAS THE
POMGNT2 FISH FOR 3 DAYS THEY
LARGE AND SHORT AND THEY HAVE
THE CHARACTERISTIC BENT TAIL.
SO THE BABY FISH IS IN A SHELL
AND USUALLY STARTS MOVING AROUND
16, 17, HOURS AND IF IT CANNOT
MOVE, THE TAIL WILL REMAIN STUCK
IN THIS BENT POSITION WHICH IS
ACTUALLY SIMILAR TO THE
CONTRACTURES THAT THE BEASHS
HAVE WITH THESE DISORDERS
BECAUSE THEY WEAK AND THEY
CANNOT MOVE WELL IN THE WOMB.
THESE FISH WILL HAVE IMPAIRED
MOBILITY THEY DISPLAY SIMILAR
FORMATIONS IN THE 1S IN THE
PATIENT WITH THE DISRUPTION OF
THE RETINALLIZATION AND ALSO IN
THE LENS OF AN END THEY WILL
HAVE THE DISRUPTIONS IN BRAIN IN
BRAIN DEVELOPMENT WHICH ARE
SIMILAR TO THE 1S IN THE
PATIENTS.
THE MOST IMPORTANT THING IS THAT
THE SAME ANTIBODIES THAT WERE
USED FOR DIAGNOSIS IN THE HUMAN
SAMPLES CAN BE USED IN THE ZEBRA
FISH.
THESE WERE ORIGE NAWILLLY
DIAGNOSED ON THE ANTIBODY ON
MUSCLE BIOPSIES, MUSCLE BIOPSIES
ARE NOT DONE THAT MUCH ANYMORE
BECAUSE WE HAVE ALL OF THE
GENETICS AND MAKES NO SENSE TO
DO AN INVASIVE PROCEDURE IN A
CHILD AT THIS TIME BUT THE DATA
FROM SEVERAL YEARS AGO SHOWS
THAT IN THE MUSCLE, AND THIS IS
JUST A MUSCLE SECTION, AND YOU
SEE THE EXTRA CELLULAR MATE
EXCITATORY AND THE GLYCOSYLATED
GLYCAN AROUND THE MY O FIBER AND
THE LOSS OF GLYCOSYLATION WITH
THE SAMPLE WITH ALSO DISRUPTION
IN THE LAM INTERFERON.
THIS MEMBRANE IS LOCALIZED INTO
THE STRUCTURES THAT ARE CALLED
MY O RECEPTORS AND THEY WILL RUN
LONGITUDINALLY AND WHEN YOU
REMOVE [INDISCERNIBLE] YOU LOSE
DPLI COSALATION OF THIS GRID
SERVICES KAN--KANA AND THIS
PARTICULAR STRUCTURE AND YOU
WILL HAVE A HIGHLY DISRUPTED
MUSCLE STRUCTURE.
THE OTHER THING YOU CAN DO IN
THE ZEBRA FISH TO RESCUE
PHENOTYPES TO ACTUALLY SHOW THE
PHENOTYPE THAT THE FUNCTION OF
THE PROTEIN IS CONSERVED AND
THAT THE PHENOTYPE IS SPECIFIC
AND WE'VE DONE A LOT OF WORK
WITH THE ANALYSIS OF MISSENSED
MUTATIONS BECAUSE THEN IF YOU
WANT TO VALIDATE YOUR MISSENSED
MUTATION YOU FIND IN THE PATIENT
YOU CAN INTRODUCE IN THE HUMAN
MRNA AND TRY TO PUT IN THE ZEBRA
FISH AND SEE WHETHER THE PROTEIN
FUNCTIONS PRESERVED IN IN
PARTICULAR CASE, THIS WAS A LOSS
OF FUNCTION MUTATION BECAUSE YOU
CANNOT RESCUE THE EFFECT OF THE
MORPHOLIN O.
SO THIS WAS A PRESENTATION OF
THE WHAT IS CALLED THE MORPHIN
WHICH IS THE MORPHOLIN O
INJECTED FISH, BUT 1 OF THE
ISSUES THERE'S BEEN A LOT OF
DISCUSSION IN THE ZEBRA FISH
FIELD TO THE LEVEL OF
NONSPECIFIC EFFECTS CAUSED BY
MORPHOLIN OS AND IN GENERAL
EVOLVED TO CRISPRs AND OTHER
GENETIC MUTANTS ALSO THE MORPH O
LINE O KNOCK DOWN IS TEMPORARY
AND SO IF YOU WANT TO DO MORE
LONG-TERM TREATMENTS STUDIES OR
STUDY DIFFERENT DEVELOPMENTAL
ASPECTS OF THE DISEASE, YOU
CANNOT REALLY DO IT IN THIS
EARLY MODELS.
AND SO WHAT WE'VE BEEN DOING FOR
THE PAST COUPLE OF YEARS IN MY
LAB, IS TO START DEVELOPING AN
ARRAY OF MUTANTS SO THAT WE CAN
THEN SEE WHAT HAPPENS IN THESE
GENETIC MUTANTS AND IN THE ZEBRA
FISH AND WHETHER WE CAN USE IT
FOR DRUG SCREENING AND FOR
TESTING DIFFERENT THERAPEUTIC
INTERVENTIONS AND SO WHAT I
WANTED TO DO TODAY WAS SHARE
SOME UNPUBLISHED DATA ON THE
BEGINNING OF THIS PROJECT AND ON
SOME OF THE MODELS THAT WE'VE
MADE AND SO 1 OF THE FIRST
MODELS THAT WE'VE BEEN STUDYING
IS POMT1, AND IF FORMS A COMPLEX
WITH POMT2, AND ATTACHES THESE
TO THE DPLI KAN--KANA PROTEIN.
AND THIS WAS LED BY CHRIS AND
BRITTANY IN THE LAB.
SO IT WAS DIFFICULT TO STUDY THE
FISH, THE MORPHIN HAD BEEN MADE
ISSUES THE PHENOTYPE WAS
REQUIRED AND THEY REARED HIGH
CONCENTRATIONS OF MORPH O LINE O
AND THEN IT BECOMES REALLY
DIFFICULT TO TELL WHETHER THAT'S
REAL PHENOTYPE OR NOT.
ONE THING THAT EMERGED IS IN THE
MRNA BY THE MOTHER, THE FEMALE
RELEASE HUNDREDS OF EGGS, SHE IS
NOT A GOOD MOM BECAUSE SHE LETS
THEM COMPETE WITH EACH OTHER
BECAUSE WHOEVER SURVIVES
SURVIVES BUT SHE WILL PROVIDE
MRNA OF SEVERAL GENES IN THE
YOLK THAT WILL SUPPORT EARLY
DEVELOPMENT BECAUSE OTHERWISE,
THEY WOULDN'T REALLY HAVE
INITIAL MRNAs TO START THE
DIVISION AND DIFFERENTIATION.
SO WE OBTAINED THESE FISH AT THE
BEGINNING OF THE PANDEMIC WOO
BECAUSE WE HAD THE MUSEUM STANTS
FROM THE ZEBRA FISH PROJECT THAT
A WERE NOT ANALYZING AND THE
MUTATION PLOT IS AT THE SANGER
CENTER, THAT I MUTATED THROUGH
THE IMMUNE SCREENS AND DOUBLE
CHECKED EVERY SINGLE GENE IN THE
ZEBRA FISH AND THE
CHARACTERIZATION THAT THEY HAVE
DONE IS ONLY UP TO 5 DAYS POST
FERTILIZATION SO THERE WAS NO
PHENOTYPE RESPORTED BUT WE
THOUGHT, WELL, LET'S JUST START
LOOKING AT THIS FISH.
IT HAD A VERY LATE TRUNCATING
STOP CO DON, BUT THERE ARE
SIMILAR MUTANT MUTATIONS IN THE
HUMANS THAT CAUSE NONSENSE
MEDIATED DECAY.
THAT HAPPEN AROUND THE SAME
AREA, SO I THOUGHT LET'S TRY
ANYWAYS.
AND IDEA IS THAT WHEN HAVE YOU
GENES THAT ARE SO HIGHLY
PROVIDED BY THE MOTHER,
SOMETIMES WHAT YOU HAVE TO DO,
YOU HAVE TO MAKE A KNOCK OUT MOM
TO REMOVE THE MATERNAL MRNA AND
THEN YOU'RE PHENOTYPE WILL
EMERGE IN THE EMBRYOS FROM THE
SEDENTARY GENERATION SO WE GAVE
THIS A TRY AND 1 THING THAT WAS
LEGALLY INTERESTING IS ACTUALLY
WE WERE NOT ABLE TO GET KNOCK
OUT MOMS BECAUSE THE KNOCK OUT
FISH START TO DIE AFTER 30 DAYS
POST FERTILIZATION AND MOST OF
THEM ARE GONE BY 60 DAYS WHICH
IS BEFORE THE TIME OF ZEBRA FISH
ARE FERTILIZEDILE.
SO THIS WAS VERY EXCITING
BECAUSE IT WAS EARLY PHENOTYPE
IN THESE FISH.
AWLINGS AT 30 DAYS WHEN THERAPY
AND STILL ALIVE THE KNOCK OUTS
ARE SIGNIFICANTLY SMALLER THAN
THE WILD TYPES AND THE HEADS AND
WHAT'S INTERESTING IS THAT THE
FEW ARE REMAINING AT 40 DAYS
THEY'RE STARTING TO RECOVER BUT
THIS IS BECAUSE THE FISH ARE
DYING IN TANK THAT FEWER FISH
COMPETE FOR FOOD THAT THEY CAN
STILL HAVE ACCESS TO FOOD.
EVEN IF THEY CAN'T SWIM QUITE AS
WELL AND I WILL SHOW YOU LATER
WHAT THAT MEANS.
SO WE CHECKED WHETHER IT WAS
TRUE THAT THERE COULD BE
MEDIATED DECAY AND WE SAW A
DECREASE IN THE KNOCK OUT IN THE
MRNA PER POMT1 AND IN ADDITION
WE SAW THAT AT 30 DAYS THE
PROTEIN WAS COMPLETELY BLOCKED
BY WESTERN BLOT AND WE HAVE A GO
ANTIBODY, I WANT TO MAKE A POINT
THAT WE HAD A LOT OF TROUBLE
FINDING THE RIGHT HOUSEKEEPING
GENE BECAUSE WHEN YOU ARE
LOOKING AT THE MUSCLE, YOU CAN'T
REALLY USE ACTIN BECAUSE ACTIN
IS DISRUPTED, AND GAB DH IS ALSO
DISRUPTED SO WE ENDED UP WITH
THE TOTAL PROTEIN SPACE TO MAKE
SURE THAT ALL OF OUR GELS WERE
EQUALLY LOADED.
SIMILAR ISSUES ALSO HAPPEN WITH
QPC R WHERE WE HAVE IT GO TO
LIKE 3 OUR 4 DIFFERENT
HOUSEKEEPING GENES THAT FIND 1
THAT WAS REFLECTIVE OF THE
AMOUNT OF MRNA.
THE OTHER THING THAT WE NOTED,
SO AS I TOLD YOU THERE'S FLIEK O
ASPECT BODY THAT SHOWS THE
PRESENCE OF THAT DPLI KAN--KANA
THAT WE'RE LOOKINGA THE THAT
CAUSED ASSEMBLED BAY THOSE
TRANSFER ACES, SARKS SEMBLE
TAXER TACHS THE FIRST 1 SO THE
DPLI KAN--KANA SHOULD BE GONE
AND IN FACT WHEN WE DID THAT
ENRICHMENT, WE SHOWED THAT AT 30
DAYS, THIS WAS COMPLETELY LOST
WHILE THE BATTA GLYCOSYLATED WAS
PRESENT IN THE ENRICHED FRACTION
SO BY 30 DAYS THE GLOI
COSALATION IS GONE.
SO IF WE LOOK AT THE MUSCLE, WE
STARTED TO SEE, WE SEE A SIGN OF
MUSCLE DISEASE SO I THINK WHAT
YOU CAN APPRECIATE IN THIS
HIGHER MAG NI5ICATION PICTURE IS
HOW THE FIBERS ARE ACTUALLY
SEPARATE FRIDAY EACH OTHER
BECAUSE THIS IS SOMETIMES WHAT
HAPPENS WHEN THERE IS LOSS OF
THE EPICELLULAR MATRIX THAT
KEEPS THEM TOGETHER AND ANOTHER
FEET THAT YOU ARE IS PRESENT IN
THE DPLI KAN--KANA FISH KNOCK
OUT IS THE FACT THAT THE MY O
SET ARE BASICALLY OPEN AND THAT
DISEASE CONTINUES AT SEVERAL
PLACES INSTEAD OF LIKE BEING
NICELY ORGANIZED.
THIS HISTOLOGICAL PICTURE WAS
INCREDIBLY DIFFICULT TO OBTAIN
BECAUSE IN FACT THE MUSCLE FROM
THESE FISH KIND OF LIKE JUST
FALLS APART.
AFTER FIXATION SO IT'S REALLY
SEVERELY AFFECTED.
WE THEN OBTAIN A SYSTEM THAT
ALLOWS TO YOU ANALYZE UP TO LIKE
96 FISH AT A TIME AND THIS IS
WHAT 1 EXAMPLE OF WHAT MY LAB
DID SO THESE ARE ALL DONE THE
SAME DAY AS 200 REQUEST 88 FISH
FROM 3 DIFFERENT MATINGS TO BE
ABLE TO RUN BEHAVIOR AND
MOBILITY ANALYSIS ON A LARGE
NUMBER OF SAMPLES AND THIS WILL
BECOME IMPORTANT IN THE FUTURE
BECAUSE WE'RE PLANNING TO USE
THE SYSTEM TO BE ABLE TO DO DRUG
SCREENINGS AS YOU CAN ADD
DIFFERENT DRUGS TO EACH 1 OF
THESE, TO EACH 1 OF THESE WELLS,
AND SO THE ANALYSIS THAT TOOK 5
DAYS, DIDN'T REALLY SHOW MUCH
CHANGE IN MOBILITY BUT WHAT WE
FOUND THAT ALREADY AT 15 DAYS
EVEN BEFORE ABOUT ANY OF THE
OTHER DEFICITS ARE OBSERVED WE
ALREADY START SEEING SIGNIFICANT
DIFFERENCES AT LEAST IN THE
VELOCITY AND IN THIS PARTICULAR
1 WAS NOT THAT MANY FISH AND SO
WE'RE GOING TO ADD, WE'RE GOING
TO ADD MORE SAMPLES BUT WE WERE
VERY EXCITED THAT THEY SEEM TO
HAVE THIS EARLY MOBILITY
PROBLEMS, BUT THEN WE WILL GET
WORSE AND WORSE AND OF COURSE
WILL LEAD TO LETHALITY BECAUSE
THEY HAVE NO ACCESS TO FOOD.
ANOTHER THING THAT WAS
INTERESTING WAS THE FACT THAT
POMT1 HAS TO ACT IN COMBINATION
OF POMT2 AND THIS WAS
CRYSTALLIZED A FEW YEARS AGO AND
WE'RE SEEING THAT EARLY IN
DEVELOPMENT POMT2, THE FISH IS
TRYING TO COMPENSATE AND
OVEREXPRESS POMT2 BUT OF COURSE,
THERE'S STILL NO GLYCOSYLATION
BECAUSE THE 2 PROTEINS NEED TO
BE TOGETHER AND THESE SEEM TO BE
VERY CLOSELY CO REGULATED.
SO, WHAT I TOLD YOU SO FAR IS
THAT POMT1 MUTANTS ARE PROMISING
NEW MODELS FOR THESE AND THEY
SHOW COMPLETE LOSS OF THE
PROTEIN, AND EARLY LETHALITY BUT
NOT AS EARLY AS THE DAG 1
MUTANTS.
THE MUSCLE DISEASE AND THE FISH
DIE, WE SEE MOBILITY DEFINITES
MUCH EARLIER, WE ACTUALLY ARE
STARTING TO SLEE ALSO OCULAR
PHENOTYPES AND SO WE'RE HOPING
TO USE THIS ABILITY TO VISION
AND END POINTS FOR DRUG
SCREENING AND TRYING TO
UNDERSTAND THE FUNCTION OF THE
POMT1 AND 2 COMPLEX DURING
DEVELOPMENT IN DIFFERENT
TISSUES.
I THINK I'M GETTING TO THE END
OF MY TIME, BUT HOW--I WAS GOING
TO TELL YOU LIKE VERY, VERY
QUICKLY, ALSO HOW WE'RE USING
CRISPR TO GENERATE ADDITIONAL
MUTANTS IN THE ZEBRA FISH, CAN
YOU USE THIS REALLY COOL
APPROACH WHERE CAN YOU DO WHAT'S
CALLED A CRISPINT AND IT
GENERATESSA I HIGHLY EMBRYONIC
EMRIO TO DO ANALYSIS OR YOU CAN
RAISE THESE FISH AND CROSS THEM
WITH WILD TYPE TO GENERATE A
STABLE LINE.
AND SO I'LL JUST SKIP VERY
QUICKLY, SO WE'VE STARTED DOING
THIS, GENERATING POMT2 CHRIS
PINTS AND DISRUPTING THE GLYCAN
AND WE DID IT WITH 2 MULTIPLE
GUIDES AND I WILL SHOW THE
RESULTS OF THE EARLY ANALYSIS OF
CRISPENT AND STOP THERE, WE
DIDN'T SEE SURVIVAL TO AFFECTED
BUT THE PHENOTYPES THAT WE RVE
ABOUTED WERE VERY SIMILAR TO
THOSE THAT WE HAD SEEN IN THE
MORPHINS.
AND WHAT I'M SHOWING HERE IS THE
CONTROL THAT WE USE TO CHECK FOR
CAS 9 AND THE CAS9 FUNCTION AND
WE SAW A COMBINATION OF SEVERE
AND MERE MILDLY AFFECTED FISH
THAT WAS REMINISCENT OF WHAT WE
SAW IN THE MORPHINS.
AND WITH THIS I WILL SKIP
THROUGH THE VERY LAST SLIDE.
WHAT I TOLD YOU TODAY THE ZEBRA
FISH CAN BE USE TOTD STUDY MUSK
LO DYSTROPHY IN THE MOUSE, AND
MAY BE THE PERFECT MODEL BUT
GIVES THE OPPORTUNITY TO STUDY
THE PROGRESSION IN THE BODY, WE
CAN USE IT TO MULTIPLEX DRUG
SCREENING FOR SPECIFIC
PHENOTYPES AND WHAT I'M
INTERESTED IN IS ALSO THE
POSSIBILITY TO USE IT TO STUDY
DISEASE MODIFIERS SINCE ZEBRA
FISH TEND TO BE LESS SEVERELY
AFFECTED AND WITH THAT, I WILL
THANK EVERYBODY IN MY LAB THAT
I'VE THANKED ALONG THE WAY AND
OUR FUNDING SOURCES AND SO YOU A
PICTURE AND TAKE QUESTIONS AT
THE END AFTER EVERYBODY'S DONE.
>> OKAY, GREAT.
THANK YOU SO MUCH CHIARA, GREAT
PRESENTATION AND WONDERFUL MODEL
AND AGAIN, EVERYONE AS A
REMINDER PLEASE SUBMIT YOUR
QUESTIONS VIA THE SEND LIVE
FEEDBACK LINK AND AGAIN I WILL
ANSWER THOSE QUESTIONS AT THE
END.
SO AGAIN, I'M HAPPY TO INTRODUCE
OUR FINAL SPIKER VERY FITTING
IT'S MICHAEL TIEMEWHY, ER FROM
COMPLEX CARBOHYDRATE RESEARCH
CENTER AT THE UNIVERSITY OF
GEORGIA EXPW ME WILL TELEUS
ABOUT GLYGEN: A RESOURCE FOR
INTEGRATING GLYCO SCIENCE
KNOWLEDGE.
OKAY, MIKE.
>> SO OVER THE LAST COUPLE DAYS
WE'VE HEARD A LOT OF PLACES
WHERE GLYCOSCIENCE MY INTERFACE
WITH MODELING AND I WANT TO TALK
ABOUT A RESOURCE THAT'S MATURING
THAT MAY HELP PEOPLE PULL
TOGETHER KNOWLEDGE IN THE FLIEK
O SCIENCE DOMAIN TO HELP
GENERATE HYPOTHESIS RELATED TO
THEIR WORK, AND LET ME JUST TALK
INITIALLY ABOUT JUSTIFICATION
FOR THIS SORT OF EFFORT.
SO THIS IS A NICE FIGURE FROM A
REVIEW THAT JAMIE MARTH THAT
LAYS OUT THE 4 DOMAINS OF
MOLECULES THAT ARE ESSENTIAL FOR
LIFE.
NUCLEIC ACIDS PROTEINS LIPIDS
AND AS JAMIE EMPHASIZED GLYCANS
AND FOR EACH OF THESE DOMAINS OF
LIFE AND FOR 3 OF THESE, THEY
ARE SUBJECT TO WELL CURATION,
WELL FUNDED SO GENBANK,
REFSEQGENE AND LIPIDS BUT WHAT'S
MISSING IS OR HAS BEEN MISSING
IN THE PAST IS THE SAME SORT OF
RESOURCE FOR GLYCANS SO WHERE
ARE THE GLYCAN DATABASES AND
WHAT'S HINDERED THEIR
DEVELOPMENT OVER THE DECADES
WELL IN MANY WAYS IT HAS TO DO
WITH THE INTRINSIC NATURE OF
THESE MOLECULES, THE GLYCANS
THAT ARE--TEND TO BE BRANCHED,
AND CAN EXIST IN THE MONOMERS
THAT BUILD THESE CAN BE LISTENED
TOGETHER IN VARIOUS SORTS OF
CHEMISTRY AND COMPLEXITIES AND
THAT'S HARD TO REPRESENT IPT
GREATER FORMATICALLY COMPARED TO
LINEAR POLYMERS LIKE PROTEINS OR
GENE SEQUENCES.
--TALK ABOUT GLYCANS AND TALK
ABOUT POST TRANSLATIONAL MODISHS
TO PROVIDE A RESOURCE THAT KLOW
PEOPLE TO INTERROGATE
GLYCOSCIENCE DATA SO GLYGEN JUST
A BIT OF BACKGROUND IS FUNDED BY
THE COMMON FUND, UO1 THAT
STARTED IN 2017.
AFRICAN AMERICAN YEAR OF
PLANNING AND WE THINK THAT'S
REALLY IMPORTANT, DURING THAT
YEAR OF PLANNING THE PROCESS WAS
TO ENGAGE STAKEHOLDERS AND THE
PEOPLE WE PRESUMED WOULD USE
THIS RESOURCE TO ASK THEM HOW
THEY WOULD--WHAT THEY WOULD
WANT, HOW THEY WOULD USE GLYGEN
AND WE TRIED TO BUILD THE
RESOURCE OFFER THE LAST 5 YEARS
TO ADDRESS THOSE NEEDS AND THOSE
DESIRES AS WELL AS WE COULD, WE
ARE IN OUR FINAL YEAR OF COMMON
FUND SUPPORT HOPING TO BRIDGE TO
OTHER SORTS OF SUPPORT IN THE
FUTURE.
AND WE CONTINUE TO ENGAGE INPUT
FROM USERS INSIDE AND OUTSIDE
THE GLYCOSCIENCE COMMUNITY TO
TRY AND IMPROVE OUR RESOURCE AND
MOST IMPORTANTLY I THINK FOR OUR
FUTURE, WE ARE REALLY NOW TRYING
TO CROSS LINK AS MUCH AS WE CAN
WITH OTHER DATA TYPES TO TRY AND
ESSENTIALLY BUILD A BROADER
KNOWLEDGE IN THE IMPORTANCE OF
GLYCANS.
I WANTED TO GO OVER THE FEATURES
AND STRUCTURE AND I WILL TURN IN
THE LAST PART OF MY BRIEF
PRESENTATION IT TALK ABOUT WHAT
WE CONSIDER SORT OF A FIRST KIND
OF KNOWLEDGE GRAPH IN THE
GLYCOSCIENCE DOMAIN FEATURE WE
CALL THE SUPERSEARCH, SHOW YOU
HOW WE HOPE THAT IT WILL ALLOW
PEOPLE TO ENTER INTO GLYCO
SCIENCE KNOWLEDGE EVEN IF THEY
KNOW VERY LITTLE ABOUT WHAT
GLYCANS ARE.
SO I JUST WANT TO START WITH THE
LITTLE BIT OF AN ENDORSEMENT OR
A PERSPECTIVE ABOUT HOW IT FIT
INTOS A LARGER WORLD OF EFFORTS
TO UNDERSTAND AND GENERATE
DATABASES AND KNOWLEDGE BASES IN
THE GLYCOSCIENCE.
THIS IS 1 OF THE FOUNDING
MEMBERS OF THE GLYSPACE ALLIANCE
THAT INCLUDES GROUPS IN THIS
JAPAN AND AUSTRALIA AND
SWITZERLAND, AND A LOT OF THIS
ALLIANCE AND THIS COOPERATIVITY
BETWEEN THESE EFFORTINGS REALLY
ROSE OUT OF EFFORTS THAT THE
COMMUNITY INITIATED TO BUILD A
REPOSITORY IN A WAY TO TO HAVE
EXCEPTIONS FOR GLYCAN STRUCTURES
SO THAT'SENTIOUS SENTIAL FOR
DEALING WITH THESE IN AN
INFORMATIC WAY IN SOMETHING YOU
CAN REFER TO THE STRUCTURE AS
CORRELATED POSED TO A CARTOON OR
A LONG HAND DESCRIBE OF THE
CHEMICAL IN NATURE.
SO GLUE MARIOUS TOUCAN TAKES
THESE EXPRESSIONS TO HARMONIZE
RECORDS AND WE SHARE THAT
FEATURE WITH OTHER EFFORTS
ACROSS THE WORLD.
AND SOME OF THOSE AS I MENTIONED
SOME OF THOSE EFFORTS ARE IN
GRAP AN GLUE MARIOUS CONNECT AND
WE FORMED THE GLYSPACE ALLIANCE
AND WE BACK EACH OTHER UP AND
MOVE FORWARD TOGETHER AND NOT IN
DIFFERENT DIRECTIONS.
SO GLYGEN IS BUILT AROUND THIS
AND IT'S IN A CENTRAL TRIAD OF
PROTEINS, GLYCANS AND HOW THESE
GL YCANS MAY BE LINKED TO THE
MODIIVES OF PROTEINS.
WOOER ALSO INTERESTED IN GLYCANS
BY THEMSELVES AND PROTEINS BY
THEMSELVES BUT THE UNIQUENESS IS
THAT WE TRY TO TIE IT TOGETHER,
GLYCOSYLATION IS A CONCEPT AND
OUR--THE DATA WE DERIVED COMES
FROM A LARGE NUMBER OF SOURCES
FROM PROTEINS CAN YOU SEE
SOME--HERE THAT YOU RECOGNIZE
FOR DPLI KAN--KANAS WE
CHARACTERIZE AND BRING IN DATA
OF DIFFERENT TYPES OF FROM
VARIOUS SOURCES AND THEN OUR
PARTNERS AND DATA PROVIDERS
ALLOW US TO INCORPORATE DPLI
COSALATION SITE INFORMATION
ALONG WITH THE PROTEIN IN GLYCAN
DATA.
SO WE CURRENTLY COVER A
RELATIVELY SMALL BUT GROWING
NUMBER OF SPECIES, WE'VE BEEN
FOCUSED FROM THE BEGINNING ON
HUMAN GLYCOSYLATION DATA AS WELL
AS EXPANDING THAT TO MOUSE AND
RAT.
WE'VE ALSO INCLUDED
INSIGNETHETIC DPLI KAN--KANAS
WITHIN OUR DATABASE AND VIRAL
CONSTRUCTS AS WELL AS DISTINCT
SPECIES AND WE'VE BEGUN TO
INCORPORATE DROSOPHILA DATA IN
OUR FINAL YEAR OF FUNDING AND
THEN EFFORT IS ONGOING.
AT A GLANCE WHAT WE HAVE IN
GLYCAN, WELL, OVER 30,000
GLYCANS OVER 12,000 GLYCO
PROTEINS, OVER 57,000 SITES
ACROSS ALL SPECIES 64,000
PROTEINS ARE ACCESSIBLE THROUGH
IN GLYCANS DATA.
BE YOU CAN GET TO THIS DATA IN 1
OF 2 WAYS.
YOU CAN GET THROUGH IT THROUGH
THE DATA PORTAL, ALL THE DATA WE
INCORPORATED IS FREELY
AVAILABLE.
YOU NEED TO ACKNOWLEDGE THAT YOU
GOT IT FROM US.
AND THESE ARE AVAILABLE AS FILES
AND THERE'S A END POINT THAT
ALLOWS YOU TO DEVELOP YOUR OWN
QUEERS AND TAKE THE DATA AND DO
WHATEVER YOU WANT SO IT'S
FREELYY AVAILABLE SO THERE'S
ACCESS TO THE DATA DIRECTLY FROM
THE DATA PORTAL THERE'S ALSO
ACCESS THROUGH THE WEB INTERFACE
AND I WILL QUICKLY SHOW YOU THE
FEATURES OF THAT INTERFACE, THIS
IS THE HOME PAGE, THIS S&P THE
GLYGENHOME PLACE AND
WWW.GLYGEN.ORGWE ENCOURAGE TO
YOU EXPLORE IT ON YOUR OWN.
THERE ARE SURFACES THAT 1 CAN
PERFORM SO THEREYA A SEARCH,
PROTEIN SEARCH, SITE SEARCH
AGAIN, THESE ARE THE SORT OF
CENTRAL TRIAD OF WHAT IT OFFERS,
AND WE OFFER A SORT OF QUICK
SEARCHES WHERE YOU CAN PUT IN
INQUIRIES AND QUICKLY SEE,
HOPEFULLY GET AN ANSWER, WE
PROVIDE SOME BACKGROUND, SOME
INSTRUCTIONAL INFORMATION,
VIDEOS THAT DESCRIBE HOW TO USE
ASPECTS OF GLYGEN BUT WE ALSO
LINKED OTHER RESOURCES BUT ALL
OF THESE SEARCHES ARE AVAILABLE
FROM PULL DOWN MENUS OR OF
COURSE FROM THESE CARDSAs WELL
SO THIS IS PART OF THE FRONT
PAGE, IF YOU SCROLL DOWN YOU SEE
ANOTHER PART OF FRONT PAGE WHERE
WE HAVE CURATED TPHREU RACING
KAN--KANA PROTEEF LISTS WHICH
ARE VERY IMPORTANT FOR THINKING
ABOUT FUNCTION AND WE WILL TALK
ABOUT THAT AGAIN IN A LITTLE
BIT.
WE HAVE WAYS TO BROWSE THROUGH
GLYKAN--KANA STRUCTURES EITHER
AS COMPOSITIONS OR AS ACTUAL
STRUCTURES THAT ARE INTERRELATED
BASED ON ISOMERIC
CONFIGURURATIONS, AGAIN, A DATA
PORTAL TO GET TO ALL THE DATA,
WAYS TO INTERACT WITH THE DATA,
STATISTICS OF OUR DATABASE, AND
IF WE SCROLL DOWN TO THE BOTTOM,
THERE'S A UNIQUE SET OF WAYS TO
UNDERSTAND WHAT GLYGEN DOES BY
TRY ME QUESTIONS THAT ARE
PRECANNED THAT,A LOW --ALLOW YOU
TO SEE WHAT GLYGEN CAN OFFER.
WE ALSO HAVE A PLAYGROUND WE
CALL THE SAND BOX WHERE WE TRY
NEW THINGS AND GENERATE NEW
TOOLS THAT ENRICH EXPERIENCE OF
GLYGEN, I WON'T TALK ABOUT THE
SAND BOX TODAY BUT IT'S AN
INTERESTING FEATURE THAT WE
CONTINUE TO DEVELOP AND MOVE
THINGS THAT FROM THE SAND BOX
INTO GLYGEN PROPER.
SO THE REST OF THE TIME I WANT
TO TALK ABOUT HOW PEOPLE MIGHT
ACCESS GLYGEN IF I THEY DIDN'T
KNOW ANYTHING ABOUT THE BIOLOGY,
MAYBE THEY READ A PAPER AND
SOMETHING POPS UP IN THE PAPER
AND YOU WOULD LIKE TO KNOW MORE
ABOUT THAT RIGHT?
SO MAYBE A PAPER LIKE THIS, YOU
ARE INTERESTED IN NOTCH, YOU'RE
INTERESTED IN NEURAL STEM CELL
DIFFERENTIATION AND YOU SLEEP
APNEA AND OBESITYY THIS PAPER
THAT LOOKS INCREEINGING, LOUIS
X-CARRYING N-GLYCANS REGULATE
THE PROLIFERATION OF MOUSE
EMBRYONIC NEURAL STEM CELLS VIA
THE NOTCH SIGNALING PATHWAY, AND
THEY SHOW THAT YOU HAVE A MUCH
HIGHER ABUNDANCE OF PROTEINS
THAT ARE MODIFIED WITH LOUIS X
AND ANTIBODIES TO LEWIS X SO THE
UNDIFFERENTIATED CELLS A LOT
MORE STANDING THAN
DIFFERENTIATED CELLS, RIGHT?
SO THAT LOOKS LIKE IT MIGHT BE
AN INTERESTING THING TO LOOK AT
BUT WHAT IS LEWIS X, WHAT
PROTEINS ARE MODIFIED WITH THIS
LEWIS X, DO YOU FIND LEWIS X ON
A LOT OF PROTEINS OR ANY OF
THOSE PROTEINS ASSOCIATE WIDE
DISEASE.
WHERE WOULD YOU GO TO FIND THAT
INFORMATION?
YOU COULD GO BACK TO THE
LITERATURE AND DO VARIOUS
LITERATURE SEARCHES, OR YOU
COULD COME TO GLYGEN AND USE
LAWN MOWER WE CALL A SUPER
SEARCH.
I WILL SHOW YOU HOW THIS ALLOWS
1 TO INVESTIGATE SORT OF
MULTIFACTORIAL CONCEPTS OF GLYCO
SCIENCE.
RIGHT?
SO THIS IS A SUPER SEARCH IRPT
FACE AND CAN YOU SEE THAT WE
COLLECTED HERE IN THESE BOXES
THE TYPE OF DATA THAT WE
ACTUALLY HAVE AT GLYGEN AND FOR
EACH OF THESE BOXES CAN YOU SEE
THE NUMBER OF INDIVIDUAL RECORDS
WE HAVE FOR THAT KIND OF DATA SO
434,000 SITES.
THIS IS ACTUALLY A BIT OLD
EMPLOY I DIDN'T REDO THE DEMO
LAST NIGHT BUT THE NUMBERS ARE
ACTUALLY A LITTLE BIT HIGHER
NOW.
SO CAN YOU SEE WHAT WE HAVE IN
THOSE BINS, AND IF YOU CLICK ON
THE ADVANCED VIEW HERE, IT WILL
ALSO TELL YOU THEN WHAT WE HAVE
ON THE EDGES.
SO, GLYGEN HAS 64,219 PROTEINS.
53,291 OF THOSE PROTEINS
TOGETHER HAVE 433,990 SITES
ASSOCIATED WITH THEM.
SO 1 CAN BEGIN TO EXPLORE WITHIN
THAT DATA SET OF CONCEPTS THAT
MAY LINK THEM TOGETHER SO WE
WILL START HERE WITH THIS NOTION
OF DOING A MOTIF, SUPERSEARCH,
SO CLICK ON THAT MOTIF BOX AND
THEN CAN YOU ENTER THE
PARAMETERS THAT YOU MIGHT BE
INTERESTED IN SEARCHING, WE'RE
INTERESTED IN INCLUDING A NAME,
AND THAT NAME IS LEWIS X SO WE
WILL ASK QUESTIONS ABOUT WHAT
PROTEINS HAVE LEWIS X ON THEM.
WHAT GLYCANS CARRY LEWIS X
EPIEPITOAPPROXIMATE E, SO THIS
IS OUR INTEREST, WE HIT SYRUP
AND THE SEARCH RESULTS SHOWS
THAT IN THE GLYGEN DATABASE
THERE ARE 86 PROTEINS ASSOCIATED
WITH LEWIS X BUT THEY MAY
INCLUDE ENZYMES THAT ARE IN THE
LEWIS X BUT THERE ARE 7 PROTEINS
THAT HAVE SIGHTS MODIFIED WITH
THE WEATHER 1 AND ON THOSE 7
PROTEINS THERE ARE 12 SITES THAT
MODIFIED SO WE CAN ASK QUESTIONS
ABOUT WHAT THE PROTEINS ARE AND
WHAT THE SITES ARE SO LET'S
START WITH THE SITES, SO THE
RESULT LIST FROM THAT SITE
SEARCH THAT CAME FROM THE SUPER
SEARCH LISTS PROTEINS BY THE
UNIPRODUCT SESSIONS AND LISTS
SITES THAT ARE MODIFIED AND WE
JUST TAKE THE TOP PROTEIN HERE
THAT'S MODIFIED AT AMINO ACID 95
AND THIS PROTEIN IS
INTER--INTERFERON ALPHA 14 AND
YOU CAN SEE THAT IN AN
ASPARRAGING 95, 1 OF THE GLYCO
FORMS OF THIS PROTEIN HAS THIS
LEWIS EPITOPE THAT INCLUDES
[INDISCERNIBLE] SO THIS AS A
LEWIS X IN THE 1 OF THE GLYCO
FORMS CAN YOU SEE GO THE TO
SEQUENCE REPRESENTATION THAT
SHOW SHOWN HERE AND I'VE PRELIE
HEIGHTED IT IS SEQUENCE WITH
FEATURES INCLUDING END LINK
SEATS SO THE RED UNDERLINE IS
THE DPLI COSALATION SITE AND
IT'S HIGHLIGHTED HERE IN GREEN,
BECAUSE THERE'S A VARIATION
KNOWN TO BE ASSOCIATED WITH THAT
ASPARRAGING AND IN FACT THAT
GLYCOSYLATION SITE, 95, THIS IS
A VERYIATION IN WHICH THAT
ASPARRAGING IS CONVERT EXPTD
THEN OF COURSE IS NO LONGER
SUBSTRATE FOR DPLI COSALATION
AND THAT'S ASSOCIATED
WITH--ASSOCIATED WITH COLORECTAL
CANCER.
SO WE'VE GONE FROM THE MOTIF
IDEA, LEWIS X TO A SPECIFIC
PROTEIN THAT AS I SPECIFIC SITE
MODIFIED BY THIS AND VARIATIONS
OF THATVIATE ARE ASSOCIATE WIDE
THE DISEASE.
SO 1 CAN GO IN AND EXPLORE WHAT
PROACTIVE TEENS WITH WITHIN OUR
DATA SET THAT CARRY THE 1 AND
HAVE A LIST OF THOSE PROTEINS,
AND THIS IS THE PROTEIN THAT WE
WERE PLEKS PLERRING ALREADY IN
THE IRPT FERON ALPHA 14 BUT
THERE ARE OTHERS YOU COULD GO IN
AND ASK WHAT SITES ARE MODIFIED
WITH THE LEWIS EPITOPE AS WELL
AND THIS BECOMES HYPOTHESIS AS
GENERATED TO SAY, IF I'M ABOUTED
IN LEWIS X WHAT MIGHT BE
IMPORTANT TO INVESTIGATOR THIS
POTENTIAL CARRIER OF LEWIS X SO
THAT'S IF 1 CAME TO GLYGEN WITH
NO KNOWLEDGE OF WHAT GLYCANS ARE
BUT YOU WERE INTERESTED IN A
FUNCTIONAL MOTIF YOU COULD GET
INFORMATION UPON I WANT TO
FINISH UP JUST SHOWING AWAY THRA
YOU CAN ACQUIRE SORT OF NOVEL
ANSWERS THAT PROBABLY AREN'T
AVAILABLE ANYWHERE ELSE TO WHAT
MANY GRIEK O SCOF THES WOULD
THINK ARE IMPORTANT QUESTIONS SO
WE WILL KK BACK TO THE SUPER
SEARCH AGAIN AND NOW WE'RE GOING
TO DO A SITE SEARCH SO WE'RE
GOING TO ASK--WE ARE GOING TO
QUERY THE DATA FOR SITE AND IN
PARTICULAR A SITE SEQUENCE AND
WE WANT TO LOOK AT ASPARRAGE
GENES THAT BE GO GLUE MARIOUS
COSALATED AND THOSE APSAR GENES
THAT WHERE THERE'S A SINGLE
NUCLEOTIDE SO WE'RE ASKING THE
QUESTION, SHOW ME ALL IN-LINK
SITES THAT ARE IMPACTED BY A
CHANGE IN THE RESIDUE WITHIN THE
NSX ST OR C SE81.
SO YOU CAN SEE THAT IS 331
PROTEINS THAT HAVE 9681 SITES
THAT HAVE ASPARRAGES THAT MAY BE
IMPACTED BY VARIATIONS, RIGHT?
SO WE CAN INVESTIGATE THESE
SITES AND WE'LL JUST TAKE A TOP
HIT HERE.
OF PROTEIN IN THIS CASE, IT'S
[INDISCERNIBLE] 4.
AND IF WE LOOK AT DECKNOLOGY,
AND LOOK AT THE SEQUENCE, AND
WE'RE LOOKING AT DISPARAGING
281, WHICH IT IS AS END LINK
CONSENSUS, AS PARAGING XT AND
THAT IS MODIFIED TO ASERIES
POINTSINE IN THIS PARTICULAR
MUTATION AND IN THIS CASE, IT'S
NOT DISEASE ASSOCIATED WITH YOU
ABOUT'S A WHOLE LIST OF SITES
THAT 1 CAN EXPLORE IN WHICH THE
CONSENSUS FRIENDLY GLYCOSYLATION
HAS BEEN MODIFIED AWAY FROM
GLYCOSYLATED SO I WILL FINISH UP
WITH SOME OF OUR FUTURE GOALS
FOR GLYGEN AS WE MOVE OUT OF
COMMON FUND FUNDING AND HOPE FOR
FUTURE SUCCESS, AND THAT IS THAT
OUR--1 OF OUR GUIDING LIGHT
SYSTEM ALWAYS TO ENHANCE DATA
ACCESSIBILITY TO FIND WAYS TO
BRING PEOPLE INTO GLYCO SCIENCE
DATA THAT DON'T NECESSARILY HAVE
A BACKGROUND IN GLYCOSCIENCE AND
WE HOPE TO DO THIS BY BUILDING
SORT OF DOMAIN SPECIFIC PORTALS
THAT PEOPLE CAN COME TO GLYGEN
DATA WITH THEIR OWN EXPERTISE.
ALWAYS WORKING TO EXPAND THE
AMOUNT OF VOLUME WE HAVE BEEN
GLYGEN WHICH IS ALWAYS A MAJOR
PART OF OUR WORK IS TO FIND AND
CURATE NEW DATA SETS, WE WANT TO
BEGIN TO INTEGRATE GLYCO
CONJUGATE FUNCTIONS IF YOU WILL
DEFINE IN GO TERMS TO GLYCANS
AND IT WILL BE DONE BY THE
MOTIFS THAT OUR GROUP HAS--MOTIF
LISTS THAT OUR GROUP HAS BUILT
AND YOU CAN LINK THOSE TO
FUNCTIONAL PROPERTIES.
BUT WE ALSO ARE CONTINUING TO
COLLABORATE WITH VARIOUS
RESOURCES TO EXPLORE HOW GLYCAN
DATA CAN INTEGRATE WITH LARGER
DATA SETS AND IN PARTICULAR OVER
THE LAST YEAR, WE'VE BEEN
COLLABORATING WITH THE COMMON
FUND DATA ECOSYSTEM, TO FIGURE
OUT WHAT THE BEST WAYS ARE TO
INTEGRATE VARIOUS GLYGEN DATA
FORM ATS AND WE'RE ALWAYS TRYING
AND LOOKING FOR OPPORTUNITIES TO
TALK WITH NONFLIEK O SCIENTISTS
AND GLYCO SCIENTISTS TO FIGURE
OUT HOW BEST GLYGEN CAN SERVE
THEIR NEEDS AND JUST TO FINISH
UP THIS WAS THE LAST TIME WE
WERE ABLE ABLE TO BE TOGETHER,
NOW SEVERAL YEARS AGO BUT THIS
IS THE TEAM THAT'S PUSHED US
FORWARD FOR THE LAST 5 YEARS AND
MANY OF US WILL MOVE FORWARD
INTO THE NEXT INCARNATION OF
GLYGEN AND I WILL STOP THERE.
AND STOP SHARING MY SCREEN AND
READY FOR QUESTIONS.
SO AGAIN, THAIRK YOU FOR ALL THE
SPEAKERS FOR GREAT TALKS AND IF
YOU CAN TURN ON YOUR CAMERAS AND
WE WILL GO TO THE CHAT.
AGAIN, INDIVIDUALS, AGAIN THE
AUDIENCE AGAIN YOU CAN SEND YOUR
QUESTIONS VIA THE SEND LIVE
FEEDBACK LINK AND GOING BACK, I
HAD ASKED HUGO A QUESTION AND
MAYBE HE CAN RESPOND, DO PHOTO
RECEPTOR VS A LIMITED CAPACITY
FOR LYSOSOMA DEGRADATION FOR
SUCH A PATHWAY TO SECRETE
MATERIALS TO OTHER CELLS SUCH AS
GLUE MARIOUSA TO DEGRADE?
>> NO, I THINK THE PHOTO
RECEPTORS ARE VERY SIMILAR TO
OTHER CELLS AND OTHER NEURONS,
WHEN YOU ACTIVATE OTHER NEURONS
YOU PRODUCE DPLIEWK O CERAMIDE
AND IT IS TRANSFERRED TO GLUE
MARIOUSA.
SIMILARLY IN THE VERTEBRATE GLUE
MARIOUSA AND NEURONS CO CULTURE
MUCH OF THE DPLIEWK O CERAMIDE
IS TRANSFERRED TO GLUE MARIOUSA
WHERE IT'S DEGRADED.
IN YOU CO CULTURE THEM, I THINK
THE MAIN DIFFERENCE IS THAT
IMPLIES IT SEEMS LIKE THIS IS
THE SOLE PATHWAY.
GLUE MARIOUSA EXPRESS THE ENZYME
TO THE GLUCOCERAMIDE AND OTHER
CELLS JUST DON'T AND THEREFORE
THEY ALL TD NEURONS HAVE TO
COMMUNICATE WITH THE VERTEBRATE,
IT'S CLEAR THAT THE ENZYME THAT
DEGRADES GLUCOCERAMIDE IS ALSO
PRESENT IN SOME NEURONS, AND
PLAYS A ROLE IN NEURONS AS WELL.
BUT IT'S CLEAR BASED ON THE
EXPRESSION DATA THAT TYPICALLY,
DPLIA EXPRESS A LOT MORE, EVEN
INVERTEBRATE DATABASES OF THE
ENZYME THAN NEURONS AND SO, ALSO
IF YOU THINK ABOUT IT, IF YOU
PRODUCE GLUCOCERAMIDE, IT'S A IN
YOUR SYNAPSE IN YOUR
NEUROMUSCULAR JUNCTION BECAUSE
THERE IS ACTIVITY, IF YOU HAVE
TO DEGRADE IT IN THE LYSOSOME
YOU WOULD HAVE TO TRANSPORT
APPROXIMATE BACK TO THE
[INDISCERNIBLE] AND THAT'S A LOT
OF ENERGY AND PATH TO GO, IT'S
PROBABLY MUCH EASIER TO JUST
DUMP IT NEXT DOOR IN YOUR DPLEEL
CELLS AND GET RID OF IT.
>> HOW MUCH OF THE DPLIEWK O
CELL SERIES POINTS MID THAT'S
ACTIVITY RELATED IN TERMS OF ITS
PRODUCTION IS COMING FROM
BIOSYNTHESIS VERSUS DEGRADATION
OF OTHER GLYCO EXTENDED GLYCO
SINGLE LIPITS?
>> I DON'T KNOW THE ANSWER BUT,
YOU SEE BARELY ANY GRIEWK O
CERAMIDE WHEN THERE IS NO
NEURONAL ACTIVITY AND WHEN YOU
INDUCE NEURONAL ACTIVITY YOU SEE
THE DPLIEWK O CERAMIDE BEING
PRODUCED AND IF YOU KNOCK OUT
THE ENZYME THAT PRODUCING THE
GLUCOCERAMIDE, YOU SEE NO
GLUCOCERAMIDE.
SO, THE ANSWER WOULD BE NOT MUCH
ABOUT THE GLYCOL SIS.
>> YOU HAVE ANY IDEA WHAT'S
GOING ON LONG FOR THE RIDE IN
THE EXOSTUDIES OF MULTIPLE
ENDOCRINES IS THAT AN
ADDRESSABLE QUESTION?
>> VERY INTERESTING QUESTION,
SPECIALLY WITH RERELATIONSHIP TO
PARKINSON'S DISEASE.
OUR DAILY BASIS THEA SUGGESTS IN
NUCLEI SO IT TURNS OUTTA WHEN
THE LEVELS ARE ELEVATE YOU TEND
TO PRODUCE A LOT MORE SIN
NUCLEIN, AND IN FACTORS RECENTLY
SHOWN THAT THE SERIES POINTS
MIDS CAN KIND OF MODEL THE
FORMATION OF SIN NUCLEIN
AGGREGATES AND BASED ON THE
PRELIMINARY DATA WE HAVE
ALTHOUGH IT'S NOT VERY SOLID
BECAUSE THERE'S NO SIN NUCLEIN
EXAM, WE NEED DO SPECIAL
EXPERIMENTS TO EXPRESS THE SIN
NUCLEIN, IT SEEMS LIKE THE SIN
NUCLEIN AGGREGATION IS PROMOTED
BY THE INCREASE IN CERAMIDES.
AND THAT THEY RIDE ON THE SAME
AX O STUDIES OF MULTIPLE
ENDOCRINES AS THE DPLU O
CERAMIDES.
--GLUCOCERAMIDES.
>> THERE'S A QUESTION FROM LYNN
FROM RAJA, THERE ARE LOTS OF
RESOURCES THAT USE DISEASE
ONTOLOGY, DO YOU HAVE EXAMPLES
OF HOW INDIVIDUAL SCIENTISTS OR
CLINICIAN RESEARCHERS MIGHT USE
DOL?
>> THANK YOU VERY MUCH NANCY.
DISCIPLINARY PUT AN ANSWER IN
THE CHAT BUT WHAT I ALSO WANT TO
MENTION IS WE GET A LOT OF WHYS
FROM MASTER STUDENT WHO IS ARE
USING THE DID, OH TO EXPLORE NOW
AREAS OF RESEARCH AND SO WE DO
PROVIDE, WITH BOTH DATA SETS
DOWNLOADING DIFFERENT PORTIONS
OF ONTOLOGY, FOR THEIR USE AS
WELL, AND THEN RESOURCES AS
WELL, BUT WE REAL LEGAL DO WORK
HAND IN HAND WITH RESEARCHERS
EVERY WEEK ON AREAS OF
EXPERTISIES, THEY WILL SUGGEST
REVISIONS, NEW TERMS, WE WORK
WITH A LOT OF CLINICIANS,
MOLECULAR SUBSTIEPSOR CANCERS
AND WE BRING THAT DATA IN THE
AND PROVIDE FEEDBACK THROUGH THE
TRACKER SYSTEM.
THANKS FOR THE QUESTION RAJA.
>> GREAT.
GREAT.
I HAD A QUESTION EXPWRUOF THE
ABOUT THE PROCESS SO FOR CASE
STUDIES, SO, YOU KNOW SOME CASE
STUDIES OBVIOUSLY HAVE MORE
INFORMATION THAN OTHERS, SO HOW
DO YOU ANNOTATE THAT YOU KNOW
WITH SUCH VARIABILITY AND WHAT
INFORMATION MIGHT BE PROVIDED IN
VARIOUS CASE STUDIES.
>> YEAH, IT LEGAL IS VERY
TRICKY.
WE HAVE TENDED TO INCLUDE ALL
CASE STUDIES WHEN THERE'S AT
LEAST 1 FAMILY INVOLVED IN THE
STUDY, WE HIGHLIGHT THESE AND
BRING THEM IN AS PUBMED
REFERENCES AND THEN WE WILL ADD
MORE INFORMATION TO THE TEXTURAL
DEFINITION IF THERE'S VARIATION
SEEN ACROSS THOSE INDIVIDUALS OR
FAMILIES.
WE DO IN THIS CONJUNCTION WITH
OMMANDED CAN THE WHAT WE MAKE
SURE WE HAVE ENOUGH THAT
EVIDENCE THERE IS A NEW SUBTYPE
OF DISEASE AND THEN WE BRING IT
AND WE ANNOTATE IT THROUGH THE
PUBLICATIONS.
>> OKAY, GREAT, THANK YOU.
THERE WAS A QUESTION FOR
[INDISCERNIBLE] THIS, IS FROM
[INDISCERNIBLE], THE QUESTION IS
MIRROR IMAGE TOMMICS PUBLICLY
AVAILABLE?
>> YES, SO, CURRENTLY THE DAILY
BASIS THEA COULD BE ACCESSED ALL
THE PROCESSED DATA ON THE ROLE
AND THE UNDERLYING DAILY BASIS
THEA COULD BE ACCESS AT THE
MITOMICS.APP WEBSITE AND WE HAVE
MOVED SINCE THE PAPER WAS
ACCEPTED SO ANYONE CAN GO AND
INTERACT WITH THE DATA, EXPLORE
IT AND DOWNLOAD IT AND REANALYZE
WHICHEVER YOU WOULD LIKE FELT
ONCE THE PAPER CURES IN WE WILL
GET SUPPLEMENTALS FROM SO THAT
IS ALL THE DATA AVAILABLE AS OF
RIGHT NOW.
>> I HAVE A FOLLOW UP QUESTION.
LIKE DO HAVE YOU SOME KIND OF
LICENSE INFORMATION ON THE
WEBSITE?
WHAT YOU VERBALLY SAID IT LOOKS
LIKE A CC-0 TYPE OF LICENSE OR
YOU DO NOT HAVE THAT EXPLICITLY
STATED THERE?
THE REASON I'M ASKING IS THAT IN
GLYGEN WE NEED TO KNOW THAT IF
YOU LET'S SAY USE ANY OF THE
INFORMATION THAT IS AVAILABLE
HOW DO WE REFERENCE IT AND HOW
DO WE SITE IT BACK AND SO ON?
>> SO FOR IF YOU USE THE DATA
YOU WOULD PROBABLY NEED
TO--SORRY CITE THE APPLICATION,
OTHERWISE WELL, OTHERWISE
WHATEVER DAT AWE GET FROM THE
WEBSITE ARE YOURS FOR ANALYZING?
>> THAT'S GOOD, THANKS.
>> THANK YOU BUT IF WE WANT TO
SUCK IT UP WITH THE GLYGEN WE
NEED SOME ARE THE SOPHISTICATED
OF LICENSE ARRANGEMENT.
>> WHAT WE TRY TO ENCOURAGE IS
THAT WHEN ANYBODY PUTS UP A
WEBSITE, THIS BRINGS BACK A
QUESTION THAT DOUG HAD ASKED
EARLIER IN THE PREVIOUS SESSION,
WHEN SOMEBODY PUTS UP A
DATABASE, HAVING AN EXPLICIT
DECLARATION OF THE LICENSE GOES
A LONG WAY, WE DID A WORKSHOP IN
BIOCURATION A FEW YEARS AGO
ABOUT THE PROS AND CONS OF THE
LICENSES AND WE DID A SURVEY AND
IT URNS OUT THAT MOST PEOPLE
LIKE YOU WOULD WANT A CC4 PBT 0
OR ZC0 BUT SOMETHING SIMILAR BUT
IT'S NOT EXPLICITLY STATED
BECAUSE IT'S NOT STATED THAT
FORMS A BARRIER FOR DATA
SHARING.
>> I SEE, THEN YEAH WE SHOULD
DEFINITELY CONSIDER AND I WILL
BRING IT BACK TO THE TEAM TO
THINK ABOUT THAT FOR SURE.
YEAH.
>> HE WOULD NOT BE ABLE TO
DOWNLOAD THE UNDERLYING
DATABASES FROM THE SIDE, YOU
WOULD DOWNLOAD THE DATA IN THE
FORM OF EXCEL SPREADSHEET IN THE
CASE BUT YEAH IT'S WORTH
DISCUSSING THINGS AND YOU
MENTIONED YOU ARE NOT GOING TO
TALK ABOUT GLYCOSYLATION OR POST
TRANSLATIONAL MODIFICATIONS BUT
IS THAT ALSO WITHIN MIGHT O
GENICS THAT THERE'S POST
TRANSLATIONAL MODIIVES DATA?
>> YES, WITH THE POMT
METHODOLOGIES AT THE POINT IN
OUR HANDS AT LEAST, MAYBE
SOMEONE ELSE OUT THERE IS
BETTER, JUST NOT COMPATIBLE WITH
SUCH A LARGE STUDY OF SEVERAL
HUNDRED SAMPLES, SO WE NEVER
ATTEMPTED THEM.
THAT SAID, I WOULD THINK 1
ACCOUNT PROBABLY FILTER THROUGH
THE CELL LINES AND PRIORITIZE
SMALL SEB SET FOR THOSE PTM
ANALYSIS IN THE CASE OF
MITOCHONDRIA I WOULD ADVOCATE
FOR ACETYLATION AS BEING THE
MOST PROMISING PTM TO ELECTRIC
AT BEFORE GLYCOSYLATION AS IT'S
KNOWN TO BE INVOLVED APPROXIMATE
WITH METABOLISM HEAVILY AND
THERE ARE LOT OF MITOCHONDRIA
PROTEINS THAT REGULATE THROUGH
ACETYLATION SO THAT WOULD BE THE
1 TO LOOK AT IT FIRST.
>> IN MY MIND.
>> I HAVE A QUESTION FOR DANIEL
QUH IF YOU DON'T MIND ME
HOGGING?
SO DAN I WAS REALLY INTRIGUED,
YOU KNOW TALKING ABOUT THE MUCUS
BARRIER, PROTECTIVE MUCUS
BARRIER OF THE EPITHELIAL LAYER
BUT ENDED UP FOCUSING ON A
COMPONENT OF THE OLIGIO SACK O
TRANSFER ACE GLYCOSYLATION AND
MUCH OF THAT BARRIER AND OLYCANS
SO MAYBE THERE'S OBVIOUSLY GOING
TO BE IMPORTANT BALANCE THAT HAS
TO HAPPEN BUT IN A THINNING
BARRIER THAT YOU SLEEP APNEA AND
OBESITYY IN THE
EPITHELIAL--EPITHELIAL APICKAL
END IS THAT LESS PROTEIN AND YOU
KNOW SO IT'S JUST A FOLDING
PROBLEM GETTING ENOUGH PROTEINS
FOLDED CORRECTLY TO GET OUT
THERE, O THERE'S ACTUALLY--OR IS
THERE ACTUALLY A GLUE MARIOUS
COMIC SHIFT IN THE MUCUS LAYER
IN THE OLIGIOTRANSFERAISE?
>> THERE ARE A COUPLE ELEMENTS
TO BARRIER ACTIVITY AND
GLYCOSYLATION SO THE MAIN EFFECT
OF IMPAIRED AND LINKED
GLYCOSYLATION APPEARS TO BE AN
EFFECT ON ER HOMEOSTASIS SO
THAT'S INTRINSIC TO THE
EPITHELIAL CELL AND THEIR
BARRIER FUNCTION RELATED TO
FORMING JUNCTIONS WITH 1 ANOTHER
AND MAKING AN IMPERMEABLE
BARRIER.
AND THEN SECONDAR TOW THAT IS
SECRETION OF THE MUSEINS AND THE
GLYCOICAL EX AND THAT'S THE
STRUCTURES AND A WHOLE SERIES OF
OTHER GENES IMPACT THOSE TYPES
OF BARRIER FUNCTIONS.
ALL RIGHT, SO, IT'S INTERESTING
TO SEE WHEN YOU DISRUPT THE
OLIGIOTRANSFER ACE HOW DOES THAT
SPILL OVER INTO MUSEIN
GLYCOSYLATION, I WOULDN'T BE
SURPRISE IF IT DOES BUT IT WOULD
BE INTERESTING TO EXPLORE IT A
BIT.
>> I AGREE, I'M SURE IT WILL.
IT'S BEEN HARD TO DISENTANGLE ER
STRESS FROM YOU KNOW THE ROUGH
ATOM TEENS THAT ARE SECRETED
THROUGH THE ER.
OOTD BEEN A CHALLENGE FOR US.
SO FOR DANIEL THERE ARE A COUPLE
QUESTIONS RELATED TO THE
MANGANESE TRANSPORTER SO, IT'S
ASKED THAT DO YOU FIND IN YOUR
SCREEN OF OTHER MEMBERS OF SLC39
BESIGHTS A8 FAMILY THAT REGULATE
DISCIPLINARY VALENTINEDENT IONS
ALSO HAVE AN IMPACT ON
GLYCOSYLATION?
>> WE DON'T, IT'S VERY SPECIFIC
FOR SLC39 A 8.
SO THE CARGO FOR 39 A8 IS ZINC
AND MANGANESE PRIMARILY BUT THEY
ALSO TRAN PORT LIKE LIKES
CADMIUM AND A FEW OTHER
DISCIPLINARY VALENTINEDENT CAT
IONS AND AMONGST THE 39 A-FAMILY
THERE ARE 4 OR 5 MEMBERS THAT
ALSO TRANSPORT DISCIPLINARY
VALENTINEDENT CAT IONS NAMELY
ZINC.
SO WHETHER WE KNOCKED OUT 39 A8,
WE HAD NO EFFECT ON ZINC.
IT ONLY EFFECTED MAINING AN EASE
SO THIS SEEMS TO BE A
NONREDUNDANT FUNCTION OF 39 A8
WITH MAINING AN EASE WHERE THE
OTHER CAT IONS CAN BE TRANSPORT
BY OTHER FAMILY MEMBERS.
>> OKAY ISSUES GREAT.
TLR WAS A QUESTION BY
[INDISCERNIBLE], WAS GLYCO
PROTEOMIC PROTILES BY MASS SPEC
DOWN IN CASES OF THE 39 A8 AND
IF THAT SHOWED ALTERED PROFILE
ABUNDANCE COMPARED TO NORMAL?
>> SO I SHOULD PREFACE THIS BY
STATING THAT WE'RE VERY MUCH
INTERESTED IN FINDING
COLLABORATORS WHO CAN HELP US
WITH DPLI COMICS AND GLYCO
PROTEOMICS, I BEING THERE'S A
HUGE OPPORTUNITY THEREENTIOUS
SPECIALLY IN GUT BARRIER
FUNCTIONS FOR LOOKING AT THESE
TYPES OF OMICS MEASUREMENTS.
HAVING SAID THAT, WE'VE DON A
LITTLE BIT WITH SOME HELP, I CAN
TELL YOU SOME KIND OF GENERAL
TAKE AWAYS ON MY IMPRESSIONS OF
WHAT WE'VE SEEN SO FAR.
SO FIRST WHEN WE'VE DONE GLUE
MARIOUS KOAMICS ON EPITHELIAL
CELLS FROM THE COLON, IT'S
INCREDIBLY DIVERSE, ALL OF THE
GLYCAN SPECIES THAT ARE
RECOVERED.
SO THERE'S I THINK A NEED TO
MORE READILY IDENTIFY EACH OF
THOSE SPECIES IN COMPUTATIONALLY
FACILE WAY, AND WITH ACCURACY.
AND SECONDARILY, THERE'S A
CHALLENGE IN BEING QUANTITATIVE
SO MAKING SO MANY MEASUREMENTS
OF DIVERSE ENTITIES THAT
DIFFERENT ABUNDANCES, CREATES A
REAL CHALLENGE FOR BEING
QUANTITATIVE.
AND SO, THINKING MORE ABOUT
POWER ANALYSIS, AND VARIANTS AND
HOW MANY SAMPLES DO WE NEED AND
THINGS LIKE THIS IS ANOTHER
CONSIDERATION THAT I THINK IS AN
UNSOLVED PROBLEM AND SO, THAT'S
KIND OF MY TWO-CENTS ON WHERE WE
ARE BUT AGAIN, I THINK IT'S
EXCITING AREA TO LOOK INTO.
>> AND THERE WAS 1 OTHER
QUESTION FROM WESLEY ROBERTS.
HE'S ASKING ABOUT LOW MANGANESE
AND THAT'S CORRELATED TO GUT
DISMORPHISM?
SO HE'S ASKING WHAT
CONCENTRATIONS MANGANESE ARE
HEALTHY WHAT'S TOO MUCH OR TOO
LITTLE AND IS LOW MANGANESE
CORRELATED TO ALL MUSEUM MAN
GENETICS OR PHENOTYPES LIKELY TO
HAVE LOW MANGANESE AND OF COURSE
APPLAUSE ON GREAT TALKS.
>> SO, MANGANESE REALLY IS A KEY
MICRONUTRIENT.
IT'S A CO FACTOR FOR MANY
DIFFERENT ENZYMES THAT PERFORM
MANY DIFFERENT FUNCTIONS AND I
THINK THE GLYCOSYLATION PATHWAY
IS 1 OF MANY.
SO IF YOU LOOK IN LARGE COHORTS
OF PATIENTS OF HEALTHY PEOPLE
WHO ARE CARRIERS FOR AT391
TVARIANT FOR SLC39 A8, WE SEE
REDUCED MANGANESE LEVELS IN THE
BLOOD.
SOPHISTICATEDY THAT'S A COMMON
ENDOPHENOTYPE FOR THIS.
BUT AS I MENTIONED, THE DISEASE
PHENOTYPES CAN VARY AND THAT'S
PROBABLY DEPENDENT ON
ENVIRONMENTAL FACTORS, ANOTHER
GENETIC FACTORS.
BUT MAINING AN EASE THERE'S A
SWEET SPOT IN HOW MUCH, YOU KNOW
TOO LITTLE IS BAD AND TOO MUCH
IS BAD.
SO TOO LITTLE IS ASSOCIATED WITH
IBD, IF YOU HAVE OTHER RISK
FACTORS IT'S ASSOCIATED WITH
SCHIZOPHRENIA, IT'S ASSOCIATED
WITH CARDIOVASCULAR TRAITS AND
THEN TOO MUCH IS SOCKED WITH
NEUROTOXICITY SO WELDERS WHO
HAVE HIGH EXPOSE TOWER MANGANESE
SOMETIMES DEVELOP TOXICITIES AND
TACKERIN SONS LIKE SYMPTOMS THAT
ARE TRANSIENT.
SO AGAIN I THINK THERE'S A GOLDY
LOCK PHENOMENON, TOO MUCH IS
BAD, TOO LITTLE IS BAD.
>> AND IN A CONVERSATION WITH
KELLEY [INDISCERNIBLE] A COUPLE
MONTHS AGO, THOSE TRANSFERAISES
THEY HAVE A HIGH MANGANESE
REQUIREMENT, MORE SO THAN OTHER
TRANSFERAISES SO THOSE ENZYMES
THAT MAKE COMPLEX GLYCANS ARE
EXZINDERITLY SENSITIVE TO
MANGANESE LEVELS.
BEFORE WE FINISH UP A HAD A
QUESTION FOR CHIARA DO I MISS IT
OR DID THE KNOCK DOWN FISH HAVE
A BRAIN PHENOTYPE.
>> SO THEY HAVE A BRAIN
PHENOTYPE BUT THEY ALSO SHOW
DROSOPHILA WITH THE MORPH O LINE
O, THE POMT 1 KNOCK OUT SO FAR
WE ONLY--WE ARE ONLY SEEING
RETINAL PHENOTYPES, WE HAVE
HAVEN'T LOOKED IN DETAIL THAT
ACT IN GUIDANCE WHICH IS AN
ISSUE IN THE MICE, BUT WHAT WE
THINK IS GOING ON IS THAT 1 OF
THE PROBLEMS WITH THE POMT 1 IMK
OUT IS THAT THERE'S MATERNAL
MRNA THAT'S PROVIDED.
THERE IS DPLIEK COSALATED TPHREU
RACING KAN--KANA FOR THE FIRST 4
OR 5 DAYS BECAUSE THE DPLI
KAN--KANA IS PRETTY STABLE SO
NEW WE'RE LOOKING AT THE EARLIER
STAGES AND THEN IT GOES AWAY.
AND SO WE CRISPR OTHER
APPROACHES WE CAN GO IN AND TRY
AND REMOVE THE MATERNAL MRNA AND
ACTUALLY SEE IF WE CAN PUSH IT
TO A MUCH MORE SEVERE PHENOTYPE.
AND ALSO DO A DOUBLE POMT1 AND 2
KNOCK OUT.
BUT YEAH, RIGHT NOW WE HAVE
OCULAR AND MUSCLE PHENOTYPES IN
THE KNOCK OUT.
>> THANK YOU.
>> WELL WE'VE GONE BEYOND OUR
TIME NANCY.
SO I THINK WE SHOULD DO 1 FINAL
THANK YOU TO ALL THE SPEAKERS
OVER THE LASTED 2 DAYS BUT
ESPECIALLY THE LAST SESSION AND
THIS RECORDING WILL BE AVAILABLE
FOR A WHILE AND YOU CAN SEE HOW
LONGOT WEBSITE FOR THE MEETING
BUT THANK TO YOU EVERYBODY FOR
YOUR PARTICIPATION.
>> AND THANK YOU TO MIKE AND
ROGER FOR ORGANIZING THIS
WONDERFUL SYMPOSIUM AND BEHIND
THE SCENES FOR PAMELA AND
AMANDA, SO AGAIN, THANK YOU
EVERYONE.
>> THANK YOU EVERYBODY.