IT'S MY PLEASURE TO HAVE HEMALI
PHATNANI A LONG-TERM
COLLABORATOR.
THE DIRECTOR FOR THE CENTER OF
NEURO GENERATIVE DISEASE KNOWN
AT NYGC AND A POINT APPOINTMENT
AT COLUMBIA UNIVERSITY.
SHE HAILS FROM BOMBAY, INDIA AND
LEARNED SHE HAD A
NON-TRADITIONAL PATH TO WHERE
SHE IS TODAY.
SHE AMASSED EXPERTISE IN SEVEN
LANGUAGES INCLUDING GERMAN AND
HER FIRST JOB WAS ACTUALLY TO
TEACH GERMAN TO STUDENTS.
SHE FINALLY MADE HER WAY BACK TO
SCIENCE AND DID HER Ph.D. AT
DUKE UNIVERSITY WHERE SHE
RECEIVED A Ph.D. IN BIOCHEMISTRY
AND MOLECULAR BIOLOGY AND LOOKED
AT TRANSCRIPTION PROCESSING.
SHE THEN CARRIED OUT HER STUDIES
IN HARVARD AND COLUMBIA
UNIVERSITIES WHERE SHE STUDIES
ALS DISEASE MECHANISMS USING
GENOMIC PROFILING METHODS AND
STUDIED INTRINSIC EFFECTS ON
MOTOR NEURONS AND IN 2014 BECAME
CO-DIRECTOR AT NYGC AND NOW THE
DIRECTOR.
THIS GROUP FORMED AN ALS
CONSORTIUM INVOLVING ALLIANCES
WITH CLINICIANS, SCIENCE TESTS
AND PRIMARY PARTNER AND DISCOVER
HOW THEY CAUSE ALS AND DISEASE
AND THE CONSORTIUM LOOKS AT
BIOINFORMATICS AND THE WORK SHE
HAS LED WHILE BEING THE DIRECTOR
THERE HAS BEEN TRANSFORMATIVE
FOR THE FIELD OF ALS GENETICS
AND GENOMICS AND MY GROUP AS
WELL AS MANY OTHERS HAVE
LEVERAGED THESE DISCOVERIES THAT
WERE MADE THERE TO FURTHER
SCIENCE MUCH BROADER THAN THE
IMPACT OF HER OWN INDEPENDENT
WORK.
IN ADDITION TO LEADING THESE
PROJECTS AT NYGC SHE RUNS A
GROUP AS A TENURE TRACK
INVESTIGATOR AT COLUMBIA AND
FOCUSSING ON GENE REGULATORY
MECHANISMS THAT UNDER LIE
COMPLEX INTERACTIONS BETWEEN
MOTOR NEURONS AND IN THE BRAIN
AND SPINAL CORD OF ALS PATIENTS
AND MOUSE MODELS AND APPLIES
BIOINFORMATIC TO UNDERSTAND THE
ROLE OF CELL TO CELL
INTERACTIONS IN PATHOPHYSIOLOGY
AND THERE'S A PAPER PUBLISHED IN
SCIENCE USING A TRANSCRIPTOMICS
METHOD TO CHARACTERIZED ALS
MODELS IN HUMANS AND TISSUES AND
USING SEQUENCERS TO REPURPOSE
THEM TO HIGH THROUGHPUT IMAGING
AND STAINING PLATFORM.
WITH THEY CAN'T WAIT TO SEE WHAT
HEMALI WILL TALK TO US TODAY
ABOUT AND GIVE YOU A WARM
WELCOME TO THE NIH.
>>THANK YOU, MICHAEL.
I'M PLEASED TO BE HERE AND
HAVING A DELIGHTFUL VISIT SO
FAR.
TO RESET EXPECTATIONS IT'S ALL
DOWN HILL FROM HERE.
SO I'M GOING TO BE TELLING YOU
HOW WE USE SPATIAL GENOMICS TO
UNDERSTAND THE CNS IN HEALTH AND
DISEASE AND THE QUESTIONS WE'RE
TACKLING ARE HOW CAN WE USE THE
POSTMORTEM HUMAN BRAIN TO STUDY
SPATIAL DYNAMICS OF DISEASE
PROGRESSION AND HOW
DISEASE-ASSOCIATED MUTATIONS
AFFECT THESE DYNAMICS.
NEEDLESS TO SAY THIS IS
COMPLICATED ESPECIALLY TO SAY OF
LATE ONSET NEURODEGENERATIVE
DISEASE.
THE SAMPLES WE USE NEED TO BE OF
GOOD QUALITY IN THE WAY THEY'RE
BANKED TO ENABLE SOPHISTICATED
MOLECULAR BIOLOGY APPROACH AND
NEED TO BE CLINICALLY WELL
PHENOTYPED TO STRATIFY COHORTS
APPROPRIATELY AND I'LL GET TO
THAT IN A BIT.
AND ANEUROPATHOLOGICALLY WELL
CHARACTERIZED TO SEPARATE THE
INCLUSIONS AND CHARACTERISTICS
OF THESE DISEASES AND IDEALLY
NEED TO HAVE THEM WELL GENOTYPED
AS WELL.
ONCE YOU SORT THAT OUT HOW DO
YOU DECIDE WHICH TECHNOLOGIES TO
USE AND HOW DO YOU COLLECT THE
DATA AND ONCE YOU HAVE IT, WHAT
DO YOU DO WITH IT TO LEARN
STUFF?
I'LL TALK ABOUT THIS IN THE
CONTEXT OF THE ALS FTD CLINICAL
SPECTRUM USING A PHENOTYPE AT
ONE END AND FRONTAL TEMPORAL
DEMENTIA AT THE OTHER WITH LOTS
OF PATIENTS BEING SOMEWHERE IN
BETWEEN.
THAT'S UNDER APPRECIATED BUT
BECOMING MORE TRACTABLE NEW.
-- NOW.
WHEN WE TALK ABOUT THE
CONSORTIUM A BIG CHALLENGE FOR A
RARE DISEASE IS HOW DO YOU
OBTAIN LARGE NUMBER OF PATIENT
DNA AND RNA SAMPLES.
EVEN ONE OF THE BUSIEST CLINICS
IN THE OTHER EAST SEE S ABOUT
400 PATIENTS A YEAR AND CAN'T
RELY ON SAMPLES FROM ANY ONE
CENTER AND THE SOLUTION WAS TO
ESTABLISH A FEDERATED PROGRAM
WITH CENTRALIZED GOVERNANCE.
A FANCY WAY OF SAYING WE GOT
SAMPLES FROM MULTIPLE DIFFERENT
STUDIES THAT SPAN MULTIPLE SITES
WORLDWIDE.
THE COLOR CODING IN THE PINS IS
THE DIFFERENT STUDIES SET UP
WHEN WE STARTED THIS TO DO
EITHER CROSS-SECTIONAL OR
LONGITUDINAL BIO BANKING AND
VARIOUS EFFORTS.
ALL STUDIES DECIDED TO COME
TOGETHER TO POOL THE SAMPLES SO
WE COULD DO THE WHOLE GENOME
SEQUENCING.
WE HAD TO DO THE HARMONIZATION
OF THE CLINICAL METADATA AND ALL
THAT STUFF AND THEN EXPANDED TO
SITES ALL OVER THE WORLD.
THAT'S THE FEDERATED ASPECT OF
THE PROGRAM.
THERE'S STANDARDIZED PROCESSES
TO ALLOW US TO WORK WITH WHAT IS
NOW 45 SITES WORLDWIDE AND
EXPANDING INDUSTRY AND ACADEMIA
AND MANUALLY CURATING AND
HARMONIZING THE METADATA AND
COORDINATING HOW THE DATA COMES
IN AND MERGING WITH THE CLINICAL
DATA AND SHARING IT WITH EVERY
PARTICIPATING SITE AND BEYOND IN
THIS CONSORTIUM.
SO DATA FROM THESE STUDIES ARE
SHARED ALL OVER THE WORLD
INCLUDING WITH INVESTIGATORS AT
NINDS.
SO IF YOU'RE INTERESTED IN
ACCESSING THE RESOURCE, PLEASE
JUST E-MAIL ME.
WE HAVE OVER 5,000 WHOLE GENOMES
AND SEQUENCES FROM THE PATIENTS.
THEN ON THE LAB SIDE, HOW DO WE
USE GENOMICS TO STUDY THE
EFFECTS OF MUTATIONS ON CELLULAR
FUNCTION?
HERE'S WHERE OUR INNOVATIVE
APPROACH TO ALS FTD COMES IN AND
TALKED ABOUT THE CONSORTIUM
EFFORTS AT NYGC AND WE HAVE
ALMOST 500PM TISSUES WITH
DIFFERENT REGIONS OF THE BRAIN
AND SPINAL CORD WE GENERATED
DATA ON.
IN PARALLEL ON THE COLUMBIA SIDE
WE USE AT MOUSE MODELS TO LOOK
AT CELLS IN A DISH AND TISSUES
FROM THE MOUSE AND HUMAN SAMPLES
AND LOOK AT HOW GENE EXPRESSION
PATTERNS CHANGE OVER SPACE AND
TIME.
WHY DO WE WANT TO SPATIALLY
RESOLVE GENE EXPRESSION IN ALS?
LIKE OTHER DISEASES IT INVOLVES
PATHOLOGIES AND MULTIPLE CELL
TYPES AND WE WANT TO UNDERSTAND
HOW THESE DIFFERENT CELL TYPES
INTERACT AS DISEASE PROGRESSES
AND WHETHER WE CAN ACCESS THE
DYNAMICS OF ALS PATHOLOGY ACROSS
TIME AND SPACE.
WHERE DOES IT STOP AND HOW DOES
IT SPREAD.
SO HOW CAN WE MEASURE GENE
EXPRESSION IN MULTIPLE CELL
TYPES AND LOCATIONS
SIMULTANEOUSLY?
THERE ARE MULTIPLE APPROACHES TO
HOW TO DO SPATIAL
TRANSCRIPTOMICS.
THEY CAN BE DIVIDED INTO TWO
BROAD CLASS.
THE SPATIAL BAR CODING METHODS
THAT DON'T RELY ON SELECTING
TRANSCRIPTS UP FRONT AND THEN
THE IMAGING BASED METHODS WHERE
YOU START WITH A KNOWN SET OF
TRANSCRIPTS AND BUILD PROBES
AROUND THEM AND THESE METHODS
CAN GIVE YOU CELLULAR AND SUB
CELLULAR RESOLUTION WHICH THE
BAR CODING BASED METHOD SO
NECESSARILY DO.
WHAT YOU LOSE IN RESOLUTION IN
ONE METHOD YOU MAKE UP FOR IN
THROUGHPUT AND SCALE ON THE
OTHER.
AN IDEAL COMBINATION WOULD BE TO
ARTFULLY COMBINE THESE TWO AND
THAT'S WHAT WE'RE WORKING
TOWARDS.
THE METHOD OF CHOICE IS NOT
COMMERCIALIZED BY 10X GENOMICS
AND THIS WAS DEVELOPED AT THE
LAB IN WE'D -- SWEDEN AND
DEVELOPED THE WORK FLOWS THAT
WERE THEN TAUGHT IN SWEDEN.
ESSENTIALLY ANYONE FAMILIAR WITH
HOUSE VISSIUM WORKS?
YOU HAVE AN ARRAY OF PROBES ON
THE GLASS SLIDE AND THEY'RE
SPOTTED IN 55 MICRON CIRCLES
WITH THE CENTER TO CENTER
DISTANCE OF 100 MICRON.
YOU CAN SEE OFF THE BACK THEY
WON'T GIVE YOU COVERAGE ACROSS
THE TISSUE AND NOT GOING TO GIVE
YOU SINGLE CELL RESOLUTION.
SO EACH OF THESE PROBES HAS A
UNIQUE MOLECULAR IDENTIFIER THAT
GIVES YOU TWO PIECES OF
INFORMATION.
WHERE ON THE GLASS SLIDE IT CAME
FROM AND HOW MANY UNIQUE SPECIES
OF AN INDIVIDUAL MOLECULE YOU
CAPTURE.
SO THEN YOU'VE GOT YOUR TISSUE
SECTION AND MICRON FRESH FROZEN
AND TAKE A PICTURE AND IT WILL
ALLOW TO RELATE WHICH MOLECULE,
HOW MANY, WHERE ON THE SLIDE,
WHERE ON THE TISSUE.
I SHOULD DO THAT WITH MY LEFT
HAND BECAUSE I CAN'T BEND THE
PINKY WITH MY RIGHT.
THEN YOU HAVE THE TISSUE
SECTION.
YOU PERMEABLIZE IT AND ALLOW THE
RNA TO DIFFUSE AND BE COLLECTED
BY THE PROBES AND WASH THE
TISSUE FROM THE SLIDE AND DO
YOUR LIBRARY PREP AND SEQUENCING
LIKE FOR ANY NEXT GEN
EXPERIMENT.
SO THE VISIUM SLIDE HAS ON ONE
SLIDE FOUR OF THESE ARRAYS EACH
WITH THE 55 MICRON SPOT AND EACH
ARRAY IS 6MM BY 6MM AND HERE'S A
CLOSE UP OF THE STAIN SECTION
OVERLAID ON THE SPOTS.
YOU'VE GOT THE DNA OLIGOS WITH
THE SPATIAL BAR CODE.
WHAT WE LIKE ABOUT THIS AND THE
REASON WE CHOSE IT, IT ALLOWS AN
UNBIASSED WAY OF ACCESSING THE
TRANSCRIPTOME AND DO THINGS AT
THE THROUGHPUT AND SCALE YOU
NEED IT.
WE OVERCAME COMPUTATIONAL
APPROACHES AND LACK OF COVERAGE
AND LACK OF CELL TYPE SPECIFIC
INFORMATION.
I'LL TELL YOU ABOUT IN A SECOND.
SO WHEN WE WERE SETTING THIS UP,
WE DECIDED TO USE THE MOUSE
MODEL OF ALS BECAUSE THERE WAS A
WHOLE BANK OF DATA THAT WE COULD
USE TO SEE IF THE THINGS THAT WE
WERE FINDING DID THEY MAKE
SENSE, COULD WE PLACE THEM IN
THE CONTEXT OF WHAT WAS ALREADY
KNOWN.
SO THE POINT OF THE MOUSE MODEL
WAS TO USE IT AS A TOOL TO BUILD
THE LAB WORK FLOWS WE NEED TO
APPLY THEM TO HUMAN TISSUE.
WE PICKED AN AGGRESSIVE MODEL
AND FOUR TIME POINTS THAT SPAN
TO PRE AND POST SYMPTOMATIC
DISEASE STAGES AND WHAT WE HAD
TO OVERCOME IN ANALYZING THIS
DATA IS THE HIGH DIMENSIONALITY
OF THE DATA SET A SCRIPTOME
SCALE AND HAS HUNDREDS I THINK
THIS IS A LITTLE OUTDATED BUT
ABOUT 1300 TISSUE SECTIONS FROM
MOUSE ABOUT 80 HUMAN SECTIONS
THAT WE DID WHEN WE DEVELOPED
THIS ANALYTICAL FRAMEWORK.
THE MOUSE SPECIMENS SPAN
MULTIPLE ANIMALS AND MULTIPLE
TIME POINTS AND GENOTYPES AND
SPAN MULTIPLE REGIONS AND THE
ENTIRE CROSS SECTION.
AND THEN THERE ARE TECHNICAL
ISSUES.
EXTENSIVE AND HIGHLY VARIABLE
ZERO INFLATION WHICH MEANS A
MEASUREMENT OF ZERO DOESN'T
NECESSARILY MEAN IT WASN'T
THERE.
IT COULD BE TECHNICAL REASONS
YOU GET DROP OFF BECAUSE YOU GET
THIN SECTIONS AND NOT EVERY SPOT
WILL ACCESS EVERY MOLECULE IN
THE TRANSCRIPTOME.
SO THERE'S VARIABILITY BETWEEN
SPOTS AND BETWEEN SAMPLES.
SO WE CAME UP WITH A WAY TO
DIVIDE UP THE SPINAL CORD TO 11
DIFFERENT ANATOMICAL REGIONS
WHETHER A SPOT FELL ON WHITE OR
DARK OR MEDIAL OR CENTRAL OR
DORSAL AND MANUALLY ASSIGNED
ABOUT 130,000 SPOTS TO ONE OF
THESE 11AARs.
YOU SEE THE FOUR MOUSE SPINAL
CORD CROSS SECTIONS ON THESE
ARRAYS AND THIS IS HOW A
CLOSE-UP VIEW LOOKS LIKE.
A GIVEN SPOT CAN HAVE A VARYING
NUMBER OF NUCLEI DEPENDING ON
WHERE ON THE TISSUE SECTION IT
FALLS.
SO ONCE WE HAVE DONE THIS, ALL
WE HAVE TO DO IS TO TAKE THE
HORNS TO REGISTER THE TISSUE
SECTIONS WITH RESPECT TO ONE
ANOTHER.
ALLOWED US TO GO FROM WHAT WAS
COARSE AND UNEVEN TO WHAT IS
DENSE AND EVEN SAMPLING ACROSS
THE CROSS-SECTION OF TISSUE AND
SAW THE EXPECTED PATTERN OF
EXPRESSION OF EXPRESSION OF
GENES.
THINGS IN THE WHITE MATTER WERE
IN THE WHITE AND THINGS IN THE
GRAY WERE IN THE GRAY MATTER AND
THINGS THAT WERE SUPPOSED TO BE
IN THE VENTRAL HORN WAS THERE
AND WE KNOW THAT REGISTRATION
ALLOWED TO US GO TO DENSE AND
EVEN COVERAGE.
NOW THAT YOU HAVE IT, HOW DO YOU
USE IT?
WE USED WITH A GROUP TOGETHER
AND CAME UP WITH A HIERARCHICAL
PROBLEMISTIC MODEL THAT IS
SPLOTCH AND IT DOESN'T STAND FOR
ANYTHING AND WE MODEL THE
EXPRESSION LEVEL OF A GENE IN
ANY GIVEN SPOT AS A FUNCTION OF
WHICH REGION IT CAME FROM.
IT'S IMMEDIATE LOCAL ANTIBODY
AND ALSO BUILT IN SPOT-LEVEL
VARIATION.
THE EXPRESSION PATTERNS IN A
SPOT ARE LIKELY TO BE MORE
SIMILAR TO IMMEDIATE NEIGHBORS
THAN TO SPOTS FURTHER AWAY AND
THE EXPRESSION PATTERNS IN LETS
SAY THE AAR FOR THE VENTRAL HORN
WOULD BE MORE SIMILAR TO EACH
OTHER THAN SOMETHING MUCH
FURTHER AWAY.
AND THEN THERE'S THIS LINEAR
MODEL THAT'S A COMPONENT OF
SPLOTCH THAT ALLOWS YOU TO
CONTRACT THE VARIABLES YOU BUILT
INTO YOUR EXPERIMENTAL DESIGN.
SO THIS CHANGES WITH EXPERIMENT
TO EXPERIMENT FOR THE UNDERLYING
MODEL FOR HIGHER MODELLING GENE
EXPRESSION STAYS THE SAME.
AND THIS ALLOWED US BECAUSE OF
THIS MODELLING WE COULD BORROW
INFORMATION FROM NEIGHBORING
SPOTS AND EVEN THOUGH IN ANY
GIVEN SPOT YOU CAN ONLY DIRECTLY
MEASURE A FEW THOUSAND
TRANSCRIPTS.
WHEN YOU COMBINE ALL THIS
INFORMATION YOU CAN INFER THE
EXPRESSION ACROSS ALMOST THE
ENTIRE TRANSCRIPTOME.
AND THIS IS WHAT ALLOWS YOU TO
DO REGION SPECIFIC DIFFERENTIAL
EXPRESSION MEASUREMENTS AND SEE
HOW MUCH STATISTICAL
SIGNIFICANCE THEY HAVE.
THIS IS AN EXAMPLE OF ONE TWO
SUCH GENES AND HOW THEY VARY
BETWEEN DIFFERENT PHENOTYPES,
THOSE ARE THE DIFFERENT COLORS,
DIFFERENT TIME POINTS, THE
DIFFERENT ROWS DIFFERENT REGIONS
OF THE CORE, THE BOXES.
YOU CAN START TO SEE HERE THE
GENE EXPRESSION STARTS TO DIFFER
BETWEEN GENOTYPES AT P70 IN THE
VENTRAL HORN BEFORE IT DIVERGES
TO OTHER REGIONS.
YOU CAN SEE WE HAVE MORE
CONFIDENCE THE TIGHTNESS OF
THESE THINGS IN THESE
MEASUREMENTS THAN THESE FOR
EXAMPLE.
THIS IS THE CHANGE AS DESCRIBED
AND THE VALIDATION THROUGH IF.
WE CAN START TO SEE IT HAPPENS
AS EARLY AS 930 AND HAPPENS IN A
SUBSET OF CELLS AND THESE CELLS
WE KNOW THESE ARE IBA POSITIVE
MICROGLIAL CELLS HAPPEN TO BE
CLOSELY ABUTTING THE AXONS OF
THE MOTOR NEURONS AS THEY EXIT
THROUGH THE VENTRAL HORN.
THOSE ARE THE TYPES OF THINGS
YOU CAN DO ON A GENE BY GENE
BASIS AND GO THROUGH YOUR
FAVORITE PATHWAYS.
THEY ALSO HAPPEN TO BE THE
EARLIEST CHANGES WE SAW AND SEE
THEM IN THE SVENTRAL/LATERAL ARA
AND WE GROUPED THEM DEPENDING ON
HOW SIMILAR THEY WERE TO EACH
OTHER AND DIVIDED THE
TRANSCRIPTS THAT WERE CHANGED
INTO SEVERAL MODULES BASED ON
THE SIMILARITY OF THE EXPRESSION
CHANGES AND MAPPED THOSE MODULES
ON SPATIAL TEMPORAL COORDINATES.
THIS IS MODULE 8 AND HOW MODULE
8 GENES CHANGE THE WILD TYPE AND
MUTANT AND THE GLIALS.
MODULE 11 AND YOU CAN START TO
LOSE THIS EXPRESSION OVER
SYMPTOMATIC TIME POINTS AND YOU
CAN SEPARATE OUT WITHOUT GETTING
DROP OUT OF CELLS.
WE THEN TREATED EACH SPOT AS A
MINI BULK AND USED ORTHOGONAL
AND SINGLE-CELL DATA SETS.
THIS DATA SET WAS ONE OF THE
FIRST WE USED TO DO THE
DECONVOLUTION AND START TO NOW
EXTRACT THE CONTRIBUTION OF
SPECIFIC TYPES OF CELLS TO THE
CHANGES IN EACH OF THESE
MODULES.
MODULE 8 YOU CAN SEE WHAT'S THE
CONTRIBUTION OF MODULE CELLS AND
ASTROCYTES AND HOW MANY CAN YOU
DO IT INTO TURNS OUT THESE TWO.
AND THEY'RE DEFINED ON
SIMILARITIES OF SPATIAL,
TEMPORAL TYPES AND SOME ON
PATTERN TYPE AND THEN DIFFERENT
CELL TYPES WITH SUBMODULES COULD
REPRESENT SUBPOPULATIONS OF
MICROGLIA.
HERE'S IBA1 MICROGLIA AND PART
OF TWO DIFFERENT MODULES.
THEY HAVE VERY DIFFERENT
PATTERNS OF EXPRESSION OVER THE
TIME COURSE OF THE DISEASE.
NOW YOU CAN START TO DO THIS
WITH DIFFERENT CELL TYPES AND
START TO BUILD ENSEMBLES
DEPENDING ON WHERE THEY ARE IN
THE PORT AND WHAT STAGE OF THE
DISEASE YOU ARE IN.
NOW THAT WE HAVE ALL THESE
METHODS HOW CAN WE STUDY DISEASE
PROGRESSION AND HOW DO YOU
APPROXIMATE THE PROGRESSION YOU
GET FROM THE MOUSE MODEL?
BECAUSE WE SPREAD THROUGH C
CONTIGUOUS REGION WE STUDIES
REGIONS THAT WERE CLOSE TO OR
FURTHER AWAY FROM THE SITE OF
ONSET OF DISEASE AND WE HAVE
PHENOTYPING ASSOCIATED WITH
THESE CASES.
WE CAN START TO BUILD COHORTS
THIS WAY.
SO THE FIRST PASS AT THIS WAS
TAKING LUMBAR ONSET PATIENTS AND
LOOKED AT CERVICAL AND LUMBAR
CORD THAT'S WHAT THIS
COMPLICATED DIAGRAM IS SUPPOSED
TO REPRESENT.
THE YELLOW THINGS ARE THINGS
CLOSE TO OR FURTHER AWAY FROM
THE SITE OF ONSET OF DISEASE.
THE PURPLE THINGS ARE CLOSE TO
OR FURTHER AWAY FROM LOWER LIMB
ONSET OF DISEASE.
WE DID THIS FOR SIX PATIENTS.
WE LEARNED ONE SIX IS NOT ENOUGH
BECAUSE THERE'S MORE INDIVIDUAL
VARIABILITY IN HUMAN SAMPLES
THAN FOR MICE AND WE NEED LARGER
COHORT.
THE MOUSE EXPERIMENTS ALLOWED US
TO DO POWER CALCULATIONS.
WE KNOW FOR ANIMALS FOUR ANIMALS
PER CONDITION AND FOUR SECTIONS.
TISSUE IS MORE THAN TO GET MORE
DATA WITH HIGH CONFIDENCE.
FOR HUMANS IT'S MORE LIKE 20 AT
MINIMAL.
THE SECOND THING WE LEARNED WAS
THAT YES, THERE IS A DEPENDENCE
ON HOW CLOSE TO OR FAR AWAY YOU
ARE FROM THE SITE OF ONSET OF
DISEASE AND COMPARING CERVICAL
AND LUMBAR ISN'T THE WAY TO GO
BECAUSE THERE'S DISEASE-DRIVEN
DIFFERENCES.
THE THIRD THING WE DID WAS TWEAK
THE STUDY DESIGN TO LOOK AT
MOTOR VORTEX AND LUMBAR CORD
FROM PATIENTS WE STRATIFIED
BASED ON SITE OF ONSET OF
DISEASE AND THOSE ARE STUDIES
THAT ARE ONGOING.
WE PUT THIS INTO A DATA
VISUALIZER BUT IT'S CASE
SENSITIVE SO YOU HAVE TO ENTER
THE GENES IN A PARTICULAR WAY
AND IT WILL GUIDE YOU THROUGH
THAT.
YOU CAN EXPLORE THE ARRAY VIEW
FOR MOUSE OR HUMAN.
YOU CAN DO DIGITAL IN SITUS FOR
YOUR FAVORITE GENE OR LOOK AT
ONE OR MULTIPLE AT A TIME FOR
MICE AND HUMANS.
THE HUMAN DATA ARE SPARSE
BECAUSE WE HAVEN'T HAD TIME TO
POPULATE IT WITH THE NEW DATA
COMING ONLINE BUT ACTIVELY
WORKING ON THAT.
YOU CAN EXPLORE THE DATA SET
THROUGH THE COEFFICIENT VIEW FOR
DIFFERENTIALLY EXPRESSED GENES
AT A PARTICULAR PLACE AND TIME
AND PARTICULAR REGION.
OR YOU CAN LOOK AT EXPRESSION
TRAJECTORIES AND GROUPS OF GENES
THAT BEHAVE SIMILARLY WITH TIME.
SO SO FAR I TOLD YOU ABOUT HOW
WE USED THE MOUSE MODEL TO BUILD
ROBUST WORK FLOWS TO APPLY IT AT
SCALE AND HOW WE DEVELOPED THE
COMPUTATIONAL APPROACHES TO MINE
THE ST DATA AND IDENTIFY
PATTERNS AND MAYBE IDENTIFIED
SUBPOPULATIONS OF GLIAL CELLS
AND BEGIN TO APPLY THIS TO THE
MOTOR SYSTEM AND THE STUDY OF
THE CORD AND MOTOR CORTEX AND
GAVE YOU A FLAVOR FOR THIS
INTERACTIVE DATA EXPLORATION
WORK.
THE APPROACH WE'RE TAKING TO THE
COGNITIVE DEFICITS ARE SLIGHTLY
DIFFERENT.
I TOLD ALS IS A SPECTRUM AND 50%
TO 80% WILL HAVE SOME COGNITIVE
DEFICIT AND FTD.
WHAT CAN WE DO WITH PATIENTS ON
THIS CONTINUUM?
YOU HAVE PATIENTS WITH A MOTOR
PHENOTYPE THAT PRESENT WITH
VARYING LEVELS OF COGNITIVE
DEFICITS FROM NONE UP TO AND
INCLUDING FTD.
THE ISSUE IS THAT THE COGNITIVE
PHENOTYPING IS A BIT HIT OR MISS
IN NORTH AMERICAN TESTING AND
NOT EVERY CLINIC WILL DO THIS
AND DEPENDS WHERE THEY'RE SEEN
AND IF WHEN THEY DO ADMINISTER
COGNITIVE PHENOTYPING, THE TESTS
THEY USE CAN VARY WIDELY.
THERE'S ONLY FOUR CLINICS IN
NORTH AMERICA SOON TO BE FIVE, I
HOPE USING A TEST WIDELY USED IN
THE ALS COMMUNITY IN EUROPE.
SO WE'RE SO WE'RE A BIT LIMITED
MOVED TO ANOTHER SITE THE
UNIVERSITY OF EDINBURGH AND IT'S
USED IN SOME CLINICS IN THE U.S.
HERE THEY DESIGN A SCREEN FOR
PATIENTS WITH PHYSICAL
IMPAIRMENT THAT TESTS ALS
SPECIFIC AND ALS NON-SPECIFIC
COGNITIVE DOMAINS AND WE'LL
LEVERAGE PATHOLOGY TO ASSESS
THIS ALONG THE SPECTRUM AND WE
KNOW THERE'S DIFFERENT PATTERNS.
IT COMES IN MANY DIFFERENT
FLAVORS.
IT CAN ALSO BE IN DIFFERENT CELL
TYPES PREDOMINANTLY NEURONAL AND
MIXED AND GLIAL.
THE RELATION BETWEEN TDP-43
PATHOLOGY IS POORLY UNDERSTAND
AND WE HAVE THIS COHORT IN
EDINBURGH WITH MOTOR AND
COGNITIVE ASSESSMENTS EVERY SIX
MONTHS AND SEMI QUANTITATIVE
STAINING.
WE PICKED TWO REGIONS AND HAVE
CORRELATES OF EXECUTIVE AND
LANGUAGE FUNCTION AND SATISFIED
THEM ON THE EXTENT OF COGNITIVE
DYSFUNCTION ON THE SCORES.
NOW WE WANT TO ASK WHAT ARE THE
CHANGES IN CELL STATE AND
FUNCTION THAT UNDER LIE THE
DEVELOPMENT OF COGNITIVE
IMPAIRMENT IN ALS FTD AND HOW DO
AGGREGATES AFFECT SURROUNDING
CELLS?
WE WANT TO IDENTIFY FEATURES AND
PROGRAMS THAT CORRELATE WITH
THIS COGNITIVE IMPAIRMENT.
WE NEED THE CLINICAL
PATHOLOGICALLY STRATIFIED COHORT
AND NEED WAYS TO MEASURE GENE
EXPRESSION I DESCRIBED AND THEN
YOU ALSO WANT WAY TO LINK THIS
TO SPECIFIC CELL TYPES MEASURES
OF PATHOMNEMONIC INCLUSIONS AND
NEED WAYS TO DO MULTIPLE
ANTIBODY STAINS AT THE SAME TIME
ESSENTIALLY.
I'LL TELL YOU ABOUT THE ANTIBODY
STUFF FIRST.
WE DEVELOPED A PROTOCOL FOR
IMAGING.
THEY DEVELOPED THIS FOR CELL
CULTURE WHERE THEY STAINED,
IMAGES MULTIPLE ANTIBODIES FROM
THE SAME GROUPS OF CELLS AND
HERE'S AN AG GR-- AGGREGATION O
ALL THE DATA AND THEY REALIZED
THERE'S CROSS LINKING OF THE
ANTIBODY TO THE ANTIGEN WHEN YOU
DO THE IMAGING.
THEY DEVELOPED WAYS TO QUENCH
THIS PHOTO CROSS LINKING BY
DOING THESE EXPERIMENTS IN
PUFFERS THAT HAVE MILD DNA
CONDITIONS.
THAT'S WHERE THE ITERATIVE
MACHINE COMES IN.
YOU DO THE STAIN, IMAGE AND DO
THIS BEFORE YOU DO YOUR NEXT
ROUND.
WE OPTIMIZED THE PROTOCOL
FOR--SECTION.
WE HAD TO TWEAK THE ILLUSION
BUFFER A LITTLE BIT.
TWEAK THE TYPE OF SLIDES WE
SECTIONS THE--ON TO WARMED THE
SLIDE WITH THE FINGER A LITTLE
BIT TO MAKE SURE IT STICKS AND
ASSEMBLED BEFORE WE DO THE
SECTIONING IB VISIUM AND AT OPT
MISSING OF THIS PROTOCOL WHERE
WE USED A REPURPOSED
DECOMMISSIONED MACHINE MACHINE
AND INCREASED THE THROUGHPUT OF
MULTI DAY EXPERIMENTS AND SHOW
REPRODUCIBILITY AND ACCURATE
LOGGING.
WE MADE USE OF THE INTEGRATED
FLUID CAPABILITIES.
THIS WAS IN COLLABORATION WITH
THE TECHNOLOGY LAB AND AN
TALENTED ENGINEER AT THE NEW
YORK GENOME KRRT.
A Ph.D. STUDENT WORKED WITH THEM
TO DESIGN THE CUSTOM BUILT FLOAT
CELL THE GLASS SLIDE WITH HOLES
IN IT TO ALLOW TUBING AND THEY
USE THE TAPE THEY PUT ON ROCKETS
AND THERE'S A COVER GLASS THAT
BUI
BUILDS LAYERS FOR MULTIPLE
LAYERS OF TISSUE AND THEY THEN
OPTIMIZED THIS FOR THE HUMAN
SPINAL CORD WITH THE DIFFERENT
ANTIBODIES AND HERE'S THE
EXAMPLE OF THE DATA YOU CAN GET
ON THE ANTIBODIES ON THE HUMAN
ONE.
IN THE FLOW CELL WE KNOW TISSUES
STAY TABLE UP TO TWO WEEKS AND
YOU HAVE TO DO OPTIMIZATION OF
THE ANTIBODIES TO MAKE SURE THEY
CAN WORK IN DIFFERENT CYCLES.
YOU CAN DO UP TO 10 CYCLES BUT
YOU HAVE TO MAKE SURE THE
ANTIBODY GIVES YOU THE SAME KIND
OF SIGNAL IN THE FIRST AS IN THE
10th CYCLE.
THE CYCLE IN WHICH YOU PUT THEM
IS IMPORTANT.
THERE'S OPTIMIZATION INVOLVED UP
FRONT.
WHEN HAVE YOU THAT WORKED OUT
YOU GET NICE DATA.
THEN THE DESIGN OF THE
MULTI-MODEL EXPERIMENTS IS YOU
HAVE ONE SECTION OF TISSUE YOU
USE AND TAKE THE SECTION AND
ASSEMBLE THE FLOAT CELL AND CAN
DO ALL THE MULTIPLEXED
IMMUNOFLUORESCENCE AND YOU CAN
USE THIS FOR WATCHING AN
ILLUSION AND TAKING PICTURES AND
TAKE A THIRD PICTURE FOR IN SITU
BASED LOCATIONS AND GET YOUR
FAVORITE TRANSCRIPT.
THE IDEA IS TO COMBINE ALL OF
THIS AND BUILD A SUITE OF TOOLS
AND ANTIBODIES TO GIVE YOU THE
MAXIMUM AMOUNT OF INFORMATION
YOU NEED TO TELL YOU WHAT'S
GOING ON WITH DISEASE.
I HAVE A LITTLE BIT OF TIME SO I
CAN TELL YOU NEW STUFF WHAT THE
DATA FOR THE CORTEX BEGINS TO
LOOK LIKE I TOLD YOU WE HAD TO
DO THIS ANNOTATION STUFF.
SO SHE DID ANNOTATION FOR DOWN
STREAM ANALYSIS.
THAT'S HOW WE'LL EXTRACT
LAYER-SPECIFIC DIFFERENCES.
SHE STARTED BY IDENTIFYING GRAY
VERSUS WHITE MATTER BOUNDARIES
BASED ON THE PRESENCE OF
NEURONS.
SHE THEN WORKED AWAY FROM THAT
TO IDENTIFY THE LARGE PARAMETER
CELLS THAT MARK LAYER 5.
THE THEN IDENTIFIED LAYER 4 BY
THE NEURONS ADJACENT TO LAYER 5
AND YOU COULD I WHY DIDN'T YOU
USE SPECIFIC MARKERS FOR THIS?
WE WANTED AN INDEPENDENT WAY OF
ASSIGNING SPOTS TO LAYERS
BECAUSE WE WANTED TO EXTRACT
CONTRIBUTION TO DIFFERENTIAL
GENE EXPRESSION.
IF WE IDENTIFIED THE LAYERS WE
WOULD BE DOING IT A BIT
CIRCULAR.
WE WANTED TO RELY ON THE
FEATURES TO DO THIS ANNOTATION.
THE GREATEST VARIATION WERE
EXPLAINED BY THE CORTICAL LAYER
AND WANTED TO USE SYSTEM -- IT
WASN'T WHETHER A SAMPLE WAS
CONTROLLED OR ALS OR WHETHER IT
HAD OR DID NOT HAVE COGNITIVE
IMPAIRMENT.
THE LARGEST VARIATION IS COMING
FROM WHICH LAYER YOU'VE ASSIGNED
A SPOT TO.
THIS IS QUANTIFYING ALL OF THAT
AND ALL THE SAMPLES THE CONTROL
ALS WITH IMPAIRMENT AND THEY
HAVE THE SAME DISTRIBUTION OF
SPOTS ACROSS ALL THE LAYERS.
NOW WE CAN TAKE THE
TRANSCRIPTOME MEASUREMENTS AND
SAY ARE WE RECAPITULATING THE
LAYER EXPRESSION AND WE ARE.
SO THEN WE CAN DO CO-EXPRESSION
ANALYSIS LIKE WE DID FOR THE
MOUSE COHORT TO IDENTIFY MODULES
OF GENESES WHO IS EXPRESSION
COVARIES AND LOOK AT THE CELL
SPECIFIC CONTRIBUTION TO THE
EXPRESSION MODULES AND BECAUSE
OF THE LINEAR MODEL HOW WE BUILD
IT WE CAN SAY HOW MUCH IS
ASCRIBABLE TO WHETHER YOU HAVE
TDP-43 INCLUSIONS AND WE'RE
RELYING ON THE STAINING THE PATH
LAB PROVIDED.
SO MODULE 4 FOR EXAMPLE IS
UPREGULATED IN THE UPPER
CORTICAL LAYERS HERE OF ALS
PATIENTS WHEN THEY HAVE
COGNITIVE IMPAIRMENT.
HERE'S A CONTROL GROUP AND ALS
WITH MOTOR ONLY AND HERE'S ALS
WITH COGNITIVE IMPAIRMENT.
YOU CAN SEE THIS IN THE UPPER
THREE LAYERS.
WHAT IS MODULE 4 MADE UP OF?
IT'S ESSENTIALLY INFLAMMATORY
SIGNALLING.
WHICH CELL TYPES CONTRIBUTE TO
THIS?
IT'S BETWEEN MICROGLIA,
ASTROCYTES AND ENDOTHELIAL CELLS
AND YOU HAVE A SIGNAL
COORDINATED BETWEEN ASTROCYTES,
MICROGLIA AND ENDOTHELIAL CELLS
HIGHLY SPECIFICALLY CORRELATED
WHETHER A POPULATION HAS
COGNITIVE IMPAIRMENTS IN
ADDITION TO PHENOTYPES AND DON'T
AND WHEN YOU SEE HOW DOES TDP-43
RELATES TO THIS, IF YOU JUST
LOOK AT THE CONTRIBUTION YOU
DON'T PICK THIS OUT.
THIS APPEARS TO BE SOMETHING
SPECIFIC TO THE COGNITIVE
IMPAIRMENT.
AND NOT NECESSARILY WHEN DRIVEN
BY THE TDP-43 PATHOLOGY.
SO NOW WE CAN SEE -- NOW WE CAN
TAKE THE ADJACENT SECTIONS WE
BANKED AND SAY HOW VALID IS
THIS?
WHAT IF YOU REALLY WENT IN AND
LOOKED AT OTHER WAYS OF LOOKING
AT TDP-43 CONFIRMATIONS?
CAN YOU START TO TEASE THIS
APART?
DOES IT HAVE SOMETHING TO DO
WITH WHERE AND WHICH CELL TYPES
AND SO ON?
SO, SPATIAL TRANSCRIPTOMICS CAN
LOOK AT PATTERNS SHARED WITHIN
CELLULAR NEIGHBORHOODS AND
STRATIFYING SUBJECTS BASED ON
COGNITIVE AND PATHOLOGICAL
PHENOTYPING CAN REVEAL DISTINCT
SETS OF GENE EXPRESSION
PERTURBATIONS.
I'M GOING TO GIVE YOU A FLAVOR
OF HOW WE'RE APPROACHING THIS IN
NON-DISEASED CNS SAMPLES THROUGH
THE COLOMBIA UNIVERSITY
SENESCENCE TISSUE SAMPLING
CENTER ON WHICH I WORK WITH
PATHOLOGISTS.
OUR GOAL IS TO BUILD AN AN ATLAS
OF SENESCENCE ACROSS THE BRAIN
AND SPINAL CORD THROUGHOUT THE
LIFE SPAN.
THIS IS CHALLENGING BECAUSE WE
DON'T REALLY KNOW WHAT
SENESCENCE LOOKS LIKE IN THE
CONTEXT OF TISSUE IN THESE CELLS
AND THAT'S THE POINT OF THE
SENESCENCE NETWORK THE COMMON
FUND PUT TOGETHER IS TO MAP
EXACTLY WHAT SENESCENCE LOOKS
LIKE ACROSS THE LIFE SPAN AND
WE'RE LOOKING AT THE SAME REGION
OF THE CORTEX WE'RE LOOKING AT
CASES AND THE LUMBAR CORD, THE
REGION IN THE FTD CASES AND
HIPPOCAMPUS WHERE WE ARE
EXPECTING TO SEE CHANGES
ASSOCIATED WITH AGE.
WE ARE RELYING ON SAMPLES FROM
THE UNIVERSITY OF EDINBURGH
BRAIN BANK AND LOOKING AT 20
MALES AND 20 FEMALES FROM EACH
AGE BIN WE'RE GOING TO BE DOING
A COMBINATION OF VISIUM LIKE I
DESCRIBED AND RNA SYNC TO BUILD
THEM BACK ON TO SPACE AND TIME.
SO IT'S RIGHT AT 12:45.
I'D LIKE TO THANK ALL THE
PATIENTS WHO PARTICIPATED IN
THESE STUDIES.
THE PEOPLE I DID THE WORK ARE
CYLUS WHO LED THE MOUSE ST AND
JOANNA WHO WORKED ON THE
AUTOMATION OF THE 4I AND WE
PARTNERED AND CONTINUED TO HAVE
A CLOSE PARTNERSHIP WITH
PHYSICALLY SHARED SPACE AT THE
NYU AND WORKED WITH A GROUP AND
THEY'RE WORKING TO BAKE INTO
SPLOTCH THESE SINGLE NUKE
MEASUREMENTS TO GET DIFFERENTIAL
EXPRESSION IN SPACE ALONG WITH
THE CONTRIBUTION OF THE CELL
TYPES AND AT UNIVERSITY OF
EDINBURGH THE WOULD NOT HAVE
HAPPENED WITHOUT THE SAMPLES
COLIN SMITH ASSEMBLED THERE WAS
A THANK YOU SLIDE FOUR GUYS THAT
APPARENTLY IS HERE.
THANK YOU FOR YOUR ATTENTION.
>>REALLY GREAT TALK.
I WAS CURIOUS IN YOUR ALS FTD
STUDY DID YOU TRY TO STRATIFY
BASED ON ANY OTHER PATHOLOGY
LIKE FTP PIT OR A PARTICULAR
COGNITIVE PHENOTYPE?
>>NOT YET.
>>THAT'S PARTLY WHAT ALL THE
IMAGING STUFF IS MEANT TO BE
ABLE TO ACCOMMODATE LATER.
>>A BEAUTIFULLY CLEAR
PRESENTATION.
DO YOU HAVE ANY WAY OF
ESTIMATING WHETHER THE CELLS ARE
LOST
>>WE CAN DO THAT FOR MICE BUT
CAN'T REALLY DO THAT FOR HUMANS.
THAT WAS WHY WE WENT TO THIS CAN
WE USE THE CLINICAL STRATIFY TO
LOOK AT EARLY VERSUS LATE IN
DISEASE AND THAT'S THE CLOSEST
WE CAN COME TO PATIENTS WHO HAVE
DIED OF THE DISEASE.
>>THREW -- THANK YOU FOR THE
TALK AND FOR PIONEERING THE
APPROACHES WE'LL GET TO USE.
I'M WONDERING WITH THE MODULES
WITH MULTIPLE CELLULAR
COMPONENTS IN THEM IS IT BECAUSE
YOU HAVE SIGNALLING THAT ARE
COVARYING OR EXACTLY WHAT'S
GOING ON THERE?
CAN YOU TAKE A DEEPER LOOK?
>>SO, THE WAY I INTERPRET IT IS
IN THAT REGION THERE'S A
CONCERTED RESPONSE BY THREE
TYPES OF CELLS.
NOW WE CAN GO BACK TO THE DISH
AND SAY IF YOU IT'S THIS OUT HOW
ARE THEY TALKING TO ONE ANOTHER?
WHICH ONE IS DRIVING WHAT?
WHICH ONE IS PRIMARY AND THEN
WHAT ARE THE EFFECTS IT'S HAVING
ON THE NEURONS AND THAT'S PARTLY
WHY WE HAVE SO MUCH FUN WORKING
WITH MICHAEL.
>>GREAT TALK.
YOU TALKED BY STRATIFYING BY
DIFFERENT GENE EXPRESSION
DIFFERENCES.
HAVE YOU GONE THE OTHER
DIRECTION SO LOOKED AT HOW
VARIOUS PATTERNS OF EXPRESSION
MIGHT ASSOCIATE WITH NOVEL
CLUSTERING OF CLINICAL
PHENOTYPES?
>>NOT YET BUT WHEN WE BUILD
THIS OUT MORE THAT'S THE KIND OF
STUFF WE WANT TO BE ABLE TO DO.
I TALKED ABOUT THE MOTOR SYSTEM
AND DLPC IN TWO SEPARATE STUDIES
BUT REALLY WHAT WE'RE DOING IS
USING THE SAME PATIENTS FROM
WHOM WE HAVE ALL THE OTHER DATA
TYPES AND STUDYING EACH REGIONS
FROM THE SAME PATIENTS TO START
TO ANSWER QUESTIONS LIKE THAT.
SO WHEN YOU GROUP ALS VERSUS NO
ALS DO YOU SEE ANYTHING THAT
CORRELATES IN THIS REGION VERSUS
THAT REGION WITH THIS A SPECIFIC
TYPE BUT TO GET THE NUMBERS TO
BE ABLE TO DO THAT RIGHT YOU
NEED TO GET TO AT LEAST 100
PATIENTS AND YOU DON'T WANT TO
MAKE YOUR GROUPS TOO SMALL
EITHER OTHERWISE YOU LOSE THE
POWER.
WE'RE ABOUT A THIRD OF THE WAY
TO WHERE I WANT US TO BE TO BE
ABLE TO ANSWER QUESTIONS LIKE
THAT.
>>HAVE YOU HAVE PLANS TO EXPAND
THE DISEASE SETS YOU INCLUDE IN
THIS BECAUSE THE GENE LIST IN
THE MODULES ARE REMINISCENT OF
OTHER DISEASES.
THERE'S SIMILAR FLAVORS OF
MICROYES -- MICROGLIA AND
ASTROCYTES THAT SHOW UP.
>>WE DO A LOT OF THAT THROUGH
COLLABORATION.
THERE'S AGE-RELATED COGNITIVE
DECLINE AND MCI ASSOCIATED WITH
AD PROGRESSION WE'RE LOOKING
INTO IN COLLABORATION WITH OTHER
GROUPS AT COLUMBIA.
THERE'S EFFORTS TO BANK ISSUES
THROUGH THE NEW IMMUNOLOGY GROUP
AT COLUMBIA AND IF YOU'RE
INTERESTED IN DOING THAT I'M
HAPPY TO TALK THROUGH HOW THAT
CAN WORK.
WE'LL BE HAPPY TO SHARE AND ANY
ALL PROTOCOLS THAT YOU NEED.
>>I'M CURIOUS TO GET YOUR
THOUGHTS ON USING DIFFERENT
REGIONS OF TISSUE FROM HUMAN
SAMPLES AND LEARNING PATHWAYS
THAT MAY BE IMPORTANT EARLY IN
THE DISEASE PROGRESSION AND TO
WHAT EXTENT YOU THINK ANIMAL
MODELS ARE USEFUL FOR THAT.
>>IT DEPENDS ON WHAT WE'RE
MODELLING.
FOR THE MOTOR SYSTEM WE DAN
DAN -- -- WE CAN -- FROM THE SOD
MODEL IT'S A VERY AGGRESSIVE
MODEL AND ANYTHING THAT CAN GO
WRONG DOES GO WRONG AND THE TIME
COURSE IS VERY VERY FAST.
THE FIRST MODEL, FOR EXAMPLE, IS
VERY DIFFERENT AND MUCH MORE
NUANCED.
WE DON'T KNOW WHICH PATHOLOGIES
CONVERGE WHEN OR IF THEY DO AT
ALL.
THEY MUST AT SOME POINT BECAUSE
THE SAME TYPES OF CELLS DIE.
THAT'S WHERE THE ANIMAL MODELS
BECOME MORE USEFUL AND THERE'S
AN ASO THAT REVERSE THE CLINICAL
PRESENTATION AND MODEL AND ONE
STUDENT IN THE LAB IS WORKING ON
THE TIME AND DOES IT CONVERGE
WITH ANYTHING IN THE SOD?
WHAT IS REVERSED BY THE ASO?
DID THEY LEAD TO THE FUNCTION IN
THE FIRST PLACE AND WHEN YOU GET
TO THAT HOW MANY ARE SEEN IN ALS
PATIENTS AND HOW MANY OF THOSE
SERVE TO SEPARATE PATIENTS INTO
DIFFERENT TYPES OF PROGRESSION?
SO THOSE ARE THE KINDS OF
APPROACHES THAT WE CAN TAKE WITH
THE ANIMAL MODELS.
>>I HAVE A QUESTION AS WELL.
I THOUGHT IT WAS COOL HOW
[INDISCERNIBLE] THIS IS
OBVIOUSLY A VERY GRAPHICALLY
ADVANCED TOOL TO MAKE SENSE WITH
DATA WITH A LOT OF MISSING
VALUES AND A LOT OF NOISE.
WHAT DO YOU THINK ARE BIG
QUESTIONS THE SPATIAL
TRANSCRIPTOMICS WILL BEGIN TO
RESOLVE IN OUR GENERATION WE
CAN'T CURRENTLY GET AT WITH
HIGHER DEPTH IN SEQ.
>>WE CAN LOOK AT PATHOLOGICAL
AGGREGATES OR OTHER SIGNALLING
PATHWAYS THAT ARE CHANGED AND
ALLOWS US TO ASK MORE NUANCED
QUESTIONS SINGLE NUC CAN GIVE
YOU A LOT OF DEPTH BUT WHEN YOU
MARRY IT WITH SPATIAL METHODS
CAN TAKE YOU FURTHER THAN EITHER
CAN GO BY THEMSELVES AND THAT'S
WHAT WE'RE HOPING TO DO.
AND NO ONE LAB CAN DO ALL THIS
BY THEMSELVES.
THAT'S THE OTHER LESSON WE
LEARNED SIT DOESN'T MAKE SENSE
TO HAVE SILOS BASED ON WHICH
DISEASE AND METHOD.
YOU NEED TO TALK TO PEOPLE AND
BE OPEN TO SHARING AND BORROWING
INFORMATION AND GETTING BY WITH
HELP FROM YOUR FRIENDS.
>>IF YOU HAD A CRYSTAL BALL DO
YOU THINK WE'LL ALL BE DOING
SPATIAL TRANSCRIPT OMICS OR
STILL PARALLEL TECHNOLOGIES?
>>I THINK WE'LL LEARN MORE ON
WHAT DRIVES THE VARIOUS
DISEASES.
THESE ARE VERY EXPENSIVE TOOLS.
EVERYBODY DOESN'T HAVE TO DO ALL
OF THEM.
WE'LL HAVE LEARNED ENOUGH ENOUGH
ABOUT THE COMMONALITIES AND
DISTINCTIONS AND HOW MUCH IS
EXPLAINED BY COMPARTMENTS AND
BARRIERS WHAT DETERMINES
SELECTIVE VULNERABILITY WHEN YOU
HAVE SO MANY PATHWAYS ALL IN
COMMON.
THAT'S WHERE THE CELL-BASED
MODELS WILL GOING TO BE VERY
INFORMATIVE.
SO IT'S GOING TO BE REALLY
EXCITING AND ALL THE IMAGING
METHODS AND THE M.L. BASED
APPROACHES TO DO THE
CLASSIFICATION AND LOOKING AT
HOW MUCH MORPHOLOGY CAN EXPLAIN
AND HOW MUCH YOU CAN EXTRACT
FROM MORPHOLOGICAL INFORMATION
WILL BE MUCH FURTHER ALONG.
YOU'LL HAVE MORE TARGETED TOOLS,
I THINK, TO BE ABLE TO PARS OUT
SOME OF THIS IN A MUCH FINER
GRAIN WAY.
>>ANY QUESTIONS?
THANK YOU, HEMALI.