>>WELCOME TO THE WORKSHOP
STANFORD UNIVERSITY SCHOOL OF
MEDICINE AND POSTGRADUATE
TRAINING IN PEDIATRICS, MEDICAL
GENETICS AND NEONATAL MEDICINE
AT BOSTON CHILDREN'S HOSPITAL
AND HARVARD MEDICAL SCHOOL.
HER FOCUS IS ON PRENATAL
GENOMICS WITH DNA SCREENING AND
DIAGNOSIS TO DEVELOP NEW
THERAPIES FOR GENETIC DISORDERS
TO BE ADMINISTERED PRENATALLY
AND A PAST PRESIDENT OF THE
PERINATAL RESEARCH SOCIETY AND
SOCIETY FOR PRENATAL DIAGNOSIS.
RICHARD HODES HAS DIRECT THE
NATIONAL INSTITUTE ON AGING OR
THE NIA SINCE 1993.
HIS HIS STEWARDSHIP THE BUDGET
HAS GROWN TO $4.2 BILLION
REFLECTING INCREASED PUBLIC
INTEREST IN AGING AS AMERICA AND
THE WORLD GROW OLDER.
DR. HODES HAS DEVOTED HIS TENURE
TO THE DEVELOPMENT OF A STRONG
AND DIVERSE RESEARCH PROGRAM
FOCUSSING ON THE GENETICS AND
BIOLOGY OF AGING, BASIC AND
CLINICAL STUDIES AIMED AT
REDUCING DISEASE AND ALZHEIMER'S
AND RELATED DEMENTIA AND
AGE-RELATED COGNITIVE CHANGE AND
THE BEHAVIORAL AND SOCIAL
ASPECTS OF AGING.
HE'S A GRADUATE OF YALE
UNIVERSITY AND RECEIVED HIS M.D.
FROM HARVARD MEDICAL SCHOOL AND
COMPLETED TRAINING IN INTERNAL
MEDICINE AT MASSACHUSETTS
GENERAL HOSPITAL AND CONTRIBUTED
TO THE FIELD OF IMMUNOLOGY
AUTHORED OVER THAN 250 RESEARCH
PAPERS.
I TURN THE PROGRAM OVER TO
DR. BIANCHI.
>> THANK YOU SO MUCH, DR. PRICE.
I'D LIKE TO WELCOME EVERYONE TO
THE BRAIN ACROSS THE LIFE SPAN
VIRTUAL WORKSHOP AND INCLUDES
THE SPEAKERS AND PANELISTS
JOINING VIA ZOOM AND AUDIENCE
MEMBERS TUNING IN VIA THE NIH
VIDEOCAST AND I BELIEVE IT WILL
BE ARCHIVED AS WELL.
I'M DR. DIANA BIANCHI AND WE'LL
REFER TO NICHD.
THIS HAS COME TOGETHER BETWEEN A
STRONG COLLABORATION THE NIH AND
BILL AND MELINDA GATES
FOUNDATION AND BUILT ON THE
COMMON GOALS OF IMPROVING HEALTH
AND DEVELOPING EFFECTIVE
ASSESSMENTS AND INTERVENTIONS --
APPROACHES FOR A VARIETY OF
DISEASES IN DIVERSE CULTURAL
CONTEXTS.
SPECIFICALLY NICHD IS ENGAGED
WITH SEVERAL PROJECTS AS PART OF
THE MATERNAL NEONATAL AND CHILD
HEALTH WORKING GROUP ALSO KNOWN
AS THE MUNCHIES.
THE WORKING GROUP IS FOCUSSED ON
PREGNANCY OUTCOMES AND NUTRITION
AND IMPORTANTLY FOR THIS
WORKSHOP NEURAL DEVELOPMENT.
AS A METRIC OF HEALTH AND WELL
BEING THE NEURAL COGNITIVE
DEVELOPMENT IN DIVERSE AND
GLOBAL SETTINGS IS A SHARED
INTEREST BETWEEN NICHD AND THE
GATES FOUNDATION.
NICHD APPRECIATES THE IMPORTANCE
OF TAKING A LIFE SPAN APPROACH
AND LIFE SPAN PERSPECTIVE ON
HEALTH.
IN FACT, AT NICHD'S 2020
STRATEGIC PLAN THERE WAS AN
ASPIRATIONAL GOAL THAT SAID WE
NEED TO IDENTIFY BIOMARKERS OF
ATYPICAL NEURAL DEVELOPMENT TO
ESTABLISH THE LIKELIHOOD OF
NEURO DEGENERATIVE DISORDERS
LATER IN LIFE.
BY IDENTIFYING SENSITIVE PERIODS
WE CAN BETTER UNDERSTAND ORIGINS
OF DISEASE AND CREATE SPECIFIC
INTERVENTIONS TAILORED TO THE
DISRUPTIVE PROCESSES.
NICHD IS AMONG SEVERAL NIH
INSTITUTES AND CENTER SUPPORT
THE ADOLESCENT BRAIN, COGNITIVE
DEVELOPMENT STUDY OR ABCD, THE
LARGEST LONG-TERM STUDY OF BRAIN
DEVELOPMENT IN CHILD HEALTH IN
THE UNITED STATES.
WE'RE ALSO PROUD TO CO-SUPPORT
THE UPCOMING HEALTHY BRAIN AND
CHILD DEVELOPMENT OR HECD STUDY
WHICH WILL RECRUIT A ROBUST
COHORT OF PREGNANT WOMEN FROM
ACROSS THE COUNTRY AND FOLLOW
THE BRAIN, COGNITIVE AND
BEHAVIORAL DEVELOPMENT OF THEIR
CHILDREN THROUGH THE FIRST FEW
YEARS OF LIFE.
STUDIES SUGGEST AS ABCD PROVIDE
A PIVOTAL LOOK AT DIFFERENCES IN
DEVELOPMENT HOWEVER, WHEN IT
COMES TO THE BRAIN, WE'RE
CURRENTLY LIMITED BY THE
AVAILABLE TOOLS TO MEASURE THE
BRAIN OVER LONGER PERIOD OF
TIME.
THUS, WE NEED BETTER APPROACHES
TO LINK DISCREET NEURO DATA TO
UNDERSTAND THE LINK BETWEEN
DIFFERENT LIFE STAGES.
THEREFORE WE'RE PLEASED TO
SUPPORT THE WORK SHOP AS A FIRST
STEP IN AT THE STATE OF THE ART
WAY TO LOOK AT THE BRAIN AND
FOSTER DISCUSSIONS FOR BRAIN
MEASUREMENT ACROSS THE LIFE
SPAN.
HOWEVER, WE DON'T HAVE TO WAIT
FOR FUTURE FUNDING
OPPORTUNITIES.
NICHD ALREADY HAS ACTIVE FUNDING
OPPORTUNITIES RELATIVE TO THE
WORKSHOP AND WE INVITE ALL WHO
ARE INTERESTED TO EXPLORE THE
NIH GUIDE TO IDENTIFY THEM.
THIS WORKSHOP HAS AN EXCITING
AGENDA INCLUDING RESEARCHERS WHO
HAVE DIVERSE EXPERIENCE IN THIS
AREA WOULD ARE WORKING ON
DIFFERENT TIME POINTS WITHIN THE
LIFE SPAN AT DIFFERENT LEVELS OF
RESOLUTION IN BOTH HUMANS AND
NON-HUMAN ANIMAL MODELS I LOOK
FORWARD TO A PRODUCTIVE MEETING
IN WHICH WE CAN EXPLORE EXISTING
AND EMERGING APPROACHES TO
ASSESS CHANGES IN BRAIN CELLULAR
IDENTITY, CONNECTIVITY AND
BETTER UNDERSTAND THEIR
IMPLICATION FOR HEALTH AND
WELLNESS THROUGHOUT LIFE.
AGAIN, I'D LIKE TO THANK THE
SPEAKERS, PANELISTS AND EVERYONE
WHO CONTRIBUTED TO THE PLANNING
OF THIS MEETING AND I WILL NOW
TURN THE PROGRAM OVER TO MY GOOD
COLLEAGUE DR. RICHARD HODES
DIRECTOR OF THE NATIONAL
INSTITUTE OF AGING.
>> AND I JOIN YOU AND IN
WELCOMING THOSE TO THE WORKSHOP.
NICHD AND NIH HAVE BEEN LONG
TERM PARTNERS WITH LIFE SPAN
THAT APPLIES TO THIS WORKSHOP ON
MEASURING BRAIN AND BRAIN
CHANGES ACROSS THE LIFE SPAN.
IT'S IMPORTANT FOR US TO
INCREASE THE MISSION OF THE SPAN
OF LONG AND PRODUCTIVE LIFE AND
UNDERSTAND THE FACTORS THAT
CONTRIBUTE FROM NEOIN A LOTT --
NEONATAL AND LIFE COURSE EVENTS
AND LOOK AT THE LEVEL OF CLINIC
RESEARCH AND LONGITUDINAL
STUDIES NOW SPANNING THE BIRTH
TO CHILDHOOD THROUGH OLD AGE AND
AN INCREASING EMPHASIS ON THE
COGNITIVE STUDIES OF CHANGES OF
BRAIN AND IMPROVE METHODOLOGIES
AND TOOLS FOR THAT TIME.
AND LOOKING AT THE SPECIAL
EVENTS EARLY IN LIFE TO
PREDISPOSE AND LOOK AT SPECIAL
POPULATIONS INVOLVED AND
DIVERSITY AND SOME SPECIAL
POPULATIONS SUCH AS THOSE
AFFECTED WITH DOWNS SYNDROME
WHICH ARE SO INFORMATIVE AND IN
THEIR OWN RIGHT IN NEED OF
STUDIES ACROSS THE LIFE SPAN AS
WE HAVE PEOPLE LIVING TO LONGER
LIVED WITH INCREASED RISK OF
NEURO DEGENERATIVE DISEASES AND
WE WORK TOGETHER WITH THE BRAIN
INITIATIVE TO LOOK AT EXTENDING
THE ATLAS OF NEURONAL AND GLIAL
CELLS FOR THE LIFE SPAN
PERSPECTIVE AND FOR THE
NEUROSCIENCE BLUEPRINT AT NIH
AND NICHD PARTICIPATING WITH 15
INSTITUTES AND CENTERS TAKE THE
HUMAN CONNECTOME TO LIFE SPAN
CONNECTOME AND STUDYING FROM
CHILDHOOD TO ADULTHOOD AND OLDER
YEARS FOR CHANGES THAT MARK
TRANSITION AND STAGES FROM
HEALTHY TO PATHOLOGIC CHANGE AND
IN DOING SO TO IDENTIFY
INTERVENTIONS TO IMPROVE THE
QUALITY OF LIFE AND BRAIN LIFE
THROUGH THAT TIME.
WITH THIS BACKGROUND I THANK YOU
ALL AND LOOK FORWARD TO THE
EXCITEMENT YOU BRING WITH YOUR
INGENUITY AND EXPERTISE AND LOOK
FORWARD TO THE NEXT FEW DAYS IN
WHICH TO FIND BETTER MEANS OF
TRACKING THE FUNCTION, STRUCTURE
OF BRAIN CHANGES ACROSS AGE AND
LIFE.
THANKS SO MUCH.
I TURN IT BACK TO AMANDA.
>> THANK YOU TO BOTH OF YOU FOR
YOUR WELCOMING REMARKS THIS
MORNING.
>> I'LL GIVE A QUICK OVERVIEW OF
THE WORKSHOP STRUCTURE AND HOW
TO GET THE MOST OUT OF THE
VIRTUAL EVENT TODAY.
FIRST, I'D LIKE TO REMIND
EVERYONE YOU CAN FIND THE AGENDA
AND FULL BIOS FOR ALL THE
SPEAKERS AND PANELISTS ON THE
MEETING WEBSITE AND THE LINK IS
ON THIS SLIDE FOR YOU.
THE OVERALL GOAL WILL BE MEASURE
THE BRAIN OVER TIME AND IDENTIFY
FUTURE DIRECTIONS FOR IMPROVING
OUR ABILITY TO MEASURE THE BRAIN
ACROSS THE LIFE SPAN.
THIS WORKSHOP IS ORGANIZED INTO
THREE SESSIONS OVER TWO DAYS
COVERING THE LATEST AND GREATEST
IN MEASURING BRAIN CELLULAR I'D
IDENTITY AND CONNECTIVITY AND
EACH DAY WILL INCLUDE A PANEL OF
SPECIFIC TOPIC OF INTEREST AND
WE'LL HEAR FROM EXPERTS TO
DISCUSS CONNECTING NEURAL
DEVELOPMENT AND NEURAL
DEGENERATION AND TOMORROW WELL
BE TREATED TO A DISCUSSION ON
SCALING TECHNOLOGIES FROM THE
INDIVIDUAL POPULATION LEVELS
PARTICULARLY IN LOW AND MIDDLE
INCOME SETTINGS.
AND THANK YOU TO DR. SONYA LEED
AS THE CO-LEAD ON THE WORKSHOP
AND TO THE BILL AND MELINDA
FOUNDATION AND WE WANT TO THANK
THE SPEAKERS AND PANELISTS FOR
BEING SO COLLABORATIVE AND FOR
YOUR TIME AND EXPERTISE.
AND THANK YOU FOR THE AUDIENCE
FOR YOUR PARTICIPATION SO WE
HAVE A GREAT DISCUSSION.
NOW I'LL TURN IT OVER TO
DR. HARRY BURGESS.
>> IT'S MY GREAT PLEASURE TO
INTRODUCE DR. OLIVER HOBERT AND
INVESTIGATOR OF THE HOWARD
HUGHES MEDICAL INSTITUTE.
THE BRAIN HAS MILLIONS OF
NEURONS THAT PERFORM DISTINCT
FUNCTIONS.
TAKING ADVANTAGE OF THE
INFORMATION SYSTEM HIS
LABORATORY PROBED MOLECULAR
PATHWAY TO HOW EACH NEURON HAS
UNIQUE IDENTIFIES AND CREATING
THE EXTRAORDINARY DIVERSITY OF
NEURONAL FORM AND FUNCTION SEEN
IN HUMANS WE THANK HIM FOR
ACTING AS CHAIR OF THIS SESSION.
>> THANK YOU SEARCH VERY MUCH
FOR THE INTRODUCTION.
I WANT TO START WITH A QUOTE
FROM SIDNEY BRENNER WHO IS ONCE
SUPPOSED TO HAVE SAID, PROGRESS
IN SCIENCE DEPENDS ON NEW
TECHNIQUES AND DISCOVERIES AND
NEW IDEAS PROBABLY IN THAT
ORDER.
AND I THINK NOWHERE MORE IS THIS
TRUE THAN IN THE FIELD THAT
WE'RE DISCUSSING MEANING THE
FIELD OF DEFINING CELL TYPES IN
THE BRAIN AND AND AWAY HAVE SEEN
OVER THE 150 YEARS OR SO JUMPS
IN TECHNOLOGY AND INTRODUCTION
OF ELECTROPHYSIOLOGY THAT HELPED
DEFINE MORE CELL TYPES FROM
DIFFERENT PHENOTYPIC CRITERIA.
THEN WITH THE INVENT OF THE
MOLECULAR AGE WE'VE SEEN NOVEL
WAYS TO MEASURE CELL TYPE
DIVERSITY BUT I THINK IT'S FAIR
TO STAY IN THE LAST FIVE TO 10
YEARS THERE'S BEEN ENORMOUS
STRIDES BASED ON SINGLE-CELL
TECHNOLOGY HELPING TO DEFINE
CELL TYPES IN MORE COMPLEX
ANNIVERSARY SYSTEMS IN THE
MAMMALIAN AND VERTEBRATE BRAIN
AND WE'LL HEAR A LOT ABOUT THIS
TODAY.
WE'LL HEAR FROM FROM AN
IMPORTANT FIGURE IN THE FIELD ED
LEIN AND HEAR FROM SOMEWHAT MORE
JUNIOR MEMBERS BRINGING IN NEW
TECHNOLOGY ANGLES THAT ARE VERY
EXCITING AND HELP US GO BEYOND
CELL TYPE DEFINITION ON THE
LEVEL OF IDENTIFY FEATURES OF
MATURE CELLS AND LOOKING AT THE
LINEAGE OF INDIVIDUAL CELLS.
IT'S VERY EXCITING.
THERE'S VERY MANY INTERESTING
TECHNOLOGY.
IN FACT OUR FIRST SPEAKER BUSHRA
RAJ HAS NOVEL APPROACHES AS A
POST-DOC IN ALEX SHEERS' LAB.
BUSHRA IS NOW AN ASSISTANT
PROFESSOR AT U-PENN IN THE
DEPARTMENT OF CELL AND
DEVELOPMENT BIOLOGY.
SHE HAS GOTTEN HER Ph.D. AT THE
UNIVERSITY OF TORONTO AT A THEN
CLOSED LAB AND WAS LUCKY ENOUGH
TO NOT TAKE UP AN OFFER AT MY
LAB AND USED CRISPR CAS 9
TECHNOLOGY TO LOOK AT CELL
LINEAGE IN THE ZEBRAFISH BRAIN
WHICH OFFERS UNIQUE
OPPORTUNITIES TO VISUALIZE AND
CATALOG CELLULAR ACTIVITY.
I'LL NOW TURN IT OVER TO BUSHRA
AND I AM MUCH LOOKING FORWARD TO
HEAR HER TALK.
>> THANK YOU FOR THE GENEROUS
INTRODUCTION AND WONDERED IF YOU
REMEMBERED MY APPLICATION TO
YOUR LAB AND I'M HERE TO SHARE
THE INSIGHTS OF MY WORK WITH
ZEBRAFISH AND THE VERTEBRATE
BRAIN DEVELOPMENT.
SO THE TITLE OF MY TALK IS
MOLECULAR ROAD MAPS OF BRAIN
DEVELOPMENT LINEAGE AND
SIGNALLING AND I'D LIKE TO START
OFF BY GIVING YOU AN OVERVIEW OF
THE GENERAL TYPES OF QUESTIONS
THAT ME AS WELL AS OTHER PEOPLE
IN THE FIELD ARE INTERESTED IN.
WHAT ARE WE TRYING TO BUILD AS
WE TRY TO UNDERSTAND BRAIN
DEVELOPMENT?
.
AND THAT WOULD INCLUDE INCLUDE
IDENTIFYING HOW MANY DISCREET
CELL TYPES ARE IN THE BRAIN AND
IDENTIFYING THE GENE EXPRESSION
PROGRAMS IMPORTANT FOR THEIR
DEVELOPMENT, ACTIVITY,
INTERACTION.
IDENTIFYING THE ORIGINS AND
PLACE OF THE BRAIN CELLS.
WHERE DO THEY COME FROM, WHAT
ARE THEIR RELATED ANCESTORS?
AND HOW DO SIGNALLING PATHWAYS
REGULATE NEUROGENESIS AND
LOOKING AT CELL AUTONOMOUS AND
NON-CELL AUTONOMOUS PROGRAMS
THAT CAN IMPACT BRAIN
DEVELOPMENT.
SO THERE'S MULT WALL WAYS OF
ADDRESSING THESE QUESTIONS.
FOR THE PURPOSE OF THIS TALK
I'LL INTRODUCE FOUR METHODS THAT
WE USED COMMONLY IN THE FIELD,
ONE IS IN ORDER TO CATEGORIZE
CELL TYPES WE HAVE
TRANSCRIPTOMICS AND IF WE EXTEND
INTO A FORM OF TIME COURSE WE
CAN DO PROFILING OVER THE LIFE
TIME OR OVER CRITICAL PERIODS OF
DEVELOPMENT AND HOW CELLS CHANGE
OVER TIME AND COMPLEXITY AND
LOOK AT THEIR HISTORY AND
UNDERSTANDING WHERE THEY COME
FROM WE CAN START GENERATING
HIGH DENSITY LINEAGE TREES THAT
MERGE THE CELL IDENTIFY WITH
THEIR CELLULAR ANCESTRY TO GIVE
US A RECORD OF WHERE IN THE
EMBRYO THEY CAME FROM AND WHICH
OTHER CELL TYPES THEY'RE RELATED
TO.
LASTLY I'D LIKE TO INTRODUCE THE
CONCEPT OF ATLASES IN THE
CONTEXT OF A DEVELOPING BRAIN
THOUGH THIS CONCEPT CAN BE
EXTENDED TO ANY ORGAN OF
INTEREST.
I WANT TO TAKE 10, 20 SECONDS
FOR INTRODUCTION OF RNA
SEQUENCING AND WE START WITH
DISASSOCIATED CELLS INTEREST A
TISSUE AND ALLOW FOR THE
ENCAPSULATION OF INDIVIDUAL
CELLS MARK BY UNIQUE BAR CODES
AND THEY CAN THEN BE CONVERTED
INTO LIBRARIES WHICH CAN BE
SEQUENCED AT HIGH THROUGHPUT TO
GIVE AN OVERVIEW OF THE
TRANSCRIPTIONAL LANDSCAPE OF
INDIVIDUAL CELLS AT THE LEVEL OF
TENS TO HUNDREDS OF THOUSANDS OF
CELLS AT A TYPE.
THE FISH GIVES EASY ACCESS TO
THE TISSUES.
AND HAVE VARIABLES AVAILABLE FOR
THE FISH AND HIGHLY TRANSPARENT
IN THE EARLY STAGES OF
EXPERIMENT CONDUCIVE TO IMAGING.
WITH RESPECT TO BRAIN
DEVELOPMENT THE FISH IS
DIFFERENT FROM THE MAMMALIAN
SYSTEM AS IT UNDER GOES
NEUROGENESIS.
THROUGHOUT THE LIFE TIME OF THE
FISH THERE'S POOLS OF CELLS THAT
UNDER GO DIFFERENTIATION AND
EXPANSION AND GIVE RISE TO NEW
NEURONS.
IN ADDITION THE FISH UNDER GOES
REGENERATION QUITE EFFICIENTLY
INCLUDING IN THE BRAIN TISSUE
AND THIS PROVIDES GREAT WAYS TO
ANSWER THE QUESTION.
AND FOR ONE OF MY STUDIES I DID
A PROFILING OF BRAIN DEVELOPMENT
STARTING FROM EARLY STAGE WHEN
THE BRAIN IS JUST ABOUT STARTING
OFF TO A STRUCTURE FROM THE IS
IT HOURS POST FERTILIZATION AND
EXTENDING TO TWO WEEKS POST
FERTILIZATION AT 15 DAYS AND SO
THE FISH HAS UNDER GONE A LOT OF
CHANGE AND IS SELF-SUFFICIENT
AND DISPLAYS DIFFERENT KINDS OF
COMPLEX BEHAVIORS.
THIS REPRESENTS A RANGE OF TIME
POINTS AND HOPEFULLY WILL GIVE
US AN IDEA OF THE INCREASE OF
COMPLEX AT THE FISH'S
DEVELOPMENT.
SO USING SINGLE CELL RNA
SEQUENCING WE LOOKED ACROSS 12
STAGES OF DEVELOPMENT AND THE
FIRST TIME POINT WE IDENTIFIED
20 MAJOR CELL TYPES THAT
CORRESPOND TO NEURO TISSUES AND
IDENTIFIED 100 CELL TYPES
ROUGHLY AND OVERALL IN THE DATA
SET WE ANNOTATED ABOUT 800
CLUSTERS AND ALL THIS IS
AVAILABLE AT A COMMUNITY
DATABASE THAT CAN BE EXPLORED
ESPECIALLY IF YOU'RE INTERESTED
IN CROSS-SPECIES ANALYSIS
LOOKING AT DEVELOPMENT FROM FISH
ALL THE WAY UP TO MAMMALIAN
SYSTEMS AND LOOKING AT THE
SIMILARITIES AND DIFFERENCES.
THIS COULD BE A GREAT RESOURCE
TO LOOK INTO THAT.
AND WE HAVE TIME ANALYSIS DONE
BY RECONSTRUCTING THE GENE
EXPRESSION TRAJECTORY THE CELLS
HAVE THE VARIOUS CELL STATES
HAVE UNDER GONE FROM EARLY TIME
POINTS TO LATER STAGES OF
DEVELOPMENT.
MOST OF THIS IS DONE BY USING
SINGLE CELL RNA SEQUENCE SETS
AND CONNECTING CELLS AS A
MEASURE OF THEIR MATURITY LEVEL,
IF YOU WILL, BASED ON THEIR GENE
EXPRESSION PROFILE.
THIS ALLOWS US TO LOOK AT EARLY
DEVELOPMENT AND STARTING WITH
FOUNDER CELLS AND AS IT CHANGES
FOR LATER AND LATER STAGES OF
DEVELOPMENT AND ALLOWS US TO
CREATE THE SPECIFICATION
TRAJECTORIES OR TREES THAT HAVE
BRANCH LEAD OFF TO DIFFERENT
TISSUE TYPES AND CELL TYPES
WITHIN A PARTICULAR TISSUE.
CELL LINEAGES MEASURE A SLIGHTLY
DIFFERENT ASPECT OF DEVELOPMENT
AND IN THIS CASE WE'RE ACTUALLY
LOOKING AT THE CELL DIVISION
HISTORY.
LOOKING AT WHICH CELLS DIVIDED
FROM WHICH CELL AND HOW THOSE
PATTERNS WERE PASSED ON TO
FUTURE GENERATIONS.
THIS IS MAYBE WHAT'S KNOWN AS
THE CLASSIC LINEAGE TREE AND C.
ELA
ELEGANS IS WHERE WE LOOK TO
EXTEND TO COMPLEX ANIMALS AND
VERTEBRA
VERTEBRATE.
WE THOUGHT THERE WAS A GREAT
OPPORTUNITY TO DEVELOP A
TECHNIQUE TO ALLOW US TO SCALE
LINEAGE TRACING IN A WAY THAT
WOULD BE USEFUL FOR LOOKING AT
HIGHER VERTEBRATES OR IN THE
CASE OF ANIMALS, DISEASE
CONDITIONS OR CANCER PROGRESSION
AND THIS SEEMS LIKE A GREAT
OPPORTUNITY TO IMPLEMENT CRISPR
CAS 9 BAR CODING TO LOOK AT
LINEAGE HISTORY OF CELLS.
WE CREATED THIS METHOD WHICH IS
A WAY OF DYNAMICALLY BAR CODING
CELL LINEAGES DURING THE
DEVELOPMENT OF AN ANIMAL.
WE START WITH THE SEQUENCE AND
IT'S COMPLETELY SYNTHETIC AND WE
CAN START INTRODUCING MUTATIONS
IN THE BAR CODE AND THAT IS DONE
BY ADDING CAS9 PROTEIN AND GUIDE
THE TARGET TO VARIOUS REGIONS ON
THE BAR CODE AND EACH TIME
THERE'S A MUTATION AND THE CELL
DIVIDES THE MUTATION WILL BE
PASSED ON TO DAUGHTER CELLS
WHERE ADDITIONAL MUTATIONS CAN
ACCUMULATE AND PASSED ON TO
GRANDDAUGHTER CELLS WHERE MORE
MUTATIONS CAN ACCUMULATE.
SO ON AND SO FORTH OVER SEVERAL
ROUNDS OF CELL DIVISIONS UNTIL
EVENTUALLY THE BAR CODE BECOMES
FULLY SATURATED WITH MUTATIONS
OR THE RE-AGENTS GET DILUTED
OVER THE COURSE OF DEVELOPMENT.
THESE EDITS ARE CUMULATIVE AND
COMBINATORIAL AND PERMANENT.
THEY'RE MUTATED WITHIN THE
GENOME WHERE THE BAR CODE HAS
BEEN INSERTED SO WE CAN THEN
EXTRACT THE BAR CODES AT A LATER
TIME POINT USING SEQUENCING.
STARTED OFF WITH A CRISPR EDITED
ANIMAL.
IN THIS CASE WE WERE USING FISH
ABOUT THREE WEEKS OLD ISOLATED
THE BRAIN FROM CRISPR EDITED
ANIMAL AND PASSED THEM THROUGH
THE SINGLE CELL PLATFORM AND
LOOKED AT THE LINEAGE BAR CODES
THEMSELVES TO HELP UNDERSTAND
WHAT THE CELL DIVISION HISTORY
OF THESE CELL TYPES WERE LIKE.
AND WE LOOKED AT FUTURE LEVELS
OF COMPLEXITY FOR FUTURE
GENERATION.
I'LL QUICKLY ZOOM INTO ONE OF
THESE TREES.
I'M SHOWING THE TREES EXTENDS
OUT AND EACH LITTLE NODE
REPRESENTS A PERIOD OF CELL
DIVISION HISTORIES.
ARE REPRESENTED AS DELETIONS OR
INSERTIONS AND THE RED BAR
REPRESENT THE SIZE OF THIS
DELETION AND WE CAN ORDER THESE
BAR CODES AND GENERATE A LINEAGE
TREE BY LOOKING AT THE PATTERNS
AND FREQUENCY OF MUTATION AND
THOSE FREQUENT THAT OCCUR IN A
LOT OF CELLS LIKELY ERODE EARLY
ON IN DEVELOPMENT AND WOULD
ANCHOR ONE OF THE EARLY NODES ON
THE TREE AND MUTATIONS MORE RARE
WOULD REPRESENT LATER AND LATER
NODE OF THE TREE.
AND WE CAN DETERMINE GENERALLY
WHAT TYPE OF CELL THEY ARE AND
ALSO GENERALLY THE REGION OF THE
BRAIN THEY CAME FROM BASED ON
EXPRESSION PATTERNS OF LANDMARK
TRANSCRIPTION FACTORS.
SO NOW I'D LIKE TO FOCUS ON THE
LAST ASPECT OF THIS TALK WHICH
IS HOW DO WE START LOOKING AT
SIGNALLING PATHWAYS AND WHAT
THEIR ROLES ARE DURING BRAIN
DEVELOPMENT.
THEY HAVE BEEN LOOKING AT SMALL
PATHWAYS OR PARTICULAR TIME IN
DEVELOPMENT AND MANIPULATING THE
SIGNALLING PATHWAY AND LOOKING
TO SEE WHAT THE EFFECTS ARE.
BUT IF WE WANT TO LOOK AT IT IN
THE CONTEXT OF DEVELOPMENT AND
WHAT'S HAPPENING AS THE ANIMAL'S
GROWING AND LOOK AT IT IN A MORE
UNBIASSED WAY ACROSS MULTIPLE
TYPES OF CELLS AND REGIONS OF
THE BRAIN, HOW CAN WE START
SCALE I
SCALING HOW WE INVESTIGATE
SIGNALLING PATHWAYS DURING
DEVELOPMENT.
I'D LIKE TO PROPOSE WE CAN ONCE
AGAIN WE LIE ON CRISPR CAS TO
LOOK AT SIGNALLING ACTIVITY ON A
LARGER SCALE.
THE IDEA IS SIMILAR WITH THE
RECORD WHICH IS NOW WE CAN
RECORD SIGNALLING HISTORY AND
CELL TYPE IDENTITY AT THIS TIME
AND DO THIS IN COMPLEX TISSUES
AND MAKE IT UPON ACTIVATION OR
INPUT OF THE PATHWAY THE SYSTEM
BECOMES ACTIVATED AND THAT
STARTS INTRODUCING MUTATIONS SO
THAT WE CAN COMBINE THAT WITH
SINGLE CELL RNA SEQUENCING TO
HAVE AN ATLAS WITH THE
SIGNALLING HISTORY AND CELL TYPE
IDENTITY AND LINEAGE
INFORMATION.
AND THERE ARE ADDITIONAL CAS
PROTEINS THAT HAVE BEEN SHOWN TO
WORK FAIRLY EFFICIENTLY IN A
RANGE OF SYSTEMS INCLUDING
ZEBRAFISH AND WE NOW HAVE A
COLLECTION OF ORE CAS PROTEINS
TO INTRODUCE COMPLEXITY IN THE
TIME I
TIMING OUR GOAL IS TO START
LOOKING AT NOTCH SIGNALLING AS A
PROOF OF PRINCIPLE.
IT'S GENERALLY IMPORTANT AND IT
PRESSES THE PRONEURAL GENES AND
HELPS MAINTAIN STEM CELL POOLS.
OUR GOAL IS TO HAVE A SYSTEM TO
TURN ON THE VARIOUS CAS PROTEINS
UPON USING AND WHEN THERE'S
SUFFICIENT SIGNALLING THE CAS
GETS ACTIVATED AND COMPLEX WITH
THEIR AND WE HAVE A PROMOTER
EXPRESSED IN THE NEURAL TUBES
BUT HERE I'M SHOWING GFP
EXPRESSION AND IT LABELS CELLS
ALONG THE FINAL PORT AS WELL AS
THE BRAIN WHERE THE CENTRAL
NERVOUS SYSTEM AND PERIPHERAL
NERVOUS SYSTEM EXISTS AND IT'S
GREAT TO START SCALING THE
ATLASES.
TO THE GOAL IS TO HAVE ORE
ORTHOLOGOUS SYSTEMS AND WE CAN
RECORD TWO OR MORE SIGNALLING
PATHWAYS AT ONES AS LONG AS WE
CAN MAKE THEM RESPONSIVE TO
MULTIPLE SIGNALLING INPUT AND
PROVIDE AS A WAY OF DOING
SCALABLE SINGLE-CELL ATLAS BY
COMBINING WITH SINGLE-CELL RNA
SEQUENCING.
THIS SYSTEM OF COURSE I'M
EXPLAINING IN THE CONTEXT OF THE
ZEBRAFISH BUT WE'D LIKE TO
INTRODUCE THIS INTO OTHER
LINEAGE AND STUDY IT OUTSIDE OF
THIS SUCH AS THE CONTEXT OF
DISEASE AND MEASURE LINEAGE
SIGNALLING, SPLICING AND
TRANSCRIPTION.
SO OF COURSE WE'LL MAKE ALL THIS
AVAILABLE TO THE WIDER COMMUNITY
AS WE MOVE ALONG IN OUR PROJECT
PROJECTS AND I'D LIKE TO QUICKLY
END BY ACKNOWLEDGING EVERYONE
WHO HAS BEEN VERY HELPFUL IN
GETTING VARIOUS ASPECTS OF THIS
PROJECT GOING AND FORMER MENTORS
AND COLLABORATORS.
>> THANK YOU FOR GREAT TALK AND
IN THE SPIRIT OF HOW THE MEETING
WILL RUN WE'LL HAVE QUESTIONS
AFTERWARDS.
AND TIM PETROS AT NICHD GOT HIS
Ph.D. IN COLUMBIA STUDYING AXON
PROJECTIONS OF GANGLION CELLS
AND DID A POST-DOC WITH STEWART
ANDERSON STUDYING INTRINSIC AND
EXTRINSIC PROGRAMS AFFECT
DIVERSITY AND HE'S BEEN AT NICHD
SINCE 2017 AND WE LOOK FORWARD
TO HEAR HIS LATEST.
TIM, TAKE IT AWAY.
>> AND WE STUDY GAB ERIC
INTERNEURONS AND HOW WE GENERATE
THIS DIVERSE POPULATION OF CELLS
THAT ARE LOCALIZED IN ALMOST
EVERY BRAIN WITH DIFFERENT
MORPHOLOGIES AND FUNCTION AND
PLAY IMPORTANT ASPECTS IN NEARLY
EVERY PART OF BRAIN FUNCTION.
TO SUMMARIZE THIS THE INHIBITORY
GABERGIC NEURONS HAVE AN AN
INCREDIBLE DIVERSITY IN TERMS
MUCH THE MORPHOLOGY AND
ELECTROPHYSIOLOGICAL PROPERTIES.
AND YOU CAN HAVE SEE THE
DIFFERENT TYPES OF INHIBITORY
INFORMATION.
HOW DO YOU GENERATE THIS
DIVERSITY IS CHALLENGING AND
EXCITING QUESTION AND WE USED
THE MOUSE AS A DEF -- MODEL AND
THE NEURON BROWN FROM THE
GANGLIONIC EMINENCES AND THEY'RE
BORN FROM THE LATERAL, MEDIAL
AND BECOMEPOST-MITOTIC AND WORK
HAS FOUND AND THERE'S DIFFERENT
GABAERGIC CELLS AND IN THE LAST
DECADE OR SO WITH THE ADVENT OF
SINGLE-CELL TECHNOLOGY ALLOWS TO
IDENTIFY THE TRANSCRIPT OME AND
HEARS ONE FIGURE FROM A SUMMARY
ARTICLE SHOWING YOU CAN DEFINE
DIFFERENT SUB TYPES OF MATURE
GABAERGIC NEURONS AND CORRELATE
THESE OBSERVATIONS TO THE MORE
TRADITIONALLY CELL TYPES BASED
ON THE MORPHOLOGY OR
ELECTROPHYSI
ELECTROPHYSIOLOGIC PROGRAMS AND
THERE'S EVIDENCE THE
PERTURBATION FUNCTION IS
CRITICAL FOR A WIDE VARIETY OF
BRAIN DISEASES AND DYSFUNCTION
AND IT'S ASSOCIATED WITH
EPILEPSY, AUTISM, BIPOLAR
DISORDER AND OTHER PSYCHIATRIC
DISEASES.
ADDITIONAL STUDIES HAVE ON THE
MANY DISEASES DISASSOCIATED
GENES ARE OFTEN EXPRESSED IN
YOUNG CELLS, SO IMMATURE
DIVIDING CELLS AND IN PARTICULAR
SOME ARE ENRICHING PROGENITORS
AND THERE'S GWAS STUDIES AND
OTHER APPROACHES THAT CHANGES IN
EPIGENETIC MECHANISMS CAN BE
ASSOCIATED WITH NEUROPSYCHIATRIC
DISORDER.
THE MAJORITY OF LOCI WITH
DISEASES ARE NOT FOUND IN CODING
REGIONS BUT OUTSIDE OF THEM
WHICH MEANS SOMEHOW THEY'RE
AFFECTING GENE EXPRESSION THAT
CAN IN TURN LEAD TO DISEASE.
THE SUMMARY OF THIS IN THE
OVERALL THEME HOW I THINK ABOUT
THIS IS WE NEED A BETTER
UNDERSTANDING AND
CHARACTERIZATION OF THE GENETIC
AND EPIGENETIC MECHANISM
REGULATE INTERNEURONAL STATE TO
UNDERSTAND DEVELOPMENT AND
DISEASE ETIOLOGIES.
I'LL SHOW YOU WORK WE'VE DONE TO
TRY TO GENERATE WHAT WE CALL AN
EPIGENOME ATLAS IN THE MOUSE
BRAIN USING TOOLS TO LOOK AT THE
DIFFERENCES BETWEEN THE SPECIFIC
REGIONS.
WE PERFORMED SINGLE NUCLEOTIDE
SEQUENCING AND SINGLE CELL RNA
SEQUENCING THAT BUSHRA
SUMMARIZED IN THE FOUR BRAIN
REGIONS THAT COMPARE AND
CONTRAST GENE AND CHROMATIN
ACCESSIBLE BETWEEN BRAINS.
WE'VE ADDED ON TO THIS BY
PERFORMING SOME NEWER TECHNIQUES
TO CHARACTERIZE THE HISTORY OWN
MODIFICATION TO GET A BETTER
SENSE WHETHER REGIONS ARE
PROMOTERS OR ACTIVE OR REPRESSED
OR ENHANCERS TO UNDERSTAND HOW
GENES ARE REGULATED IN DIFFERENT
PARTS OF THE BRAIN AND PERFORMED
HIGH C TO LOOK AT LARGER
CHROMATIN CONFIRMATION STRUCTURE
AND SEE HOW IT'S ORGANIZED
DIFFERENTLY BETWEEN BRAIN
REGIONS AND UNDER LIES
DIFFERENCES IN GENE EXPRESSION
AND EPIGENETICS.
ATAX HAS HAS A WIDE VARIETY OF
STUDIES WITH DIFFERENT TIME
POINTS OR BRAIN REGIONS TO
UNDERSTAND THE TRANSCRIPTOME IN
THE BRAIN BUT MANY STUDIES HAVE
BEEN CRITICAL WHEN ONE THINGS OF
A HETEROGENEOUS ENVIRONMENT YOU
NEED SINGLE CELL TO UNDERSTAND
DIVERSITY AND UNDERSTAND
DIFFERENCES BETWEEN CELL TYPES.
WHAT A SINGLE ATAC CAN IDENTIFY
OPEN REGIONS OF CHROMATIN AND
THEY CAN INDICATE PROMOTERS OR
ENHANCERS AND THE TRANSPOSEES
CAB ACCESS AND ADAPT TO THEN GO
THROUGH A PROCESS OF GENERATING
SEQUENCING THE REGIONS AT THE
SINGLE-CELL LEVEL KNOW WHETHER
GENOMIC LOCI IS ACCESSIBLE OR
OPEN OR CLOSED OFF.
GOING THROUGH THE WORK FLOW WE
USED IN THE LAB FOR THIS
EXPERIMENT WE TOOK THE MOUSE AND
CAN DISSECT OUT THE REGIONS
VISIBLE AND THE OG, MG AND CG
AND PERFORMED EITHER SINGLE CELL
OR SINGLE LOCI ED --
ASSOCIATIONS AND LOOK AT THE
SEQUENCING OR MORE RECENTLY
MULTIOMIC EXPERIMENT TO OBTAIN
BOTH SCREEN EXPRESS AND
CHROMATIN ACCESSIBILITY IN THE
SAME CELLS AND GIVE IT TO THE
SEQUENCING CORE TO ANALYZE THE
DATA TO TRY TO UNDERSTAND THE
DIFFERENCES BETWEEN CELL TYPES
AND DIFFERENT REGIONS OR
DIFFERENT TIME POINTS.
THIS IS WHERE WE SPEND A LOT OF
OUR TIME FIGURING OUT THE BEST
WAY TO MASSAGE THE DATA
TO BETTER UNDERSTAND.
THIS IS KIND OF WHAT THE INITIAL
FIRST PASS ANALYSIS LOOKS LIKE.
IN THIS PLOT THE DOT REPRESENTS
A CELL OR IN THIS CASE NUCLEUS
AND CLOESER THE DOTS THE MORE
ACCESSIBILITY AND WE HIGHLIGHT
THE BRAIN REGIONS AND YOU CAN
SEE MOST THE CELLS ARISE FROM
THE CORTEX AND CLUSTER TOGETHER
AND FROM THE MG CLUSTER TOGETHER
AND LESS KNOWN DIFFERENCES
BETWEEN THE LG AND CG AND YOU
CAN SEE THOSE REGIONS ARE
CLUSTERED TOGETHER HERE.
YOU CAN LOOK AT PREDICTED
DISTINCT CELL TYPES AND THERE'S
ABOUT 25 OR SO POTENTIAL
CANDIDATE DIFFERENT CELL TYPES
IN THE DATA SET.
WE CAN ALSO BREAK IT DOWN LOOK
AT DIFFERENT PROGENITORS AND
BLUE IS A POST-MITOTIC NEURON TO
LOOK AT DIFFERENT STAGES AND
PERFORM ANALYSIS THAT CAN GIVE
US INFORMATION FOR THE EARLIER
CELL TYPES VERSUS LATER
IMPORTANT POST-MITOTIC.
I WON'T BORE YOU WITH GENES BUT
HIGHLIGHT WHAT WE CAN OBTAIN
FROM THIS DATA.
IF YOU LOOK AT THE ACCESSIBILITY
OF PROMOTERS OF SOME GENES YOU
SEE DIFFERENTIAL ACCESSIBILITY.
AND THIS IS A SPECIFIC
TRANSCRIPTION FACTOR ONLY
EXPRESSED IN THE MG AND THE
PROMOTER IS ONLY ACCESSIBLE IN
THE MGE AND YOU SEE THE CORTICAL
SPECIFIC TRANSCRIPTION FACTOR
AND IT'S ONLY EXPRESSIBLE IN THE
CORTEX.
WE CAN LOOK AT THE ACCESSIBILITY
DATA IN DIFFERENT WAYS.
IF WE ORGANIZE AND CLUSTER BASED
ON THE REGION YOU CAN SEE THIS
IS ONLY ACCESSIBLE IN THE MG AND
IN THE OTHER REGIONS AND NEUROD6
SHOWS ACCESSIBILITY TO THE
CORTEX AND NOT OTHER REGIONS AND
YOU CAN LINE THESE UP FROM THE
EARLIEST PROGENITORS IT NESTED
AS A GREAT GENE WITH ALLELE
CELLS AND IT'S ACCESSIBLE AND RE
-- DECREASES OVER TIME AND SO
THERE'S A NICE CORRELATION
BETWEEN ACCESSIBILITY OF
PROMOTERS WITH KNOWN GENE
EXPRESSION BOTH IN TERMS OF OVER
DEVELOPMENT OF TIME AND LOOKING
BETWEEN DIFFERENT IMAGES.
THIS SAY PRETTY COMPLICATED
FIGURE AND WE HAVE TAKEN THE 25
CLUSTERS AND GROUPED THEM
TOGETHER TO LOOK AT DIFFERENTIAL
ACCESSIBILITY PEAKS.
FOR EVERY CLUSTER HOW UNIQUE IS
THE ACCESSIBILITY OF THE GENOME.
AND SO WHAT YOU SEE HERE ALONG
THE DIAGONAL IS COMPARING EACH
CLUSTER TO ITSELF AND IF YOU
LOOK AT THE CLUSTER UP HERE THAT
CONTAINS PROGENITORS FROM THE
CORTEX AND HAS A LARGER AMOUNT
OF DIFFERENTIATED EXPRESSED
PEAKS AND IF YOU COMPARE TO A
POSTMITOTIC CELL FROM MG THERE'S
LITTLE SIMILARITY FROM THE
DIFFERENTIALLY EXPRESSED PEAKS.
THIS WOULD LOOK DIFFERENT FROM
RNA TRANSCRIPTION AND EACH
CLUSTER OF CELLS HAVE A UNIQUE
SET OF CELLS DISTINGUISHING IT
FROM DIFFERENT BRAIN REGIONS AND
DIFFERENT SUBSETS.
YOU CAN DIG INTO THIS DATA A
LITTLE BIT MORE.
FOR EACH ACCESSIBLE REGION WE
CAN SAY WITHIN THAT REGION ARE
THERE SPECIFIC SPECIFIC
TRANSCRIPTION FACTOR BINDING
SITES.
THIS IS CRITICAL FOR DEVELOPMENT
OF GABAERGIC CELLS AND THE MOTIF
IS RESTRICTED SPECIFICALLY TO
THE CELLS CONVERSELY THIS IS
CRITICAL FOR CORTICAL
DEVELOPMENT AND THE BINDING SITE
IS ONLY PRESENT IN CORTICAL
CELLS AND NOT PRESENT IN THE
ACCESSIBLE AREAS OF THIS.
THERE'S OTHER WAYS TO DIVE INTO
THE DETE BUT IT GIVES AN
OVERVIEW OF WHAT WE CAN GENERATE
FROM THESE GENES AND WE LOOK AT
REGIONS CO-ACCESSIBLE.
WE HAVE A PROMOTER FOR GENE
EXPRESSION.
AND MOST ARE LOCATED FURTHER
AWAY WE WANTED TO SEE IN THE
DATA CAN WE FIND REGIONS
PROMOTERS AND IN THE SAME CELL
FIND GENOMIC LOCI WHICH COULD BE
INDICATIVE OF A POSSIBLE
ENHANCER.
WE USED THIS ANALYSIS CALLED
CISERO AND ALL THESE BLUE LINES
THE BLUE ARCHES CREATE A REGION
UPSTREAM OF THE GENE AND WITHIN
THE SAME CELL IS OFTEN
CO-ACCESSIBLE.
THIS COULD INDICATE THAT A
REGION COULD POSSIBLY BE AN
ENHANCER AND CHECKS WITH THE
PROMOTER TO REGULATE GENE
EXPRESSION.
YOU ONLY SEE THIS PATTERN IN THE
MG WHERE THE GREEN IS EXPRESSED
AND NOT IN OTHER REGIONS.
WE CAN LOOK AT THIS TYPE OF
ANALYSIS AND GENE AND ALSO LOOK
AT IT BETWEEN REGIONS AND LOOK
AT IT THROUGH DEVELOPMENT OF
TIME.
AND THIS IS A POSTMITOTIC GENE
AND COMES ON LATER IN
DEVELOPMENT AND THE CHROMATIN
CO-ACCESSIBILITY DOESN'T EXIST
BUT IN THIS OTHER CELL YOU SEE A
MORE MATURE PATTERN AND YOU CAN
DO THE SAME THING IN YOUR
FAVORITE GENE.
THE ACCESSIBILITY INFORMATION IS
GREAT BUT WE WANT TO MAKE SURE
IT MAKES SENSE AND FITS WITH THE
RNA EXPRESSION.
WE PERFORMED SINGLE CELL RNA
SIKH AND INTEGRATED THE DATA
TOGETHER SUCH THAT IN THE SAME
COMPUTATIONAL SPACE IN DIFFERENT
CELLS WE CAN LOOK AT GENE
EXPRESSION PATTERNS AS WELL AS
ACCESSIBILITY AND YOU CAN DO THE
SAME ANALYSIS FINDING CLUSTERS
AND IF WE GROUP GENES WITH
SIMILAR EXPRESSION PROFILES TO
SIMILAR FAMILIES WE CAN SEE A
SET OF GENES THAT ARE EXPRESSED
HIGHLY DURING NEURO GENIC CELLS
AND GET DOWN REGULATED WITH
POST-MITOTIC CELLS AND OTHERS
GET UPREGULATED OVER TIME.
AND BECAUSE WE INTEGRATE THE
DATA TOGETHER WE CAN LOOK AT
GENE EXPRESSION AND THE GAS AND
ENHANCERS.
AND YOU CAN FOLLOW BOTH THE
GREEN EXPRESSION AND PROMOTER
AND ACCESSIBILITY AND WHAT WE
SEE IS THAT GENES ENRICHED EARLY
IN DEVELOPMENT THEN GO DOWN AS
THOSE BECOME POST-MITOTIC AND
HAVE DIFFERENT LEVELS PART OF
THE PROMOTER ENHANCER BEING
TURNED OFF AND IF YOU LOOK AT
GENES UPREGULATED OVER TIME YOU
CAN SEE BOTH THE PROMOTERS AND
ENHANCERS START TO BECOME
ACCESSIBLE PRIOR TO RNA
EXPRESSION.
ONE EXAMPLE IS WHERE THE ACTUAL
MRNA IS EXPRESSED AND SEE BOTH
IN TERMS OF THE PROMOTER AND
ENHANCER THE REGIONS BECOME
ACCESSIBLE PRIOR TO RNA WHICH IS
A COMMON THEME WE SAW THROUGHOUT
THE DAY.
NOW, THIS IS GREAT BUT DOESN'T
DIRECTLY TELL ANYTHING ABOUT
ENHANCER AND PROMOTER
INTERACTIONS AND SO TO DIG INTO
THIS DIGGER WE WANTED TO UTILIZE
ANALYSIS OF HISTONE
MODIFICATIONS WHICH HAS BEEN
KNOWN TO LABEL ENHANCERS.
AND WE ANALYZE ONE IS A
PROMOTER AND ENHANCER AND
THERE'S A HISTONE MODIFICATION
THAT INDICATES REPRESSIVE MARKS.
WE DEVELOPED THIS AND IT'S
CHEAPER AND HAS LESS CELLS WHICH
IS WHY IT WAS APPEALING TO US
AND YOU CAN ADD AN ANTIBODY TO
YOUR NUCLEI.
IT RECOGNIZES SPECIFIC
MODIFICATION AND HISTONE.
YOU THEN ADD A TRANSPOSING THAT
RECOGNIZES THE ANTIBODY AND
ACTIVATE IT TO CUT THE DNA AND
ADD TAGS ON TO IT AND EXTRACT
AND SEQUENCE IT AND IT WILL TELL
YOU WHERE YOU HAVE THIS SPECIFIC
HISTONE TAG THAT COULD INDICATE
A PROMOTER OR ACTIVE ENHANCER OR
REPRESSER.
THIS IS A MARK ACTIVE GENE
EXPRESSION AND WE HAD AN RNA
ACCESSIBILITY AND LOOKING AT
ACTIVE OR REEXPRESSEXPRESSED AND THIS SAY
GENE PREDOMINANTLY ENRICHED IN
THE CG AND EXPRESSED IN LOW
LEVELS IN THE OTHER BRAIN
REGION.
IF YOU LOOK AT THE ATAC DATA YOU
DON'T SEE ANY DIFFERENCE.
ONLY LOOKING AT THE CHROMATIN
ACCESSIBILITY DOES NOT PROVIDE A
LOT OF INFORMATION ABOUT THE
GENE EXPRESSION OR FUNCTION.
WHEN YOU ADD IN THE HIS TONE
MARKS THE PROMOTER IS ONLY
ACTIVE IN THE CG AND LOW LEVELS
OF OTHER GENES AND THE
REPRESSIVE MARK IS NOT SHOWN BUT
REPRESSED IN OTHER REGIONS.
THIS IS A COMMON THEME THAT ONLY
LOOKING AT ONE MODALITY GIVES A
LITTLE BIT OF INFORMATION BUT
WHEN YOU START TO COMBINE
MULTIPLE MODALITIES TOGETHER YOU
CAN GET A BETTER UNDERSTANDING
OF THE STATE OF THE GENE WITH
THE EXPRESSION AND EPIGENETICS.
AND THIS IS A CELL ENRICHED AND
PREVIOUS STUDIES HAVE LOOKED AT
THIS AS A POSSIBLE ENHANCER OR
ASCL1 BUT DIDN'T SHOW THE
EXPRESSIVE PATTERN.
IT'S CO-ACCESSIBLE WITH THE
PROMOTER BUT WHEN YOU LOOK TO
THE SPATIAL RESOLUTION AND IF
YOU LOOK AT THE ACTIVE ENHANCER
IT'S STRONGLY K27 ACETYL SIGNAL
IN THE CORTEX AND THE REGION
IT'S NOT EXPRESSED AND IT HIT
DOESN'T LOOK LIKE A GREAT
CANDIDATE FOR ENHANCER BECAUSE
THE HISTONE MARK IS NOT ENRICHED
IN THE AREAS WHERE THE GENE IS
EXPRESSED AND WE FOUND OTHER
REGIONS FOR THE DOWN STREAM
CO-ACCESSIBLE WITH THE PROMOTER
AND SHOW A HIGHER ENRICHMENT OF
THIS ACTIVE ENHANCER MARKS
SPECIFICALLY IN THE GANGLIONIC
EMINENCES AND THE REGIONS WHICH
HAVE NOT BEEN STUDIES ARE BETTER
CANDIDATES FOR ENHANCER TO
REGULATE THIS GENE COMPARED
PREVIOUSLY STUDIED THAT DIDN'T
HAVE THE RESULT.
WE CAN DO THIS FOR A VARIETY OF
BRAIN REGIONS AND THE OTHER
THING WE'VE DONE IS HIGH C
LOOKING AT HIGHER CHROMATIN
INTERACTIONS AND TO HIGHLIGHT
THIS COMPARING THE REGIONS
HERE'S A REGION WHERE WE SEE A
DIRECT CONTACT BETWEEN THE
PROMOTER AND THE REGION UP
STREAK AND THIS IS SPECIFIC TO
THE MGE AND NOT FOUND IN OTHER
BRAIN REGIONS.
AGAIN, WE CAN COMPARE THIS AND
COMBINE WITH OTHER DATA SO THAT
THE NKX REGION WE SEE A DIRECT
INTERACTION BETWEEN THE PROMOTER
AND THE LOCI OVER HERE NOT FOUND
IN THE OTHER BRAIN REGIONS AND
THE CONVERSE IS TRUE WITH THE
GENES EXPRESSED AND SEE THE
INTERACTION WITH THE LOCI WITH
THE REGION NOT FOUND IN THE MG.
WE CAN DO THIS IN A VARIETY OF
BRAIN REGIONS AND REALLY QUICK
AS IT'S IMPORTANT TO MAKE THE
INFORMATION PUBLICLY ACCESSIBLE.
ALL THE DATA IS AVAILABLE ON THE
UCSD BROWSER WITH ALL THE RNA
INFORMATION, ACCESSIBLE AND THE
CONNECTIONS AND THE HISTONE
MODIFICATIONS AS WELL AS THE
HIGH C DATA AND CAPTURE SEQ
BELOW.
WE LOOKED AT THE FUTURE I WON'T
GO THROUGH THIS DUE TO TIME
CONCERNS BUT I DO WANT TO
HIGHLIGHT THAT I THINK SOME OF
THE MOST IMPORTANT THINGS ARE
MAKING THE DATA AS PUBLICLY DATA
AS POSSIBLE AND INTEGRATING A
WIDE VARIETY OF MODALITIES IS
CRITICAL FOR UNDERSTANDING GENE
AND CELL FUNCTION THROUGHOUT
DEVELOPMENT AND AT DIFFERENT
TIME POINTS AND DIFFERENT
SPATIAL REGIONS AND I THANK MY
ENTIRE TEAM CRITICAL FOR RUNNING
THE PROJECT AND THE
COLLABORATION AND THE
BIOINFORMATICS SEQUENCING CORE
AT NICHD.
THANK YOU FOR THE DATA.
>> THANK YOU, VERY MUCH, TIM.
WE'LL MOVE ON TO YE ZHANG FROM
THE UNIVERSITY OF CALIFORNIA IN
LOS ANGELES.
YE DID HER POST-DOCTORAL WORK
WITH UCSF STUDYING FLY
DEVELOPMENT AND MOVED ON TO DO A
POST-DOC WITH BEN BURRIS WHERE
SHE PIONEERED INTERESTING
TECHNOLOGY TO SORT DIFFERENT
CELLS PROVIDING THE OPPORTUNITY
TO LOOK AT GLIAL CELL TYPE
DIVERSITY IN GREATER DETAIL.
AND THIS IS WORK SHE HAS BEEN
CONTINUING AT UCLA AND WE LOOK
FORWARD TO HEAR THE LATEST, YE,
PLEASE, TAKE IT AWAY.
>> THANK YOU, OLIVER FOR THE
KIND INTRODUCTION AND I'D LIKE
TO THANK THE ORGANIZERS FOR
PUTTING TOGETHER A FANTASTIC
WORKSHOP AND I'VE HEARD A LOT OF
FROM THE FIRST TWO TALKS.
I'M TALK ABOUT IMMUNOPANING FUR
FICTION AND TRANSCRIPT OME
PROFILING OF GLIAL CELLS.
IN THE HUMAN CENTRAL NERVOUS
SYSTEM HALF THE CELLS ARE GLIAL
CELLS AND IN RECENT YEARS MANY
LABS HAVE SHOWN THAT GLIA CELLS
ARE IMPORTANT FOR THE
DEVELOPMENT AND FUNCTION CENTRAL
NERVOUS SYSTEM AND THERE'S THESE
SYNAPSES AND NEURONS FORM FEW
SYNAPSES IN VIVO WITHOUT
ASTROCYTES AND THESE ARE AN
IMMUNE TYPE AND MICROGLIA ARE
DEVELOPMENT IN THE SYNAPSE AND
SCULPTING OF NEUROCIRCUITSES
AND THESE DENDRITE CRITICAL FOR
THE METABOLISM AND HEALTH OF
AXONS.
SO TO UNDERSTAND BRAIN
DEVELOPMENT, IT'S ESSENTIAL TO
UNDERSTAND THE GLIA FUNCTIONDERSTAND THE G LIA FUNCTION.SO TO UNDERSTAND BRAIN
DEVELOPMENT, IT'S ESSENTIAL TO
NDERSTAND THE GLIA FUNCTION.
I'LL GOING TO TALK ABOUT A
METHOD OF PURIFICATION FOR GLIAL
CELL AND TWO METHODS AND THE
TRANSCRIPTOME PROFILING AND WE
WERE ABLE TO DO CROSS-SPECIES
COMPARISONS OF HUMAN ASTROCYTES
AND CHARACTERIZING HUMAN
ASTROCYTE TRANSCRIPT OME CHANGES
ACROSS THE LIFE SPAN AND I'LL
TALK ABOUT STRENGTH AND
LIMITATIONS OF CURRENT METHODS.
THIS WAS DONE IN BARRES LAB AND
NOW WE CAN HAVE THIS APPLICABLE
TO MANY CELL TYPES AND ACROSS
MOUSE, AND HUMAN SPECIES.
BACK WHEN I WAS A POST-DOC WE
WANTED TO CONSTRUCT A MOUSE
BRAIN CELL TYPE TRANSCRIPTOME
DATA SET WITH PURIFICATION OF
DIFFERENT CELL TYPES AND WERE
ABLE TO DEVELOP PURIFY METHODS
AND NEURONS IN THREE STAGES IN
THE OLIGO DENDRITE CELLS AND THE
NEURAL FORMED OLIGO DENDROCYTES
AND WE PERFORMED THE RNA
SEQUENCING AND HERE'S THE PURITY
OF THE ISOLATED CELL TYPES.
THE CELL TYPE MARKERS ARE
CLEARLY EXPRESSED IN A SPECIFIC
MANNER.
AFTER THIS WORK WE WERE HOPING
TO EXPAND THE TRANSCRIPTOME DATA
SET OF GLIAL TYPES AND ISOLATED
MICROGLIA AND OLIGO DENDROCYTES
AND ASTROCYTES AND DATA SETS.
TO MAKE DATA ACCESSIBLE WE
GENERATED A WEBSITE WHICH IS
SEARCHABLE YOU CAN TYPE THE NAME
AND SEE THEIR EXPRESSION OF THE
GENE ACROSS CELL TYPES IN MOUSE
AS WELL AS IN HUMAN.
AND SHOWN HERE IS AN EXAMPLE
WHICH IS AN ALZHEIMER'S RISK
GENE.
CAN SEE IT'S TREM 2 IS ENRICHED
IN MACROPHAGES AND OVER THE
YEARS WE EXPANDED OUR WEBSITE
AND MANY FORMER TRAINEES HAVE
COLLECTED ADDITIONAL DATA SETS
FOR GLIA AND HERE IF YOU CLICK
YOU CAN SEE MICROGLIA
DEVELOPMENT TRANSCRIPTOME
CHANGES IN MICE FROM THE DATA
SET AND HERE'S ANOTHER DATA SET
FOR MOUSE ASTROCYTE CHANGES AND
WE ADDED A STUDY FROM MY OWN LAB
LOOKING AT HOW ASTROCYTES CHANGE
IN THE PERI TUMOR
MICROENVIRONMENT AND YOU CAN
CLICK AND FIND OUR DATA THERE.
OVER THE PAST DECADE OR SO MANY
LABS HAVE GENERATED USEFUL
TRANSCRIPTOME SEQUENCING DATA
SETS AND SOME LABS HAVE NICE
DATA SET WEBSITES TO MAKE IT
ACCESSIBLE BUT MANY OTHER LABS
DO NOT HAVE THE EXPERTISE OR
BANDWIDTH TO MAKE WEBSITES AND
MAKE DATA IN SEARCHABLE ACCESS
ABLE FORM LEAVING USEFUL DATA
SETS HIDDEN IN SOME REPOSITORIES
AND ONLY ACCESSIBLE TO PEOPLE
WITH INFORMATICS EXPERTISE AND
THE DATA MINING BANDWIDTH.
WITH OUR ONGOING WORK WE WANTED
TO MAKE DATA ACCESSIBLE BY
BUILDING A UNIVERSAL WEBSITE
BUILDING TOOL SO THE GOAL IS ANY
LAB CAN UPLOAD AN EXCEL SPREAD
SHEET FOR THEIR TRANSCRIPTOME
DATA AND OUR TOOL CAN CONVERT
THAT TO A SEARCHABLE WEBSITE
THAT RESEMBLED THE SIMPLICITY OF
OUR WEBSITE.
AND ANOTHER TOOL THAT WE'RE
BUILDING THAT'S MORE SPECIFIC TO
GLIA RESEARCH IS A WEB HUB FOR
GLIA TRANSCRIPTOME DATA SET.
THERE'S MANY GREAT DATA SETS
PUBLISHED BUT FOR SOMEONE NEW TO
GLIA MAY NOT KNOW ALL THE DATA
SETS AND THESE INFORMATION ARE
DISTRIBUTED IN EACH INDIVIDUAL
PAPERS AND WHAT WE WANT TO DO IS
TO HAVE A CURATED WEB HUB SO
ANYONE NEW TO THIS FIELD CAN GO
TO THIS DATA SET AND SEE WHAT'S
AVAILABLE AND PERFORM DATA
MINING.
WE WANTED TO NAME THIS TO
BARRESEQ.
NEXT, I'LL TELL YOU TWO AUTO
IMMUNO PANNING AND THIS IS
INVOLVED IN ENVIRONMENTAL
SYNAPSE ELIMINATION AND
REGULATION OF BLOOD FLOW AS WELL
AS POTASSIUM HOMEOSTASIS.
AND ASTROCYTES ARE DYNAMIC CELL
TYPES.
IN DISEASES AND INJURIES THEY
UNDER GO A PROCESS AND THEY HAVE
BENEFICIAL AND DETRIMENTAL ROLES
IN DISEASE CONTEXT DEPENDENT
MANNER.
SO FAR WHAT WE KNOW ABOUT
ASTROCYTES ARE MOVED -- MOSTLY
BASED ON MOUSE MODELS AND WE
WANTED TO DO A COMPARISON BUT
PREVIOUS METHODS HAVE
LIMITATION.
AN EARLIER METHOD DEVELOPED OVER
40 YEARS AGO AT UCLA CAN OBTAIN
HUMAN ASTROCYTES AND WITH THIS
METHOD YOU GROW ALL CELLS FROM
THE BRAIN IN THE SERUM
CONTAINING MEDIUM AND AFTER
WEEKS OF CULTURE, MOST CELL
TYPES DIE EXCEPT A GROUP OF
ASTROCYTE PROGENITOR TYPE CELLS
THAT PROLIFERATE IN VITRO AND
THEY LOOK POLYGONAL IN SHAPE AND
DIFFERENT IN THEIR MORPHOLOGY
FROM THE IN VIVO PROCESS IN
MORPHOLOGY OF ASTROCYTES.
IN ADDITION TO MORPHOLOGICAL
DIFFERENCES THERE'S ALSO OTHER
LIMITATIONS FOR THIS METHOD.
FIRST, THIS IS NOT AN ACUTE PUR
FICTION METHOD.
YOU ONLY GET ASTROCYTES AFTER
DAYS TO WEEKS OF CULTURE AND
EXPANSION.
IN THIS PROCESS GENE EXPRESSION
COULD CHANGE.
INDEED WE ALREADY KNOW SERUM CAN
INDUCE REACTIVE ASTROGLIOSIS AND
IT MAKES IT MORE DIFFICULT TO
STUDY HOW RESTING HEALTHY
ASTROCYTES CHANGE IN RESPONSE TO
DISEASE-RELEVANT GENERATION.
ALSO THESE CELLS RELY ON A
CERTAIN GROUP OF ASTROCYTES
MAKING THEM MORE DIFFICULT TO
STUDY MATURE PROPERTIES AND
ASSESS PROPERTIES ACROSS THE
LIFE SPAN.
SO SINCE WE DEVELOPED
IMMUNOPANNING METHOD WE OVERCAME
ALL THE PROBLEMS AND WE WERE
ABLE TO COMPARE HUMAN VERSUS
MOUSE ASTROCYTES.
FIRST, I'LL SHOW YOU
PURIFICATION OF HUMAN MOUSE
ASTROCYTE FROM HEALTHY BRAINS
AND ASSESSING THEIR
TRANSCRIPTOME PROFILES USING
WITHOUT CULTURE AND WE FOUND
THERE ARE SUBSTANTIAL
CONSERVATION AND HERE I
HIGHLIGHTED SOME GENES SHOWING
THE HIGHER EXPRESSION IN MOUSE
ASTROCYTES AND MANY OF THEM ARE
LOCATED WITH MITOCHONDRIA
INVOLVED AND IF YOU LOOK AT
HIGHER IN HUMAN ASTROCYTES THAN
IN MOUSE AND MANY GENES ARE
SECRETED CYTOKINE MOLECULES IN
DEFENSE RESPONSE AND WE
IDENTIFIED THE GENE SIGNATURES
AND WONDERED WHETHER THEY'RE
INTRINSICALLY PROGRAMMED OR
INFLUENCED BY THEIR DIFFERENCES
IN BRAIN ENVIRONMENT SUCH AS
DIFFERENCES IN NEURONS.
AND TO ADDRESS THIS QUESTION A
TALENTED POST-DOC COLLABORATED
WITH OTHER LABS AND TRANSPLANTED
HUMAN ASTROCYTES INTO MOUSE
BRAINS AND ALLOWED THE CELLS TO
FOR A FEW MONTHS IN MOUSE BRAINS
AND THEN PERFORMED IMMUNOPANNING
TO ISOLATE THEM AND THEN
PERFORMED RNA SEQUENCING AND WE
FOUND THE HUMAN ASTROCYTES GROWN
IN THE MOUSE HOST BRAIN
ENVIRONMENT HIGHLY RESEMBLE
HUMAN IN VIVO ASTROCYTES
DEMONSTRATING THE HUMAN
SIGNATURE ARE LARGELY
INTRINSICALLY PROGRAMMED.
AND SINCE ASTROCYTE CHANGED
THEIR PROPERTIES AND DISEASES IN
INJURIES WE'RE INTERESTED IN HOW
THE CHANGES ARE SIMILAR OR
DIFFERENT BETWEEN HUMAN AND
MOUSE ASTROCYTES.
WITH IMMUNOPANNING PURIFICATION
METHOD WE CAN COMPARE THE MICE
ON THE CULTURE CONDITIONS AND
TREAT THEM WITH DISEASE-RELEVANT
STIMULATIONS AND EXAMINE HOW
THEY CHANGE AND THIS IS WORK LED
BY A TALENTED POST-DOC IN THE
LAB.
AND THE CELLS WERE TREATED WITH
STIMULATION AND FOR THE INTEREST
OF TIME I'LL ONLY MENTION
HYDROGEN PEROXIDE WHICH
INTRODUCED OXIDATIVE STRESS.
WE FOCUSSED ON THIS STRESS
BECAUSE IT'S A KEY PATHOLOGICAL
COMPONENT OF MANY TYPES OF
NEUROLOGICAL CONDITIONS
INCLUDING NEURODEGENERATION AND
STROKE AND TRAUMATIC INJURY.
AND SAW THE STRIKING DIFFERENCE
IN SURVIVAL.
THE HUMAN ASTROCYTES ARE MORE
SUSCEPTIBLE TO OXIDATIVE STRESS
THAN MOUSE ASTROCYTES AND DID
METABOLISM AND MOLECULAR STUDIES
COLORED IN THE RECENTLY
PUBLISHED PAPER NOT GOING TO
INTO DETAIL BUT I JUST WANT TO
SAY THAT THESE DIFFERENCES COULD
HAVE IMPORTANT IMPLICATIONS FOR
MODELLING OF DISEASE.
MANY LABS HAVE NOTICED THAT
COMMONLY USED MOUSE MODELS OF
NEURODEGENERATION HAVE MILDER
PHENOTYPE COMPARED WITH HUMAN
PATIENTS.
WHY IS THAT?
WE THINK IT'S PROBABLY BECAUSE
MULTIPLE REASONS AND ONE OF THE
REASONS SUGGESTED BY OUR FUNDING
IS THAT MOUSE ASTROCYTES MAY BE
BETTER AT SURVIVING UNDER
OXIDATIVE STRESS AND IN OUR
MOLECULAR STUDIES COMPARE THE
DIFFERENCES IN THE PATHWAYS
RELATED TO OXIDATIVE STRESS, WE
CAN SUGGEST WAYS TO IMPROVE
MODELLING OF NEURODEGENERATION
INCLUDING MOUSE MODELS.
IN THE SECOND EXAMPLE OF
APPLICATION OF IMMUNOPANNING
PURIFICATION OF GLIAL CELLS
WE'RE LOOKING AT HOW HUMAN CELL
TRANSCRIPTOMICS CHANGE WITH
COLLABORATION WITH UCLA AND
OTHER INSTITUTIONS.
OVER THE YEARS WE AND OUR
COLLABORATORS HAVE COLLECTED
FRESH SURGICALLY RECEPTED BRAIN
TISSUE AND WE WERE ABLE TO PURE
PURIFY THE ASTROCYTE IMMUNO
IMMUNOPANNING AND WE LOOKED AT
THE ASTROCYTES ACROSS
DEVELOPMENT AND WE NOTICED A
SHIFT AT TRANSCRIPTOME AT ABOUT
8 TO 12 YEARS OF AGE AND OUR
FAVORITE HYPOTHESIS IS IT'S THE
PEAK OF SYNAPTIC GENESIS WHERE
AFTER IT'S A PEAK OF SYNAPSE
PRUNING AND AS TROECYTES HAVE
DIFFERENT DIFFERENT STAGES IN
SUPPORT OF THE CIRCUITS AND WE
ALSO LOOKED AT ASTROCYTE CHANGES
IN YOUNG ADULTS VERSUS MORE
MATURE ADULTS AND WE SEE WITH
AGE MANY GENES INVOLVED IN
ENERGY METABOLISM ARE GOING DOWN
ALSO ARE GENES INVOLVED IN
INTERACTIONS BETWEEN ASTROCYTES
AND SYNAPSES.
THIS IS A GLUTAMATE TRANSPORTER
DOWNLETTINGED -- DOWN REGULATED
WITH SOME ASTROCYTES AND
INVOLVED IN SENESCENCE.
I'LL SUMMARIZE THE STRENGTH AND
LIMITATIONS OF IMMUNOPANNING
PURIFICATION AND RNA SEQ
PROFILING OF GLIAL CELLS
COMPARED TO RELATED METHODS.
A SIMILAR METHOD TO PURIFY RNA
FROM A SELECTED CELL POPULATION
IS RIBOTAG AND HOLD DOWN A
RIBOSOMAL PROTEIN AND SEQUENCE
THE RNA ASSOCIATED.
AND ONE ADVANTAGE OF THE
IMMUNOPANNING COMPARED TO
RIBOTAG IS IMMUNOPANNING DOES
NOT REQUIRE TRANSGENIC MOUSE
STRAINS OR VIRAL VECTOR
TRANSDUCTION AND THIS IS
IMPORTANT FOR GENETICALLY IN
TRACTABLE SPECIES LIKE HUMANS
AND FOR MOUSE STUDIES IT'S
USEFUL WHEN HAVE YOU AGED MICE
FOR EXAMPLE OR A MOUSE MODEL OF
DISEASE SO YOU CAN DO
IMMUNOPANNING WITH THE MICE YOU
HAVE RIGHT AWAY WITHOUT HAVING
TO CROSS IT TO ANYTHING.
WHERE RIBO TAG REQUIRES TRANS
DISCUSSION.
AND IMMUNOPANNING OBTAINS WHOLE
CELLS WHERE IT CAN EXTRACT WHOLE
RNA AND RIBOTAG IS ACTIVELY
TRANSLATING RNA AND LOOKING AT A
DIFFERENT POPULATION IN THE
DYNAMICS OF RNA.
AND ONE ADVANTAGE OF RIBOTAG IS
YOU CAN TARGET ANY CELL TYPE
LABELLED BY A CREE LINE AND WE
LOOKED AT IMMUNOPANNING IN MOUSE
BUT HAVEN'T FOCUSSED ON
DIFFERENT SUBTYPES OF NEURONS
AND THAT'S NOT AVAILABLE TO
DIFFERENT CELL TYPES.
AND I'D ALSO LIKE TO COMPARE
IMMUNOPANNING COMPARED TO SINGLE
CELL NUCLEUS SEQ.
WE PRODUCED CULTURES OF PURIFIED
CELLS AND THAT'S IMPORTANT FOR
OUR STUDY OF GLIA FUNCTION FROM
MOUSE AND HUMANS WHEREAS FOR
SINGLE CELL RNA SIEQ THE CULTURE
NOT ONE OF THE GOALS AND THIS
METHOD REQUIRES FRESH TISSUE AND
THAT'S NOT AN ISSUE FOR HUMAN
STUDIES BUT FOR MOUSE IT'S
DIFFERENT AND WITH IMMUNOPANNING
WE GET A POPULATION OF CELLS AND
WITH SINGLE CELL APPROACHES
THERE'S MORE INFORMATION FOR SUB
POPULATION DIVERSITY.
LASTLY, I WANT TO SAY WITH
EITHER METHOD IT'S CRITICAL TO
VALIDATE FINDINGS USING RNA
SCOPE ORTHOLOGOUS METHODS AND
I'D LIKE TO THANK OUR
COLLABORATORS AND THE FORMER
BARRES LAB MEMBERS AND FUNDING
AGENCIES.
THANK YOU.
>> TERRIFIC, THANK YOU VERY
MUCH.
SO WE'LL MOVE ON TO OUR LAST
SPEAKER IN THIS PART OF THE
MEETING.
ED LEIN FROM THE ALLEN INSTITUTE
IN SEATTLE.
ED DID HIS Ph.D. AT U.C.
BERKELEY AND DID HIS POST-DOC
AND HAS BEEN AT THE ALLEN SINCE
2004 AND HAS LED A NUMBER OF
REALLY AMAZING PROJECTS THERE
THAT OF COURSE LATELY HAVE
HUGELY PROFITED FROM THE ADVENT
OF SINGLE CELL TECHNOLOGY.
THE RESOURCES THE ALLEN
INSTITUTE AND ED HAVE
ESTABLISHED REACHING LEGENDARY
STATUS WE ALL USE IN ONE FORM OR
ANOTHER AND EXCITED TO HEAR
ABOUT HIS LATEST EFFORTS.
ED, TAKE IT AWAY.
>> THANK YOU.
THANK YOU FOR THE OPPORTUNITY
AND FOR THOSE WHO LAID OUT THE
TOOLS FOR STUDYING DIVERSITY IN
THE BRAIN.
I'D LIKE TO TAKE THE OPPORTUNITY
TO REPRESENT THE WORK WE'VE BEEN
DOING AS PART OF THE BRAIN
INITIATE NETWORK WITH A
PARTICULAR EMPHASIS ON THE ADULT
BRAIN AND ON USING THE TOOLS TO
BE ABLE TO UNDERSTAND DIVERSITY
IN HUMAN TISSUES OR TISSUES IN
NON-GENETICALLY TRACTABLE MODEL
ORGANISM.
THERE'S DEVELOPMENT AND AGING
STUDIES IN OTHER EFFORTS WHICH
USE THESE SAME TOOLS AND BUILD
OFF THE REFERENCE BUT I'LL FOCUS
MAINLY ON THE ADULT REFERENCE
TODAY AS THE RELATIVELY STABLE
MIDDLE POINTS OF THE LIFE SPAN
THAT COULD BE THE TARGET FOR
AGING STUDIES.
OLIVER, TO BUILD OFF YOUR
COMMENTS, PROGRESS DEPENDS ON
TECHNOLOGY.
AND THIS IS CERTAINLY THE CASE
IN TRYING TO BUILD CELL ATLASES
AND TRY TO MOVE THEM TO THINGS
THAT COULD BE STUDIED IN HUMAN
BRAIN AND THE TECHNOLOGIES HAVE
DRAMATIC PROCESS FROM THE STATE
OF FIVE YEARS AGO IN BEING ABLE
TO DISSECT CELLULAR DIVERSITY IN
A VARIETY OF BRAIN TISSUES.
SOME OF THESE ARE FAIRLY MUNDANE
IN TISSUE PREPARATION BUT
RELEVANT IN HUMAN STUDIES AND
THE COHORT OF SINGLE CELL
TECHNOLOGIES AND TRANSCRIPTOMICS
AND EPIGENOMICS AND SPECIAL
TRANSCRIPTOMICS AND FUNCTIONAL
ANALYSIS IN HUMAN LIVING TISSUES
OR TISSUES OF OTHER MODEL
ORGANISM AND GENETIC TOOLS THAT
COME DIRECTLY OUT OF THE SINGLE
CELL GENOMIC WORK TO ALLOW CELL
TYPE SPECIFIC MANIPULATION
ACROSS SPECIES USING A.V.s WITH
ENHANCERS.
THE WORK IS BASED AROUND A
REMARKABLY PRODUCTIVE AND WELL
ORCHESTRATED CONSORTIUM OR
BICCN.
THIS IS A LARGE CONSORTIUM
AROUND BUILDING CELL ATLASES IN
THE MOUSE BRAIN AND DEVELOPING
THE TECHNOLOGIES TO APPLY TO THE
HUMAN AND NON-HUMAN PRIMATE
BRAIN AS THE NEXT STAGE TO BE
CALLED THE BRAIN ATLAS AND THIS
CAME OUT WITH 17 ARTICLES AND A
FLAGSHIP DESCRIPTION SHOWING HOW
DIFFERENT TECHNOLOGIES CAN GAIN
INSIGHT INTO THE FINE
ARCHITECTURE AT THE CELLULAR
LEVEL OF DIFFERENT BRAIN TISSUES
AND PRIMARILY THE PRIMARY MOTOR
CORTEX.
THE IDEA WAS TO TAKE A PAGE FROM
GENOMICS SUCH AS THE ENCODE
PROJECT WHICH LOOKED AT 1% OF
THE GENOME INITIALLY TO LOOK AT
ONE REGION OF THE BRAIN AND HAVE
A VARIETY OF RESEARCHERS WITH
DIFFERENT TECHNOLOGY TO FOCUS ON
THE ONE REGION TO COME TO A
SYNTHETIC UNDERSTANDING OF THE
CELLULAR AND SECTOR ARCHITECTURE
OF THE REGION AND -- CIRCUIT
ARCHITECTURE.
AND IT'S CLEARLY HOMOLOGOUS
ACROSS REGIONS AND AS I'LL
DESCRIBE BRIEFLY THE DIFFERENT
CONTRIBUTORS USED DIFFERENT
TECHNIQUES FROM SINGLE CELL
GENOMIC TO SPATIAL ANALYSIS AND
CONNECTIONAL ANALYSIS TO DERIVE
AT CELLULAR TAXONOMY AND SPATIAL
MAP AND CHARACTERIZATION OF THE
PROPERTIES OF THE CELL TEX.
THE UNDER PINNING FOR THIS WHICH
YOU HEARD QUITE A BIT ABOUT ARE
SINGLE CELL GENOMICS.
THESE HAVE BEEN GAME CHANGERS
FOR LOOKING AT OTHER MODEL
SYSTEMS AND IT'S POSSIBLE TO
TAKE A TISSUE AND DISASSOCIATED
AND CHANGE IT AND IN ONE FELL
SWOOP GENERATE A CLASSIFICATION
OF CELL TYPES.
I'LL DESCRIBE THE OUTPUT IN A
LITTLE BIT BUT CONCEPTUALLY,
THIS BINDS TO THE COMPLEXITY OF
THE SYSTEM TO A SERIES OF CELL
TYPES THAT CAN THEN BE PROBED TO
UNDERSTAND THE PROPERTIES OF THE
CELLS.
FURTHERMORE THAT CAN BE USED TO
HARNESS CELL TYPE DEREGULATION
TO FUNCTIONALLY MANIPULATE THE
CELL TYPE POPULATIONS IN A
VARIETY OF SYSTEMS INCLUDING
HUMAN.
BESIDES THE SINGLE CELL
ASSOCIATED ANALYSIS, ANOTHER
TRANSFORMATIVE SET OF TECHNOLOGY
THE TRANSCRIPTOMIC TECHNOLOGIES
THAT ALLOW US TO TAKE THE
SOMEWHAT ABSTRACT CLASSIFICATION
AND MAP IT BACK TO ITS TISSUE
ARCHITECTURE.
SO SHOWING HERE ON THE LEFT SIDE
IS WORK USING A TECHNIQUE TO
HAVE A 500 GENE PANEL WHICH CAN
DISCRIMINATE THE MORE THAN 100
TYPES OF CELLS IN THE MOUSE
MOTOR CORTEX AND MAP THEM TO GET
THE SPATIAL STATISTICS OF THEIR
ORGANIZATION.
THIS TECHNOLOGY HAS NOW BEEN
COMMERCIALIZED THROUGH A COMPANY
AND WE'VE BEEN USING THIS AND
HAVE SHOWN IT CAN BE APPLIED TO
MACAQUE AND HUMAN TISSUES AND
ALLOWS TO YOU MOVE THE FIRST
STEP OF DEFINING THE TYPES TO
THE SECOND STEP OF DEFINING THE
SPATIAL ORGANIZATION IN
FUNCTIONAL TISSUE ARCHITECTURE.
A THIRD MAJOR APPROACH HAS BEEN
TO CHARACTERIZE THE
TRANSCRIPTOMICLY DEFINED CELL
TYPES TO LOOK AT THIN SLICES
WHERE YOU FORD A CELL AND FILL
IT WITH A DYE AND CAN MEASURE
THE TRANSCRIPTOME OF THE CELL
AND MAP IT BACK TO THE
TRANSCRIPTOMIC CLASSIFICATION.
THIS CAN BE SCALED UP TO BE DONE
SYSTEMATICALLY ACROSS THE
COMPLEX TISSUE.
THIS IS SHOWING SUMMARY FIGURES
LOOKING AT THE MOUSE MOTOR
CORTEX AND LOOKING AT THE
PROPERTIES OF CELLS WITH THIS
TYPE OF APPROACH WHICH HAS NEVER
BEEN POSSIBLE BEFORE TO DO.
THERE'S A ROBUST TRANSCRIPTIONAL
TRANSCRIPTIONALLY BASED
CLASSIFICATION AND CELL TYPES
FOR WHICH WE KNOW THE IDENTITIES
AND THE MOLECULAR SIGNATURES OF
THESE CELLS AND PROPORTIONS,
SPATIAL ORGANIZATION OF THE
CELLS AND THE PROPERTIES OF THE
CELLS FOR ALL THE CELLS YOU
HEARD ABOUT TODAY FROM THE OTHER
SPEAKERS.
THE EXCITATORY AND INHIBITORY
AND NON-NEURONAL CELL
POPULATION.
WE HAVE A GOOD ATLAS TO SERVE AS
A REFERENCE FOR THE REST OF THE
COMMUNITY TO BUILD ON.
I WANT TO HIGHLIGHT THIS IS THE
FIRST STAGE AND IT'S A BEEN
LARGELY EXTENDED TO THE BRAIN
AND ADULT REFERENCE IS VERY
QUICKLY BECOMING REALITY.
ANOTHER IMPORTANT THING IS THEY
CAN BE APPLIED TO HUMAN,
MARMOSET AND MOUSE AND CAN GO
ACROSS SPECIES AND WE CAN BEGIN
TO SEE THE CRAIG LAR
ARCHITECTURE IS VERY WELL SERVED
ACROSS MAMMALIAN ORGANISMS AND
MOST THE SPECIES DIFFERENCES ARE
DOWN AT THE FINEST OF TYPE LEVEL
BUT ALL THE MAJOR BRANCHES ARE
WELL CONSERVED ACROSS SPECIES.
THIS IS I THINK HUGELY IMPORTANT
ON THE ONE HAND BECAUSE IT
ALLOWS US TO INFER PROPERTIES IN
HUMAN THAT ARE NOT REALLY
POSSIBLE TO MEASURE AT THIS
POINT SUCH AS LONG-RANGE
PROJECTIONS OR DEVELOPMENTAL
ORIGINS, FOR EXAMPLE, BUT WE CAN
INFER THEM BASED ON INFORMATION
FROM MODEL ORGANISM.
ON THE OTHER, IT ALLOWS US TO
COMPARE APPLES TO APPLES AND
UNDERSTAND TO WHAT EXTENT
CERTAIN CELLULAR PHENOTYPE ARE
CONSERVED IN SPECIES.
IF WE CAN DO THIS IN MOUSE,
MARMOSET AND HUMAN, YOU CAN DO
THIS IN ANY SPECIES.
AND WE'VE BEGUN TO EXPLORE WHAT
CAN BE LEARNED BY TAKING THE
IDEA OF CELL TYPE MORPHOLOGY AND
LOOK ACROSS MORE SPECIES AND
UNDERSTAND EVOLUTIONARY
VARIATION AND SIMILAR TO LIMB
HOMOLOGY WHERE YOU HAVE SPECIES
VARIATION THAT CAN LEAD TO
DIFFERENT FUNCTION THE SAME IS
TRUE FOR CELL TYPES.
THE OVERALL CELLULAR BLUEPRINT
IS WELL CONSERVED BUT THEN YOU
GET SPECIES SPECIALIZATIONS THAT
CAN BE PROFOUND IN SOME CASES.
TO GIVE A FEW EXAMPLE EXAMPLES WE'VE
LOOKED AT PRIMARY MOTOR CORTEX
FROM ARMADILLO TO HUMAN AND AT
THE INTERMEDIATE LEVEL OF
GRANULARITY THE CELLULAR
BLUEPRINT IS EXTREMELY WELL
CONSERVED AND WE CAN ALIGN SUB
CLASSES ACROSS THE SPECIES.
WE CAN ALSO IDENTIFY HIGHLY
CONSERVED CELL MARKERS ACROSS
ALL THE SPECIES WHICH INDICATES
THESE MUST BE UNDER EVOLUTIONARY
CONSTRAINT LIKELY TO BE
FUNCTIONALLY ESSENTIAL FOR CELL
IDENTITY OR CANONICAL CELL
PROPERTIES AND THIS INCLUDES
MANY THINGS LIKE TRANSCRIPTION
FACTORS.
ON THE OTHER HAND, IT CAN SHOW
SIGNIFICANT DIFFERENCES.
IF ONE LOOKS AT THE EXCITATORY
AND INHIBITORY RATIO IN THE
MOTOR CORTEX THE TEXTBOOK NUMBER
FOR THAT RATIO IS 5:1 COME FROM
RODENT STUDIES.
WHEN WE FIRST LOOKED AT PRIMATES
WE DISCOVERED THE RATIO IS MORE
LIKE 2:1 IN THE HUMAN AND
MACAQUE.
IT'S NOT A PRIMATE
SPECIALIZATION BUT RODENTS.
AND YOU CAN ONLY GET FOOLED BY
LOOK AT A COUPLE SPECIES.
ANOTHER IMPORTANT OBSERVATION IS
BESIDES THE CONSERVATION OF THE
CELL TYPES THE GENE EXPRESSION
WHICH MAY INCLUDE THINGS LIKE
RECEPTORS FOR DRUG TARGETS ARE
NOT CONSERVED IN THEIR
SPECIFICITY.
IT SEEMS THE MAJORITY OF GENES
ARE SPECIES SPECIFIC AND THE
RELATIVE MINORITY CONSERVED
ACROSS SPECIES.
FINAL
FINALLY THERE'S A SOME
DIVERSITY.
AND THE UPPER LAYERS OF THE
CORTEX ARE EXPANDED IN HUMAN
CORTICAL EVOLUTION TO INCLUDE
MORE CELLS THAT COMMUNICATE THE
CORTEX COMMENSURATE WITH THE
INFECTIOUS IN CORTICAL AREA AND
IT TURNS OUT THE INCREASE IN
SIZE AND IN DEPTH IS ACCOMPANIED
BY AN INCREASE IN DIVERSITY AND
SOME DON'T APPEAR TO BE IN THE
DEEPER PARTS OF THE CORTEX.
AND WHILE THIS ONE REGION OF
CORTEX WORKED ITS WAY TO
COMPLETION, THE REST OF THE
WHOLE MOUSE BRAIN GOT SEQUENCED
ESSENTIALLY.
THIS IS ABOUT 3,000 OR SO
GENOMICCALLY DEFINED CLUSTERS
ACROSS THE BRAIN.
AND THIS IS THE NATURE OF THE
BEAST IF WE WANT TO UNDERSTAND
THE FULL LIFE SPAN OF A SYSTEM
THAT COMPLEX.
AT THE SAME TIME THE TECHNIQUES
HAVE BEEN APPLIED TO HUMAN WITH
A SURVEY ACROSS THE BRAIN AND
ESTABLISHED THIS CAN BE DONE AT
THE SAME TYPE OF GRANULARITY IN
HUMAN AND THIS IS NOW ONE OF THE
MAJOR FOCUSES OF THE CELL ATLAS
NETWORK OR BICAN.
I WANT TO QUICKLY ACKNOWLEDGE
THE CONTRIBUTIONS OF NIA IN
FUNDING STUDIES IN MOUSE AND
ALSO IN HUMAN AT THE ALLEN
INSTITUTE WE HELP TO RUN A GRANT
FUNDED BY NIA TO BUILD OFF THE
BRAIN INITIATIVE CELL CENSUS TO
UNDERSTAND WHAT HAPPENS IN THE
COURSE OF DISEASE AND ALSO IN
AGING.
I'M NOT REALLY GOING TO SHOW AN
AGING TRAJECTORY HERE BUT I WANT
TO POINT OUT WE'RE ABLE TO MAP
CELLS FROM VERY AGED INDIVIDUALS
AND INDIVIDUALS WITH ALZHEIMER'S
DISEASE EFFECTIVELY TO THE
NEUROTYPICAL REFERENCE FROM
YOUNGER INDIVIDUALS SHOWING IT'S
A CONSERVED BLUEPRINT CONSERVED
ACROSS AGING BUT OF COURSE
THERE'S AGING AND DISEASE
SIGNATURES ACROSS THAT AND A
HOPE IT'S A PARADIGM FOR OTHER
DISEASES AS WELL.
AND OPEN DATA ACCESS IS AN
ESSENTIAL COMPONENT OF THE
WELL-FUNDED EFFORT TO CREATE A
REFERENCE FOR THE COMMUNITY AND
THE BRAIN INITIATIVE REFERENCES
THROUGH THE BRAIN CELL DATA
CENTER AND ARCHIVES ALSO AT THE
ALLEN INSTITUTE ASPIRE TO MAKE
THESE EASILY ACCESSIBLE TO THE
COMMUNITY.
I WANT TO END ON ONE FINAL
OUTCOME OF THESE CELL ATLASES
WHICH I THINK WAS NOT ENTIRELY
ANTICIPATED AT THE OUTSET AND
THAT'S THE EPIGENOME ATLASES
LEAD DIRECTLY TO FINDING
FUNCTIONAL ENHANCER ELEMENTS
THAT CAN FIT INTO ADENO
ASSOCIATED ANALYSIS TO ALLOW
CELL-TYPE SPECIFIC MANIPULATION.
THE SINGLE CELL EPIGENOMICS CAN
BE USED TO CLUSTER AND ALIGNED
TO THE TRANSCRIPTOME AND USE IT
TO FIND SHORT ENHANCER ELEMENTS
DISTAL TO GENES ONLY OPEN IN A
CELL TYPE OF INTEREST AND IT
TURNS OUT MANY OF THESE ARE
FUNCTIONAL ENHANCER THAT CAN
CONFER THAT SPECIFICITY IN OF
THEMSELVES.
TO GIVE A FEW EXAMPLES OF THESE
AND THIS IS ONLY A FEW MUCH MANY
WE SEEM TO BE ABLE TO TARGET ANY
CELL WE HAVE THIS TYPE OF
INFORMATION FOR AND INTERNEURONS
AND MANY ENHANCERS TURN OUT TO
BE TO MAINTAIN THE SPECIFICITY
ACROSS SPECIES.
WHILE WE DEVELOPED INITIALLY IN
THE MOUSE, THEY FREQUENTLY
CONFER THE SAME SPECIFICITY IN
MONKEY OR IN HUMAN SPLICE.
THAT'S REALLY A KEY OBSERVATION
AND KEY THING MOVING FORWARD AND
ANOTHER PRIORITY FOR THE BRAIN
INITIATIVE WITH THE
ARMAMENTARIUM IDEA AND WE HAVE
SPECIFIC MANIPULATION IN MANY
MODEL ORGANISMS AND CAN BE USED
IN ANY THAT'S THE RIGHT MODEL
FOR A PARTICULAR BEHAVIOR OR
DISEASE.
AND FURTHERMORE LOOKING FORWARD
TO HUMAN APPLICATION, WE ALREADY
HAVE AVs IN THE CLINIC FOR GENE
REPLACEMENT AND THERAPY BUT SO
FAR THEY'RE FAIRLY BLUNT
INSTRUMENTS BUT NOW WE HAVE THE
OPPORTUNITY TO BE ABLE TO TARGET
SPECIFIC CELLS AND DELIVER A
THERAPEUTIC TO A SPECIFIC CELL
TO A VULNERABLE POPULATION IN
THAT DISEASE.
WE'RE ASKED TO PROVIDE GAPS IN
OPPORTUNITIES AT THE END HERE
AND I THINK MY FIRST STATEMENT
WOULD BE I THINK ALL THESE
TECHNOLOGICAL ADVANCES CAN BE
EQUALLY APPLIED TO STUDY
DEVELOPMENT AND AGING WITH
SPECIES AND IT'S TO CREATE A
REFERENCE TO EACH LAB DOESN'T
NEED TO BE DOING THIS ALL OVER
AGAIN.
THEY CAN MAP TO THE REFERENCE
AND BUILDING KNOWLEDGE BASE
AROUND THAT REFERENCE.
THAT WILL INTERN PROVIDES A
FRAMEWORK FOR MORE TARGETED
QUESTION TO START TO ASK ABOUT
THE DEVELOPMENT PROCESSES
RELEVANT TO THE EMERGENCE OF
CIRCUITRY OR SUSCEPTIBLE TO
DISEASE AND PHENOTYPES AND BUILD
FROM THAT FOUNDATIONAL
STANDPOINT.
AND SECONDLY, THESE TOOLS OF
ENHANCERS CAN BE EQUALLY
DEVELOPED FOR DEVELOPMENT STAGES
AND HITTING DIFFERENT CELLS
PERHAPS PROGENITORS OR NEW
NEURONS EARLY IN DISEASE WHEN
IT'S RELEVANT TO DISEASE AND
THESE NEW TECHNOLOGY HAVE OPENED
THE DOOR TO BEGIN TO
CHARACTERIZE BUT THERE'S A LOT
OF WORK TO DO STILL TO FULLY
CHARACTERIZE THE HUMAN BRAIN TO
STUDY HUMAN BRAIN DEVELOPMENT IN
AGING AND UNDERSTAND HOW IT
UNDER LIES DIFFERENT DISEASES
AND DEVELOPMENT DISEASE AS IN
AGING RELATED DISEASES AND A BIG
GAP I'D LIKE TO HIGHLIGHT IS
ACCESS TO HIGH-QUALITY TISSUES
TO STUDY HUMAN BRAIN DEVELOPMENT
IN PARTICULAR AND STUDYING HUMAN
BRAIN AS A WHOLE THAT WOULD
ACCELERATE THE FIELD IF A
GREATER EFFORT IN BRAIN DONATION
COULD BE MADE.
WITH THAT I'D LIKE TO END AND
THANK MANY PEOPLE.
I'VE REPRESENT THE WORK OF MANY
AT THE ALLEN INSTITUTE AND BRAIN
INSTITUTE AND THE STAFF MANY
OTHER COLLABORATORS AND THE
NATIONAL INSTITUTE ON AGING.
THANK YOU VERY MUCH.
>> TERRIFIC, THANK YOU, ED.
ALL RIGHT.
SO ALL THE SPEAKER NOW ASKED TO
PLEASE TURN ON THEIR VIDEO AND
WE'LL GO AND START WITH THE Q&A
SESSION.
I HAVE COLLECTED ALL THE
QUESTIONS SO FAR FROM THE
AUDIENCE AND I'LL JUST POSE
THESE QUESTIONS TO THE
PRESENTERS IN THE ORDER OF THE
PRESENTATIONS.
WE HAVE A QUESTION HERE FOR
BUSHRA.
I'LL READ THE QUESTION HERE, IS
IT FEASIBLE TO USE GESTALT FOR
ZEBRAFISH MODELS?
>> IT'S POSSIBLE TO USE GESTALT
TO LOOK AT MUTANT -- DIFFERENT
DIFFERENCES IN LINEAGES AND THE
THING YOU'D HAVE TO GENERATE IS
A TRANSGENIC LINE TO HAVE THE
BAR CODE SXRIFD
EXPRESSED IN THE ZEBRAFISH AND
IT CAN BE APPLIED TO LOOK AT ANY
ASPECT OF DEVELOPMENT IN THE
FISH OR ANY OTHER MODEL ORGANISM
WHERE YOU CAN ADAPT THIS.
GENERALLY I'D SAY THE LIMITATION
WITH GESTALT IS THE MUTATIONS
MAY NOT BE AS IMPORTANT TO
UNDERSTANDING THE CHANGES OR
DIFFERENCES IN THE LINEAGE AFTER
THE MUTATION STARTED SATURATED.
THE TIMING IS ALWAYS A BIT OF AN
OOSH AND WE'D LIKE A SYSTEM TO
HAVE MORE CONTROL OR SLOW DOWN
THE RATE AT WHICH MUTATIONS
OCCUR.
>> THANK YOU.
AND WE HAVE A QUESTION HOW LEAKY
ARE THE PROMOTERS YOU USED AND
IF IT'S A PROBLEM AND IF SO HOW
DO YOU USE THIS?
>> THE INDUCIBLE SYSTEMS ALWAYS
HAVE SOME LEVEL OF LEAKINESS.
IN GENERAL THE WAY WE ACCOUNT
FOR THIS IS AT LEAST WITH
ZEBRAFISH BECAUSE WE END UP
SCREENING A LOT OF FISH TO LOOK
FOR TRANSGENIC ANIMALS WHERE WE
HAVE TITER REGULATION OF
EXPRESSION.
THAT'S ONE WAY OF DOING IT.
THERE ARE BETTER INDUCIBLE
RECORDERS.
PERHAPS USING THE CRAE 2 SYSTEM
WITH TAMOXIFEN HELPS REGULATE
THE LEAKINESS TO SOME EXTENT AND
ALSO GENERATING MORE TIGHTLY
REGULATE
REGULATED OTHER SYSTEMS WHERE
THERE'S BASEBALL ENGINEER OR
SEQUENCE CHANGES MADE TO MAKE IT
MORE TITER.
IN GENERAL GAS LEAKINESS WILL
ALWAYS BE A SMALL ISSUE IN THE
SYSTEMS.
FOR US IT'S NOT A HUGE CONCERN
TO HAVE A LOW BASAL LEVEL OF
LEAKINESS AND IN THE DAY THE CAS
9 NEEDS TO BE TURNED ON TO A
CERTAIN LEVEL IN ORDER FOR THE
MUTATIONS TO ACCUMULATE AND IF
THERE'S A LOW LEVEL IT'S NOT
SUFFICIENT TO SATURATE THE
SYSTEM AND YOU CAN ALWAYS HAVE
ADDITIONAL LEVELS OF INFORMATION
ON TOP OF ANY BASAL ACTIVITY
THERE.
OVERALL, IF THERE IS ACTIVITY AS
A BACKGROUND IT WILL BE LESS
THAN 5% OF THE POPULATION.
>> A FOLLOW-UP TO GESTALT AND
PARTICULARLY WHAT YOU FOUND,
YOUR LINEAGE CONCLUSION, IF I
UNDERSTAND CORRECTLY, THERE'S
QUITE A BIG DEAL OF LINEAGES.
WHERE YOU BASICALLY HAVE SIMILAR
CELL TYPES THAT YOU HAVE FROM
DIFFERENT LINEAGES.
IF I UNDERSTAND THIS CORRECTLY
TO WHAT LEVEL OF GRANULARITY CAN
YOU TAKE THAT WHICH IS BASICALLY
ASKING HOW SURE YOU ARE ABOUT
THE CELL TYPE IDENTITY.
CAN YOU STATE IF YOU HAVE
IDENTICAL CELL TYPES THAT COME
FROM DIFFERENT LINEAGE BRANCHES
OR CAN YOU ONLY SAY THAT THERE
ARE SOME REGIONAL CONVERGENCES
WITH CORE NEURON POPULATION
DESCRIBED FROM THE DIFFERENT
LINEAGES.
>> I THINK IT'S AN IMPORTANT
QUESTION.
IN TERMS OF CONVERGENCE, SO
THERE'S A RESOLUTION LIMIT TO
GESTALT WHERE THE LINEAGE
RECORDING DID NOT HAPPEN ACROSS
THE WHOLE PERIOD OF DEVELOPMENT.
WE LOOKED AT RELATIVELY EARLY
DURING BRAIN DEVELOPMENT THE
DECISIONS MADE AND THERE ARE
MOST LIKELY ADDITIONAL LEVELS OF
LINEAGE DIVERGENCES THAT
OCCURRED AFTER WE FINISHED
RECORDING THEIR HISTORIES.
AND SO THOSE WERE LIKELY MISSED.
SO IN SOME WAYS WE CAN'T RULE
OUT THE POSSIBILITIES THE CELL
TYPES DIDN'T OCCUR LATER ON AND
WE DIDN'T CAPTURE THAT
INFORMATION.
WITH THE TIMING WE ARE LIMITED
WITH THE METHOD OF RECORDING AND
SO ASKING THOSE GRAN YUU
SO ASKING THOSE GRAN YLAR
QUESTIONS WHEN THE CELL TYPES
DIVERGED, I THINK WE NEED ONE
MORE STEP IN ORDER TO ADDRESS
THAT QUESTION.
>> THANK YOU.
ALL RIGHT, NEXT QUESTION TO TIM.
DO YOU THE PROPORTION MODIFIED
OVER TIME AND SECOND OF THE
DYNAMIC REGIONS AND WHAT'S THE
DIFFERENCE IN GENETIC
DIFFERENCES ACROSS THE LIFE
SPAN.
>> THOSE ARE GOOD AND IMPORTANT
QUESTIONS.
TO THE FIRST ONE IN TERMS OF THE
CONSISTENCY OVER THE LIFE SPAN I
SHOWED ONE SNAPSHOT HOW THE
EPIGENOME LOOKS IN THE DIFFERENT
BRAIN REGIONS.
WE'VE DONE SINGLE CELL ATAC IN
THE MOUSE AND WHEN WE CLUSTER IT
WITH THE TIME POINT THE
EMBRYONIC TISSUE CLUSTERS FAR
FROM THE ADULT.
THE DIFFERENT BRAIN REGIONS ARE
MORE SIMILAR TO EACH OTHER AND
THE EMBRYO THAN TO THE ADULT
TISSUE AND THAT'S NOT SO
SURPRISING.
THIS HITS TO THE BIG CHALLENGE
IN BIOLOGY IN LINKING DIVIDING
CELLS WITH AND THERE'S A HUGE
CHANGE IN TRANSCRIPT AND
EPIGENOME VERSUS THE EMBRYO AND
THE MATURE CELL TYPE.
ONE CAN EITHER DO LOTS OF
DIFFERENT TIME POINTS OTHER LABS
HAVE DONE TO LINK EARLY RNA OR
EPIGENOME OR OTHER COMPUTATIONAL
TECHNIQUES TO TRY TO INVESTIGATE
THAT.
THE MAJORITY WILL BE DIFFERENT
THAN IN THE MATURE BREAK AND
THERE'S SOME GENES EXPRESSED
EARLY ON AND MAINTAINED LIKELY
BE SIMILAR.
AND WE ARE NOW INVESTIGATING
CERTAIN MUTATIONS AND GENES TO
SEE WHEN A GENE IS PERTURBED,
HOW DOES THAT AFFECT THE
EPIGENOME AND YOU CAN LOOK AT
HOW ACTIVITY AFFECTS THE
EPIGENOME STATES THOSE ARE THE
QUESTIONS AND EXPERIMENTS WE
HOPE FOR THE FUTURE TO
UNDERSTAND HOW ENVIRONMENTAL
CHANGES OR BEHAVIOR AFFECT THE
EPIGENETIC STATE AND
CONNECTIVITY PATTERNS.
>> YOU'RE SHOWING ACCESSIBILITY
AND TRANSCRIPTION AND YOU'VE
DONE CORRELATION WITH HISTONE
MODIFICATIONS AND WHERE DO YOU
NOT SEE ACCESSIBILITY BUT SEE
TRANSCRIPTION IN THE LOCUS.
DOES THAT HAPPEN OR IS IT RARE?
>> WE SEE LOCUS ACCESSIBLE IN
THE PROMOTER BUT KNOW THE GENE
IS NOT EXPRESSED AND THAT'S ONE
THING WE HIGHLIGHTED AND THERE'S
ONE GENE WHERE THE PROMOTER WAS
ACCESSIBLE IN ALL FOUR BRAIN
REGIONS BUT WE AND OTHERS HAVE
SHOWN THE GREEN IS NOT EXPRESSED
IN THE CORTEX OR GLE.
-- LGE AND ONE PIECE OF DATA
YOU CAN BE FOOLED BUT LOOKING AT
THE ENTIRETY OF THE DNA IT MAKES
MORE SENSE AND I DON'T KNOW
WHERE THE PROMOTER WAS CLEARLY
REPRESSED BECAUSE IT WOULDN'T
MAKE A WHOLE LOT OF BIOLOGICAL
SENSE BUT THE OPPOSITE LOGIC WE
DO.
SOMETIMES IT'S THE PROMOTER OPEN
PRIOR TO RNA AND SOMETIMES THE
PROMOTERS ARE OPEN IN REGIONS
WHERE WE KNOW IT'S NOT EXPRESSED
AND WE DON'T KNOW WHY THAT IS
BUT TO ANSWER YOUR QUESTION WE
DO SEE MISMATCHES OF LOGIC BUT
IN GENERAL THE OVERALL THEME IS
THE EPIGENOME SEEMS TO BE IN A
POSITION YOU'D EXPECT ON RNA
ROLES.
>> WE HAVE A TECHNOLOGY QUESTION
TO YOU TIM AND YE.
WHAT MOUSE STRAINS WERE USED BY
DOCTORS PETROS AND ZHANG AND ARE
THERE COMPARISONS ACROSS MOUSE
STUDIES ON SINGLE USE GENOME?
>> WE USE THE C57 BLACK MOUSE
LINE AND NOW INVESTIGATING MOUSE
MUTANTS WITH THE SAME SCREEN.
>> WE HAVEN'T DONE THE SAME
ANALYSIS WITH THE OTHER STRAINS
AND THE PERSON ASKED ABOUT HUMAN
STUDIES USING MOUSE STUDIES AND
SINGLE GENOME, THAT IS TRUE.
SO IN OUR RNA SEQ DATA WE LOOKED
AT THE VARIANTS ACROSS
INDIVIDUALS AND IT'S LARGER FROM
OUR HUMAN STUDIES THAN FROM OUR
MOUSE STUDIES.
BUT WHEN WE FIRST OBTAINED HUMAN
ASTROCYTE SPECIFIC SIGNATURES WE
WONDERED WHETHER THAT IS REALLY
HUMAN VERSUS BLACK 6 MICE OR ALL
THAT AND WE HAVE AN INDIRECT WAY
TO LOOK AT THIS.
WE LOOKED AT ANOTHER DATA SET
THAT IS NOT ASTROCYTE SPECIFIC
AND THE WHOLE TISSUE HIPPOCAMPUS
BRAIN TISSUE FROM A GROUP IN THE
JACKSON LABS WHERE THEY COMPARED
MANY MOUSE SCREENS AND WE SEE
THE TOP HUMAN ASTROCYTES ARE
HIGH IN HUMAN ASTROCYTE BUT LOW
IN MOUSE ASTROCYTE GENES ARE
ACTUALLY CONSISTENT ACROSS
SPECIES.
AND IT'S NOT LIMITED BUT MORE
THOROUGH STUDIES ARE REQUIRED TO
ADDRESS DIFFERENCES IN MOUSE
GENES.
>> IS IT POSSIBLE TO USE
IMMUNOPANNING AS AN ENRICHMENT
STEP PRYOR TO SINGLE CELL
SEQUENCING TO SEE IT CERTAIN
TYPES OF ASTROCYTES RESPOND
DIFFERENTLY TO THE ENVIRONMENT
OR OTHER STIMULI?
>> YES, THAT'S DEFINITELY A
REASONABLE THING TO DO.
IT'S A GOOD IDEA AND WE HAVE
DONE THAT AND WHEN WE DO THE
MOTIVATION IS IF YOUR INTEREST
IS IN SUBTYPES YOU DON'T WANT TO
SPEND SO MUCH MONEY TO SEQUENCE
A LOT OF CELLS WHERE THE
MAJORITY ARE NEURONS SO WE DO
ENRICHMENT FIRST AND SINGLE CELL
SEQUENCING.
>> THANKS.
AN INTRIGUING QUESTION FROM THE
AUDIENCE.
HOW DOES THIS CELL TYPE
CONSERVATION ACROSS SPECIES MAP
TO THE ADULT ANIMAL OF HUMAN
BRAIN DEVELOPMENT.
ANY COMMENTS ON THAT?
>> IT'S A TERRIFIC QUESTION I
THINK ULTIMATELY WILL BE
ADDRESSED VERY WELL BY
COMPARATIVE DEVELOPMENT
ANALYSIS.
I THINK I DON'T KNOW THE ANSWER
THERE YET BUT THE HINTS ARE
THERE FROM PRIOR WORK WE HAVE
DONE DEVELOPMENT ANALYSES IN
HUMAN AND NON-HUMAN PRIMATE AND
DIFFERENT PARTS OF THE CORTEX
WHICH MATURE AT DIFFERENT RATES
AS WELL PRE FRONTAL AND AT THE
MORE BULK LEVEL THIS IS
EXTREMELY CLEAR.
YOU CAN SEE THE DEVELOPMENT
TRAJECTORIES AND EXTEND ED IN
CERTAIN BRAIN REGIONS.
I THINK THE PHENOMENON OF
DIFFERENTIAL MATURATION WOULD BE
EXTREMELY OBVIOUS WITH THE RIGHT
ASSAY BUT ARE SOME DEVELOPING
THE THE SAME RATE AND OTHERS
NOT.
I THINK WE'LL SEE SURPRISES.
SOMETIMES THERE'S THINGS
GENERATED EARLIER AND HAVE MORE
PROTRACTED MATURATION.
SOME ARE COORDINATED ACROSS
REGIONS SUCH AS SYNAPTOGENESIS
AND ESPECIALLY FOR DEVELOPMENTAL
DISORDER WHERE IT MAY WHEREBY
THINGS BEGIN TO GO WRONG.
>> IS THERE A WAY TO COMBINE
OMIC APPROACHES?
>> IN THE ADULT BRAIN I THINK
PROBABLY SOME MEMBERS OF THE
AUDIENCE MAY HAVE A BETTER
HANDLE ON EXTRA TRICKS THAT CAN
BE BROUGHT FOR DEVELOPMENT
CONNECTIVITY.
WHAT WE TRIED TO DO HAS BEEN TO
LINK CONNECTIVITY TO THE
MOLECULARLY DEFINED CELL TYPES.
SIMILAR TO WHERE YOU SEQUENCE
WITH PHYSIOLOGY YOU SEQUENCE
WITH SOME FORM OF ANATOMY AND
ONE VERSION OF THIS IS TE TO
RETRO GRADUALLY LABEL CELLS AND
FIGURE OUT WHO THE CELLS ARE BY
SEQUENCING THEM.
ANOTHER IS TO GO IN THE OTHER
DIRECTION AND TO WHOLE BRAIN
RECONSTRUCTION AND WHAT MAKES
THE PROBLEM SO DIFFICULT IS THE
PROS -- PROMISS
IT'S A RATHER CHALLENGING THING
AT THE MOMENT.
THERE ARE VERY PROMISING
TECHNIQUES FROM TONY ZADAS'S
GROUP TO SEQUENCE CELLS TO MANY
LOCATIONS.
I THINK THE TECHNOLOGIES ARE
COMING.
BUT AT THE MOMENT IT'S STILL
HARD-FOUGHT INFORMATION TO GET
CONCRETELY.
>> SO, HAL BEAT ME TO THE PUNCH
TO A QUESTION.
YOU MENTIONED THERE ARE 3,000,
DO YOU MEAN THIS REFLECTS THE
NORMAL SUBTYPES.
ASK YOU TO VENTURE GUESSES FOR
NUMBERS IN THE HUMAN BRAIN.
>> ED: OKAY, THAT'S GREAT.
SO FIRST OF ALL, I HAVE TO SAY
I'M REPRESENTING OTHERS' WORK
ON THIS MOUSE BRAIN, SO PLEASE
TAKE THAT INTO CONSIDERATION.
THIS IS COMING FROM MY
COLLEAGUE HONG QI ZHANG'S GROUP.
WHAT IS USED FOR THE MOTOR
CORTEX, APPLIED TO SIMILAR DATA
GENERATED ACROSS THE ENTIRE
MOUSE BRAIN.
AND THIS IS SORT OF THE ORDER
WITH THAT KIND OF THRESHOLDING
THAT IS OBSERVED ACROSS THE
ENTIRE BRAIN.
AND IT TURNS OUT THAT ACTUALLY,
THE MAJORITY OF THE DIVERSITY
COMES FROM SUB CORTICAL
STRUCTURES.
I THINK A LOT OF THE CORTICAL
-- WOULD THINK IT WAS IN THE
CORTEX, BUT IT'S ARCHITECTURE
THAT GRADES IN DIFFERENT
FASHIONS IN THE CORTEX.
THERE ARE MANY TYPES OF CELLS
THAT DON'T HAVE SUCH A
HIERARCHICAL ORGANIZATION IN
SUB CORTICAL STRUCTURES.
BUT THAT IS KIND OF THE WHOLE
PICTURE.
OF COURSE THIS DOESN'T INCLUDE
OTHER PARTS OF THE CNS, THE
SPINAL CORD OR RETINA, WHICH
WOULD ADD TO THAT NUMBER.
THE SECOND PART OF YOUR
QUESTION TO VENTURING A
QUESTION IN HUMAN.
ONE OF THE THINGS WE HAVE
REALLY BEEN STRUCK BY IS THE
CELLULAR DIVERSITY IN A
HOMOLOGOUS REGION SEEMS TO BE
EXTREMELY CONSISTENT ACROSS
MAMMALS.
IT IS NOT DRAMATICALLY MORE
DIVERSE IN THE HUMAN CORTEX
COMPARED TO THE MOUSE CORTEX.
THERE'S A LOT MORE OF IT.
AND I THINK YOU CAN GET GREATER
DIVERSIFICATION, IN THE CORTEX
BECAUSE YOU HAVE MORE REGIONS
AND THEY BECOME MORE
SPECIALIZED TO SOME DEGREE.
BUT FOR THE MOST PART, THE
DIVERSITY IS VERY SIMILAR.
I THINK THAT IS PROFOUND IN ONE
WAY.
THE ALSO PRAGMATICALLY REALLY
IMPORTANT BECAUSE IT MEANS IT'S
NOT 1,000 TIMES THE PROBLEM TO
MAKE A HUMAN CELL OUT OF THIS.
THIS IS A DOABLE THING TO TRY
TO MATCH THAT LEVEL OF
DIVERSITY.
THE PROBLEM BECOMES ONE OF HOW
DO YOU ADEQUATELY SAMPLE A
BRAIN WHICH IS 1,000 TIMES
BIGGER TO CAPTURE THAT
DIVERSITY.
BUT IT DOESN'T APPEAR THE
DRAMATICALLY DIVERSE.
WE'RE NOT TALKING ABOUT EVEN A
TWO-FOLD.
I THINK IT'S NOT MUCH MORE
DIVERSE IN THE HUMAN.
>> I WANT TO ELABORATE A LITTLE
BIT ON THIS, AND THIS IS SORT
OF BASED WITH -- ALSO ASKING
WHAT ARE THE LIMITATIONS IN
IDENTIFYING NEURO TYPES BY
TRANSCRIPTIONAL PROFILING.
I WANT TO COMMENT ON WHAT IS
EMERGING IN -- WE HAVE BASED
ON OUR SINGLE CELL ATLAS, THE
GREAT DATA SET.
WE HAVE VERY NICE -- OF THE
DIFFERENT DREL TYPES.
BUT WE ARE LOOKING AT TROJAN,
WE LOOK BY TAGGING WITH G.F.P.
AND LOOKING WHETHER PROTEIN IS
EXPRESSED.
THERE ARE ACTUALLY INTRIGUING
DIFFERENCES, MAYBE NOT TOO
UNEXPECTED BECAUSE OF ALL THE
STUFF THAT HAS TO HAPPEN WITH
TRANSCRIPTION AND MAKING OF A
PROTEIN.
COMING BACK TO HAL'S QUESTION,
I'M WONDERING IF YOU HAVE
THOUGHTS ABOUT WHETHER THEY ARE
SORT OF, YOU KNOW, DEEPER
LAYERS OF DIVERSITY SETS THAT
ARE NOT HAPPENING ON THE
TRANSCRIPTIONAL LEVEL BUT ON
THE LEVEL OF TRANSLATION
CONTROL, MICRONASE AND ALL THAT
STUFF.
MAYBE TO FOLLOW-UP ON THAT, IS
THE INSTITUTE THINKING OF
PURSUING THAT FOR EXAMPLE,
LARGE SCALE GFP TAGGING OR
REGISTERING ANTIBODY STAINS OF
NUCLEAR PROTEINS AGAINST
TRANSCRIPTIONAL PROFILES TO GET
A SENSE OF HOW MUCH MORE
DIVERSITY YOU CAN GET OUT OF A
TRANSCRIPTION DATA SET?
>> ED: THOSE ARE ALL REALLY
GREAT QUESTIONS.
I WILL START BY SAYING WE SHIED
AWAY FROM GETTING INTO THE
PROTEIN SIDE OF THINGS.
IN PART, BECAUSE VERY OFTEN
THEY ARE DEPENDENT ON
ANTIBODIES AND WE HAVE LIMITED
HIGH-QUALITY ANTIBODIES TO WORK
WITH.
COMPARED TO HAVING THE FULLY
GENERALIZABLE NUCLEOTIDE
APPROACHES.
I GUESS LET ME STEP BACK.
TO ME, ONE OF THE REALLY QUITE
REMARKABLE THINGS IS THAT, YOU
CAN TAKE AN UNBIASED VIEW AT
THE GENOME, AND GET A PRETTY
CONSISTENT CLUSTERING OR
CLASSIFICATION OF SUBTYPES AS
YOU WOULD IF YOU PICKED A SET
OF GENES YOU THINK WOULD BE
PARTICULARLY FUNCTIONALLY
IMPORTANT.
YOU CAN OFTEN REPLICATE IT WITH
SOME, NEURONS ARE WELL
DIFFERENTIATED WITH GENES
ASSOCIATED, YOU CAN LARGELY
RECAPITULATE THE WHOLE THING.
YET, EMBEDDED WITHIN THAT ARE
PROTEIN CODING GENES,
NON-CODING RNA'S, VARIOUS OTHER
THINGS.
WE GET LARGELY THE SAME RESULTS
IF WE LOOK WITH METHYLATION
ANALYSIS OR ATTACK ANALYSIS OR
SINGLE CELL OR SINGLE NUCLEUS.
THEY SEEM TO BE PRETTY
FUNDAMENTAL UNITS THESE ARE
DIFFERENT ASPECTS OF THEM.
THAT BEING SAID, I'M SURE THAT
IF YOU REALLY DOVE IN AND
FOUND, YOU CAN FIND PLACES YOU
CAN BETTER DIFFERENTIATE WITH
RNA'S OR SUB PROTEINS.
AND THERE ARE PLACES WHERE THE
TRANSCRIPTON ISN'T CLEARLY
DESCRIBING EVERYTHING FROM
PHENOTYPING PERSPECTIVE WHAT WE
HAVE SEEN SO FAR.
I WOULDN'T LIKE TO GIVE THE
IDEA I BELIEVE EVERYTHING IS
REPRESENTED IN THE
TRANSCRIPTONE.
I'M SURE THERE'S MORE, BUT IT'S
A GOOD EARLY APPROXIMATION.
>> THANK YOU.
SO WE HAVE TWO MORE QUESTIONS
THAT I WOULD ACTUALLY LIKE TO
TRANSITION NOW TO THE MORE OPEN
DISCUSSION PART.
THIS IS ACTUALLY A QUESTION,
EVEN THOUGH ONE WAS DIRECTED TO
ED, THAT I WOULD LOVE TO HEAR
ALL OF THE PRESENTERS COMMENT
ON.
THEY ARE BOTH VERY IMPORTANT
GENERAL QUESTIONS.
I WILL POSE BOTH OF THEM, AND
MAYBE EACH ONE OF YOU CAN
COMMENT ON BOTH.
ONE IS FOR ALEXANDRIA, WHAT ARE
THE MAJOR CHALLENGES YOU SEE IN
INTEGRATING DATA SETS FROM
DIFFERENT LABS?
THIS IS, OF COURSE, A VERY
COMMON QUESTION THAT AFFECTS
ALL OF YOU.
I WOULD LOVE TO HEAR ABOUT YOU.
AND THE SECOND QUESTION AND
EQUALLY BIG PICTURE QUESTION.
THAT IS DIFFERENCES BETWEEN THE
MALE AND THE FEMALE.
BUSHRA, DO YOU WANT TO START
WITH COMMENTING ON THAT?
THERE ARE STILL MULTIPLE --
HOW DO YOU FEEL ABOUT DATA
INTEGRATION.
VERY INTERESTING SEXUAL
DINANYSMS IN THE BRAIN.
>> YEAH, SO WITH RESPECT TO
INTEGRATING DATA SETS, I THINK,
YEAH, THAT DOES REMAIN A FAIRLY
BIG CHALLENGE.
I THINK ONE OF THE BIGGEST
THINGS IN TERMS OF THE DATA
QUALITIES, AND HOW MUCH, YEAH,
HOW MUCH INFORMATION ARE YOU
GETTING FROM THE SEQUENCING.
AND THIS CAN VARY BASED ON THE
CELL TYPES, SOME ARE EASIER TO
SEQUENCE, YOU GET A LOT MORE
INFORMATION, THEY ARE BIGGER,
THERE'S A LOT MORE RA.
AND THEN YOU COME TO CELLS LIKE
THE BRAIN, ESPECIALLY IN THE
FISH, THEY TEND TO BE REALLY,
REALLY SMALL.
AND DATA QUALITY DOES
DEFINITELY SUFFER.
I DON'T KNOW IF I HAVE A GREAT
RESPONSE TO HOW TO, YOU KNOW,
ADDRESS THIS CHALLENGE.
I GUESS AS WE ARE WORKING IN
THE COMMUNITY TO PROVIDE DATA
SETS THAT OTHER PEOPLE CAN USE,
THIS DEFINITELY STARTS TO
BECOME AN ISSUE.
BUT I DO THINK THAT A LOT OF
THE NEW GENERATION ANALYSIS
PIPELINES ARE TAKING THAT INTO
ACCOUNT.
AND ARE GENERATING WAYS IN
WHICH YOU CAN ACCOUNT FOR
DIFFERENCES IN THE QUALITY OF
THE DATA TO SOME EXTENT.
I THINK THAT IS AT LEAST A
STARTING POINT.
AS WE HAVE A MORE GENERALIZED
PROTOCOL AVAILABLE FOR MAYBE
PREPARATION OF THE VARIOUS
TISSUES, ASSOCIATION OF
PARTICULAR CELLS, THAT WOULD
HELP IN SORT OF AVERAGING OR
MAINTAINING THE DIFFERENCES TO
A LOWER LEVEL.
WITH RESPECT TO THE MALE VERSUS
FEMALE DIFFERENCES, SO FOR
EXAMPLE, IN THE STUDIES THAT
I'VE BEEN INVOLVED IN, WE HAVE
BEEN LOOKING AT DEVELOPMENT AND
THAT TIME POINT, THE FISH HAS
AN ACTUAL SEXUALLY DYNAMICALLY
MORE, WE CAN'T REALLY TELL.
THERE'S NO GENETIC, THEY DON'T
HAVE SEX CHROMOSOMES SO WE
CAN'T REALLY TELL THEM APART
BASED ON THAT EITHER.
SO I THINK WHEN YOU REACH THE
SEXUAL MATURITY STAGE AND YOU
ARE LOOKING AT OLDER FISH, THE
QUESTION OF MALES AND FEMALES
CAN BE MORE INTERESTING, BUT
FOR OUR STUDIES WE HAVEN'T
LOOKED AT IT BECAUSE WE ARE
LOOKING AT VERY EARLY
DEVELOPMENT.
>> UNDERSTOOD, YEAH.
TIM, DO YOU WANT TO SAY
SOMETHING ABOUT ACROSS LABS AND
ALSO SEX AS A PARAMETER?
>> TIM: DEFINITELY N.I.H. HAS
MADE A PUSH TO LOOK AT MALES
AND FEMALES FOR DIFFERENT
STUDIES.
WE ARE LOOKING AT 12, WHILE WE
CAN SEX THE MICE, SOME
EXPERIMENTS WE HAVE, WE DON'T
KNOW HOW DIFFERENT THE MALE AND
FEMALE BRAINS ARE IN 12.
BUT WHENEVER POSSIBLE, THE
ASSAYS INVOLVE POOLING MULTIPLE
EMBRYOS TOGETHER, WE TRY TO
POOL MALE AND FEMALE TOGETHER.
BUT ONE COULD BE OPPOSITE,
SEQUENCED MALES VERSUS FEMALES
AND LOOK AT THE DIFFERENCES.
BUT CONCEPTUALLY, ESPECIALLY IN
ADULT MODEL SYSTEMS AND HUMAN
PRIMATES AND THINGS THAT
QUESTION IS VERY IMPORTANT,
BECAUSE OBVIOUSLY A VARIETY OF
FACTORS COULD INFLUENCE
CIRCUITRY DIFFERENT.
AS FAR AS INTEGRATING DIFFERENT
DATA FROM DIFFERENT LABS AND
DIFFERENT SPECIES, PEOPLE AT
THE -- INSTITUTE, -- GENOME
CENTER ALSO DOES AN EXCELLENT
JOB TRYING TO OVERCOME THESE
CHALLENGES.
I WON'T SPEAK FOR AT AN, I
FORGET THE NAME OF THE WEBSITE
BUT HE IS TRYING TO INTEGRATE
ALL THESE DIFFERENT DATA SETS.
IF YOU HAVE SINGLE NUCLEAR TACK
IN AN ORGAN YOU CAN PUT IT IN
THEIR DATA SET AND ACTUALLY
READ OUT WHAT THE RNA
TRANSCRIPTION IS.
EVEN THOUGH DIFFERENT CELL
TYPES.
THAT KIND OF INTEGRATION IS
REALLY IMPORTANT FOR
UNDERSTANDING THESE MULTIONLY
TYPES OF ANALYSIS, ONE TYPE OF
DATA IS NOT SUFFICIENT TO DO IT.
IT'S IMPORTANT, AS BUSHRA SAID,
THE DATA QUALITY SET NEEDS TO
BE GOOD.
MAYBE TEN YEARS AGO THEY DIDN'T
PROTECT THE WORK WHERE IT WAS
TODAY, YOU NEED GOOD QUALITY
DATA SETS, MATCH TIME POINTS
AND IDEALLY SPATIAL REGIONS, IN
TERMS OF WHAT WE THINK ABOUT,
SINGLE CELL DEVELOPING BRAIN,
TAKING THE ENTIRE FOREBRAIN
MUSHING IT UP AND LOOKING AT
IT, WE KIND OF MICRO DISSECTED
THESE REGIONS.
THERE ARE QUESTIONS THAT COME
WITH THAT IN TERMS OF
INTEGRATING IT, I THINK ED
MIGHT BE ABLE TO ADDRESS THOSE
ISSUES.
>> BEFORE WE GO TO ED FOR THE
QUESTIONS, LET'S ASK ABOUT YE
ABOUT THE GLIA PROBLEM.
>> SO, I SHOULD START WITH SEX
-- SOMETHING?
>> UH-HUH.
>> YEAH, WE ACTUALLY DID
EXAMINE MALE VERSUS FEMALE
TRANSCRIPTTOME IN HUMANS.
THE DIFFERENCES ARE QUITE SUBLE.
WE HAVE A SHORT GENE LIST THAT
IS EPIGENETIC, DIFFERENT FROM
MALE AND FEMALE IN THE HEALTHY
BRAIN.
OUR GUESS IS THAT IN THE
HEALTHY BRAINS, MALE AND FEMALE
ARE QUITE SIMILAR.
BUT IN DISEASE CONDITIONS THEY
COULD BE VASTLY DIFFERENT, AS
WE ALL KNOW MALE AND FEMALE
HAVE DIFFERENT SUSCEPTIBILITY
TO A VARIETY OF DISEASES BUT IN
THE HEALTHY BRAIN, OUR
COGNITIVE FUNCTION ARE REALLY
SIMILAR.
MANY PEOPLE IN THE FIELD HAVE
REPORTED MICRO GLIAL, SEXUAL
MORPHISM WHICH IS INTERESTING,
WE SEE COMPARED WITH MICRO
GLIA, AT LEAST UNDER THE
HEALTHY CONDITION.
>> OLIVER: GOOD, GOOD.
GREAT.
ED, WHY DON'T YOU COMMENT ON
THESE POINTS.
THESE SHOULD BE OUR LAST WORDS
FROM YOU, ACTUALLY EVERYONE FOR
THIS SESSION BEFORE WE BREAK.
BUT YOU HAVE A FEW MINUTES TO
TALK ABOUT THESE IMPORTANT
ISSUES.
>> ED: THANK YOU.
FIRST OF ALL, I REALLY WANT TO
HIGHLIGHT THIS IS REALLY BIG
DATA SCIENCE HERE WITH THESE
ENORMOUS DATA SETS.
AND IT REQUIRES A LOT OF
COMPUTATIONAL EXPERTISE.
AND I THINK ONE OF THE
SUCCESSES OF SOME OF THE BIGGER
CONSORTIA HAVE BEEN TO BRING IN
HARD CORE COMPUTATIONAL
BIOLOGISTS OR EVEN OUTSIDE OF
THESE FIELDS TO TACKLE THESE
KINDS OF QUESTIONS.
YOU KNOW, THESE SORT OF TRICKLE
DOWN TO THINGS MANY LIVES CAN
APPLY TO THEIR OWN RESEARCH.
AND SO ACTUALLY, -- WORK ON
AZIMUTH IS THE NAME OF THE TOOL.
HAVING THIS METHOD AND APPLY TO
YOU CAN MAP NEW DATA SETS
AGAINST THE OLD.
YOU KNOW, WHEN DATA IS MEASURED
INDEPENDENTLY, EITHER BY THE
SAME GROUP BUT DIFFERENT
METHODS OR ACROSS DIFFERENT
GROUPS THAT CREATES A PROBLEM
OF TRYING TO NORMALIZE AND
INTEGRATE THOSE DATA SETS.
ONE OF THE REALLY POSITIVE
THINGS FROM THE SINGLE CELL
WORLD IS THAT IT'S POSSIBLE TO
INTEGRATE THESE QUITE
EFFECTIVELY.
I ALMOST HAD A SLIDE IN MY
PRESENTATION THAT SHOWED PART
OF THE CELL CENSUS EFFORT IN
THE MOUSE WHERE THERE THERE
WERE MULTIPLE TRANSCRIPTOME
METHODS, CELLS AND NUCLEI.
THEY COULD BE COMPARABLE.
THESE KINDS OF DATA KIND OF
LEND THEMSELVES WELL TO THAT.
BUT THERE ARE STILL INTEGRATION
PROBLEMS.
IF YOU COULD A TACK SEEK AND
RNA SEEK, YOU CAN ONLY ALIGN AT
A CERTAIN LEVEL OF CERTAINTY.
AND SO I THINK MORE AND MORE WE
ARE GOING TO BE NEEDING THE
COMBINED METHODS.
WHERE WE MEASURE THEM AT THE
SAME TIME.
AND THE COMPANIES ARE SEEING
THIS.
10 X NOW HAS MULTIOME.
WE FOUND HAVING A SMALL AMOUNT
OF MULTIOME ALLOWS YOU TO
INTEGRATE LARGER SINGLE
MODALITY SETS.
I THINK THIS IS GOING TO BE AN
ONGOING CHALLENGE FOR THE FIELD.
BUT ONE THAT THERE'S A HUGE
AMOUNT OF PROGRESS FOR.
AND I THINK IT REALLY IS WORTH
SOME SIGNIFICANT INVESTMENT
FROM N.I.H. IN FOSTERING THE
COMPUTATIONAL SIDE OF THINGS.
ON THE QUESTION OF SEXUAL
DIMORPHISM.
IT'S A CRITICAL QUESTION AND
ONE THAT ALL OF THE NAMED ATLAS
PROJECTS ARE MORE OR LESS
OBLIGATED TO TAKE ON, FOR GOOD
REASON.
AND YOU KNOW, OF COURSE YOU CAN
DIFFERENTIATE ON SEX CHROMOSOME
GENE EXPRESSION VERY EASILY.
BUT YOU CAN SEE SEXUAL
DIMORPHISMS IN MANY CASES.
I DON'T KNOW HOW MANY SURPRISES
HAVE BEEN PROMOTED SO FAR.
YOU SEE HYPE THALAMIC
DIFFERENCES DIFFERENTLY.
BUT THAT'S BEEN DESCRIBED IN
THE PAST.
CLEARLY THERE ARE DIFFERENCES,
PERHAPS THEY WILL MANIFEST MORE
ROBUSTLY DURING DEVELOPMENT AS
WELL.
I THINK THIS IS AN ESSENTIAL
THING THAT ALL THESE BIG
EFFORTS SHOULD HAVE AS PART OF
THE EXPERIMENTAL DESIGN SO WE
CAN BEGIN TO UNDERSTAND THESE
THINGS.
>> ONE QUICK FOLLOW-UP, ED.
IS THERE A DIFFERENCE, THOSE
DIFFERENCES THAT YOU SEE THOSE
RELATIVELY FEW DIFFERENCES, ARE
THEY WITHIN CELL TYPES?
OR DO YOU THINK THEY ARE LIKE
INVERTED NERVOUS SYSTEM
SEX-SPECIFIC CELL TYPE, THAT
ONLY EXIST IN ONE SEX VERSUS
THE OTHER?
>> ED: I WOULD HATE TO DEFER ON
THAT QUESTION, BUT I'M
REPRESENTING OTHERS' WORK THAT
I WOULD HESITATE TO GET WRONG.
LET'S JUST SAY THE QUESTION IS
UNDER ACTIVE INVESTIGATION.
BUT I THINK THERE ARE MORE
ROBUST DIFFERENCES IN CERTAIN
PARTS OF THE BRAIN.
>> OLIVER: I SEE.
THANK YOU.
ALL RIGHT, WE ARE PRETTY MUCH
AT THE END OF THIS MORNING
SESSION.
SO WE WILL NOW TAKE A 20-MINUTE
BREAK.
AND THEN WE WILL HAVE SESSION 2
START AT 1:40.
WONDERFUL.
SEE YOU GUYS THEN.
THANK YOU.
AND THANKS AGAIN TO THE
SPEAKERS.
>> THANKS, OLIVER, FOR RUNNING
THE SESSION.
>> ED: THANKS VERY MUCH.
THAT WAS FUN.
IT REALLY SHOWS THE PROBLEM WE
NEED TO ADDRESS IN NEURO
SCIENCE AND BRAIN SCIENCE.
PARTICULARLY ON THE LEFT, IF WE
LOOK AT THE SIZE OF THE
QUESTIONS WE ARE ASKING, MANY
OF US ARE WORKING AT DIFFERENT
LEVELS OF SCALES OF THE BRAIN.
FROM THE MICRON SYNAPTIC LEVEL,
NEURON TO THE CELLULAR LEVEL,
UP TO THE WHOLE BRAIN LEVEL.
AND THIS IS THE PROBLEM WE HAVE
TO DEAL WITH AND PART OF THE
DISCUSSION TODAY IN THIS
SESSION WILL BE LOOKING AT
BRAIN STUR STRUCTURE AND
FUNCTION AT THESE DIFFERENT
LEVELSMENT BUT DON'T FORGET P
ABOUT THE FOURTH DIMENSION,
TIME.
OUR BRAIN WORKS IN VERY
DIFFERENT SCALES OF TIME.
FROM MILLI SECONDS.
TO HOURS TO DAY, TO MONTHS AND
YEARS, ESPECIALLY FOR --
GENERATION AND OTHER BEHAVIORAL
PROCESSES.
SO HERE TERRY SHOWED THE
STATE-OF-THE-ART IN 1988.
THIS IS STATE-OF-THE-ART IN
2014 WHERE HE IS LISTING
DIFFERENT METHODS TO MEASURE IN
DIFFERENT TIME SCALES AND
DIFFERENT SCALES OF SIZE.
AND I THINK WE CAN FILL THIS IN
WITH A LOT OF REVOLUTIONARY
TECHNIQUES DISCUSSED AND
DEVELOPED TODAY.
SO CAN I HAVE THE NEXT SLIDE,
PLEASE.
SO TODAY WE ARE GOING TO BE
TALKING ABOUT, BASICALLY TWO
DIFFERENT LEVELS.
WE WILL BE TALKING ABOUT
MEASURING BRAIN CONNECTIVITY.
AND DR. WILL BE TALKING ABOUT
--
TRYING TO COMBINE MESO
MEASUREMENTS WITH HIGHER
RESOLUTION MEASUREMENTS.
AND THEN WE MOVE TO MODEL
SYSTEMS WHERE MEI ZHEN WILL BE
TALKING ABOUT WIRING CHANGES
ACROSS THE LIFE SPAN.
AND FINALLY TO SYSTEM WITH
ELLIE HECKSCHER TALKING FROM
STEM CELL TO CIRCUIT.
THIS IS A TALK IN SCALES AND
SOMETHING I THINK WE CAN
DISCUSS IN THE DISCUSSION WHAT,
THERE IS A BIG GAP HERE SO WHAT
WILL FILL THAT GAP.
WE WILL START RIGHT OFF WITH
DR. SETSOMPOP.
HE RECEIVED HIS MASTERS IN
SCIENCE FROM OXFORD UNIVERSITY.
AND COMPUTER SCIENCE FROM M.I.T.
POSTDOCTORAL FELLOW FROM THE
MARTINEZ CENTER.
HIS RESEARCH FOCUSES ON THE
DEVELOPMENT OF THE NOVEL M.R.I.
ACQUISITION METHODS AND THE
GOAL OF CREATING IMAGING
TECHNOLOGIES THAT COULD BE USED
TO HELP BETTER UNDERSTAND BRAIN
STRUCTURE AND FUNCTION FOR
APPLICATIONS IN HEALTHCARE AND
HEALTH SCIENCE.
DR. SETSOMPOP, TAKE IT AWAY.
>> THANK YOU FOR THAT
INTRODUCTION.
LET ME SHARE MY SCREEN.
CAN EVERYONE SEE MY SCREEN OKAY?
FOR THE OVERVIEW OF THE
SECTION, LOOKING FORWARD TO
LEARNING MORE ABOUT THROUGH
THESE TALKS.
SO MY TALK WILL BE TOWARDS
PRECISION MESOSCALE M.R.I.
ACROSS THE LIFE SPAN.
THESE ARE MY DISCLOSURES.
I WOULD LIKE TO SHOW TECHNOLOGY
MY LAB HAS BEEN PUSHING FORWARD
IN TERMS OF M.R.I. ACQUISITION,
TO ALLOW US AT THE MESOSCALE
PRECISELY AS WELL AS RAPIDLY.
I WILL FOCUS ON TWO AREAS IN
THIS TOPIC, QUANTITATIVE
IMAGING AND ADVANCED DIFFUSION
IMAGING.
STARTING WITH QUANTITATIVE
IMAGING, I WOULD LIKE TO
DESCRIBE SOME METHODS WE WOULD
BE USING TO GET TO RAPID
REPEATABLE.
LOOKING AT QUANTITATIVE
IMAGING, WE WANT TO IMAGE THE
UNDERLYING QUANTITATIVE TISSUE
RATHER THAN THE TYPICAL
CONTRAST WAY IMAGES ARE DONE.
IN THE HOPE WE COULD MOVE
TOWARD MORE PRECISE AND
REPEATABLE INFORMATION.
AS WELL AS DO MORE QUANTITATIVE
ANALYSIS.
THESE THINGS WILL BE IMPORTANT
WHEN DOING LARGE SCALE STUDY
AND ACROSS THE LIFE SPAN.
QUANTITATIVE IMAGING IS A
PROMISING WAY TO DO THINGS,
HOWEVER IT COULD TAKE A LONG
TIME TO DO BECAUSE IT'S MORE
INTENSIVE IN TERMS OF IMAGING
ENCODING.
A POPULAR APPROACH HAS BEEN
FINGERPRINTING, IMAGING M.R.I.
IS DONE WITH COHERENT SPACE
TIME AND CONTRAST TO REALLY
SPEED THINGS UP AND EACH
ACQUISITION OF THIS M.R.I.
SCAN, EACH POPULATION WILL
POSSESS TEMPORAL FINGERPRINT TO
ALLOW YOU TO REPLICATE AS SHOWN
HERE.
THIS APPROACH WAS INVENTED IN
2013 BY A GROUP AT CASE WESTERN.
ONE OF THE MOST EFFICIENT
ACQUISITION AT THE TIME.
TAKES AROUND 10 SECONDS PER
IMAGING SLICE TO GET ALL THESE
PARAMETERS.
WHICH IS GREAT BUT AT THE SAME
TIME TRYING TO TARGET VERY HIGH
RESOLUTION ACROSS THE WHOLE
BRAIN OF 200-300 SLICES.
IT COULD STILL TAKE 30 MINUTES
OR LONGER MAKING IT HARD TO
TRANSLATE AND USE ROUTINELY.
OVER THE LAST FEW YEARS THERE'S
BEEN A LOT OF ADVANCEMENT TO
TRY TO IMPROVE ON M.R.I.
ACQUISITION.
SOME OF WHICH I WILL FOCUS ON
HERE IN TERMS OF MAJOR
ADVANCEMENT.
FIRST IN TERMS, INSTEAD OF ONE
SLICE AT A TIME, WE ARE NOW
DOING MULTIPLE OR 3D IMAGING.
THESE VOLUMETRIC ALLOWS YOU TO
UNDERSTAND THE DATA ACROSS MORE
DIMENSIONS.
THERE'S ALSO BEEN A LOT OF WORK
IMPROVING, AS WELL AS PRIOR
INFORMATION ABOUT OUR SIGNAL
INFORMATION, PARTICULARLY
THROUGH THE METHOD OF LOW
TEMPORAL SUB SPACE, WHERE YOU
HAVE A SIGNAL EVOLUTION OF
THESE DIFFERENT TISSUES ACROSS
500 DIFFERENT TIME POINTS YOU
ARE TRYING TO RESOLVE.
BUT YOU CAN NOTE THAT THESE
SIGNAL EVOLUTION ACTUALLY LIVE
IN A SMALL SUB SPACE OF THE
TEMPORAL BASIS, SO INSTEAD OF
TRYING TO RECONSTRUCT 500
IMAGING VOLUMES YOU ONLY NEED
TO RECONSTRUCT 5 VOLUMES OF
THESE SUB SPACE SPACES, MAKING
THE RECONSTRUCTION PROBLEM A
LOT EASIER, ALLOWING YOU TO DO
MUCH FASTER IMAGING WITH GOOD
QUALITY.
WE HAVE DONE A LOT OF WORK IN
TERMS OF SEQUENCE OPTIMIZATION,
FLIP ANGLE AND THINGS LIKE
THAT, TO PROVIDE MORE UNITS OF
FINGERPRINT TISSUE TO ALLOW FOR
MORE SIGNAL SEPARABILITY.
WHERE DOES THIS ADVANCEMENT GET
US TO?
THIS IS SOME OF THE LATEST
RESULTS FROM MY LAB, WHERE WE
ARE NOW ABLE TO ACHIEVE ORDER
OF MAGNITUDE FASTER IMAGING
WITH M.R.F., ONE MILLIMETER
ISOTROPIC, WE CAN DO THIS IN
LESS THAN TWO MINUTES, T1 AND
T2 MAPS.
USE THIS INCREASE OF EFFICIENCY
OF IMAGING ENCODING TO PUSH FOR
HIGHER RESOLUTION.
THIS IS 0.66 MILLIMETER BRAIN,
REQUIRING FOUR MINUTES.
YOU CAN APPRECIATE THE
INCREASING DETAIL AS WE PUSH
FOR A HIGHER RESOLUTION WHERE
WE CAN SEE SOME OF THE
PARAVASCULAR SPACE HERE.
IT'S STILL SURPRISING SOMETIMES
LOOKING AT THIS WE HAVE
SUFFICIENT SNR ENCODING ABILITY
TO DO THIS ON A CLINICAL THREE
TESLA SCANNER.
AND THE MAIN DRIVE IN OUR
ABILITY TO DO THIS, WE ARE
USING M.R.I. SCANNER IN AN
EFFICIENT WAY, DOING CONTINUOUS
VOLUMETRIC RESOLUTION, WE ARE
ACQUIRING DATA AT A TIME AND WE
ARE POOLING ALL THIS DATA
TOGETHER IN A NICE
RECONSTRUCTION TO PROVIDE IVE
INFORMATION QUICKLY.
SO NOW THAT I HAVE SHOWN YOU
SOME OF THE METHODS, LET'S LOOK
AT SOME OF THE BENEFIT OF
QUANTITATIVE IMAGING.
I THINK THIS IS QUITE A NEAT
EXAMPLE WHERE SHOW
REPEATABILITY OF SCANS, NOT
ONLY ACROSS TIME POINTS, BUT
ALSO ACROSS SCANNER VENDORS ON
A HEALTHY VOLUNTEER.
ONE MILLIMETER WHOLE BRAIN
M.R.I. SCAN TWO MINUTES,
SIEMENS SCANNER.
SIX MONTHS LATER, GE PREMIERE
ON SAME HEALTHY VOLUNTEER.
DO SUBTRACTION AND SCALE THINGS
UP BY A FACTOR OF 10.
YOU CAN SEE THESE MINIMAL
DIFFERENCES BETWEEN THESE TWO
SCANS, SHOWING GREAT
REPEATABILITY AND RELATEBLY
HIGH RESOLUTION.
SO OVER THE LAST YEAR OR TWO OF
ALSO TRYING TO PUSH THIS
TECHNOLOGY FURTHER, INFUSING IN
SOME OF THE ADVANCED MACHINE
LEARNING FOR OUR IMAGING, AS
WELL AS OUR ABILITY TO PROVIDE
-- WE ARE STARTING TO RULE
SOME OF THIS OUT TO THE CLINIC
AT THE STANFORD HOSPITAL AS
WELL AS AT THE CHILDREN'S
HOSPITAL.
SO HERE IS SOME OF OUR LATEST
RESULTS OF PRELIMINARY DATA.
WHILE WE ARE ABLE TO GET ONE
MILLIMETER ISOTROPIC WHOLE
BRAIN OF T1, T2 AND SIM PATIC
CONTRAST WITH ONE MINUTE SCAN
WITH RECONSTRUCTION, THESE ARE
THE CLINICAL CONTRASTS WE ARE
ABLE TO SYNTHESIZE, HAVE GOOD
CORRESPONDENCE TO A CLINICAL
SCAN NORMALLY USED, TAKES
AROUND 30 MINUTES.
WITH THIS HOPEFULLY I CAN SHOW
YOU DEVELOPING TECHNOLOGY TO
MOVE US TO EXAM AT HIGH
RESOLUTION IN JUST A FEW
MINUTES WITH FAST ONLINE
RECONSTRUCTION AND ACCURATE
SYNTHESIZED CONTRAST WEIGHTED
IMAGES.
AND HOPEFULLY THIS WILL BE
REALLY USEFUL FOR LARGE-SCALE
STUDY, AS WELL AS IMAGING
ACROSS THE LIFE SPAN.
CONTINUING ON THIS THEME,
MOVING FROM MR DP*, WE ARE ALSO
DEVELOPING ANOTHER TECHNIQUE,
ECHO TIME RESULT OR E.P.T.I.
THIS UTILIZES WHAT I WOULD CALL
TIME RESULT IMAGING SIMILAR TO
M.R.F., WE ARE USING SCANNER
NOT AS A CAMERA WHICH IT WAS
USED BEFORE, BUT MORE AS A
VIDEO.
NOT TAKING A FEW IMAGES AND
TRYING TO GET TO QUANTITATIVE
MEASURE BUT CAPTURING A TIME
SERIES OF 500-1,000 IMAGES AND
REALLY TRACK THE SIGNAL
EVOLUTION TO GET REALLY NICE
QUANTITATIVE INFORMATION.
SO IN ORDER TO DO THIS, WE HAVE
TO DO A LOT MORE ENCODING.
WE HAVE TO DO CASE BASE FOR
ENCODING, NOT ONLY ACROSS A FEW
VOLUMES BUT ACROSS THOUSANDS OF
VOLUMES.
WE HAVE TO COME UP WITH A WAY
TO ACQUIRE THIS DATA IN AN
EFFICIENT MATTER, SO WE COME UP
WITH ACQUISITION IN THIS TIME
SPACE WHERE WE CAN HIGHLY
SAMPLE OUR ACQUISITION USING
SOME APPROACHES OF SPARSITY AND
CONTROL ALIASING, AS WELL AS
SPATIAL TEMPORAL, SO WE CAN
RESOLVE MORE TIME RESOLVE
HUNDREDS OF DIFFERENT IMAGES
ACROSS OUR ACQUISITION.
HERE IS AN EXAMPLE OF E.P.T.I.
ACQUIRES DATA FOR 9180 SPIN
ACQUISITION, TRACKING THE STAR
SIGNAL EVOLUTION AS WELL AS T2
RECOVERY.
WE ARE GETTING MORE THAN 100
IMAGES, WHICH ARE PRETTY SHARP
CRISP IMAGES ACROSS THESE
DIFFERENT SIGNAL.
SO WE CAN ACQUIRE THIS RAPIDLY.
UTILIZING THIS TECHNIQUE, OF
THIS DATA ACQUISITION, WE
DESIGN OUR SEQUENCE TO BE
SENSITIVE TO T1, T2 STAR SIGNAL
VARIATIONS, IN JUST A THREE
MINUTE SCAN WE CAN GENERATE
MORE THAN 1,000 WHOLE BRAIN AT
100 METER ISOTROPIC.
FROM THIS, WE ARE ABLE TO THEN
DERIVE ACCURATE QUANTITATIVE
MEASURES OF TISSUE PARAMETERS
SHOWN HERE.
WE HAVE DONE QUITE A BIT OF
SCAN, RESCAN REPEATABILITY
ACROSS MULTIPLE HEALTHY
SUBJECTS OF THIS CASE, E.P.T.I.
SCAN WE CAN GET THE
QUANTITATIVE T1 MAP TO DO AUTO
BRAIN SEGMENTATION INTO
DIFFERENT REGIONS.
FROM THESE REGIONS WE THEN LOOK
AT SCAN/RESCAN REPEATABILITY OF
THESE QUANTITATIVE MESHS.
IT HAS GREAT SCAN/REPEAT SCAN
REPEATABILITY, BIAS SHOWN HERE
ACROSS THESE PARAMETERS.
WITH THIS TECHNIQUE WE CAN ALSO
ACHIEVE HIGH SPATIAL RESOLUTION
ACCEPTABLE SCAN TIME ON A
COMMERCIAL THREE TESLA SCANNER.
0.7 MILLIMETER ISOTROPIC IN
JUST NINE MINUTES.
FROM THIS WE CAN ACTUALLY START
TO LOOK AT CORTICAL DEPTH
PROFILE.
T1, T2 AND T2 STAR, WE CAN
SEGMENT THE BRAIN USING OUR T1
MAP.
LOOKING AT DIFFERENT CORTICAL
LAYERS IN THE CORTEX INFLATE UP
INTO SURFACES AND THEN LOOK AT
THESE QUANTITATIVE PARAMETERS
AT DIFFERENT CORTICAL DEPTHS,
AS WELL AS DIFFERENT BRAIN
REGIONS, AS SHOWN HERE.
YOU CAN START TO PLOT THE --
OOPS.
GO BACK ONE.
YEP, YOU CAN START TO PLOT THE
CORTICAL PROFILE AT THESE
DIFFERENT BRAIN REGIONS AS
SHOWN HERE AT THESE DIFFERENT
PARAMETERS, ASSUMING INTO ONE
OF THESE REGIONS.
WE CAN LOOK AT REPEATABILITY.
AGAIN, THESE ARE ACROSS
SUBJECTS, AS WELL AS
SCAN/RESCAN WHERE WE HAVE
CONSISTENT CORTICAL PROFILE OF
THESE QUANTITATIVES PARAMETERS.
LOOKING AT THIS DATA A BIT MORE
CLOSELY WE CAN SEE THAT WE HAVE
LOWER INTRA SUBJECT VARIABILITY
THAN INTERSUBJECT VARIABILITY.
POINTING TO AN EXCITING
POTENTIAL WE MIGHT BE ABLE TO
START TO DETECT INDIVIDUAL
DIFFERENCES IN THESE
QUANTITATIVE MESHES, EVEN IN
HEALTHY VOLUNTEER COHORTS.
SO TO BE ABLE TO DO PRECISION
QUANTITATIVE M.R., IT'S ALSO
IMPORTANT TO BE MOTION ROBUST
PARTICULARLY WHEN IMAGING
ACROSS THE LIFE SPAN WITH YOUNG
CHILDREN AS WELL AS OLDER
ADULTS.
SO DEVELOP WAYS TO DO THIS
USING A RAPID 3D NAVIGATOR TO
BE ABLE TO INSERT THIS INTO THE
DEAD TIME OF THE SEQUENCE TO
TRACK MOTION AS WELL AS FIELD
VARIATION IN THE SCANNER THAT
CAN BE CAUSED BY SOME OF THESE
MOTIONS TO GET PRECISION
IMAGING.
SO HERE IS SOME OF OUR TRACKING.
HERE IS SOME OF THE
QUANTITATIVE MAPS THAT WE ARE
ABLE TO GET WITHOUT ANY MOTION
AND WITH MOTION SUBJECT THAT WE
THEN ESTIMATE AND CORRECT FOR
IN OUR RECONSTRUCTION AND WE
CAN SEE HERE THAT YOU ARE ABLE
TO GET PRETTY GOOD
CORRESPONDENCE BETWEEN THE
MOTION-FREE REFERENCE AND
MOTION-CORRECTED RECONSTRUCTION
OF MOTION CORRECT DATA.
WE ARE MOVING TOWARD PRECISION
QUANTITATIVE M.R.I. WHERE WE
HAVE RAPID AND REPEATABLE
QUANTITATIVE IMAGING WITH MORE
TISSUE PARAMETERS ACQUIRED IN
MOTION ROBUST WAY AT HIGH
ISOTROPIC RESOLUTION.
LET ME GO OVER THE SECOND PART
OF THIS TALK, ADVANCED EFFUSION
IMAGING.
OVER THE LAST DECADE OR SO, MY
LAB HAS REALLY BEEN TRYING TO
PUSH THE SPATIAL RESOLUTION
LIMIT OF IN VIVOM.R.I., TAKING
ADVANTAGE OF SOME OF THE
ADVANCED HARDWARE IN
DEVELOPMENT, IN TERMS OF HIGH
SHIFTING CAPABILITY AND HARDWARE
HAVE ALSO DEVELOPED THE
ACQUISITION AND RECONSTRUCTION
APPROACHES TO BE ABLE TO ACQUIRE
DATA MORE PRECISELY AS WELL AS
BETTER SMR AS WELL AS DEVELOPING
MOTION CORRECTION AND DENOISING
APPROACHES.
SO OUR MOTIVATION FOR THIS STEMS
MAINLY FIRST FROM THE EX VIVO
WORK PEOPLE HAVE DONE AT 250
MICRON.
HERE'S AN EXAMPLE IN THE CORTEX
FROM THE LAB WHERE AT THIS TYPE
OF RESOLUTION YOU START TO BE
ABLE TO SEE INTRACORTICAL
FIBERERS RUNNING TANGENTIALLY
WITHIN THE CORTEX.
HERE'S WE'RE WORKING HARD TO TRY
TO PUSH THROUGH THAT RESOLUTION.
WE'VE GOT TO ABOUT 780 MICRON IN
THIS CASE WITH GOOD DIFFUSION.
ZOOMING INTO THE REGION YOU CAN
SEE MULTIPLE CROSSES IN THE
REGION AND YOU SEE FIBERS AS
EXPECTED.
HERE'S ANOTHER MOTIVATION WHY WE
WANT TO DO THIS AT HIGHER
RESOLUTION TO GET TO THE
INFORMATION SUCH AS THE U FIBERS
WHICH CANNOT BE SEEN IN THE
STANDARD SEEING THAT WELL IN THE
STANDARD DATA AND HERE'S OUR IN
VIVO ACQUISITION GETTING TO THE
NEW FIBERS AS SEEN HERE
INTERESTINGLY THEY MAKE UP MORE
THAN THE WHITE FIBER PEOPLE HAVE
BEEN USING DIFFUSION MI TO
STUDY.
IT REPRESENTS IMPORTANT MISSING
INFORMATION WE'RE STARTING TO
SEE WHEN WE GET TO A HIGH ENOUGH
RESOLUTION AS WELL.
SO IN GETTING TO THAT TYPE OF
RESOLUTION AND GETTING TO IT IN
A PRECISION, PRECISE MANNER WE
HAVE TO FIX SOME ARTIFACT
ASSOCIATED WITH THE DIFFUSION
AND WE HAVE IMAGE DISTORTION IN
THE MRI SCANNER ONCE YOU PUT THE
SUBJECT IN SO WE'LL WORK
TOGETHER WITH THE GROUP AT NGH
WHERE THEY'VE DEVELOPED THIS
AC/DC SHIMMER RAY WHICH
PERFORMED WITH RECEIVE B ZERO
FIELD TO ALLOW FOR BETTER
SHIMMING OF THE HOMOGENEITY.
THIS IS THE BOTTOM PART OF THE
BRAIN WHERE IT'S HARD TO IMAGE
WELL AND YOU GET A LOT OF
DISTORTION WITH THE DYNAMIC
SHIMMING FROM THE HARDWARE YOU
REDUCE THE DISTORTION COMBINED
WITH ADVANCE POWER AND WE'RE
GETTING MORE THAN TENFOLD
REDUCTION IN THE DISTORTION AND
GET STRUCTURAL IMAGING THAT
TAKES LONGER TO DO AS SHOWN
HERE.
NOW WITH SOME OF THE TECHNIQUES
WE'RE ABLE TO IMAGE DIFFUSION
ACQUISITION AT THE BASE OF THE
BRAIN REALLY WELL AT HIGH
RESOLUTION.
THINK THIS IS AROUND 700 MICRON.
WE'VE GOT DISTORTION-FREE
DIFFUSION IMAGES AND A SINGLE
DIRECTION OF DIFFUSION,
ACQUISITION ACROSS MULTIPLE
DIRECTION AND YOU CAN SEE GOOD
REDUCTION AND THE COLOR OF THE
MAPS AND WE ALSO TRIED TO PUSH
THE SPATIAL RESOLUTION AND USING
THE HARDWARE AVAILABLE AT
STANFORD AND TWEAKING OF OUR
CONSTRUCTION FURTHER HERE'S
PRELIMINARY RESULT I'M EXCITED
TO SHARE WITH YOU AT 500 MICRON
ISO TROPIC RESOLUTION IN VIVO.
STILL A BIT NOISY BUT THE DATA
ALREADY STARTED TO SHOW SOME OF
THE NICE DETAIL WE CAN SEE AT
THIS HIGH ISO TROPIC RESOLUTION
SCAN.
IT'S IMPORTANT TO GET TO THE
HIGH RESOLUTION BUT IT'S ALSO
IMPORTANT TO IMAGE THIS IN A
CLINICALLY RELEVANT TIME FRAME.
WE'RE DEVELOP SOME WORK WITH OUR
COLLABORATOR AT THE BRIGHAM AND
WOMEN'S HOSPITAL WITH DIFFUSION
SPACE AND THIS IS OUR TYPICAL
IMAGING WHERE AT 860 MICRON WE
CAN APPLY 640 FUSION DIRECTION
AND IT TAKES 20 MINUTES TO DO
AND THIS IS ONE OF THE DIFFUSION
DIRECTION IT'S QUITE NOISY YOU
CAN DO FOUR AVERAGES OF THIS TO
GET BETTER SNR OR COMPRESS TO GO
THE OTHER WAY TO A 10-MINUTE
SCAN AND GET GOOD SMR SHOWN.
IS WITH SOME THE TECHNOLOGY
WE'RE HOPING TO MOVE TOWARD
DIFFUSION PROTOCOL AND JUST IN A
10-MINUTE SCAN THAT CAN BE DONE
ON A CLINICAL SCANNER FOR THE
STUDY AND LIFE SPAN AND
HOPEFULLY I'VE SHOWN YOU WE'RE
MOVING TO DIFFUSION MR AND HAVE
DIFFUSION IMAGING THAT CAN BE
OBTAINED IN A CLINICALLY
RELEVANT TIME FRAME.
I'VE SHOWN YOU WORK ON PRE
VISION -- PRECISION
QUANTITATIVE MR THAT IS ROBUST
AND REPEATABLE AS WELL AS HAVE
THE ABILITY TO ROBUSTLY STUDY
DETAIL INTRACORTICAL DEPTH
PROFILE FOR CONSTRUCTION AND
DESCRIBE SOME OF THE ADVANCE
DIFFUSION IMAGING TO GET HIGH
SCALE DIFFUSION AND A QUICK END
HERE IN TERMS OF FUTURE
DIRECTIONS, STILL QUITE A BIT OF
WORK TO ALLOW SOME TECHNOLOGIES
TO HAVE WIDESPREAD USE IN
CLINICAL STUDY.
MACHINE LEARNING AND WE WANT OUR
ACQUISITION TO BE REALLY MOTION
ROBUST AND MOTION PRONE
RELATIONS SO WE'RE DEVELOPING
TECHNIQUES FURTHER THAN THAT.
THERE'S WORK TO BE DONE IN TERMS
OF OPTIMIZING, STANDARDIZING
PROTOCOL AND VALIDATING THE
TECHNOLOGY AND EXCITINGLY
MAPPING MORE TISSUE IN TERMS OF
THE MICROSTRUCTURES THE WORK
WE'VE STARTED LOOKING AT MYELIN
WATER AND LOOKING AT THE
TECHNIQUES MENTIONED AND LASTLY
AS THIS SECTION HAS ALLUDED TO
IT'S IMPORTANT TO LOOK INTO
CROSS-MODALITY ANALYSIS OF SOME
OF OUR IN VIVO IMAGING WITH
MICROSCALE EX VIVO IMAGING TO
UNDERSTAND THE LENGTH OF THE
DATA SET AND WHAT WE'RE IMAGING
IN VIVO AS WELL AS BUILDING
INFORMATION INTO OUR
CONSTRUCTION AND ANALYSIS TOOL
TO FURTHER IMPROVE OUR IMAGING.
WITH THAT I'D LIKE TO THANK MY
LAB AND THE FOLLOWING
INSTITUTIONS AND GRANT SUPPORT
AND THANK YOU FOR YOUR
ATTENTION.
>> THANK YOU FOR A BEAUTIFUL
TALK.
AS WITH THE PREVIOUS SESSION
WE'LL HOLD QUESTIONS UNTIL THE
DISCUSSION BUT PLEASE PUT YOUR
QUESTIONS IN THE CHAT AND I'LL
GATHER THEM FOR THE DISCUSSION
SESSION.
OUR NEXT SPEAKER IS AANASTASIA
YENDIKI AND HER POST-DOCTORAL
TRAINING WAS DONE AT THE MARTIN
CENTER.
HER RESEARCH FOCUSES ON
OBTAINING ACCURATE MODELS OF
WHITE BUNDLE FIBERS FROM AN
TOPIC TRACING AND DEVELOPING
METHODS THAT CAN TAKE ADVANTAGE
OF THE POSTMORTEM MODELS TO
INFER CONNECTIONAL ACTIVITY FROM
IN VIVO DIFFUSION MRI.
TAKE IT AWAY.
>> THANK YOU FOR THE KIND
INTRODUCTION.
IN VIVO IMAGING WITH MRI WE HAVE
MANY THINGS AT OUR DISPOSAL TO
PROBE THE STRUCTURE AND FUNCTION
OF THE HUMAN BRAIN.
WITH STRUCTURAL MRI WE GET
CORTICAL THICKNESS AND WITH
DIFFUSION MRI WE GET LOCAL
ESTIMATES AND ORIENTATIONS OF
BUNDLES TO THEN FOLLOW ACROSS
THE BRAIN TO RECONSTRUCT
PATHWAYS THAT CONNECT DIFFERENT
BRAIN REGIONS AND WITH
FUNCTIONAL MRI WE GET TIME
COURSES RELATED TO BLOOD
OXYGENATION THAT ALLOW US TO
INFER WHICH ARE ACTUATED IN THE
SCANNER.
FOR MOST STUDIES THAT COLLECT
THE DATA IN VIVO THE RESOLUTION
IS SOMEWHERE IN THE ORDER OF 1
TO 2 MILLIMETERS BUT THAT'S THE
GENERAL SCALE.
WHAT CAN WE GET AT THAT SCALE
SPECIFICALLY IF WE WANT TO
COMBINE LARGE AMOUNTS OF DATA
ACROSS THE LIFE SPAN?
THIS IS AN EXAMPLE FROM A VERY
RECENT AND QUITE REMARKABLE
STUDY.
REMARKABLE IN TERMS OF THE
NUMBER OF DATA SETS THAT WERE
COMBINED.
IT WAS 124,000 SCANS FROM ABOUT
100,000 DIFFERENT SUBJECTS
RANGING FROM FETAL TO ALL THE
WAY TO 100 YEARS OF AGE.
WHEN COMBINING THIS MANY DATA
SETS ONE HAS TO TYPICALLY
COMPROMISE IN TERMS OF THE
QUALITY OF THE DATA AND THE
ANALYSES POSSIBLE.
THIS LOOKED AT WHITE MATTER AND
VENTRICULAR MATTER FROM
STRUCTURAL MRI.
SO NOT RELEVANT TO CONNECTIVITY
PER SE BUT THOSE THE POTENTIAL
POSSIBILITY, IF WE'RE ABLE TO
COMBINE THIS MANY DATA SETS.
THANKFULLY THERE HAVE BEEN
LARGE-SCALE INITIATIVES
COLLECTING IN VIVO HUMAN IMAGE
DATA START FROM THE HUMAN
CONNECTOME PROJECT WHICH HAS
NOVEL TECHNOLOGIES FOR MRI AND
SCANNERS AND GRADIENTS TO
COLLECT BETTER FUSION MRI AND
SOME OF THE ACCELERATED
SEQUENCES TO IMPROVE THE ANGULAR
RESOLUTION OF THE DIFFUSION MRI
AND THE TEMPORAL RESOLUTION AND
THIS IS FROM LARGE-SCALE DATA
COLLECTION FIRST FOR YOUNG
ADULTS AND EXTENDED ACROSS THE
LIFE SPAN AS WELL AS WITH
ADDITIONAL PROJECTS LIKE THE
ABCD WHICH FOCUSES IN YOUTH AS
WELL AS WITH THE U.K. BIO BANK.
SO WHAT ARE SOME CHALLENGES OF
COMBINING THE AVAILABLE DATA?
ONE CHALLENGE HAS TO DO WITH THE
FACT THAT MOST OF THE AVAILABLE
DATA SETS ARE CROSS-SECTIONAL.
EACH SUBJECT IS SCANNED ONLY
ONCE AND REPRESENTS ONLY ONE
AGE.
THE AGE AT WHICH THEY WERE
SCANNED.
UNFORTUNATELY WE'RE LOOKING
SMALL WITHIN SUBJECT EFFECT
CHANGES ACROSS THE LIFE SPAN IN
THE PRESENCE OF VERY LARGE
SUBJECT VARIANTS SO IT'S NOT THE
BEST AT ALLOWING US TO DETECT
SMALL CHANGES.
IF WE WERE ABLE TO INSTEAD OF
COMPARING TWO DIFFERENT SETS OF
SUBJECTS REPRESENTING DIFFERENT
AGE GROUPS IF WE WERE ABLE TO
SCAN THE SAME SUBJECTS AT
DIFFERENT AGE GROUPS WE WOULD BE
ABLE TO TELL IF THERE'S NO TREND
AT ALL BECAUSE THE BRAIN
MEASURES ARE GOING UP IN SOME
SUBJECTS AND DOWN IN OTHERS OR
IF THERE IS A TREND EVEN IF THAT
TREND REPRESENTS ONLY A VERY
SMALL WITHIN SUBJECT CHANGE.
SO IT HAS BEEN KNOWN FOR A WHILE
OF COURSE THAT LONGITUDINAL
DESIGNS INCREASE STATISTICAL
POWER HOWEVER, IT'S BEEN KNOWN
THAT WE NEED TAILORED DATA
ANALYSIS TOOLS TO GET TO THAT
STATISTICAL POWER OUT OF THE
LONGITUDINAL DATA.
AND SO THERE WAS AN EFFORT NOT
THAT LONG AGO TO DEVELOP TOOLS
FOR ANALYZING SPECIFICALLY
LONGITUDINAL DATA AND THIS WAS
DONE FOR STRUCTURAL DATA BY MY
COLLEAGUE AND THEN WE EXTENDED
THAT WORK TO ANALYZING
LONGITUDINAL DIFFUSION IMAGING
DATA AND PERFORMING LONGITUDINAL
TOPOGRAPHY STUDIES.
THESE TOOLS ARE NOW AVAILABLE TO
THE COMMUNITY AND HAVE BEEN FOR
A FEW YEARS.
AND ANOTHER CHALLENGE WHEN WE
WANT TO COMBINED LARGE AMOUNTS
OF DATA SETS THEY WON'T BE
COLLECTED WITH PROTOCOLS OF HIGH
ENOUGH QUALITY TO BE PUT THROUGH
SOME OF THOSE ANALYSIS TOOLS AND
THIS IS MOTIVATED RECENT EFFORTS
TO SYNTHESIZE HIGHER RES IMAGES
TO LOWER RES ALLOWING THE LOWER
RES IMAGES TO BE PUT THROUGH THE
SAME ANALYSIS AND SOME WORK
SHOWED IT'S POSSIBLE TO USE
HIGH-QUALITY MODELS OF BRAIN
PATHWAYS FROM FUSION MRI TO
TRAIN AN ALGORITHM TO LOOK AT
MORE MODEST QUALITY DATA AND
THIS ALLOWS US TO EXTEND THE
BENEFITS OF HAVING ONE OF ONLY A
HANDFUL OF SUCH SCANNERS IN THE
WORLD TO ALL THE STUDIES OUT
THERE THAT DON'T HAVE ACCESS TO
SUCH A SCANNER.
HOWEVER, EVEN AFTER WE SOLVED
ALL THOSE PROBLEMS THERE'S STILL
LIMITATIONS WITH DIFFUSION MRI
MEASUREMENT ARE PRESENT EVEN IN
THE HIGHEST QUALITY DATA WE
HAVE.
AND I WOULD ONLY BRIEFLY TRY TO
EXPLAIN THIS SO WHEN THERE'S
ONLY A SINGLE AXON BUNDLE SHOWS
GREATER POWER TO THE AXON BUNDLE
ALLOWING US TO DETECT THE MAIN
AXIS OF AXON BUNDLE AND FOLLOW
IT SUCCESSFULLY.
WHEN THERE'S MULTIPLE IN A VOXEL
FUNDING IT WON'T HAVE A CLEAR
ACCESS TO FOLLOW AND WORK IN THE
FIELD OVER THE LAST COUPLE
DECADES FOCUSSED ON WHAT IS
KNOWN AS AN ODF ORIENTATION
DISTRIBUTION FUNCTION TO ALLOW
US TO FIT MULTIPLE AXON
POPULATION FOR VOXEL.
A PROB WE HAVE HOWEVER, IS THAT
EVEN THOUGH WE HAVE DONE VERY
GOOD AT FITTING THESE ODFs
BECAUSE WE HAVE HIGH QUALITY
DATA THANKS TO THE ADVANCES MADE
POSSIBLE BY THE HUMAN CONNECTOME
PROJECT TOPOGRAPHY WILL STILL
GET THINGS WRONG SOMETIMES.
THAT'S BECAUSE THERE'S MULTIPLE
CONFIGURATIONS OF DIFFERENT AXON
POPULATIONS IN A VOXEL THAT CAN
GIVE RISE TO SIMILAR ODFs SO WE
DON'T KNOW WHICH OF THE PEAKS TO
FOLLOW AT A GIVEN VOXEL AND HAVE
TO CHOOSE WIDELY BECAUSE WE
DON'T KNOW WHICH OF THE POSSIBLE
AXON CONFIGURATIONS ON THE LEFT
GAVE RISE TO THE ODF.
LEADS TO ERRORS EVEN WITH THE
HIGHEST QUALITY DATA WE HAVE.
SO WHAT CAN WE DO MOVING
FORWARD?
SOME OF THE HIGH RESOLUTIONS
METHODS CAN HELP AND SO THIS
WORK ALSO LED BY OUR GROUP IN
COLLABORATION SHOWS THAT
SPECIFIC DEEP BRAIN CIRCUITRY
REQUIRES RESOLUTION AT THE SUB
MILLIMETER LEVEL.
WHAT'S SHOWN ON THE LEFT IS ONE
OF THE HIGH QUALITY DATA SETS ON
THE CONNECTOME SCANNER AND THIS
CAN BE COMBINED AT THE HIGHER
RESOLUTION BUT THE OTHER BUNDLES
CAN ONLY BE RECONSTRUCTED IN THE
SUB MILLIMETER RESOLUTION DATA
AND NOT IN THE ONE DATA SET
THOUGH THEY WERE COLLECTED IN
THE SCANNER AND THIS SHOWS THE
IMPORTANCE OF HIGH RESOLUTION
FOR THE DEEPER CIRCUITRY.
THE SUB MILLIMETER RESOLUTION
SET WAS SCANNED WITH A SINGLE
SUBJECT TWO HOURS EACH TIME.
NOT IN SUBJECTS CAN FOLLOW THIS
AND POST MORTEM BRAIN SCAN
TOLERATED IT JUST FINE AND
WITHIN THE CONNECTOME 2.0
PROJECT A BRAIN INITIATIVE
PROJECT LED OUR OTHER GROUP WE
HAVE LOOK AT THE ACQUISITIONS
POSSIBLE TO ACHIEVE MESO SCALE
RESOLUTION DIFFUSION MRI.
THIS IS NOT EASY EVEN WITH A
SCANNER AND WITH THE BETTER
CONNECTOM SCANNER WE WILL GET
SOON REQUIRES CUSTOM MADE COILS
AND METHODS TO MITIGATE THE
ARTIFACTS SPECIFIC TO THE EX
VIVO ACQUISITIONS AND WE'LL
ADDRESS THE TECHNOLOGICAL
CHALLENGE.
WHAT'S THE CLINICAL RELEVANCE?
WHAT CAN WE GET OUT IN THE REAL
WORLD IF WE ARE ABLE TO MAP
THESE LITTLE BUNDLES DEEP IN THE
BRAIN?
ONE EXAMPLE HAS TO DO WITH
NEUROMODULATION.
THERE'S FIBERS IN THE DEEP BRAIN
IF STIMULATED CAN LEAD TO
OPTIMAL THERAPEUTIC OUTCOMES
WHERE OTHER BUNDLES NEXT TO THE
GOOD BUNDLES CAN LEASE TO
DETERIORATION OF DEPRESSION
SYMPTOMS.
SO IT'S VERY CRITICAL TO MAP THE
DEEP POINT CIRCUITRY ACCURATELY
AND CHALLENGING.
SO RIGHT NOW THIS IS BEYOND THE
CAPABILITIES OF CURRENT IN VIVO
IMAGING METHODS.
SO MOST OF WHAT WE KNOW ABOUT
THE ORGANIZATION OF THESE
BUNDLES COMES FROM AN ATOMIC
TRACING EXPERIMENT IN NON-HUMAN
PRIMATES.
IN COLLABORATION WITH A GROUP
HAVE BEEN MAPPING SOME OF THESE
TOP
TOPPOGRAPHICAL ORGANIZATIONS
DEEP IN THE WHITE MATTER AND
HAVE SHOWN IT'S POSSIBLE TO
RECREATE SOME OF THOSE
TOPOGRAPHIES USING DIFFUSION MRI
DATA POSTMORTEM IN THE MACAQUE
AND AS WELL AS IN VIVO IN THE
HUMAN HOWEVER, THERE ARE THINGS
THAT GO SERIOUSLY WRONG WITH MRI
MEASUREMENTS.
TO GET TO THE BOTTOM OF WHAT ARE
THOSE THINGS THAT ARE GOING
WRONG AND HOW TO IMPROVE THEM,
WE HAVE BEEN COLLECTING DATA IN
THE SAME MRI DATA IN THE SAME
NON-HUMAN PRIMATE BRAINS THAT
RECEIVED TRACER INJECTIONS IN
SUSAN'S LAB SCANNING THE BRAINS
FOR 40 PLUS HOURS SOMETIMES AND
AT HIGH RESOLUTION WITH HIGH
DIFFUSION CONTRAST AND
RESOLUTION.
WE HAVE USED SOME OF THE DATA
SETS TO ENGAGE THE COMMUNITY AND
THE DISTRIBUTION FUNCTION NOT
ACCURATE SPECIFICALLY WHERE THE
AXONS DO NOT CROSS BUT INSTEAD
TURN OR BRANCH OR FAN.
THIS POINTS TO A POTENTIAL
AVENUE FOR FUTURE IMPROVEMENT OF
METHO
METHODS.
HERE WE USED THE TRACING DATAS
AWAY TO CALIBRATE A POST MORTEM
IMAGING METHODS THAT CAN BE USED
IN THE HUMAN BRAIN AND IN THE
HUMAN BRAIN IN VIVO AND
SPECIFICALLY DIFFUSION MRI.
AND WHAT IF WE CAN APPLY IT AT
THE MICROSCALE AND THIS IS AN
APPROACH THAT RELIES ON THE
MYELIN TO OBTAIN MEASUREMENTS AT
THE MICROSCOPIC SCALE.
SO THE MAP ON THE RIGHT ARE THE
DIRECT MEASUREMENTS OF THE
AXONAL ORIENTATIONS AND ON THE
LEFT IS MYELIN CONTENT AND IS
ANOTHER OUTPUT OF THIS
TECHNIQUE.
THERE'S SPECIFIC ADVANTAGES OVER
THE STAINS.
A PROB -- PROBLEM IS YOU CAN
HAVE IT HARD TO ALIGN FROM ONE
SECTION TO THE OTHER WHICH IS
CRITICAL FOR BEING ABLE TO
FOLLOW AXONS LONG RANGE ACROSS
THE BRAIN.
WE IMAGED THE SUPERFICIAL LAYER
BEFORE IT'S DISTORTED AND THE
SECTIONS COME OUT SCANNED
WITHOUT MISS ALIGNMENTS OR
DISTORTIONS SO AND IN ADDITION
TO THAT WE DO NOT ACQUIRE AN
IMAGE OF THE TISSUE WE THEN
INTEREST HAVE TO EXTRACT THE
AXONS AND ESTIMATE THE
ORIENTATIONS.
WE GET A DIRECT ESTIMATE OF THE
VECTORS AND THIS ALLOWS US TO
RIGHT OUT OF THE BOX PERFORM THE
TOPOGRAPHY AT SCALE IN THE HUMAN
BRAIN.
THE TECHNOLOGY HAS ADVANCED AND
SO COMPARED TO THE FIRST
GENERATION SYSTEM WHAT IS
DEPLOYED AT THE MARTIN CENTER
HAS BETTER CONTRAST TO NOISE
RATIO BUT ABOUT SEVEN TIMES
FASTER SO A TISSUE THAT USED TO
TAKE FOUR DAYS TO SCAN NOW WE
CAN SCAN IN LESS THAN A DAY AND
THIS IS IMPORTANT PARTICULARLY
WHEN THINKING OF SCALING TO
LARGER VOLUMES.
AND YOU DO NOT SEE CONTRASTS
HERE BUT IT NEEDS TO BE
ENHANCED.
AND THIS IS POSSIBLE BY
SUBMERGING THE TISSUE IN THE
SOLUTION THAT ALLOWS THE FIBERS
TO BE FOLLOWED ALL THE WAY INTO
THE CORTEX SHOWN HERE AT THE
BOTTOM COMPARED TO THE PBS
IMMERSED TISSUE ON THE TOP.
WE EXTRACT THE ORIENTATION OF
THE AXONS PERPENDICULAR TO THE
ILLUMINATION AND WE CONNECT WITH
TWO DIFFERENT ILLUMINATION
ANGLES AND WORK SHOWS THIS ALLOW
US TO HAVE THE BENEFIT OF OCT
THAT WE DO NOT HAVE DISTORTIONS
ACROSS LICENSE THIS WILL ALLOW
US TO FOLLOW AXON ORIENTATIONS
ACROSS SECTIONS AND ACROSS THE
BRAIN.
ONE QUESTION SPECIFICALLY
RELATING TO IMAGING DEVELOPMENT
SAMPLES IS THAT THIS CONTRAST
RELIES ON THE MYELIN SO THE
QUESTION IS IT CAN BE USED IN
TISSUE NOT FULL MYELIN.
THIS IS PRELIMINARY RESULTS
COLLECTED BY DR. WANG'S GROUP
WHO STUDIES DEVELOPMENT
POPULATIONS IN OUR CENTER AND
THIS IS A ONE-MONTH-OLD SAMPLE
SHOWING THE CONTRAST ON THE
RIGHT AS WELL AS WHAT ALLOWS
THEM TO EXTRACT GRANULAR
THICKNESS IN THE CEREBELLUM.
GOING FORWARD AND ATOMIC TRACING
REMAINS THE MAIN SOURCE OF
INFORMATION WE HAVE ABOUT BRAIN
CONNECTIVITY.
IT'S ONLY FEASIBLE IN NON-HUMAN
PRIMATES BUT WE HAVE AN
OPPORTUNITY TO USE IT TO
OPTIMIZE AND CALIBRATE METHODS
THAT CAN BE USED TO IMAGE POST
MORTEM ACROSS SPECIES.
WE HAVE CALIBRATED DIFFUSION MRI
AND USING ATOMIC TRACING TO
CALIBRATE TO IMAGE AXONAL
ORIENTATIONS AT THE MICRO SCAPE
AND ACROSS VOLUMES AND ALLOWS US
TO SURVEIL IN THE BRAIN AND
OBTAIN TRUTH FOR ALGORITHMS FOR
ANALYZING OUR IN VIVO DIFFUSION
MRI DATA GOING FORWARD.
I'D LIKE TONED BY THANKING MY
COLLABORATORS WHO HAVE MADE THIS
RESEARCH POSSIBLE AND THANK YOU
FOR YOUR ATTENTION.
>> THANK YOU.
BEAUTIFUL TALK.
AGAIN, WE'RE GOING TO HOLD
QUESTIONS UNTIL THE END OF THE
DISCUSSION BUT UPLOAD THEM
EITHER IN THE CHAT OR IN THE
VIDEOCAST SYSTEM YOU CAN UPLOAD
QUESTIONS AS WELL.
THANK YOU DR. YENDIKI.
NOW WE MOVE TO A MUCH DIFFERENT
SCALE AND I'LL INTRODUCE
DR. ELLIE HECKSCHER FROM THE
UNIVERSITY OF CHICAGO.
SHE RECEIVED HER Ph.D. FROM THE
UNIVERSITY OF SAN FRANCISCO IN
THE LAB OF GRAY DAVIS AND
CONTINUED AT THE UNIVERSITY OF
OREGON.
HER GROUP LOOKS AT LINEAGE
TRACING APPROACHES WITH
CONNECTOMICS AND STATE OF THE
ART SYSTEMS, NEUROSCIENCE
APPROACHES AND HER RESEARCH IS
FOCUSSED ON HOW MOTOR CIRCUITS
ARE GENERATED STARTING FROM
NEURONAL STEM CELLS.
>>
>> HI, I'M ELLIE.
INE ASSIST AND THE PROFESSOR IN
THE DEPARTMENT OF MOLECULAR DEN
GENETICS AND CELLULAR BIOLOGY IN
THE UNIVERSITY OF CHICAGO AND
TALK ABOUT A DIFFERENT SCALE
FROM YOU'VE BEEN THINKING ABOUT
THE MOLECULAR CELLULAR AND
SUBCELLULAR SCALE.
SO JUST TO ORIENT YOU TO HOW I
THOUGHT I'D SPEND MY TIME
TALKING TODAY.
I'LL START BY INTRODUCING A
QUESTION AND THE MODEL SYSTEM
AND THEN MOVING ON TO HOW WE
MEASURE BRAIN CONNECTIVITY,
FUTURE DIRECTIONS OF THE
APPROACHES IN THE SYSTEM AND BIG
PICTURE GAPS IN THE SYSTEM.
SO WE'LL START HERE WITH A
QUESTION AND THE MODEL SYSTEM.
AND SO THIS IS THE BRAIN ACROSS
LIFE SPAN WORKSHOP I THOUGHT I'D
ORIENT YOU TO THE TIME SPAN THAT
I'M FOCUSSING ON AND SO
SPECIFICALLY WE'RE FOCUSSED ON
THE START OF NEUROGENESIS TO THE
START OF BEHAVIOR AND I'M A
DEVELOPMENT BIOLOGIST BY
TRAINING AND THERE'S THE CARTOON
OF HUMAN DEVELOPMENT.
STARTING HERE WITH SPERM AND EGG
FERTILIZING AND WITHIN A WEEK OR
SO YOU'LL HAVE RECOGNIZABLE
EMBRYO AND AT THAT POINT YOU'LL
SEE STEM CELLS.
THIS IS WHAT I MEAN BY THE START
OF NEURO GENESIS.
IN THE COMING WEEKS THE FETUS
WILL DEVELOP AND IT WILL START
TO MOVE AND MOVE BECAUSE THOSE
NEURONS HAVE STARTED TO MAKE
SYNAPSES AND WIRE UP IN SPECIFIC
CIRCUITS.
THIS THIS PERIOD FROM THE START
OF NEUROGENESIS TO THE START OF
BEHAVIOR I'LL BE TELLING YOU
ABOUT TODAY.
SO THE SPECIFIC QUESTION I'LL
FOCUS ON IS HOW IS IT CIRCUITS
SELF-ASSEMBLE STARTING FROM STEM
CELLS?
A STEM CELL SHOWN HERE IN THE
BIG BLUE CIRCLE IS A PLURIPOTENT
CELL THAT WILL DIVIDE
ASYMMETRICALLY WAY AND THIS WILL
HAPPEN OVER AND OVER AGAIN TO
GENERATE WHAT WE HAVE A LINEAGE
OF NEURONS.
SO ALL OF THESE NEURONS COME
FROM THE STEM CELL PARENT.
SO WHY DO WE CARE ABOUT THIS
PARTICULAR QUESTION AND THE BIG
REVEAL HERE AND WE LIKE TO KEEP
OUR QUESTIONS FUNDAMENTAL TO
HAVE WIDE-RANGING IMPLICATIONS
FOR A LOT OF FEEL.
AND FOR DEVELOPMENT WE THINK
ABOUT HOW THE BRAIN DEVELOPS IS
PERHAPS ONE OF THE MOST COMPLEX
ORGAN MORPHOGENESIS QUESTION.
FROM NEUROBIOLOGY THIS WHAT
CONSTRAINTS CIRCUIT FUNCTION AND
THIS IS WHAT CONSTRAINTS
PERCEPTIONS AND ACTIONS.
FOR THE FIELD OF ROBOTICS, WE'RE
HOPING WE CAN GIVE COMPLEX
NETWORKS AND HOPEFULLY FOR THE
MEDICAL AUDIENCE UNDERSTANDING
HOW STEM CELL WIRE UP TO CREATE
CIRCUITS MAY HELP UNDERSTAND
WHAT GOES WRONG IN DISEASE AND
PROVIDE INSIGHT INTO HOW TO USE
STEM CELLS THERAPEUTICALLY.
I THINK THIS IS AN IMPORTANT
QUESTION BUT I WANT TO POINT OUT
WE REALLY DON'T KNOW MUCH ABOUT
THE ANSWER AND THAT'S BECAUSE
THE QUESTION HAS BEEN
INTRACTABLE FOR A LONG TIME.
THERE WERE TOOLS BUT COULDN'T
GET AT THE CIRCUITS BECAUSE THE
CELLS WERE SMALL BUT WE COULD
GET ELECTRODES INTO CIRCUITS BUT
DIDN'T HAVE THE GENETIC TOOLS TO
STUDY STEM CELL.
BRIDGING THE DIVIDE WAS
TECHNICALLY NOT POSSIBLE.
IS THE SPECIFIC SYSTEM WE USE IS
THE EGG IS THE STAGE IN WHICH
DRIVE CIRCUITS AND THE LARVAE
WILL GROW AND EAT AND SHED THE
CUTICLE TO MAKE A SECOND LARVAE
TO GROW AND EAT AND ONCE YOU GET
TO THE THIRD ENSTAR AND YOU'RE
BIG ENOUGH YOU WILL BECOME A
PUPA AND YOU HAVE REMODELLING
HAPPEN AND HATCH INTO ADULTS.
AND ADULTS DO NOT GROW.
THEY'RE ADAPTED JUST FOR MATING
AND DISPERSAL.
I WANT TO POINT OUT IT SEEMS
LIKE A WEIRD MODE OF DEVELOPMENT
BUT IT'S NOT MUCH DIFFERENT FROM
WHAT HAPPENS IN MANY LIKE HUMANS
WHERE YOU HAVE A GROWTH PHASE
WITHOUT REPRODUCTIVE
CHARACTERISTICS.
AS THE MOTHER OF A TEENAGER I
THINK IT'S GREAT THEY JUST DO
ALL THE REMODELLING IN THE PUPA
STAGE.
THERE'S THE LARVAL STAGE AND I
WANT TO TALK ABOUT WHAT ARE THE
PERIODS.
THERE'S A PERIOD WITHIN 24 HOURS
WITHIN THE EMBRYO.
THERE'S APPROXIMATELY 1,000 STEM
CELLS SET ASIDE AND THEY'LL
DIVIDE TO GIVE RISE TO NEARLY
15,000 NEURONS.
THE 15,000 NEURONS WILL WIRE UP
TO MAKE CIRCUITS THAT DRIVE THE
LARVAE AND IT WILL BE ABOUT 3
MILLION SYNAPSES.
ONCE THE LARVAE HATCHES THE
NEURONS WILL DRIVE LARVAL
BEHAVIOR THROUGHOUT.
THERE'LL BE NO ADDITIONAL
NEURONS CONTRIBUTING TO THE
LARVAL SECTORS.
THEY'LL JUST GET BIGGER AS THE
ANIMAL GROWS AND THE NUMBER OF
SYNAPSES WILL INCREASE.
OTHER THAN THAT WE DON'T
ACTUALACTUAL
LY -- ACTUALLY DON'T KNOW MUCH
ABOUT THE STEM CELLS AN AS THEY
GROW BUT AS THE LARVAE STARTS TO
GROW, THE STEM CELLS WILL COME
OUT OF QUIESCENCE AND START TO
MAKE ADDITIONAL NEURONS ON THE
ORDER OF 100,000 OF THEM.
THEY'LL BE IMMATURE UNTIL PU
PUPATION HAPPENS.
THERE'S A WHOLE OTHER SECOND
PERIOD OF NEUROGENESIS THAT'S
INTERESTING TO THINK ABOUT FOOP
AND MANY HAVE THESE GENES.
WE HAVE SYSTEMS WHICH HAVE THE
ROLE OF DROSOPHILA RESEARCH.
THAT'S WHAT I WANTED TO COVER
AND NOW I WANT TO GET INTO MORE
OF THE DETAILS ABOUT HOW WE IN
OUR SYSTEM MACHINE BRAIN
CONNECTIVITY.
AND WE USE THE RESOURCE IN THE
RESEARCH A LOT.
I'M SHOWING THE PICTURE OF THE
DROSOPHILA LARVAL CONNECTOME.
IT'S A SIX-HOUR OLD FEMALE
LARVAE.
YOU THE ESSENTIAL BRAIN AND
NERVE CORD WHICH IS LIKE YOUR
SPINAL CORD, HERE ARE CELL
BODIES AND THE AXONS AND
DENDRITES FORM SYNAPSES IN THESE
CENTRAL REGIONS.
THE YOU CAN SEE THE MEMBRANES
SECTIONED AND IMAGED BY TEM AND
THE SECTIONS WERE ALIGNED INTO A
PLANE AND YOU CAN SEE THEY WERE
ALIGNED IN THREE DIMENSIONS.
THIS IS THE WORK OF RICK FETTER
AND OTHERS AND IT'S A HIGH
RESOLUTION SINGLE IMAGE AND I'LL
SHOW A LITTLE BIT MORE IN THE
NEXT SLIDE.
HERE'S JUST A SLICE OF THE DATA.
HERE YOU CAN SEE THE OUTLINES OF
THE CELLS AND MITOCHONDRIA.
OVER 20 LABS ALL OVER THE WORLD
HAVE BEEN MANUALLY
RECONSTRUCTING THESE AND YOU PUT
A PINK DOT ON THE CELL OF
INTEREST AND SCROLL IN THE NEXT
SLICE AND THIS IS HOW YOU BUILD
UP THE MORPHOLOGY OF THE NEURON.
THE OTHER TYPE OF ANNOTATION DO
AND THE RUN NEED TEM AND THIS IS
SYNAPSING ON TO THESE THREE.
TO GIVE INTUITION ABOUT NUMBERS,
ANY ONE NEURON AND MAKE ABOUT
100 TO 200 SYNAPSES.
IT LETS US AND STEM CELLS WE
ALREADY KNOW ABOUT IN THE
SYSTEM.
THINK HOW THEY MAP TO THE
CONNECTOME AND THE CONNECTOME
LETS US KNOW HOW THAT RELATES TO
ANATOMICAL CIRCUITS AND
FUNCTIONAL BEHAVIOR.
AND THIS IS ENABLED BY THE VAST
COLLECTION OF GENETIC TOOLS AND
HUGE POWER THAT IS DROSOPHILA
GENETICS AND ENABLED BY THE FACT
THAT NEURONS INVARIANT.
I'M SHOWING A STEM CELL CALLED
3-3 AND SELF-RENEWS BUT WILL
ALSO MAKE A BUNCH OF NEURONS.
AND IN LINEAGE TRACING WE INDUCE
A GENETIC CHANGE IN A STEM CELL
AS IT'S DIVIDING.
IT'S GOING TO LABEL ONE CELL IN
ONE FLUORESCENT COLOR AND THE
OTHER CELL IN ANOTHER
FLUORESCENT COLOR BECAUSE IT'S A
SELF-RENEWING CELL AND PASS IT
ON TO THE REMAINDER OF THE
PROGENY.
IF WE INDUCE THE CHANGE AT A
DIFFERENT TIME WE GET A
DIFFERENT PATTERN.
THIS IS WHAT SOME OF THE DATA
LOOKS LIKE.
IN PURPLE YOU SEE CELL BODIES
AND WHEN YOU INDUCE THE CLONE IN
THIS PARTICULAR CASE YOU SEE TWO
RED CELLS AND ONE GREEN CELL
LABELLED.
IT TELLS US THE GREEN CELL IS
THE THIRD FROM LAST CELL BORN
FROM THE STEM CELL.
YOU CAN ALSO GO IN AND LOOK AT
HIGH RESOLUTION AT THE ANATOMY
OF THIS CELL AND IN THIS
PARTICULAR CASE AND SO INVARIANT
YOU CAN FIND THE MATCH IN THE
CONNECTOME.
SO ONCE WE FOUND THE NEURON --
LET THE JUST ORIENT YOU, THIS IS
THE SAME ONE IN YELLOW BUT NOW
IT'S SHOWN IN BLACK.
WHAT YOU CAN DO IS GO TO THE
CONNECTOME AND ASK WHO ARE THE
ANATOMICAL INPUTS.
IN THIS CASE THE NEURON IS
GETTING INPUTS FROM THE SENSORY
NEURON AND MAKING SYNAPSES, 13
HERE AND TWO HERE.
YOU CAN DO THE SAME THING ASKING
THE OUTPUTS AND YOU CAN SEE THE
NEURON E3 IS ACROSS THE MID LINE
AND WILL OUTPUT ON THE GREEN
CELL.
GENERATING A CONNECTOME IS LABOR
IN SENSE BUT WE KNOW THE LEFT
AND RIGHT SIDES ARE MIR IMAGES
AND WE CAN LOOK OR THE SAME
NEURON THE OTHER SIDE OF THE CNS
AS A TECHNICAL REPLICATE AND A
WANT YOU TO NOTICE IT LOOKS
SIMILAR THOUGH THE NUMBERS OF
SYNAPSES BETWEEN ANY TWO CELLS
ARE DIFFERENT.
SO FROM THESE TYPES OF DATA WE
CAN BUILD UP A WIRING DIAGRAM
AND I DON'T CARE YOU THINK ABOUT
THE DETAILS HERE BUT THERE'S THE
CELL E3 AND SOME OF ITS
SIBLINGS.
THEY ALL GET INPUT FROM
PROPREPR
PROPREPRIOCREEPTORS AND WE CAN USE
IT AND MAKE PREDICTIONS.
WE THINK THESE EL NEURONS GET
INFORMATION FROM PROPRIOCEPTORS
AND MAYBE WE CAN GET ASYMMETRY.
AND WE HAVE ACTIVATED ALL THE
ELs USING OPTOGENETICS AND WE
CAN ABLATE THEM AND THINK IN
THIS CASE WE SCRAMBLED THE P E
PROPRIOCEPTOR INFORMATION AND
THE FIRST THING WE LEARNED IS
THE RULE AND THAT'S LINEAGES ARE
REORGANIZED AND AS IT A GROUP OF
NEURONS BORN FROM A STEM CELL
OVER TIME.
PROPRIOVENT
AND WE HAVE SOME THAT ALL
PARTICIPATE IN A PROPRIOCEPTOR
CIRCUIT AND HERE'S WE HAVE A
MECHANO SENSORY STIMULATION.
THAT LEADS TO THE IDEA THERE'S
LITTLE DEVELOPMENT CHUNKS OF
LINEAGES ORGANIZATIONAL UNITS.
SO IT'S THESE KINDS OF RULES
WE'RE INTERESTED IN DISCOVERING
USING THE METHODOLOGY.
MORE BROADLY I WANT TO DRAW YOUR
ATTENTION TO WHAT WE CAN DO IN
THE SYSTEM WHICH IS TO INTEGRATE
DIFFERENT LEVELS OF ANALYSIS.
I HAVEN'T GOTTEN MUCH IN THE
MOLECULAR BUT WE HAVE EXCELLENT
TOOLS IN DROSOPHILA AND WE CAN
GET TO SYNAPTIC CONNECTIVITY AND
I SHOW YOU THE CELLULAR DATA AND
WE CAN MAKE PREDICTIONS ABOUT
BEHAVIOR.
WE ALSO ARE BEGINNING TO BE ABLE
TO DO THIS STANDING TIME.
I SHOWED YOU DATA LINKING
EMBRYONIC TO LARVAL.
THAT'S SORT OF WHAT I WANTED TO
TELL YOU ABOUT THE APPROACHES
AND WHAT WE CAN DO IN THE SYSTEM
AND I ALSO THOUGHT THE FRAMEWORK
WOULD BE A GOOD WAY TO INTRODUCE
WHAT A THINK ARE SOME OF THE
FUTURE DIRECTIONS OF THE
APPROACHES WE NEED TO USE IN THE
SYSTEM.
AND SO THIS LINKS BACK TO THE
FIRST SET OF TALKS MEASURING
CELL IDENTITY AND CHROMATIN
STATES AND OTHER THINGS.
NOW THAT WE HAVE THIS CONNECTOME
WE HAVE A DETAILED RESOURCE.
WE ALSO NEED TO BE ABLE TO LINK
IT SINGLE CELL LEVEL AND LINK IT
TO CIRCUIT BEHAVIOR.
AND CAN WE GET CONNECTIVITY
INFORMATION OVER TIME FROM
EMBRYOS FROM LATE LARVAE AND
FROM PERTURBATIONS?
LIKE ZEBRAFISH LARVAE ARE
OPTICALLY CLEAR.
ON THE WISH LIST IS THE ABILITY
AND PEOPLE ARE MAKING GREAT
STRIDES FOR THIS BEING ABLE TO
IMAGE ACTIVITY OF ANIMALS --
SORRY, ACTIVITY OF NEURONS IN
ANIMALS AND FINALLY I THINK
BECAUSE WE HAVE SUCH HIGH
RESOLUTION INFORMATION ABOUT
CONNECTIVITY WE NEED HIGHER
RESOLUTION INFORMATION ABOUT
BEHAVIOR.
IN PARTICULAR WE NEED TO
UNDERSTAND BEHAVIOR AT THE LEVEL
OF SINGLE MUSCLE CONTRACTIONS
BECAUSE THAT'S REALLY THE
INTERMEDIATE BETWEEN THE NERVOUS
SYSTEM AND BEHAVIOR.
OKAY.
I'LL WRAP UP IN THE LAST 30
SECONDS WITH WHAT I THINK ARE
BIG PICTURE GAPS IN THE SYSTEM.
SO WE'RE BEGINNING TO UNDERSTAND
WHAT THE RELATIONSHIPS ARE
BETWEEN STEM CELL AND CIRCUIT
AND WE HAVE MORE TO LEARN BUT WE
ALSO NEED TO KNOW HOW THE
RELATIONSHIPS VARY AT DIFFERENT
CONTEXTS.
WE TOLD YOU WHAT'S HAPPENING IN
ONE SEGMENT BUT WE'RE INTERESTED
IN ALL THE SEGMENTS AND HOW IT
VARIES ACROSS LIFE STAGE AND
ORGANISMS.
WE NEED TO UNDERSTAND HOW THE
RELATIONSHIPS ARE BUILT ON THE
MOLECULAR AND CELLULAR LEVEL AND
THE THREE THINGS WE NEED TO KNOW
ARE WHAT'S GOING ON IN THE STEM
CELL AND THE NEURON AND IN THE
ENVIRONMENT AND THEN THE LAST
SET OF THINGS WE NEED TO DO IS
PERTURBTIVE ANALYSIS AND HOW'S
IT BREAK AND WHEN AND WITH THAT
HERE'S MY LAB.
THANK YOU FOR FUNDING FOR PEOPLE
WHAT CAN DO ANNOTATION AND FOR
THE ATTENTION.
>> THANK YOU, ELLIE, BEAUTIFUL.
I WISH WE COULD ALL CLAP.
I'LL INTRODUCE DR. MAI ZHEN A
SENIOR SCIENTIST AT THE
LUNENFELD-TANNENBAUM INSTITUTE
AND VISITING PROFESSOR OF
PHYSICS AT HARVARD
INVESTIGATION.
SHE GOT HER Ph.D. AT UNIVERSITY
OF COLUMBIA AND DID HER
POST-DOCTORAL AT UCSD.
HER WORK COMBINES ELECTRON
MICROSCOPY AND HOW THE NERVOUS
SYSTEM WORKS IN C ELEGANS AND
OTHER MODELS.
TAKE IT AWAY.
>> THE FOCUS OF MY TALK IS AN
EMERGING AREA THAT ADDRESS THE
FUNDAMENTAL QUESTION IN BIOLOGY,
HOW DOES WIRING AND FINDING A
SYNAPTIC CONNECTIVITY CHANGES
ACROSS THE ANIMAL'S LIFE SPAN.
TO UNDERSTAND THE ARCHITECTURE
OF THE BRAIN SPECIFICALLY HOW
IT'S FORMED AND THE CHANGE OF
THE FORM FACILITATING THE
ANIMAL'S ABILITY TO ADAPT TO ITS
GROWING BODY AS WELL AS THE
CHANGING ENVIRONMENT.
DURING DEVELOPMENT THE WIRING
MATURES DRIVEN BOTH BY THE
ANIMAL'S GENETIC PROGRAMS,
INTRINSIC PROGRAM AND THE
ANIMAL'S INTERACTION WITH THE
ENVIRONMENT.
WE HAVE USED HIGH RESOLUTION TO
RECONSTRUCT EVERY CELL AND MAP
EVERY SINGLE CHEMICAL SYNAPSE OF
THE C. ELEGAN'S BRAIN TO
ADULTHOOD AND LOOKING AT THE
STAGES WE'RE ABLE TO INFER A FEW
POTENTIAL RULES THAT MAY GOVERN
THE MATURATION PROCESS.
TO ME THERE'S A FRAMEWORK UPON
WHICH THE CONNECTIVELY TO UNDER
LINE THE ANIMAL BEHAVIOR.
CONNECTOMICS HAS BEEN ACTIVE
ACROSS ANIMAL SPECIES MOST
NOTABLY IN THE C. ELEGANS AND
OTHERS AND THERE'S THE ABILITY
TO GENERATE SENSORIMOTOR
BEHAVIORS BOTH ROBUST AND
ADAPTIVE.
C. ELEGANS ALLOWS TO US COMPARE
AT A SINGLE SYNAPSE RESOLUTION
AND LOOK AT THE ENVIRONMENT.
THE C. ELEGANS NERVOUS HAS A
BRAIN AND THE C. ELEGANS HAS THE
PROCESS WHY IT'S SENSORY AND
INTERNEURONS WORK IN THE SENSORY
PROCESSING.
THE OTHER IS THE BODY COURSE.
THE C. ELEGANS EQUIPMENT OF THE
PERIPHERAL NERVOUS SYSTEM AND
ASCENDING AND ESCENDING SYSTEMS
AND THEY COMPLIED THE CONNECTOME
AND THIS CLASSIFIES 300 NEURONS
INTO 117 CELL TYPES.
THIS IS PURELY MORPHOLOGY AND
CONNECTIVITY AND IT SEEMS TO
HAVE FAIRLY GOOD CORRELATION
WITH THE MOLECULAR FINGERPRINTS
NOW THAT WE HAVE THE SINGLE CELL
RNA SEQ DATA AND WE HAVE
CELL-CELL CONNECTIONS MOST
DRIVEN BY CLEM -- CHEMICAL
SYNAPSES AND LIKE ALL ANIMALS,
THE NEWLY MATCHED C. ELEGANS HAS
TO UNDER GO SEVERAL STAGES
BEFORE BECOME BEING ADULT AND
IT'S MAPPED BY THE CELL
LINEAGES, HARD WIRING INVOLVES
DURING THE STAGES AND HOW LONG
REMAINS UNKNOWN.
MOREOVEDURING THE STAGES AND HOW LONG
MOREOVER,MOREOVER, KNOW ENVIRONMENT CAN
CHANGE THE C. ELEGANS'
ENVIRONMENTAL DECISIONS AT A
CRITICAL DEVELOPMENT STAGE WHEN
ANIMALS ARE CHALLENGED WITH A
HARSH ENVIRONMENT THEY CAN HALT
UNTIL THE ENVIRONMENT IMPROVES.
THIS STAGE HAS BEEN ANALYZED
METABOLICALLY BUT PRECISELY HOW
THIS IS AFFECT THE ENVIRONMENT
IS UNKNOWN.
WE ASKED HOW DOES THE NERVOUS
SYSTEM CHANGE DURING
DEVELOPMENT?
WHAT MECHANISMS MAY GOVERN THIS
MATURATION PROCESS AND WHETHER
THE ENVIRONMENT CAN ALTER THE
WIRING.
THE APPROACH WE TOOK IS HIGH
RESOLUTION AND THEN HIGH
SEMI-MICROSCOPY TO RECONSTRUCT
THE EVERY CHEMICAL SYNAPSE OF
THE ANIMAL FROM BIRTH TO
ADULTHOOD.
ALL THE DATA SETS HAVE BEEN MADE
AVAILABLE THROUGH AN INTERACTIVE
WEBSITE WHERE WE POST THE
NETWORK AS WELL AS THE 3-D
STRUCTURE THAT PROVIDES THE
SPATIAL LOCATION OF ALL THE
SYNAPSES.
IN THE CONTEXT OF THE REST OF MY
TALK THE C. ELEGANS HAS 180
NEURON
NEURONS AND THE MAJORITY OF THE
CELLS IS ALREADY PRESENT AT
BIRTH AND FOR EIGHT INDIVIDUALS
OF A DIFFERENT DEVELOPMENT TIME
POINT WE HAVE CONSTRUCTED EVERY
SINGLE CELL AND THEN WE
IDENTIFIED EVERY SINGLE CELL TO
COMPARE THEM.
OUR FINAL DATA SET HAS THE
LOCATION AND SIZE OF THE
PHYSICAL CONTEXT FOR EACH CELLS
IN THE BRAIN AND THIS CAN INFORM
THE TOPOLOGY OF THE BRAIN OF
SEVEN INDIVIDUALS STAGE FROM L1
TO ADULT.
THE SECOND DATA SET THE
CONNECTOME WHERE THE LOCATION
AND THE NUMBERS OF EACH
CONNECTIONS IS DEPICTED AND THEY
REPRESENT THE Y DIAGRAMS OF THE
EIGHT INDIVIDUALS TO ADULT ALSO.
WITH THE DATA SETS WE ADDRESS
THE PROCESS AT FOUR DIFFERENT
LEVELS.
THE SCAFFOLD, SYNAPSE,
CONNECTION AND THE NETWORK.
AND THE APPROACH WE TOOK IS TO
EXAMINE THE RELATIONSHIPS ACROSS
AND BETWEEN THE TWO PHYSICAL
MATRICES THE COMPACTOME AND
CONNECTOME.
FROM THE COMPACTOME FROM
COMPARING ACROSS DEVELOPMENT WE
KNOW WHEN AND WHERE AND HOW MUCH
NEURON MAKES PHYSICAL CONTACT
AND COMPARING THOSE CHANGES
ALLOWS US TO ASSESS THE TOPOLOGY
CHANGES.
AND FROM THE HORIZONTAL
COMPARISON WE KNOW WHERE AND HOW
MANY SYNAPSES ARE PRESENT AND
HOW MUCH OF THE NETWORK REQUIRES
EXCHANGES.
FINALLY, BY COMPARING THE
EXCHANGES WE CAN ADDRESS THE
RELATIONSHIPS BETWEEN THE
TOPOLOGY AND CONNECTIVITY
DEVELOPMENT.
FOLLOWING THE SUM OF OUR KEY
FINDINGS, FIRST, WE FIND THE C.
ELEGANS BRAIN WE FIND THE
NEURONS OF EXTEND LINEARLY AND
BY FIVEFOLD AND ALL REACH OUT TO
EACH OTHER AND MAINTAIN THE
RELATIVE PHYSICAL CONTACT WITH
EACH OTHER AT THE SAME
GEOLOGICAL LOCATIONS BUILDING
THE STABLE SCAFFOLD.
UPON THIS SCAFFOLD THE NUMBER OF
SYNAPSES INCREASES LINEARLY AND
THIS FIVEFOLD SYNAPSE INCREASE
FROM L1 TO ADULTHOOD SERVE TWOS
TURN.
THEY STRENGTHEN THE EXISTING
SYNAPTIC CONDITIONS ALREADY
PRESENT AT BIRTH.
YOU SEE THE AVERAGE NUMBER OF
CONNECTION INCREASES AND SECOND
A SMALL NUMBER OF THE SYNAPSES
ARE USED TO BUILD MANY NEW
CONNECTIONS AND THE NUMBER OF
CONNECTIONS HAS INCREASED BY
TWOFOLD EXPANDING THE
CONNECTIVITY AMONG THE SAME
NUMBER OF NEURON.
THE CHANGES OCCUR THROUGH A
GLOBAL ADDITION OF SYNAPSES WITH
ALMOST COMPLETE ABSENCE OF
SYNAPSE PRUNING.
BEING ABLE TO IDENTIFY THE
GLOBAL TREND OF SYNAPSE WEIGHT
CHANGES ALLOWS US TO DESIGN
STRATEGIES TO COMPARE
DIFFERENCES BETWEEN CONNECTOMES.
THE PREMISE IS TO EVALUATE EACH
CELL-CELL CONNECTION BY THE
SYNAPTIC WEIGHT AGAINST THE
CONNECTIONS THAT EXHIBIT A
FASTER INCREASE REPRESENTING
CONNECTIONS THAT ARE ADDED
DURING DEVELOPMENT, CONNECTION
WITH NO INCREASE OF THE C.
ELEGANS PRUNING AND BECAUSE EACH
TIME POINT WE ONLY HAVE ONE
SAMPLE THAT MEANS ONE
CONNECTOME.
WE WANTED TO INCREASE THE
CONFIDENCE OF OUR CONCLUSIONS BY
TWO MEANS.
FIRST WAS MENTIONED BY ELLIE, WE
INCREASE THE STATISTIC POWER OF
OUR DATA SETS BY EXAMINING
INDIVIDUAL CONNECTIONS OF THE
LEFT-RIGHT CELL PAIR FOR EACH
CLASSES AND INCREASING THE
SAMPLE SIZE FROM 1-2.
SECOND, BECAUSE ADULT CONNECTOME
REPRESENT THE MATURE FORM WE ARE
ALLOWED TO SEPARATELY CONNECT
AND ASSESS THE SIMILARITY
DIFFERENCE BETWEEN ADULT
CONNECTOMES AND OVERLAP OF THE
CONNECTIONS REGARDLESS OF THE
SYNAPTIC WEIGHT.
FORCE THIS PURPOSE WE RECRUIT
THE LEGACY DATA SET FROM JOHN
WHITE THUS GENERATING MORE THAN
30 YEARS AGO.
TOGETHER THE ANALYSIS REVEALED
EACH CONNECTOME OF INDIVIDUALS
CONSISTENT OF THREE TYPES OF
CONNECTIONS.
STABLE CONNECTIONS THAT ARE
PRESENT AND INCREASES STEADILY
IN SYNAPTIC STRENGTH.
AND THE DYNAMIC CONNECTIONS
SELECTIVELY ADDED, PROMINENT
DURING THE EARLY OR LATE
DEVELOPMENT STAGES AND THE
VARIABLE CONNECTIONS THAT ARE
FORMED AND EXHIBIT NO OBVIOUS
TREND.
TOGETHER, WE CONCEDED A STABLE
AND DEVELOPMENTALLY DYNAMIC
CONNECTIONS MAKE UP THE CORE OR
THE PORTION OF THE C. ELEGANS
CONNECTOME AND FORM THE VARIABLE
PORTIONS OF INDIVIDUALS.
TO ASSESS WHERE THE VARIABLE AND
INVARIABLE CONNECTION
DISTRIBUTES WE LOOK AT
MODULATORY CONNECTOMES AND WE
CAN SEE FROM THE WIRING DIAGRAMS
THE VARIABLE CONNECTION MORE
BROADLY PRESENT BETWEEN AND
ACROSS MOST CELL TYPES WHEREAS
THE STABLE CONNECTIONS ARE
DISTRIBUTED.
TO VISUALIZE THIS MORE CLEARLY
PLOTTED ONLY THE INVARIABLE
CONNECTIONS IN THE ADULT
CONNECTOME BY THE SYNAPTIC
WEIGHT AND WE COLOR CODED THE
CONNECT.
FROM THIS DIAGRAM YOU CAN SEE
CLEARLY WHERE THE MOST PROMINENT
DEVELOPMENT CHANGES OCCUR SLOWLY
AND IN CONTRAST CONNECTIONS
AMONG MOST INTERNEURONS WHICH
CONSTITUTE THE CORE DECISION
MAKING SECTOR IS REMARKABLY
STABLE.
THUS, THIS ANALYSIS REVEALS TWO
UNEXPECTED PROPERTIES OF THE
DEVELOPMENT WIRING CHANGES.
ISO GENIC INDIVIDUALS CAN
ACTUALLY RAISE UNDER THE SAME
CONDITION AND STILL DEMONSTRATE
WIRING PROCESSING AND THEY'RE
LARGELY ESTABLISHED ALREADY AT
BIRTH BY SENSORY INTEGRATION AND
MOTOR REASONS CAN REMAIN PLASTIC
AFTER BIRTH.
LASTLY, WE FOUND THAT THE
SYNAPSE CHANGES CAN ALTER THE
NETWORK STRUCTURE.
WE USED WEIGHTED BLOCK MODELLING
TO BLOCK NEURONS INTO
DISTINCTIVE MODULES AND APPLIED
IS AND THIS RESULTED IN SIX
DISTINCTIVE MODULE AND EACH CAN
BE NAMED BY THE KNOWN BIOLOGICAL
FUNCTION OF THE CELLS THEY'RE
ENRICHED IN.
AND WHEN WE ARE APPLY THIS
CONNECTOME WE FOUND THE MODULAR
STRUCTURE FORMS DURING LATER
DEVELOPMENT.
FOR EXAMPLE, THE TWO DIFFERENCE
OF MODULES THAT ARE SEPARATED IN
THE ADULT CONNECTOME ONLY EMERGE
DURING THE LATE LARVAL STAGE.
THEREFORE THE SYNAPTIC GROWTH
REFINES SOME NETWORKS FOR
SENSORY OR MOTOR SENSES AND
THEY'RE BUILD STRONGER AND MORE
INVARIABLE CONNECTIVITY AND THEY
WANTED TO BECOME MORE MODULAR.
THIS MEANS SYNAPTIC GROWTH OR
ADDITION IS NOT RANDOM.
THEY'RE TARGETED WITH THE
COLLECTIVE GOAL.
THE REASON THAT WE'RE EXCITE
ABOUT THIS IS THIS EFFECTIVELY
TRANSLATES THE SECOND QUESTION,
WHAT MECHANISMS MAY GOVERN THE
MATURATION PROCESS INTO A
CONCRETE RESEARCH QUESTION.
WHAT ARE THE SYNAPSE AND HOW HAS
THE SIGNALLING MOLECULES TARGET
THIS ADDITION?
THERE'S MANY APPROACHES TO GO
ABOUT THIS.
THE BEGINNING APPROACH WE TOOK
WAS TO FURTHER EXAMINE THE
RELATIONSHIP.
IN THIS CASE WE'RE EXAMINING THE
CORRELATION OF THE PROPERTY OF
THE NEWBORN BRAIN OF THE
COMPACTOME AND CONNECTOME AND
IDENTIFY THE FEATURES OF THE L1
TOPOLOGY AND SYNAPTIC
CONNECTIVELY THAT CAN PREDICT
THE STRUCTURE OF THE ADULT
CONNECTO
CONNECTOME.
WE IDENTIFIED SOME POTENTIAL
ROLES.
WE KNOW UNIFORM NEURO ITE GROWTH
IN GROWTH NON-UNIFORM
SELECTIVELY STRENGTHENS THE
FINDING AND THE CONTEXT SIZE CAN
PREDICT THE LIKELIHOOD TO HAVE
NEW SYNAPSES AND THE NEW NEURONS
AT BIRTH HAVE HIGHER PROPENSITY
TO HAVE NEW CONNECTIVITY INPUT
AND OUTPOUT AND STRENGTHEN
EXISTING CONDITIONS WITHOUT
ADDING MORE CONNECTIVITY AND
SYNAPTIC CONNECTIONS RECEIVE
MORE SYNAPSES TO STRENGTHEN
THEM.
IN THE LAST QUESTION I'D LIKE TO
POINT TO A GENETIC FINGERPRINT
THAT DETERMINES THE WIRING
DIAGRAM.
AND THE ENVIRONMENT ALTER THE
WIRING.
FOR THIS WE RETURN TO THIS MOST
HARSH ENVIRONMENTAL CONDITIONS
THAT C. ELEGANS CAN FACE.
YOU RECALL I SAID AT THE
BEGINNING WE ALREADY KNOW
EXPOSURE TO THE HARSH
ENVIRONMENT AT THE END OF R1
STAGE HOW THE POST-EMBRYONIC
DEVELOPMENT CAN GET BETTER AND
THE ANIMALS CAN STOP FEEDING BUT
DEMONSTRATE DIFFERENT MORPHOLOGY
AND BEHAVIOR.
WE PERFORMED CONNECTOME BEHAVIOR
AND RECALL WE IDENTIFIED OVER
1,000 CONNECTIONS.
REGARDLESS OF THE STAGES THOSE
CONNECTIONS ARE THERE AND THEN
HAVE A SIMILAR RATE IN THE
NETWORK.
AND TO OUR SURPRISE THAT THOSE
CONNECTIONS ONLY ABOUT
TWO-THIRDS IS SHARED IN THE
CONNECTOME.
ABOUT 237 CONNECTIONS IS ABSENT
IN THE DATA SET AND IN ADDITION,
AT LEAST THREE OUT OF FOUR HAVE
NEW CONNECTIONS ABSENT FROM OUR
CORE CONNECTOME.
SO THIS REALLY SUGGESTIONS THAT
ENVIRONMENT CAN FUNCTION
TOGETHER WITH GENES TO SHAPE THE
SECTOR MATURATION OF THE PATIENT
AND SOMETHING CORE TO WHAT I'M
INTERESTED IN THE QUESTION OF
DESTINY IN PLASTICITY.
IN CLOSING NEED OF THE NERVOUS
SYSTEM TO GROW AND ADAPT IS
UNIVERSAL I DO AGREE WITH
EVERYBODY HERE THAT COMPARATIVE
STUDIES ARE CRUCIAL TO UNLOCK
WIRING RESOLUTION AND I WAS
REQUESTED TO IDENTIFY THE
REMAINING GAPS AND FUTURE
OPPORTUNITIES.
THESE ARE THE REMAINING GAPS IN
WHICH WE'RE ACTIVELY WORKING ON.
WE NEED TO GET ELECTRICAL CLEM
CAL SYNAPSES NOBODY TALKED ABOUT
AND MOLECULAR MAPPING AND USING
MUTANT MAPPING TOFIDE THE
GENETIC MECHANISMS OF THE WIRING
AND INTERPLAY BETWEEN GENES AND
ENVIRONMENT.
WITH THIS I WANTED TO THANK
EVERYBODY AND MY WONDERFUL
COLLEAGUES AND COLLABORATORS TO
MAKE THE WORK POSSIBLE AND I
WANT TO THANK JOHN WHITE WHO HAS
BEEN A MENTOR AND AN EXTREMELY
SUPPORTIVE MEMBER WHO HAS BEEN
TREMENDOUSLY SUPPORTIVE IN THE
LAST FEW YEARS WHEN THIS WORK
WAS ACTUALLY PRETTY DIFFICULT TO
DO.
THANK YOU VERY MUCH.
>> THANK YOU VERY MUCH.
BEAUTIFUL DATA.
GREAT.
IT'S TIME FOR SOME DISCUSSION.
I HAVE A FEW QUESTIONS.
I ENCOURAGE PEOPLE TO HAD MORE
QUESTIONS TO THE CHAT OR SEND
THEM THROUGH US AND CAN ALL THE
SPEAKERS TURN ON THEIR VIDEO AND
UNMUTE.
GREAT.
SO I HAVE A COUPLE QUESTIONS.
I'LL START WITH DR. SETS OMPOP.
BOTH SUGGESTIONS SUGGEST HIGH
RESOLUTION DWI CAN ALLOW ONE TO
RESOLVE FIBERS EITHER U OR SUB
CORTICAL TRACTS.
THAT CLINICAL RESEARCH QUALITIES
CANNOT.
I WAS WONDERING IF THE
INTERPOLATION OF SCANS OF
MILLIMETER RESOLUTION WAS TESTED
TO SEE IF THE SCANS COULD WE
INVOLVE THE TRACKS.
>> THANK YOU.
I'LL START A LITTLE BIT IF
THAT'S OKAY.
>> WE'RE LOOKING AT IT'S TYPES
OF TRACTS WE ARE LOOK AT THE
FIBERS AND IT WOULD BE A WAY TO
INFER HIGHER TO LOWER RESOLUTION
TO HELP WITH SOME OF THAT.
SO THERE'S TWO PRONGS TO WORK
WITH BETTER ACQUISITION AND
UTILIZE THE BEST DATA WE HAVE
AND TRY TO USE THAT AS PRIOR TO
RECONSTRUCT THE LOWER RESOLUTION
DATA.
I'LL LEAVE IT AT THAT BECAUSE
I'M SURE ANASTASIA HAS QUITE A
FEW THINGS TO SAY AS WELL.
>> THANKS, KAWIN.
THAT'S A GREAT QUESTION,
ACTUALLY.
WE HAVE A PROPOSAL TO DO
REVIEWED THAT AND SUPER
RESOLUTION TECHNIQUES CAN HELP
IN THAT REGARD AND I THINK IT'S
AN EXCITING DIRECTION TO USE WE
HAVE THE LUXURY TO COLLECT
HIGH-QUALITY DATA SETS TO
ENHANCE MORE CLINICALLY FEASIBLE
PROTOCOLS.
>> FOR DR. YENDIKI WHAT DO YOU
THINK THE ROLE OF POST MORTEM
CONNECTIVELY ROLE WILL BE GIVEN
THE LIMITATION OF RESOLUTION IN
FUNCTIONAL IMAGING STUDIES?
>> THAT'S ALWAYS A TOUGH ONE AND
A FAVORITE ONE.
HOW THE FUNCTIONAL CONNECTIVITY
RELATES TO STRUCTURAL
CONNECTIONS.
SINCE WE'RE ON THE TOPIC OF
CHANGES OVER THE LIFE SPAN,
DEFINITELY FUNCTIONAL
CONNECTIVITY AND STRUCTURAL
CONNECTIVITY ARE DIFFERENT TIME
SCALES AND STRUCTURAL
CONNECTIVITY TENDS TO CHANGE
MUCH SLOWER OVER TIME AND
FUNCTIONAL CONNECTIVITY IS
HIGHLY DYNAMIC EVEN WITHIN A DAY
DEPENDING ON HOW MUCH COFFEE YOU
HAD THAT DAY OR HOW MUCH SLEEP
YOU HAD, ETCETERA.
WE DEFINITELY DO NOT EXPECT THE
TWO TO AGREE AND THEY CONVEY
COMPLIMENTARY INFORMATION.
DEFINITELY STRUCTURAL
CONNECTIVITY HAS SPECIFICALLY AT
THE HIGHER RESOLUTIONS WE CAN
ACHIEVE MOST -- POST MORTEM CAN
INFORM FUNCTIONAL STUDIES AND
THERE'S PARALLEL AND SEGREGATED
CIRCUITS TO JUSTIFY WHERE
SOMETIMES THE PICTURE IS MORE
COMPLEX.
SO BEING ABLE TO DO THAT KIND OF
MAPPING AND HIGH RESOLUTION IN
THE HUMAN BRAIN WILL ALLOW US TO
SHED LIGHT ON SOME OF THESE
QUESTIONS.
>> I HAVE ONE FROM DANIEL GLEN
WHICH IS RATHER LONG BUT
INTERESTING.
>> I THINK IT MUST HAVE GOTTEN
CUT BECAUSE I DIDN'T SEE THE
QUESTION.
>> A FEW COMMENTS.
EFFORTS WITH PETER BASSLER AND
DR. SALIM ON HIGH RESOLUTION
MACAQUE WITH MATCHING HISTOLOGY
INTEGRATION ALLOWED US TO
RECENTLY CREATE A NEW HIGH
RESOLUTION ATLAS FOR THE MACAQUE
BRAIN.
I AGREE WITH THE ADVANTAGES OF
LONGITUDINAL CHANGES VERSE THIS
H DIFFERENCES THOUGH IT'S
IMPORTANT TO REALIZE THE ERROR
ASSOCIATED WITH EACH MEASUREMENT
AND CORTICAL THICKNESS IS OFTEN
CALCULATED ON THE CORTEX.
THOSE ARE SENSITIVE TO THE
INCONSISTENCY ACROSS SESSIONS OR
EVEN EXTRA ZERO SLICES AT THE
LARGEST POINT OF POINT
MILLIMETER AND IT MAY STILL
REACH STATISTICAL SIGNIFICANCE
ON A LARGE GROUP.
DO EITHER OF YOU WANT TO
RESPOND?
>> WHAT'S THE QUESTION?
>> HE'S CONCERNED ABOUT THE
VARIABILITY ACROSS TIME IS
LOOKING FOR DIFFERENCES IS
SENSITIVE TO ACQUISITION AND
RESAMPLING ON THE GRID.
>> YEAH, IT IS.
>> THAT'S THE ONE THING WE WORK
HARD AT TRYING TO HIGH
RESOLUTION AND REMOVING SOME OF
THE BIAS.
A LARGE PART OF THE WORK IN THE
LAB IS LOOKING AT THE
QUANTITATIVE IMAGING AT VERY
HIGH RESOLUTION.
SO WE'RE GETTING RID OF THE
VARIABILITY IN TERMS OF THE
VOXEL SIZE RESAMPLING AS WELL AS
DIFFERENT SCAN CASES AND
HOPEFULLY THAT WILL HELP IN
TERMS OF THE LARGE-SCALE STUDIES
AND ANALYSIS.
>> AND TO CLARIFY THAT WAS NOT
FROM DANIEL GLEN JUST FROM
COMMENTS.
I HAVE A QUESTION.
HOW MUCH DO YOU THINK THAT
MACHINE LEARNING AND ARTIFICIAL
NATURAL GAS CAN HELP GOING
FORWARD IN INCREASING THE
RESOLUTION AND POSSIBLY EVEN
BRIDGING THE GAP BETWEEN MRI AND
OTHER MODAL ANALYZING STRUCTURE
IN POSTMORTEM SAMPLES, FOR
EXAMPLE.
>> WE NEED THE POST MORTEM
MAPPING BECAUSE WE CANNOT TAKE
ADVANTAGE OF METHODS BECAUSE WE
DON'T HAVE THE GROUND TRUTH.
WHAT WE CAN USE AS THE GROUND
TRUTH AS A SUBSTITUTE OF THE
GROUND TRUTH IS MAYBE HIGHER
RESOLUTION SCANS, FOR EXAMPLE.
BUT STILL IT DOESN'T GET TO EVEN
THE HIGHER RESOLUTION MRI SCANS
HAVE THEIR OWN LIMITATIONS.
AND SO UNTIL WE REALLY HAVE THE
GROUND TRUTH OF THE CIRCUITRY OF
THE BRAIN WE WILL NOT TRULY BE
ABLE TO HARNESS THESE MACHINE
LEARNING APPROACHES AND THAT'S
EXACTLY ONE IMPORTANT DIRECTION
OF THE POST MORTEM WORK.
>> I'LL ADD THE IMPORTANCE OF
THE GROUND TRUTH IS IMPORTANCE
SO THE MACHINE LEARNING
APPROACHES SO GET IN VIVO DATA
THAT ANASTASIA MENTIONED SOME 18
HOURS OF SCANNING ACROSS NINE
SESSIONS FOR SOME OF THE
DIFFUSION SCAN BUT STILL IT'S
NOT AT A RESOLUTION WHERE WE
HAVE SOME OF THESE EX VIVO
SAMPLES WE CAN DO.
DEVELOPING THE RIGHT MACHINE
LEARNING TOOL TO UTILIZE THAT
WILL BE IMPORTANT.
IN TERMS OF THE ACQUISITION SIDE
AND MRI, I WOULD WANT TO USE IT
MAINLY FOR SPEEDING UP THE
RECONSTRUCTION RATHER THAN USING
IT AS AN EXTRA PRIOR.
I THINK WE HAVE AN APPROACH
BASED ON PHYSICS TO DO WELL IN
TERMS OF ACQUISITION BUT WE'RE
GETTING DATA AT A RATE THAT IS
CRAZY NOW.
YOU'RE GETTING SUBMILLIMETER
VOXEL ACROSS THE WHOLE BRAIN.
HAVE YOU 500, 600 TIME POINTS IN
A COUPLE MINUTES AND HOW DO YOU
RECONSTRUCT THAT PARALLEL.
YOU CAN SCAN FOR TWO MINUTES BUT
YOU CAN'T WAIT FOR 10 HOURS TO
DO THE RECONSTRUCTION AND GIVE
IT TO ANALYSIS.
YOU NEED TO BE ABLE TO HAVE
INSTANTANEOUS ONLINE
RECONSTRUCTION OF THE DATA AND A
THINK THAT'S WHERE MACHINE
LEARNING WILL HELP US A LOT.
>> DID YOU WANT TO ASK A
QUESTION?
>> I'M A MOLECULAR GENETICISTS
AND WHEN THE HUMAN GENOME DATA
AND WE WORKED TO IDENTIFY THE
FIRST POSITIVE MUTATIONS FROM
SOME THINGS WE'RE TESTING AND WE
STARTED TO DO DE NOVO SEQUENCING
THAT COMPARED THE MOLECULAR
CHANGES SIBLINGS AND THEIR
PARENTS I WONDERED WITH THE
BRAIN IMAGING APPROACH AND SOME
APPROACHES LIKE THAT, THAT'S A
BIT MORE TARGETED BUT WOULD THAT
BE MORE HELPFUL TO IDENTIFY -- I
WOULDN'T SAY POSITIVE BUT
SOMETHING THAT REDUCED LIKE
PINPOINT MORE SPECIFIC
POTENTIALLY PATHOLOGICAL OR
MORPHOLOGICAL MORE RELIABLE
CONNECTIVITY CHANGES?
>> I THINK ONE OPEN QUESTION AT
WHAT SCALE DO WE NEED TO
OPERATE?
DO WE REALLY NEED EVERY SINGLE
AXON IN THE HUMAN BRAIN?
I THINK IT'S QUITE POSSIBLY WE
DO NOT BECAUSE IT'S NOT GOING TO
BE A SINGLE AXON THAT MAKES THE
DIFFERENCE BETWEEN PATHOLOGICAL
BRAIN AND A HEALTHY BRAIN.
AND IT'S UNLIKELY THERE'S ONE
SINGLE AXON THAT DIFFERENTIATES
US FROM OTHER BRAINS.
ONE PERSON'S BRAIN FROM ANOTHER.
I THINK IT'S OPERATING AT A
SCALE TO CLINICAL REFERENCE AND
IS THE SWEET SPOT WHERE WE NEED
TO BE.
>> GREAT.
HOW DO THEY REWIRE TO INNERVATE
ADULT MUSCLES?
IS THERE ANY GENETIC
RELATIONSHIP TO REGENERATION?
>> 10% OF OUR ADULT SYSTEM IS
BORN IN THE EMBRYO AND GETS
REMODELLED AND AS THE MOTE MOTOR
NEURONS AND THE AXONS RETRACT
INTO THE CELL BODY AND THEY GROW
OUT AGAIN DE NOVO.
THERE'S THE MUSHROOM BODY WHICH
GETS MASSIVELY REMODELLED PEOPLE
HAVE USED TO STUDY THE
QUESTIONS.
THERE'S ALSO SENSORY NEURON
DENDRITE GET MASSIVELY
REMODELLED.
THEY LOOK LIKE THE NEURON
BETWEEN DR. HUGANIR'S HEAD AND
YOU CAN DO STUDIES OF
REMODELLING AND REGENERATION IN
THOSE CONTEXTS.
THERE'S A HUGE NUMBER THAT ARE
INTERESTING HAVING TO DO WITH
THE REMODELLING EVENTS.
>> HERE'S A QUESTION FOR
DR. ZHEN.
THANK YOU.
I'D LIKE TO KNOW WHAT DO YOU
SPECULATE ABOUT WHY CONNECTIONS
AMONG INTERNEURONS ARE MOST
STABLE?
COULD THIS EXPLAIN INTERNEURON'S
VULNERABILITY DURING AGING AND
AGE-RELATED DISEASES?
>> THAT'S A GREAT QUESTION.
WE HAVE DIFFERENT OPINIONS WHAT
THIS MEANS.
AND THIS IS A C. ELEGANS
CEREBELLUM AND DIFFERENT REGIONS
THAT LOOK AT THE BEHAVIOR.
MY PERSONAL TAKE IS MAYBE THIS
IS AN ENVIRONMENTAL STRATEGY
TAKEN FROM A SPECIES WITH A
SHORT LIFE SPAN AND SHORT TIME
AND THEN THE MOMENT IT GETS OUT
IT NEEDS TO MOVE AROUND.
WHEN YOU LOOK AT THE
DISTRIBUTION OF INVARIABLE
CONNECTION AND THOSE WITH
DEVELOPMENT PLASTICITY BUT IS
NOT VARIABLE IS CONNECTIONS
BETWEEN SENSORY NURNZ AND ALSO
THE CONNECTIONS FROM THE LAST
LAYER SENSORY INTERNEURONS INTO
THE FIRST LAYERS ARE THE MOST
DEVELOPMENTALLY PLASTIC.
MY INTERPRETATION IS THEY THINK
THE BEST THING TO DO IS TO BUILD
UP HOW THE SENSORY IS PROCESSED
AND THEY DON'T CHANGE IT AND
ONCE THEY COME OUT BECAUSE THE
ENVIRONMENT IS A LITTLE BIT
UNPREDICTABLE THEY CAN FURTHER
DELAY OR ACCELERATE OR EVEN
CHANGE THE CONNECTIONS THROUGH
THE OTHER CIRCUIT LAYER.
THAT'S WAY THEY'RE CHANGING THE
WAY THEY CROSS-TALK AND GET
INPUT FROM THE BRAIN BUT THE
PROCESSING ITSELF DOES NOT NEED
TO CHANGE.
THIS MAY BE A VERY ECONOMICAL
WAY TO MAINTAIN STABILITY AND
WITHOUT COMPLETELY LEAVING
EVERYTHING UNNEUURTURED BECAUSE
THEY DON'T HAVE THE TIME WINDOW.
I'M HAPPY TO TALK ABOUT.
AND ONE THING ABOUT AGING, I
DON'T KNOW ABOUT AGING WE
HAVEN'T DONE THAT BUT WE KNOW
THIS PART NEEDS TO BE PROTECTED
BECAUSE THAT'S THE THING WE WERE
SURPRISED HALF THE CONNECTIONS
ARE IN THE SO-CALLED INVARIANT
THE COMPLETE INTERNEURON
CONNECTIONS AND LIKE THEY CAN
CHANGE WHEN THEY'VE BEEN PUSHED
TO THE EXTREME.
THAT WAS ENCOURAGING NEWS AND WE
CAN PROBABLY FIND OUT A BIT MORE
WHAT THEY DO ONCE WITH WE
CONFIRM THE UNPUBLISHED STUDIES.
>> BECAUSE OF THE MENTION OF
ABSENCE OF SYNAPTIC PRUNING IS
SYNAPSE MAINTENANCE HARD WIRED
AND STABLE?
>> GOOD QUESTION.
WE HAVEN'T DONE THOSE EXPERIMENT
S -- EXPERIMENTS WITH THE
DIFFERENT INVERTEBRATE STUDIES
AND THE LACK OF PRUNING IT COULD
BE FOR ECONOMICAL REASONS.
YOU CAN IMAGINE C. ELEGANS WAS
PRETTY MUCH BORN IN THE GOOD
ENVIRONMENT AND ALMOST READY TO
GO IN THE BRAIN.
THE BODY'S A DIFFERENT STORY I
DON'T HAVE TIME TO TALK ABOUT.
BECAUSE THEY HAVE TO FEND FOR
THEMSELVES IT DOESN'T MEAN THE
PLASTICITY DOESN'T HAPPEN IN THE
EARLIER STAGE.
WE HAVE TO PUSH BACK THE TIME
WINDOW SEE IF THERE'S SYNAPTIC
PRUNING OR WHAT BEEN OBSERVED IN
THE VERTEBRATE SYSTEM AND
CONVINCINGLY HAPPENS IN THE
EMBRYONIC STAGE.
WE JUST DID NOT EXPECT IT WHEN
WE STARTED TO DO THE
EXPERIMENTS.
SENSORY PERCEPTION, I COME FROM
A LAB WHERE WE DEVELOPED THE
FIRST GENETIC MARKERS TO SCREEN
SYNAPSE FORMATION IN C. ELEGANS.
I HAVE DONE SOME.
AND OTHER GROUP WERE ABLATING
SOME NEURONS AND CHANGES THE
MECHANO SENSORY NEURONS AND SOME
SEEM TO SO THE A LOT OF
PLASTICITY AT THAT LEVEL.
I WOULD NOT BE SURPRISED THEY
ARE NOT -- THEY'RE NOT HARD
WIRED AND THEY'RE NOT STABLE.
>> HERE'S A QUESTION FROM DAVID
AND IT WAS ANSWERED IN THE CHAT.
AND LOTS OF PEOPLE DON'T SEE THE
CHAT.
THE ADVANCES IN FUNCTIONAL MRI
COMPARABLE TO WHAT YOU SHOWED
FOR INSTRUCTIONAL DIFFUSION MRI.
>> THANK YOU.
WE'VE BEEN WORK QUITE A BIT ON
THAT AS WELL.
I JUST DIDN'T HAVE ENOUGH TIME
TO SHOW THAT IN THE TALK.
WE HAVE BEEN PUSHING FUNCTIONAL
MRI AND IN THAT SENSE THERE'S
LIMITATION IN TERMS OF SPATIAL
AND TEMPORAL RESOLUTION WHICH WE
HAVE TO OVERCOME IN TERMS OF THE
IMAGING BUT THERE'S ALSO THE
BIOLOGICAL RESOLUTION AND WHAT I
MEAN BY THAT IS THAT WE'RE
MEASURING BLOOD SIGNAL AND THE
ABILITY OF THAT TO CORRELATE IS
NOT PERFECT.
THERE'S SOME SPATIAL SPREADING
AS WELL AS TEMPORAL DELAY IN
CHANGES AND WE'RE LOOKING TO
OVERCOME THOSE.
>> WE ONLY HAVE A FEW MORE
MINUTES LEFT MAYBE I CAN OPEN
THE DISCUSSION TO THE WHOLE
PANEL.
ONE THING I'M PARTICULARLY
INTERESTED IN HOW DO WE BRIDGE
THE GAP BETWEEN THE LEVELS OF
ANALYSIS?
EVEN WITH ARTIFICIAL
INTELLIGENCE I DON'T THINK WE'LL
BE ABLE TO DO THAT.
THIS IS ASKING YOU TO BE
SPECULATIVE AND DISCUSS THE
TOPIC.
>> I'LL START BY SAYING I THINK
ONE THING I THINK ABOUT IS
REALLY WHAT IS THE SYSTEM GOOD
FOR AND WE'RE NEVER GOING TO PUT
A LARVA INTO AN MRI MACHINE AND
BE ABLE TO DO THAT AND PART OF
THE ANSWER IS WHAT IT IS DO YOU
WANT TO LEARN FROM YOUR SYSTEM.
ONE GUESS -- QUESTION I HAVE FOR
THE MRI FOLKS AND THIS MAY BE
PRETTY NAIVE BUT TO WHAT EXTENT
DO YOU THINK IT WILL EVER BE
POSSIBLE TO GET PRIOR KNOWLEDGE
A DISEASE STATE WAS COMING?
YOU MENTIONED MAYBE ONE AXON --
YOU DON'T NEED THAT LEVEL OF
RESOLUTION TO REALLY TELL THE
BRAIN IS DYSFUNCTIONAL BUT WHERE
DO YOU THINK YOU'D NEED TO GO TO
HAVE PREDICTIVE POWER FROM
IMAGING BEFORE THINGS GO REALLY
WRONG?
>> WITH THE INCREASE RESOLUTION
AND ACCURACY OF MRI WILL WE BE
ABLE TO SEE SMALL CHANGES IN
BRAIN STRUCTURE AND FOR EXAMPLE
DO MORE RAPID CLINICAL TRIALS OR
DETECT MORE SUBTLE CHANGES IN IN
BRAIN STRUCTURE FOR A VARIETY OF
DISEASES, SCHIZOPHRENIA OR EVEN
DEPRESSION.
WHAT ARE YOUR THOUGHTS ABOUT
THAT?
>> I HOPE SO AND THAT'S THE
MOTIVATION FOR THE WORK WE'VE
BEEN PUSHING.
WITH MRI YOU CAN HAVE A LARGE
NUMBER OF FLURRY IMAGES WITH
LARGE-SCALE STUDY TO DETECT
SOMETHING OR POLISH THE LENS AND
TO THE QUESTION OF WHAT WE NEED
TO DETECT THESE THINGS.
THIS IS AN OPEN QUESTION AND
HAVING THE LARGE SCALE STUDIES
IS HELPFUL BECAUSE IF YOU ARE
ABLE TO MINE THAT DATA AND LOOK
AT BOTH MRI AND OTHER DATA
MODALITY THAT HAVE BEEN
COLLECTED YOU CAN START TO LOOK
AT SOME OF THESE AND SEE WHAT
ARE WE SENSITIVE TO I THINKS
THIS IS AN AREA ANASTASIA IS AN
EXPERT IN SO I'LL LET HER TALK.
>> WHAT I'M SOMETIMES CALLED IS
A PESSIMIST AND I DON'T KNOW IF
YOU CAN PREDICT THE FUTURE FROM
A MAP I THINK A MAP FOR
MODULATION APPROACHES IS A
FEASIBLE TARGET.
I DON'T KNOW IF WE'LL EVER HAVE
A MAP OF THE BRAIN THAT CAN
PREDICT THE FUTURE.
>> YOU'RE LOOKING AT
LONGITUDINAL STUDIES AND IF YOU
LOOK AT STRUCTURE US SHOULD BE
ABLE TO DETECT BETTER, RIGHT?
>> AND IN ACUTE STAGES OF FOR
EXAMPLE, TRAUMATIC BRAIN INJURY
WHERE YOU HAVE STRUCTURAL
CHANGES THAT OCCUR AT A SLIGHTLY
SHORTER TIME SCALE THAN NORMAL,
THAT WOULD BE ANOTHER POTENTIAL
OPPORTUNITY FOR USING THESE
METHODS.
>> THE INTRIGUING THING FOR ME
IS HOW DOES THE FUNCTIONAL MRI
STRUCTURE OR TRACK CORRELATE TO
THE 3,000 CELL TYPES IDENTIFIED
BY MOLECULAR FINGERPRINTS
BECAUSE TO ME I FOUND THE ONLY
WAY TO TACKLE WITH LARGE BRAINS
WITH HUGE NUMBER OF NEURONS IS
TO FIRST IDENTIFY THE DEGREE OF
REDUNDANCY SO YOU KNOW HOW MUCH
ANATOMICAL ACTIVITY YOU NEED TO
GO INTO DETAILS.
I WAS INTRIGUED BY DIFFERENT
OMICS DATA YOU CAN CROSS INTO
CELL TYPES BUT IT'S ALSO KNOWN
BY SINGLE CELL TECHNOLOGY ALONE
YOU CAN HAVE MORE BECAUSE ION
CHANNELS CAN CREATE THE SAME
SYSTEM APPROACH.
SO THE SAME THING HERE.
BY PROJECTIONS CAN YOU NARROW
DOWN TO SEE IF THERE'S SOME WAY
TO CORRELATE TO ME I THINK IF
YOU CAN CORRELATE THE
TRAJECTORIES THAT YOU CAN
IDENTIFY DISSECTING THE BRAIN
INTO HUNDREDS OF BRAIN REGIONS
AND HAVE A BETTER OVERLAP WITH
THE MOLECULAR FINGERPRINTS.
FROM THERE YOU ARE GOING TO A
SYNAPSE LEVEL.
THAT MIGHT BE SOMETHING I SAW
THAT I WOULD LIKE TO SEE HOW IT
WORKS IF IT'S POSSIBLE.
>> I DON'T STUDY CELLS, I STUDY
AXONS AND I THINK THE ANSWER
LIKELY VARES DEPENDING ON WHAT
SCALE YOU NEED TO LOOK AT.
THERE'S SOME PATHWAYS MORE
CLEANLY TOPOGRAPHICALLY
ORGANIZED AND WHEREAS THERE ARE
OTHER PATHWAYS MESSIER AND
POTENTIALLY IN THOSE PATHWAYS
YOU NIGHT TO LOOK AT A -- NEED
TO LOOK AT A HIGHER SCALE.
I THINK THERE ISN'T A SINGLE
ANSWER THAT WOULD BE OPTIMAL FOR
THE ENTIRE BRAIN.
AT LEAST FOR SOMETHING AS
COMPLEX AS THE HUMAN BRAIN.
>> THINK THAT'S PROBABLY A GOOD
PLACE TO STOP.
I THINK IF WE COULD MERGE MRI
WITH SPECIFICITY WE COULD GET
THERE.
WE'RE RIGHT ON 3:40.
WE'LL TAKE A BREAK FOR 10
MINUTES.
GREAT TALKS, EVERYBODY.
THANK YOU AND FUN DISCUSSION.
>> WELCOME BACK.
I'M A PROGRAM DIRECTOR AT NICHD
AND I'M IT'S PLEASURE TO
INTRODUCE DAVID van ESSEN
ENDOWED PROFESSOR AT WASHINGTON
IN ST. LOUIS AND LOOKS AT THE
CONNECTIVITY AND DEVELOPMENT OF
CEREBRAL CORTEX AND IN RECENT
YEAR THE LAB USED NEUROIMAGING
AND DATA COLLABORATIVELY WITH
OTHER INSTITUTIONS.
THE MAJOR EMPHASIS IS ON THE
DEVELOPMENT AND UTILIZATION OF
METHODS FOR COMPUTERIZED BRAIN
MAPPING AND NEUROINFORMATICS
TOOL TO INFORM DATA MINING AND
SERVED AS THE HUMAN INVESTIGATOR
FOR A LARGE SCALE EFFORT THAT
ACQUIRED AND ANALYZED DATA FROM
1200 HEALTHY ADULTS AND
CURRENTLY A CO-P.I. OF THE HUMAN
CONNECTOME PROJECTS.
THE MAJOR FOCUS OF THE LAB IS TO
USE THE HUMAN CONNECTOME
PROJECTS AND OTHER HIGH-QUALITY
DATA SETS TO BETTER UNDERSTAND
CORTICOPARSLATION IN HUMAN AND
NON-HUM
NON-HUMAN PRIMATES.
HE MOVED TO WASHINGTON
UNIVERSITY IN 1992 WHERE THE
CHAIRED THE DEPARTMENT OF ANAT
ANY AND NEURAL BIOLOGY AND
SERVED IN THE ORGANIZATION FOR
HUMAN BRAIN MAPPING AND RECEIVED
THE CORTICAL DISCOVERY AWARD AND
THE GLASS BRAIN AWARD FROM THE
ORGANIZATION FOR HUMAN BRAIN
MAPPING AND THE GEORGE A. MILLER
PRIZE FROM THE COGNITIVE
NEUROSCIENCE SOCIETY AND THE
CARL AND CORY FACULTY
ACHIEVEMENT AWARD FROM
WASHINGTON UNIVERSITY SCHOOL OF
MEDICINE.
HE'S A FELLOW OF THE AMERICAN
ASSOCIATION FOR THE ADVANCEMENT
THE SCIENCE AND MEMBER OF THE
NATIONAL ACADEMY OF SCIENCES.
DR. VAN ESSEN.
>> THANK YOU, DR. HARTMAN FOR
THE OPPORTUNITY TO PRESENT AT
THIS SESSION AND TO INTRODUCE
THE NEXT LEVEL OF DISCUSSION OF
THE BRAIN ACROSS THE LIFE SPAN.
I'M GOING TO GIVE YOU TWO
PERSPECTIVES.
FIRST IS AS A NEUROANATAMISCT
AND ACCURATE SPATIAL
LOCALIZATION IS VITAL AND
DIFFICULT BUT CAN BE DONE AND IT
HAS TO DO WITH THE TOPOLOGY AND
THERE'S CONVOLUTED CEREBELLUM
AND THE SUBCORTICAL NUCLEI AND
THEY'RE CONNECTED BY WHITE
MATTER TRACTS YOU HEARD ABOUT
EARLIER.
ANOTHER LEVEL OF COMPLEXITY
RELIES ON OVERLAID ON THE
STRUCTURE AND UNFOLDING OF THE
CORTEX IS A VERY ELEGANT BUT
FUNCTIONAL FUNCTIONAL
ORGANIZATION KNOWN AS A
PARSLATION THAT CONTAINS 180
AREAS OF THE LATEST HEMISPHERE
AND IN THE SUBCORTICAL DOMAIN
THERE'S HUNDREDS OF NUCLEI AND
UNKNOWN NUMBER OF PARCELS IN THE
CEREBELLUM.
AND ADD TO THAT THE CORTICAL
FOLD S ARE VARIABLE AND VARIABLE
IN THEIR SIZE, TWO TO THREE FOLD
VARIABILITY AND IN THE
RELATIONSHIP TO THE FOLDS.
AND THERE'S CHANGES THAT OCCUR
ACROSS THE LIFE SPAN PROFOUNDLY
IN EARLY DEVELOPMENT AND
SUBSTANTIAL CHANGES OCCURRING IN
LATE AGING AS WELL.
WE HEARD EXAMPLES OF HOW THE
EXPLOSION OF DATA FROM MEGABYTES
WHEN I WAS YOUNGER TO GIGABYTES,
PETABYTES AND COMING SOON LOTS
OF EXBYTES THE WORLD WILL HAVE
TO DEAL WITH.
THERE'S GENE EXPRESSION ATLASES
FROM THE ALLEN INSTITUTE AND
OTHERS AND I'LL LOOK AT EXPAND
THE LIFE SPAN.
AND THE HUMAN CONNECTOME PROJECT
SCANNED ADULTS AND INTRODUCED
THE CONCEPT OF HDP STYLE
NEUROIMAGING AND GETTING THE
HIGHEST DATA POSSIBLE AND REMOVE
NOISE AND SHARE THE DATA WITH
OPENNESS.
THAT APPROACH HAD BEEN CONTINUED
WITH NOW MANY OTHER PROJECTS.
AND THE NIH CONNECTOME AND THE
LIFE SPAN PROJECTS MENTIONED A
LITTLE WHILE AGO FOR DEVELOPMENT
IN AGING AND MORE ACRONYM SOUP
WITH THE ABCD PROJECT AND THE
HBCD.
THEY'RE ALL WONDERFUL PROJECTS
WITH THE BRITISH BIO BANK
EFFORT.
THE DATA IN THE NEUROIMAGING
DOMAIN HAS ONE SET OF DATA
RESOURCES LIKE CONNECTOME DB AND
THE NIMH DATABASE AND THERE'S A
GROWING NEED FOR RESOURCES TO
SHARE EXTENSIVELY ANALYZE DATA
SUCH AS THE DEAP ABCD PROJECT
AND OUR LAB'S EFFORT.
ANOTHER MAJOR CHALLENGE TOUCHED
UPON IS THE DATA HARMONIZATION
IS A HUGE CHALLENGE TO DEAL WITH
PROJECT SCANNERS AND PROTOCOLS
WHEN USED TO COMPARE ACROSS
GROUPS AND AGES.
HAVE AN ASPIRATION THAT GOOGLE
EARTH AND GPS POSITIONING
SATELLITES THAT CHANGE THE WAY
WE INTERACT WITH THE WORLD
AROUND US WILL HAVE COMPARABLE
DEVELOPMENTS IN THE COMING
DECADES FOR THE BRAIN WHERE
WE'LL BE ABLE TO QUERY ANY
REGION OF INTEREST AND ANY
SPECIES THAT HAS BEEN CAREFULLY
STUDIED AND OBTAIN VAST AMOUNTS
OF INFORMATION ABOUT STRUCTURE
DEVELOPMENT AND CONNECTIVITY AND
THE LIKE.
WITH THAT AS AN ASPIRATION,
LET'S MOVE ON TO OUR FIVE
SPEAKERS.
YOU'LL EACH HAVE FIVE MINUTES
FOR THEIR PERSPECTIVE BEFORE WE
GO INTO OPEN DISCUSSION MODE.
OUR FIRST SPEAKER IS ALEXANDER
BADEA AT DUKE UNIVERSITY.
HER RESEARCH FOCUSES ON
ALZHEIMER'S DISEASE WHICH SHE
STUDIES USING DIFFUSION IMAGING
COMBINED WITH GENETICS AND
BEHAVIOR AND OTHER METRICS THAT
LEADS TO BIOMARKER
IDENTIFICATION.
I'LL STOP SHARING MY SCREEN AND
HAND IT TO ALEX AN DRA.
>> THANK YOU FOR BEING HERE AT
THE AND OF A BUSY AND EXCITING
DAY AND FOR THE FUNDERS TO MAKE
THE WORK POSSIBLE.
I'LL TALK TO MY LINE OF RESEARCH
AND WE HAVE LOOKED AT MODELLING
AND OUR BIG CLINICAL IMAGING
USING HIGH FIELD MRI AT THE 100
MICRON RESOLUTION --
>> CAN YOU USE THE WHOLE SCREEN,
PLEASE.
>> I WILL DO MY BEST.
>> GREAT, THANK YOU.
>> WE DO USE EX VIVO IMAGING AT
5.4 TESLA AND WE ENHANCE IMAGING
CONTRAST AND SIGNAL TO NOISE
RATIO TO ACQUIRE FASTER IMAGES.
WE HAVE USED COMPRESS TESTING
FOR DIFFUSION AND YOU CAN SEE WE
CAN DISCERN CORTICAL AND
CELLULAR LAYERS AT THIS LEVEL OF
RESOLUTION EX VIVO AND GET THE
DENSE CONNECTIVITY IN EX VIVO
DIFFUSION IMAGES.
SO WE HAVE USED OUR EFFORTS TO
GENERATE HIGH SPATIAL RESOLUTION
DIFFUSION IMAGING AND THAT
ALLOWED US TO LABEL A MOUSE
BRAIN WITH 332 REGIONS TO
GENETIC POPULATION AND
CONNECTOMES AND WE HAVE
COLLABORATED TO CREATE AND APPLY
METHODS FOR DISCRIMINATING FOR
DIFFERENT MODELS OF ALZHEIMER'S
DISEASE AND LOOKING AT COMPONENT
ANALYSIS AND IT ALLOWS DEFINED
THE TOP CONNECTIONS
DISCRIMINATING GENOTYPES AND WE
CAN COMPARE FURTHER DOWN THE
LINE PROPERTIES OF TEXTURE.
AND WE CAN SEE WHEN WE LOOK AT
BRAIN CONNECTIVITY IN MOUSE
MODELS HAVING TARGETED
REPLACEMENT FOR APOE GENOTYPES
THE WIRING IS DIFFERENT FOR THE
CONNECTION BETWEEN THE CORTEX
AND HIPPOCAMPUS AND THIS REFERS
TO THE COMBINING IN THE
CONNECTION.
THERE'S DIFFERENT WIRING AND
DIFFERENT RELATIVE SIZING IN
BETWEEN THE TWO GENOTYPES.
MOREOVER THE GENOTYPES TEND TO
CLUSTER THE CONNECTOME AND MAYBE
THERE'S A TYPE FOR CLUSTERING
REPRESENTED WITH BLINDS FOR
MALES AND CIRCLES FOR FEMALES.
ONCE WE ALIGN THE DIFFERENT
GENOTYPES WE CAN COMPARE THE
DISTRIBUTION OF DIAMETERS AND
ONCE WE START DISCRIMINATING WE
CAN SEE SOME OF THE UNIFORM
DIFFERENCES AND SOME ARE
NON-UNIFORM DIFFERENCES ALONG
THE TRACKS.
WE HAVE USED APPROACHES THAT ARE
ANALOGOUS ONCE USED IN HUMANS IN
A MOUSE MODEL EXPRESSING THE
MUTATIONS GENERATED AND WE CAN
SEE THAT WE HAVE EFFECT OF
GENOTYPE AND AFFECT OF AGE IN
THE TRANSGENIC MICE ALLOWING FOR
CONTROLS WE CAN DETECT ON A
RELATIVELY SHORT TIME FRAME,
SEVEN WEEKS AFTER EXPRESSION AND
WE CAN LOOK AT THE INTERACTION
BETWEEN PHENOTYPE.
WE HAVE ALSO USED ENHANCED MRI
IN CONJUNCTION WITH BEHAVIOR
WHEN WE IMPLANT EIMPLANTED MANGANESE AND
LOOKED AT SUSCEPTIBILITY OF THE
IRON DEPOSITION AND WE DEVELOPED
APPROACHES TO MODEL BEHAVIOR
USING THE REPRESENTATION OF THE
IMAGING PHENOTYPES AND WE'VE
DISCOVERED WE HAVE BETTER
PREDICTIVE ABILITIES FOR
BEHAVIOR IF WE COMBINE THE THREE
BIOMARKERS.
AND WE ARE APPLYING MORE SIMILAR
METHODS TO LOOK AT NEURO IMAGING
GENETIC RISK FOR ALZHEIMER'S
RISK IN HUMAN POPULATIONS.
WE'RE DOING IMAGING TO GET
VARIOUS CONTRAST FOR EXAMPLE T1
WEIGHTED IMAGE FOR VOLUME
CHANGES AND SUSCEPTIBILITY AND
DIFFUSION AND WE CAN SEE WE CAN
OBSERVE ACTIONS IN BOTH VOLUME
BETWEEN APOE AND APOE 3 AND 4 AT
RISK FOR ALZHEIMER'S DISEASE
BEFORE ANY OTHER DISEASE.
SIMILARLY WE HAVE DEVELOPED RISK
SIGNATURE THAT INCORPORATED
COGNITION.
AND APOE GENOTYPE AND AGE AND
LOOK PRINCIPLE COMPONENT
ANALYSIS TO LOOK AT BRAIN
NETWORKS THAT DIFFERENTIATE APOE
3 AND APOE 4 CARRIERS AND
IDENTIFYING THE VULNERABLE
NETWORKS.
AND THIS CAN GENERATE HYPOTHESIS
FOR LARGER COHORTS FROM PUBLIC
DATABASES BUT IT CAN BE APPLIED
TO DIFFERENT TIME POINTS ACROSS
SPACES.
THANK YOU.
>> NEXT IS IRINA CONBOY LOOKING
AT TISSUE MAINTENANCE AND
REPAIR.
DR. CONBOY.
>> I GLAD WE CAN DO REMOTE
BECAUSE I HAVE AN OLD FASHIONED
COLD TODAY.
THANK YOU FOR ORGANIZING THE
MEETING.
WHAT WE HAVE BEEN FOCUSSING ON
FOR A WHILE IS THE EFFECTS OF
YOUNG OR OLD BLOOD ON
NEUROGENESIS, BRAIN INFLAMMATION
AND CAPACITY USING SMALL ANIMALS
SUCH AS MICE AS EXPERIMENTAL
SYSTEM.
RECENTLY WE EXPANDED OUR WORK TO
CLINICAL STUDIES AND THE WORK IS
STILL UNPUBLISHED AND HOPEFULLY
I'LL BE ABLE TO SHARE IT NEXT
TIME AROUND.
SO WHAT YOU CAN SEE HERE IS THE
MINIATURIZED PROCEDURE OF
EXCHANGE IN BLOOD BETWEEN MICE
WHICH IS A PROCEDURE THAT LAST
30 MINUTES AND THEY GO SEPARATE
WAYS AND WE SEE NEUROGENESIS OF
THE HIPPOCAMPUS OR THE NUMBERS
OF PROLIFERATING CELLS DECLINE
NOT ONLY WITH AGE, THIS IS YOUNG
EXCHANGE ANIMALS AND INJURED
EXCHANGE THAT ARE INJURED BUT
DECLINES WHEN YOUNG MICE ARE
EXCHANGED WITH OLD BLOOD JUST
ONCE AND PARTICULARLY WHEN THESE
ANIMALS ARE INJURED IN THEIR
SKELETAL MUSCLE.
THE COMBINATION OF INJURY AND
OLD BLOOD DIMINISHING
HIPPOCAMPUS NEUROGENESIS VERY
QUICKLY.
OLD ANIMALS DO NOT BECOME
BETTER, THEY'RE NOT REGENERATED
WITH RESPECT TO THE HIPPOCAMPAL
REGENESIS EVEN WITH YOUNGER
BLOOD AND MICE ARE PUT IN AN
INVERTED POSITION AND IT'S NOT
THE BRUT FORCE TEST SO IN THE
TRAINING SESSION YOUNG MICE ARE
NOT DOING MUCH BETTER THAN OLD
MICE.
THEN IN THE TEST IF YOUNG MICE
HAVE YOUNG BLOOD THEY LEARN HOW
TO HANG AND WITH RESPECT TO THE
OLD ANIMALS YOUNG BLOOD DOES NOT
IMPROVE THIS COGNITIVE SHORT
MEMORY RESPONSE TO REMEMBER THEY
DON'T WANT TO DROP AND DOES NOT
AFFECT AGILITY AND THIS IS
DIFFERENT WHERE IF YOU
PHYSICALLY SUTURE THE ANIMALS
TOGETHER AND THEY RUN AROUND
SEVERAL WEEKS THEN YOU SEE BOTH
DECLINE OF HIPPOCAMPAL
NEUROGENESIS IN THE PAIR AND
SLIGHT INCREASE BUT IF YOU LOOK
AT THE SCALE YOU LOOK AT THE
PRECURSOR CELLS.
INTERESTINGLY WE KNEW THIS
OUTCOME BY 2003 BUT THIS WAS
REVIEWED A COUPLE TIMES IN
NATURE BUT WE SHARED THE DATA
WITH OUR STANFORD NEIGHBOR AND
HE FOLLOWED UP AND PUBLISHED ED AED AS
YOU KNOW INTERESTING WORK IN
NEUROPLASTICITY BUT SIX YEARS
LATER THIS WAS PUBLISHED IN
NATURE.
THE BOTTOM LINE IS THERE'S A
DIFFERENCE BETWEEN BLOOD
EXCHANGE AND I'LL BE HAPPY TO
SPECULATE AS TO WHY.
THE BLOOD EXCHANGE IS YOU DO NOT
NEED TO EXCHANGE YOUNG OR OLD
BLOOD YOU CAN THE CIRCUITRY
ENVIRONMENT WITH ANY FLUID YOU'D
LIKE TO TEST AND IN THE FIRST
TEST WE SIMPLY DILUTED OLD
PLASMA USING SALINE AND WHAT
HAPPENS THERE IS THERE WAS
IMPROVEMENT IN COGNITION OF OLD
ANIMALS IN NOVEL COGNITION
TESTS.
SO TYPICALLY YOUNG MICE ARE
INQUISITIVE AND EXPLORE THEIR
ENVIRONMENT AND AFTER SINGLE
PROCEDURE OF OLD PLASMA DILUTION
THEY BEHAVE AS YOUNG.
THIS RESULT IS ARE
NEUROINFLAMMATION AND SUDDENLY
YOU GET BRAIN SENESCENCE SIMILAR
TO THAT AS WHEN THEY USED THIS
63 AND THESE ARE SMALL IMAGES
THAT SHOW THE PROFILE OF THE
CIRCUITRY PROTEOME OF MICE AND
PEOPLE UNDERGOING THE PROCEDURE.
THE REMAINING PROTEINS WHICH ARE
NOW UP REGULATED AND SO WHAT WE
THINK IS GOING ON IS THAT WE
INITIALLY DILUTE THE CIRCUITRY
PROTEIN AT THIS STAGE AND THE
PROTEIN IS AN INHIBITOR OF ALL
THOSE YOUNG FACTORS THAT DECLINE
WITH AGE AND SO ONCE IT'S
DILUTED AT THE LEVEL OF GENE
EXPRESSION AND EPIGENOME YOU
THEN UNLEASH MORE PRODUCTIVE
LEVELS OF SO-CALLED POSITIVE
REGULATORS OF FUNCTION,
MAINTENANCE AND REPAIR.
SO THIS IS THE SIMULATION WHICH
IS JUST FOR ILLUSTRATIVE
PURPOSES BUT HAVE A CAPACITY TO
AND YOUNG PROTEINS HOPEFULLY
ONCE YOU PHASE OUT THEY NEED FOR
PLASMA EXCHANGE AND DEVELOP
RATIONALE PHARMACOLOGIC
APPROACHES.
I'D LIKE TO REACH OUT TO THE
REGENERATION RESEARCH AND
STARTING AS THE NEW
EDITOR-IN-CHIEF.
THANK YOU SO MUCH FOR YOUR
ATTENTION.
>>
>> JILL GOLDSTEIN AT HARVARD
MEDICAL SCHOOL AND FOUNDER AND
DIRECTOR ON SEX CHANGES IN
MEDICINE AT MASS GENERAL AND
LOOKS AT ENDOCRINOLOGY WITH THE
AIM OF UNDERSTANDING SEX
DIFFERENCES AND DISORDERS OF THE
BRAIN AND THE CO-OCCURRENCE WITH
OTHER EVENTS SUCH AS CARDIO
VASCULAR DISEASE.
>> I'M GOING ASK FOR MENTAL
FLEXIBILITY BECAUSE I'M SHIFTING
GEARS HERE TO A MORE HIGHER
LEVEL DISCUSSION AROUND AND WE
UNDERSTAND NEURO DEVELOPMENT IS
UNDERSTANDING THE BRAIN AND WE
STUDY SEX DIFFERENCES IN THE
RISK OF THE DISORDERS OF THE
BRAIN AND CO-OCCURRENCE WITH THE
DISORDERS OF THE HEART AND WE
FOUND SHARED PATHOPHYSIOLOGY
ACROSS THE DISORDERS THAT
DIFFERS BY SEX AND THEN BEGINS
IN FETAL DEVELOPMENT AND MY LAB
FOCUSES ON SEX DIFFERENCES IN
THE RISK FOR DEPRESSION AND
CO-OCCURRENCE WITH CARDIO
METABOLIC DISEASE AND THE RISK
FOR ALZHEIMER'S DISEASE.
AND THERE'S DISORDERS OF THE
BRAIN AND HEART AND
AUTOIMMUNITY.
ARE THERE WINDOWS OF
OPPORTUNITIES FOR SEX
DIFFERENCES WHEN THEY EMERGE
WHEN THE BRAIN IN THE BODY ARE
FLOODED WITH GAN ANNAN --
GHANANO HORMONES AND WE CAN USE
THESE WHEN SEX DIFFERENCES
EMRERJ TO NOT ONLY UNDERSTAND
THE DIFFERENCES OF THE CAUSES OF
THE DIFFERENCES BUT TO DEVELOP
THERAPEUTICS WHAT WE CALL
SEX-DEPENDENT THERAPEUTICS
TARGETED EARLY EVEN PRIOR TO THE
MANIFESTATION OF DISEASE.
HAVE USED THE PRENATAL STRESS
IMMUNE MODELS OF STRESS AND IT
AFFECTS EVERY CHRONIC DISEASE WE
KNOW AND THE CIRCUITRY THAT
REGULATES STRESS IS SOME OF THE
MOST HIGHLY DIMORPHIC STRESS IN
THE BRAIN AND REGULATES ES --
REGULATES ANXIETY AND THE MOOD
AND THE HEART AND STEROID
HORMONE PHYSIOLOGY AND THE
GANANO AXIS AND THE IMMUNE
PHYSIOLOGY AND SOME OF THE SAME
BRAIN REGIONS THAT REGULATE
STRESS, MOOD AND THE HEART ALSO
REGULATE MEMORY.
SO THE MODELS WE HAVE BEEN USING
WE USE PRENATAL STRESS MODELS
AND PREGNANCY COMPLICATIONS AS
OUR MODELS OF PRE-NATAL STRESS
PREECLAMPSIA AND FETAL GROWTH
RESTRICTION AND WE HAVE FOUND
AND OF COURSE BOTH AT THE HUMAN
AND ANIMAL LEVEL THAT THIS
CHANGES THE MATERNAL IMMUNE
RESPONSE.
SHE THEN MOUNTS THE
GLUCOCORTICOID RESPONSE AND WHEN
THAT OCCURS DURING CRITICAL
PERIODS AND THE PHYSIOLOGY
ASSOCIATED WITH THE CIRCUITRY
MEDIATES THE DIFFERENCES THROUGH
CARDIOVASCULAR RISK THROUGH
DYSREGULATION OF THE HEART AND
WE'RE LOOKING AT SOME OF THE
SAME PHYSIOLOGIC AND EARLY
PREOCCURERS ARE RISKS FOR MEMORY
DECLINE AND ALZHEIMER'S DISEASE.
WE WORK WITH ANIMAL MODELS
WORKING OUT SOME OF THE BASIC
MOLECULAR MECHANISMS.
I DON'T HAVE TIME TO GO INTO
THOSE NOW BUT HAPPY TO DO SO IF
PEOPLE HAVE QUESTIONS ABOUT WHAT
WE HAVE DONE.
AND THE MOTHERS WERE FOLLOWED
THROUGH THEIR PREGNANCIES, BLOOD
WAS STORED.
IT'S NOW AT NICHD AND THE KIDS
WERE FOLLOWED FOR SEVEN YEARS.
ALL SORTS OF ASSESSMENTS WERE
DONE THROUGH THIS PERIOD OF
TIME.
IT'S A PUBLIC DATA SET AND THE
ORIGINAL STUDIES WERE ABOUT
NEUROLOGICAL DISORDERS IN KIDS.
AND OVER THE LAST 30 YEARS MY
COLLEAGUES AND I HAVE BEEN
FOLLOWING THESE ADULT OFFSPRING
IN THEIR 20s, 30s, 40s, 50s AND
NOW TURNING TO THEIR 60s AND WE
DO DEEP PHENOTYPING.
WE DO CLINICAL AND COGNITIVE
ASSESSMENTS AND DO STRUCTURAL
AND FUNCTIONAL IMAGING AND A LOT
OF PHYSIOLOGY.
WE'RE INTERESTED IN THE
PHYSIOLOGY AND WE COLLECTED
BLOOD NOT ONLY FOR DNA BUT NOW
WE COLLECT CELLS AND
TRANSCRIPTION WE'RE PARTICULARLY
INTERESTED IN SHARED IMMUNE
PATHWAYS SO WE'VE BEEN ANALYZING
MONOCYTE CELLS AND TRANSCRIBING
THEM TO LOOK AT THE PATHWAY
DYSREGULATI
DYSREGULATION.
LASTLY I THINK MY FIVE MINUTES
IS LIKELY UP, I JUST WANT TO SAY
THAT THESE TYPES OF STUDIES, THE
DEEP PHENOTYPING STUDIES OF
HUMANS REALLY TAKE A VILLAGE.
AND SO I WANT TO THANK MY
COLLEAGUES PARTICULARLY STEVEN
BUCCA AT BROWN AND HE AND I HAVE
BEEN FOLLOWING THESE ADULT
OFFSPRING OVER THE LAST 30 YEARS
AND FINALLY I WANT TO THANK THE
FUNDING SOURCES AT NIH AND NIMPH
AND THE OFFICE OF RESEARCH OF
HUMAN HEALTH AT THE NIA BECAUSE
THESE STUDIES TAKE A VILLAGE AND
THEY'RE VERY LABOR INTENSIVE AND
TAKE A LOT OF FUNDING.
WE'RE INCREDIBLY GRATE FWLFUL
FOR FUNDING THE OVER SO MANY
YEARS AND WANT TO CREATE THIS
UNIQUE COHORT AS A RESOURCE FOR
THE NEXT GENERATION TO BE
STUDYING INTO OLDER AGE.
SO THANK YOU VERY MUCH.
AND PLEASE COME VISIT US BY THE
WAY AT OUR WEBSITES AND YOU'D
LIKE TO JOIN THE EFFORT.
THANK YOU.
LET'S MOVE TO OUR FOURTH
PANELIST MARISA SPANN AT
COLUMBIA UNIVERSITY.
HER EXPERTISE IS IN CLINICAL
NEUROPSYCHOLOGY AND PERINATAL
EPIDEMIOLOGY.
HER RESEARCH AIMS TO IDENTIFY
EARLY IMMUNE, BRAIN AND EARLY
PSYCHOLOGICAL RISKS.
DR. SPANN.
>> THANK YOU AND THANK YOU FOR
THE INVITATION TO BE HERE.
I'LL HIGHLIGHT A FEW THINGS FROM
MY WORK THAT ARE REALLY SORT OF
REASONS I THINK TO THINK ABOUT
THE DEVELOPING BRAIN AS JILL
MENTIONED IN THE CONTEXT OF THE
EARLY STAGES OF DEVELOPMENT
THROUGH SENESCENCE.
WE KNOW THE BRAIN GROWS RAPIDLY
DURING THE PERINATAL PERIOD AND
MY WORK PARTICULARLY FOCUSES ON
THE FETAL PERIOD THROUGH BRAIN
DEVELOPMENT WITHIN THE FIRST
YEAR OF LIFE TO IDENTIFY EARLY
PSYCHIATRIC RISK MARKERS.
I'M NOT DOING WORK ON THE NEURO
NEURODEGENERATION SIDE THERE'S
NEUROCOGNITION AND DEVELOPMENT
THAT THIS EARLY WINDOW IN LIFE
COULD BE POTENTIALLY PREDICTIVE
AND IMPORTANT TO THINK ABOUT IN
THE CONTEXT OF LATER STAGES IN
DEVELOPMENT.
AND OBVIOUSLY THERE'S EXPANSIVE
GROWTH AND SYNAPSE FORMATION
THAT ARE PRETTY PRETT --
CRITICAL TO EARLY STAGE FUTURE
DEVELOPMENT.
WE OBVIOUSLY LOOKED AT PRENATAL
EXPOSURES AND PARTICULARLY
IMMUNE BUT ALSO ONE OF THE
THINGS WE'VE BEEN THINKING ABOUT
IS HOW COMPLEX THE ENVIRONMENT
THAT CHILDREN GROW UP IN ARE.
AND SO WE STARTED TO TRY TO LOOK
AT AND CONSIDER THE COMPLEX
ENVIRONMENT IN TERMS OF
POTENTIALLY IDENTIFYING COMMON
BRAIN REGIONS THAT MIGHT BE
REALLY CRITICAL OR ASSOCIATED
WITH PSYCHIATRIC ARREST.
AND SOME OF MY COLLEAGUES TODAY
HAVE MENTIONED THE VALUE OF THE
ENVIRONMENT.
AND THINKING OF THE CONTEXT OF
MENTAL HEALTH IN OUR WORK
RECENTLY IN PSYCHO PHARMACOLOGY
AND WE IDENTIFIED SOME COMMON
BRAIN REGIONS THAT WERE
ASSOCIATED WITH FRATERNAL
STRESS, DEPRESSION AS WELL AS A
MEASURE OF PREGNANCY, ANXIETY
A
AND CORTISOL AND ALSO CHRONIC
HEALTH CONDITIONS.
WE LOOKED AT FRATERNAL B MMI AND
WE IDENTIFIED INCREASED
CONNECTIVITY BETWEEN AN
ASSOCIATION WITH INCREASED BMI
OF THE MOM AND INCREASED
THALAMIC CONNECTIVITY AND THIS
WAS AN IMPORTANT FINDING BECAUSE
THERE WERE MODELS THAT WERE ABLE
TO IDENTIFY THE HYPOTHALAMUS
ROLE IN FOOD RESOLUTION.
-- REGULATION AND THINKING OF
SOCIAL FACTORS.
THERE'S RECENTLY UNPUBLISHED
WORK UNDER REVIEW AT PRESENT.
WE LOOKED AT THE AFFECTS OF
MATERNAL AFFECTS OF
DISCRIMINATION DURING PREGNANCY
AND FOUND REDUCED CONNECTIVITY
BETWEEN AMYGDALA AND THE
PREFRONTAL CORTEX.
THE GOAL ULTIMATELY WITH THE
FIRST PAPER THE DATA I SHOWED IS
TO REALLY TRY TO LOOK AT THE
FACTORS IN CONCERT AND HAVE MORE
COMPLEX MODELLING TO IDENTIFY
PATHWAYS THAT MAY INCREASE RISK.
AND I HINTED AT THE IMMUNE
SYSTEM MY LAB IS PARTICULARLY
INTERESTED IN PRENATALLY.
BOTH THE INNATE AND ADAPTIVE
IMMUNE SYSTEMS AND LOOKING AT
INFECTIONS AS WELL.
SOME OF OUR RECENT WORK USING
MULTI-MODAL IMAGING AND THE ME
BORN BRAIN IDENTIFIED THE
INTERLEUKIN AND CONSIDERING THE
METABOLITES IN THE BRAIN AND WE
ALSO IDENTIFIED SIMILAR BRAIN
REGIONS AND THIS IS ONE EXAMPLE
OF METABOLITE AND AGAIN THIS IS
ASSOCIATED WITH INCREASED
INTERLEUKIN SETS.
THAT'S ALL I HAVE FOR YOU.
AND I WANT TO THANK ANY
COLLABORATORS AND BRADLEY
PETERSON AND COLLABORATINING MY
DATA AND NIHM AND NICHD AND THE
LEE FOUNDATION.
>> THANK YOU.
THE LAST OF OUR FIVE PANELISTS
IS DR. MORIAH THOMASSON IN
POPULATION HEALTH IN THE NEW
YORK UNIVERSITY SCHOOL OF
MEDICINE.
HER RESEARCH ADDRESSES
PRINCIPLES OF NEURODEVELOPMENT
BEGINNING IN UTERO AND
ENVIRONMENTAL FACTORS THAT
AFFECT THE CIRCUITRY OF THE
DEVELOPING BRAIN.
>> WE'RE LOOKING AT THE F MERES
AND HUMAN BEHAVIOR AND THAT
PLAYS A BIG ROLE IN OUR
RESEARCH.
WE HAVE WEARABLES AND
NATURALISTIC ASSESSMENTS IN THE
HOME AND FINALLY THE
OPPORTUNITIES AVAILABLE TO ALL
OF US IN TERMS OF BIO SPECIMENS
PRETTY REMARKABLE AND
DR. SPANN'S WORK IS INTEGRATING
WHAT WE UNDERSTAND ABOUT THE
BODY WITH WHAT WE OBSERVE IN THE
BRAIN.
MY PRINCIPLE APPROACH IS TO USE
PERSPECTIVE LONGITUDINAL
STUDIES.
THIS IS A SCHEMATIC REPRESENTING
A DETROIT COHORT WE BEGAN TO
RECRUIT IN 2021 AND THE KIDDOS
HAD MULTIPLE BRAIN STUDIES AS
THE PLACENTAL STUDIES AND MANY
FOLLOW-UP
FOLLOW-UPS AND THERE'S A NEW
YORK BASED COHORT COMPROMISED OF
MORE THAN 1,000 WOMEN AND HALF
RECRUITED IN THE EARLY
POST-NATAL PERIOD AND WE CAN SEE
HOW DENSE THE SAMPLING IS AND
HOW MUCH TIME WE'RE SPENDING
WITH THE FAMILIES AND NOW HAVE
FUNDING TO FOLLOW UP A SUBSET
AND WE'RE CONTINUING TO DO THAT.
OVERALL THE GOAL OF OUR RESEARCH
IS TO UNDERSTAND THE IMPACT OF
PSYCHOSOCIAL DIVERSITY AN NEURO
NEURODEVELOPMENTAL AFFECTS AND
INTOXICANTS AND I KNOW WE'RE
EXCITED TO HAVE A DISCUSSION
HERE AND I WANT TO THINK ABOUT
HOW THE BRAIN AS A NON-LINEAR
ORGAN AND DEVELOPMENT REGIONALLY
SPECIFIC.
THESE ARE EXAMPLES AT THE TOP AT
THE CELLULAR LEVEL AND
FUNCTIONAL LEVEL AND AT THE
WHITE MATTER LEVEL.
WE SEE THE BRAIN IS DEVELOPING
AT DIFFERENT RATES AT DIFFERENT
PLACES.
THIS IS SOMETHING IMPORTANT TO
ATTEND TO AND THIS IS AN IMAGE
FROM A NATURALLY LOST CHILD
TOOTH WHERE WE'RE MAPPING OUT
LEVELS OF LEAD.
THE BABY TEETH BEGIN TO FORM
DURING WEEK 15 INFESTATION AND
HAVE RINGS LIKE A TREE AND WE
CAN LINK THEM UP TO HOW THE
CHILD DEVELOPS AND I HAVEN'T
SHOWN SPECIFIC TOPICS BUT THIS
IS THE GOAL UNDERSTANDING THE
EXPOSURES OF THE INDIVIDUAL WE
CAN MEASURE LEAD AT EVERY
PREGNANCY AND SEEING THE
TEMPORAL SAMPLING AND WHEN I
MEASURE A PARTICULAR PREDICTOR
IT MAY HAVE AN ASSOCIATION WITH
AN OUTCOME EXTERNALIZING
BEHAVIOR IN CHILDHOOD.
YOU HAVE ON THE VERTICAL AXIS
THE AGE AND YOU SEE MANGANESE IS
PREDICTIVE AND LEAD IS
PREDICTIVE OF LOWER EXECUTIVE
FUNCTION SCORES.
AND SOMETHING TO THINK ABOUT AS
WE TALK ABOUT THE DEVELOPMENT
PERSPECTIVE, WHAT IS OUR
POTENTIAL FOR SAMPLING.
THE CHARGE OF THIS PANEL AND
WE'LL TURN TO THIS NOW IS TO
BRIDGE THE LIFE SPAN PERSPECTIVE
HOW WE WEAVE THESE TOGETHER IN
IN EARLY LIFE THE PRESSURES ARE
DIFFERENT LATER AND WE'LL MOVE
THROUGH THE PRESSURES
POTENTIALLY HAVING A NOT-SMOOTH
FUNCTION.
THIS HAS COME UP IN SOME OTHER
TALKS BUT IT'S NOT LIKE WE'RE
GETTING A SMOOTH FUNCTION OVER
THE LIFE SPAN.
WE'RE LOOKING AT PERIODS WHERE
THERE'S BURSTS OF PLASTICITY,
PERIODS OF PROGRESSION AND
REGRESSION.
AN IT SEEMS TO ME THEY LINE UP
WITH SOCIAL TRANSITION.
WE THINK OF ADOLESCENTS,
PARENTHOOD WAS MENTIONED
EARLIER.
THERE'S ALSO CHANGES THAT HAPPEN
WHEN THE FAMILIES REORGANIZE AND
THE CHILDREN LEAVE THE HOME OR
IN RETIREMENT.
SO HOW DO WE THINK ABOUT THE
BRAIN IN THE CONTEXT OF THE
SOCIAL WORLD THAT PROGRAMS IT
AND HOW DO WE THINK ABOUT HOW WE
STUDIED ALL THESE WITH POTENTIAL
AND FINALLY ANOTHER TOPIC WE
WANT TO EXPLORE SOME OF WHICH
HAS COME UP IS SEX AND
DEMOGRAPHIC DIFFERENCES.
SOMETHING REALLY IMPORTANT FOR
US TO DO IN OUR STUDIES IS TO
THINK ABOUT NEURAL DIVERSITY AND
MAKE SURE THE PARTICIPANTS IN
OUR RESEARCH REPRESENT THE
DIFFERENCES IN THE PLANET AND
RESOURCES AND HEALTH DISPARITYIES
AND LOOKING AT THE TOPICS WITH
THE HIGHLY QUALIFIED GROUP OF
PEOPLE.
>> THANK YOU FOR SETTING UP THE
STAGE FOR THE DISCUSSION PERIOD
WE'RE ENTERING INTO.
AND THINKING OF PARTICIPANTS IN
THE VIRTUAL WORLD TO COME UP
WITH QUESTIONS YOU CAN PUT IN
THE CHAT AND DISCUSS THOSE AS
THEY COME ONLINE.
I HAVE QUESTION CAME IN PRIOR TO
THE MEETING TO GET OURSELVES
ENERGIZED IN DISCUSSION MODE.
AND CHALLENGING EACH OTHER AS
WELL AS RESPOND TO THE INPUTS
COMING FROM THE LARGER
COMMUNITY.
LET ME START WITH A QUESTION
THAT CAME UP IN ADVANCE OF THE
MEETING.
THE QUESTION I DON'T KNOW WHO
IT'S FROM BUT SAYS CAN WE BEGIN
TO USE NEUROIMAGING TECHNIQUES
COMBINED WITH PHENOTYPING TO
DETERMINE NEW BIOMARKERS AND
MILESTONES FOR DEVELOPMENT IN
COGNITIVE DECLINE.
HOW CAN INFORMATIVE BIOMARKERS
SERVE AS AN OUTCOME MEASURE AND
INTERVENTION STUDY WHICH IS
ACCEPTABLE TO REGULATORY
AGENCIES.
I'D LIKE TO ASK ALEXANDRA TO BE
THE FIRST TO RESPOND TO THAT
SINCE IT IS IN HER WHEELHOUSE SO
TO SPEAK.
>> WE STARTED LOOKING INTO
COMBINING BIOMARKERS IN
BEHAVIOR-BASED PHENOTYPES.
WE STARTED TO DEFINE A RISK
FACTOR IN THE CONTEXT OF
ALZHEIMER'S DISEASE THAT
INCLUDES GENOTYPE WITH AGE AND
SEX AND WE INTEGRATE THIS WITH
IMAGING WITH CORRELATION WHICH
BASICALLY RESULTS IN A RANK
ASSIGNED TO EACH OF THE RISK
FACTORS INCLUDING TRAITS OR
PHENOTYPES AND THESE ARE
GENERALIZABLE AND ON THE OTHER
SIZE TO BRAIN NETWORKS.
SO THIS IS MY APPROACH.
IT'S CERTAINLY NOT UNIQUE SO I
WELCOME OTHER COMMENTS.
>> ANYONE ELSE WANT TO CHIME IN
ON THIS ISSUE.
>> IT DEPENDS ON YOUR BIOMARKER.
CAN GET DOWN TO THE MOLECULAR
LEVEL.
WE HAVE USED THE DEEP
PHENOTYPING TO GET AT PHYSIOLOGY
AND HOW THE BRAIN REGULATES THE
PHYSIOLOGY AND USING PHYSIOLOGIC
MARKERS AS SOME OF THE
BIOMARKERS FOR WHAT'S HAPPENING
IN THE BRAIN.
AND SO THEY'RE ACCESSIBLE, FOR
EXAMPLE, BY BLOOD PANELS AND BY
CELLS.
ONE WAY TO GET AT IN THE NEVER
HUMAN BIOMARKERS IN ASSESSING
IMMUNE AND METABOLIC FUNCTION
AND VASCULAR FUNCTION AND LOOK
AT IT IN TANDEM WITH WHAT THE
BRAIN'S DOING WHILE WE IMAGE
THEM.
THAT'S ONE WAY WE DO THIS AND WE
DO IT ACROSS THE LIFE SPAN.
>> SO ONE OF THE THINGS THAT I
TEACH MY STUDENTS IN THE LAB IS
THAT WE DON'T HAVE A GROUND
TRUTH FOR THE FETUS.
SO A LOT OF TIMES THERE'S AI
TENDENCY TO ANTHROPOMORPHIZE THE
BRAIN AND UNDERSTAND THE
BEHAVIOR FROM OUR COGNITION AND
OBSERVATIONS AND PLAYS THESE
FUNCTION ON THE BRAIN BUT A
FETAL BRAIN IS TRYING TO DO A
DIFFERENT JOB THAN SAY EVEN AN
INFANT BRAIN OR AN AGING BRAIN
IS TRYING TO DO.
WHAT A PARTICULAR AREA OF THE
CORTEX MAY BE TRYING TO DO IN
THE FETUS MAY NOT LOOK LIKE ITS
FUTURE DESTINY.
I FIND A LOT I HAVE TO SEPARATE
THE STUDENTS FROM THE IDEA THE
AMYGDALA KNOWS WHAT IT'S GOING
TO DO IN THE FUTURE.
RIGHT, LIKE IT'S STILL THE SAME
SYSTEMS.
IT'S STILL WIRING UP TO HAVE THE
SAME FUNCTIONS BUT WE SHOULDN'T
NECESSARILY PUSH THESE CAN ONIC
ONICONI
ONIC -- CANONICAL VIEW VIEWS AND
SOME WILL SAY HOW CAN THIS
REGION BE DOING THIS THING AND
I'M SAYING, I DON'T KNOW IF IT'S
DOING THAT THING.
WE HAVE TO TEST OUR HIGH BOTH
THESE IN A MORE DATA-DRIVEN
APPROVE WHICH MAKES IT MORE
CHALLENGING TO STUDY THESE PARTS
OF DEVELOPMENT.
>> PERHAPS I DID NOT EXPLAIN
THINGS BECAUSE I HAVE A SHORT
TIME LIKE EVERYBODY ELSE.
BUT IN OUR PREDICTIVE MODELLING
APPROACHES AND I HAVEN'T SHOWN A
LOT OF RESULTS WE FOUND IF YOU
STUCK BIOMARKERS RELATED TO
BRAIN ATROPHY TO SIGNAL
INTENSITY AND SIGNAL ACTIVITY
BECAUSE REDUCING MANGANESE TAKEN
UP THROUGH CALCIUM CHANNELS AND
MAGNETIC SUSCEPTIBLE CAN BETTER
PREDICT THE TRAITS LIKE MEMORY
WE ASSESS THAN USING ANY SINGLE
BIOMARKER.
>> I'M A Ph.D. NEURO ANATAMIST
AND I GOT INVOLVED IN STUDYING
fMRI TO STUDY AUTISM AND WAS
NAIVE HOW COULD SEE AN AUTISTIC
CHILD -- IT SEEMED LIKE A SLAM
DUNK WE'D SEE BEHAVIORAL
DEFICITS AS PROFOUND AS AUTISM
COULD BE AND TWO DECADES LATER
THE FIELD IS STILL STRUGGLING TO
GET ANYTHING CONVINCING.
THERE'S A LOT OF IDEAS BUT WE'VE
RAN UP AGAINST THE HURDLES OF
TECHNICAL ARTIFACTS LIKE
AUTISTIC KIDS TEND TO WIGGLE
MORE IN THE SCANNER AND WE HAVE
COME TO THE REALIZATION THAT
AUTISM IS BY NO MEANS A SINGLE
DISORDER OF DISEASE IT'S A
SPECTRUM MUCH BETTER CALLED THAT
THAT IS VERY MULTI-DIMENSIONAL
AND ONE AUTISTIC BRAIN IS NOT
GOING TO BE LIKE ANOTHER ONE.
WE HAVE TO FACTOR IN THE
INCREDIBLE INDIVIDUAL
VARIABILITY THAT I TOUCHED UPON
AND OTHERS HAVE MENTIONED TODAY.
AND THEN THE HARSH REALITY ALSO
IS THAT THE OBSERVATIONS WE MAKE
ABOUT USING TRACTS TO IDENTIFY
STRUCTURAL CONNECTIVITY IT'S AN
ESTIMATE OF PATTERNS OF CONNECTS
BUT AS WE'VE SEEN ALREADY THE
NUMBER OF WAYS IN WHICH ONE
COULD HAVE FALSE POSITIVES AND
FALSE NEGATIVES IN CURRENT TOP
OGRAPHY -- TOPOGRAPHY DATA IS
LARGE AND WE HAVE FUNCTIONAL
CONNECTIVITY BUT THOSE ARE A
LONG WAYS FROM ANATOMICAL
CONNECTIONS.
THE SOBERING REALITY IS THAT
IT'S AN IMMENSELY COMPLEX
PROBLEM.
I'M STILL AN OPTIMIST BUT NOT
WITH A SENSE THAT WE'RE A YEAR
OR TWO AWAY FROM MAKING A
DRAMATIC EVENT BUT RATHER THAT
WE NEED TO ABSOLUTELY PERSEVERE
AND ABSOLUTELY PUSH TO THE
LIMITS TO GET BETTER DATA,
BETTER ANALYZED AND BETTER
SHARED ASSESSED IN RELATION TO
COMPLEX DISORDERS.
I WAS PARTICULARLY AMONG THE
MANY FASCINATING PRESENTATIONS
WE HEARD OVER THE DAY I WAS
PARTICULARLY IMPRESSED ON THE
ADVANCED MADE IN GETTING HIGHER
QUALITY, FASTER, ACQUISITION,
HIGHER RELEVANT SCANNING IS ONE
WAY IN WHICH CONTINUED POUNDING
HARD ON METHODOLOGICAL ADVANCES
EXTEND THE FIELD FORWARD AND
THAT'S MY VIEW ON BIOMARKERS.
JILL.
>> THERE'S ALSO THE ROLE OF
CONVERGENCE OF USING DIFFERENT
LEVELS OF ANALYSIS WHETHER WE
WORK WITH BASIC SCIENTISTS
WHETHER WE WORK AT ONE LEVEL OF
ANALYSIS AND WE TRY TO TAKE
INFORMATION.
WE LEARN ABOUT MECHANISMS FROM
THEM AND TEST IT AT THE HUMAN
LEVEL AND VICE VERSA.
I THINK USING MULTIPLE
STRATEGIES TO TACKLE THESE
ISSUES OF QUESTIONS OF
BIOMARKERS AND THE TIMING OF
THOSE BIOMARKERS WHICH IS A
CRITICAL DEVELOPING THERAPEUTICS
AT DIFFERENT POINTS ACROSS THE
LIFE SPAN WILL BE AN IMPORTANT
TOOL WE CAN USE NOW WHILE WE
WAIT FOR HIGHER LEVEL
TECHNOLOGIC ADVANCES OF IMAGING
ACROSS THE LIFE SPAN.
>> THANK YOU.
LET ME MOVE TO ANOTHER QUESTION
THAT CAME IN.
WHAT ARE METHODS WE CAN USE TO
APPROACH CO-MORBIDITY WHEN
STUDYING HOW BEHAVIOR CHANGES
RELATE TO STRUCTURAL AND
FUNCTIONAL CHANGES TO BRAIN AS
WE AGE.
I HAVE MY FINGER FIRST POINTED
TO JILL, GIVEN YOUR INTEREST IN
COMORBIDITIES CAN YOU TAKE A
STAB AT THAT?
>> YES.
AND THEY WERE ASKING ABOUT
SHARED PATHOPHYSIOLOGY ACROSS
THESE.
I DID NOT PUT THE QUESTION IN
THE QUESTION BANK.
IT'S A FANTASTIC QUESTION.
I THINK IT'S UNDER STUDIED BUT
OF COURSE THE COMORBIDITY OF
PSYCHIATRIC DISORDER WITH
GENERAL MEDICINE IS JUST HUGE.
ALL YOU HAVE TO DO IS LOOK AT
SIDE EFFECTS OF PSYCHIATRIC
MEDICINES ON OTHER SYSTEMS, THE
GUT AND THE HEART AND THE LIVER
AND ALL SORTS OF ORGAN SYMPTOMS
TO KNOW COMORBIDITY DOES EXIST
BUT MEDICINE HAS GROWN UP IN
SILOS AND THAT IS SORT OF HOW
NOT ONLY MEDICINE HAS GROWN OUT
UP BUT HOW WE DEVELOP
THERAPEUTIC TO ONE ORGAN SYSTEM.
I THINK REALLY BRINGING IN ONE
OF THAT'S ONE OF THE REASONS WE
TALK ABOUT THE HEART AND HOW THE
BRAIN REGULATES THE HEART AND IT
TURNS OUT IT DOESN'T ONLY
REGULATE THE HEART ELECTRICALLY
TO THE VAGUS NERVE BUT IT GOES
TO THE GUT AND THE AXIS AND
PEOPLE ARE STUDYING NOW.
IT'S IMPORTANT WE BELIEVE
VARIABILITY IN THE FUNCTIONING
OF THESE AND THE REGULATION OF
THESE CIRCUITS NOT ONLY DIFFERS
BY SEX WHICH WE STUDY OF COURSE
BUT ALSO HAS DIFFERENTIAL
AFFECTS ON THE DIFFERENT ORGAN
SYSTEMS.
BRINGING IN ORGAN SYSTEM THE
FAVORITE BRAIN REGIONS ARE
REGULATING WE BELIEVE IS REALLY
CRITICAL TO UNDERSTANDING AU THE
BODY AND BRAIN DELIVER.
>> DO YOU WANT TO EXPAND ON
THAT?
>> I WANT TO TALK ABOUT THE
COMORBIDITIES OF OTHER ORGAN
SYMPTOMS AND HOW TO THEY AFFECT
BRAIN AND IF PERIPHERAL TISSUE
IS INJURED AND THE SYSTEMIC
ENVIRONMENT IS ALSO OLD AND
ELEVATION OF SENESCENT CELLS AND
PERHAPS OTHER PATHOLOGICAL
ORGANS AND CAN HELP UNDERSTAND
PROGRESSION THROUGH LIFE.
>> THANK YOU.
MARISA DO YOU WANT TO ADD
ANYTHING TO THE TOPIC OF
COMORBIDITIES?
>> AS MORIAH WAS SAYING IN EARLY
DEVELOPMENT WE DON'T NECESSARILY
KNOW WHAT BRAIN REGION IS
ASSOCIATED WITH WHAT PARTICULAR
FUNCTION IN EARLY DEVELOPMENT
AND SIMILARLY WHEN WE'RE WORKING
WITH INFANTS, WE DON'T
NECESSARILY KNOW THAT THEY'LL GO
ON TO HAVE A PARTICULAR
PSYCHIATRIC DISORDER OR WHETHER
THEY'LL HAVE COMORBID DISORDERS.
OUR APPROACH WHERE WE'RE LOOKING
AT A DIFFERENT SYSTEM SUCH AS
BEHAVIORAL REGULATION AND
FOCUSSING ON SORT OF THE
FUNCTIONAL DEVELOPMENT AND
NOTALLY PUTTING IT INTO POCKETS
OF DISEASE AND I'M NOT SAYING
THAT WILL NECESSARILY WORK WITH
ADULTS ACROSS THE LIFE SPAN BUT
IT'S AN APPROACH THAT HAS WORKED
AND ONCE WE STARTED TO BUILD
AROUND THE FRAMEWORK I THINK THE
WORK HAS MADE IT MORE SENSE THAN
IF WE HAD MORE IMPACTFUL
FINDINGS.
>> CAN I MAKE ONE MORE COMMENT?
>> PLEASE.
>> I'M ACTUALLY RATHER EXCITED
THAT WE'RE LEARNING ABOUT
COMORBIDI
COMORBIDITIES SOME WE'VE KNOWN A
LOT FOR A TIME BUT PERHAPS
HAVEN'T DONE ENOUGH AS A
COMMUNITY TO ADDRESS THOSE AND
I'M TALKING ABOUT THE CONTEXT OF
ALZHEIMER'S DISEASE WHICH ARE
LATE ONSET TYPE OF DISEASE.
HOWEVER, WE KNOW HYPERTENSION,
AR THEIRO -- ATHEROCLEROSIS I
CAN HAPPEN EARLY ON AND
REPURPOSING DRUGS CAN BE USED
LATER FOR THE DISEASES OF OLD
AGE.
I THINK THERE'S OPPORTUNITIES
THAT SHOULD BE EXPLOITED.
>> HOW CAN WE HAVE MODELLING AT
MULTI-SCALE.
THIS IS A QUESTION THAT CAME UP
IN THE PRECEDING SCLUGS
AND ONE WAY TO BRING THAT INTO
THE DISCUSSION IS BRIDGING THE
GAP NOT SO MUCH BETWEEN EARLY
DEVELOPMENT IN AGING BUT BETWEEN
MACRO CONNECTOMES AND MESO
CONNECTOMES AND MICROCONNECTOMES
WE HEARD SPECTACULAR PROGRESS ON
EARLIER BUT STILL A WIDE RANGE
BETWEEN THOSE DOMAINS.
ANY THOUGHTS?
>> MORIAH.
>> ANOTHER PLACE WHERE IT'S BEEN
HELPFUL AND YOU MENTIONED DATA
SHARING AS BEING AN IMPORTANT
STEP FOR MOVING THE SCIENCE
FORWARD, DR. VAN ESSEN, I SEE IT
HELPING IN TWO WAYS.
ONE IN UNDERSTANDING THE
FUNDAMENTAL BIOLOGICAL QUESTIONS
THAT IS MUCH OF THE FOCUS WE'RE
TALKING ABOUT TODAY AND TWO IS
TO AID OUR METHODOLOGIES AND AS
AN EXAMPLE, IN MY LAB WE'VE
FACED THE CHALLENGE OF
EXTRACTING THE FETAL BRAIN FROM
THE SURROUNDING TISSUE WHICH
SOUNDS VERY BASIC BUT WHEN
YOU'RE TRYING TO REMOVE 360
INDIVIDUAL TIME POINTS THAT ARE
THREE-DIMENSIONAL IT'S A BIG
PROBLEM WE USED DEEP LEARNING TO
DO THAT EXTRACTION PROCESS
ITSELF.
SO IT'S GOING TO SPEED UP THE
SCIENCE BECAUSE WE NOW ARE ABLE
TO KIND OF BYPASS SOME OF THE
THINGS WE COULDN'T DO AND I KNOW
THAT APPLIES TO A LOT OF THE
TALKS AND HOW WE'VE ACCELERATED
OUR ABILITY TO ANALYZE THE DATA
IN MORE OBJECTIVE WAYS AND MORE
RAPIDLY.
IT'S TWO THINGS THAT IT'S GOING
TO DO FOR US AND CONTINUE TO DO
IS ONE OUR METHODOLOGIES AND TWO
IS TO ACTUALLY ANSWER DEEPER
QUESTIONS ABOUT BIOLOGY.
>> I'D LIKE TO ADD ANOTHER LAYER
THAT AND HOW TO USE SOME OF THE
TECHNOLOGIES OVER TIME WITHIN
THE SAME INDIVIDUAL WHICH IS
WHAT WE DO AND THIS IS A BIG
CHALLENGE FOR AN IMAGEER LIKE
OUR LAB WHICH IS IF YOU HAVE
RECRUITED PEOPLE INTO THE
LONGITUDINAL STUDIES AND NOW IN
THEIR 20s AND 30s AND NOW
THEY'RE 50 AND 60 OVER THE LAST
20 ODD YEARS THE METHODOLOGIES
HAVE CHANGED.
IF YOU START WITH THE 1.5T AND
NOW WE'RE UP TO 7 I LOVED THE
TALK.
I WAS TRYING TO LOOK THROUGH MY
NOTES QUICKLY TO SEE WHICH
PERSON HAD DESCRIBED IT OF AND
HOW TO MERGE THAT WITH THE 3T
TESLA AND INTERESTED THERE WERE
NEW METHODOLOGIES AROUND DO THAT
BUT NEED THAT KIND OF WORK TO BE
FOLLOWING THE SAME INDIVIDUAL
BECAUSE THAT'S REALLY WHERE
YOU'RE GOING TO SEE SOME OF THE
EARLY BIOMARKERS, FOR EXAMPLE
THEY WERE TALKING ABOUT FOR
ALZHEIMER'S DISEASE LATER IN
LIFE SINCE WE KNOW 15 TO 20
YEARS EARLIER ARE THE PRE
CURSORS TO ALZHEIMER'S DISEASE.
THAT'S WHERE WE WANT TO BE
FOCUSSING FOR OUR THERAPEUTICS.
SO HOW DO WE DO THAT IN A
TECHNOLOGIC WAY AND IT'S
IMPORTANT AS AN IMAGEER THAT WE
HAVE PEOPLE FOCUSSING ON THAT.
I'D LOVE PEOPLE TO CONTACT ME IF
THEY HAVE APPROACHES FOR DOING
THIS SINCE WE HAVE 1.5 AND 3T
DATA IN THE SAME INDIVIDUALS IN
THE COHORT.
>> JILL, THERE'S SOMETHING I CAN
TELL YOU WHICH IS HYPER FINE
THIS LOW-FIELD MRI IMAGING IS
PICKING UP NOW AS A REMARKABLE
TOOL AND THERE'S INCREDIBLE WORK
BEING DONE THERE I THINK WOULD
BE IMPORTANT TO YOU.
>> THAT LEADS US TO ANOTHER
QUESTION THAT WAS OPPOSED WHICH
IS SHOULD WE BE EMPHASIZING
LONGITUDINAL STUDIES OR
CROSS-SECTIONAL AND YOUR
PERSPECTIVE ON THE STRENGTHS AND
LIMITATIONS.
JILL, YOU POINTED OUT ONE OF THE
CHALLENGES BUT WHERE THERE'S
HOPE FOR GETTING AT LEAST PART
WAY AROUND SOME OF THE
LIMITATIONS OF TECHNOLOGY NOT
DRIFT BUT TECHNOLOGY ADVANCES.
YOUR THOUGHTS ON THE AXIS.
>> I AGREE BOTH APPROACH ARE
REALLY IMPORTANT AND FROM A
CROSS-SECTIONAL POINT OF VIEW
YOU CAN INCORPORATE LARGER DATA
SETS AND USING THE DATA MINING
AND MACHINE LEARNING STRATEGIES
IN THE LARGE SAMPLES.
BUT THERE REALLY IS AN IMPORTANT
VALUE TO FOLLOWING PEOPLE OVER
TIME.
AND ONE OF THE OBVIOUS ONES IS
THAT IT'S AN AMAZING CONTROL FOR
CONFOUNDING AND THAT'S REALLY
CRITICAL IN UNDERSTANDING
BECAUSE WE KNOW THE BRAIN
CHANGES BASED ON LOTS OF THINGS
HAPPENING IN THE ENVIRONMENT.
SO REALLY HAVING THE SAME PERSON
IMAGED OVER TIME JUST A GIFT
FROM REALLY SEEING INDIVIDUAL
VARIABILITY AND BEING ABLE TO
UNDERSTAND THAT WITHOUT SOME AND
DOING IT WITHIN A COHORT THAT'S
A CERTAIN AGE RANGE AGAIN SO
YOUR FOLLOWING A CERTAIN AGE
RANGE OVER TIME AS WELL.
SO THAT WILL LIMIT A LOT OF THE
VARIABILITY AGAIN WITH AGING.
WITHIN THE COHORT.
>> OKAY.
SO WE HAVE A QUESTION THAT JUST
CAME IN FROM CHAT.
WE HAVE ONLY FIVE MINUTES LEFT
SO THIS MIGHT BE OUR ULTIMATE OR
PENULTIMATE QUESTION DEPENDING
ON HOW DEEP WE DIVE INTO IT.
A VA M. ASKS WHAT WOULD IT TAKE
TO CREATE A STANDARDIZED METHOD
FOR BIOLOGICAL SOCIAL ADVERSITY
AND AFFECTS ON DIFFERENT
POPULATIONS.
THAT'S A SERIOUS QUESTION.
DEFINITELY WORTHY OF POND IRG.
-- PONDERING.
WHAT DO PEOPLE THINK ABOUT WHAT
WOULD IT TAKE?
>> I CAN SAY SMALL ANIMAL MODELS
CAN OFFER A WAY AND I'M AWARE OF
COHORTS STUDYING CHILDREN IN LOW
ECONOMIC STATUS AND IT'S
VALUABLE BUT WE SHOULD NOT
NEGLECT THE SMALL ANIMAL MODELS.
I WANTED TO PRESENT ANOTHER
STATEMENT AWAY NEED TO
ACKNOWLEDGE BOTH SIDES AS WE
MOVE FORWARD.
>> THAT'S A GOOD START.
TWO QUICK THOUGHTS.
ONE IS THAT IT CAN BE HELPFUL TO
SQUASH IN A VARIABILITY IN A
COFOUNDER THAT MAY AFFECT THE
VARIABLE.
STRESS AND SES ARE CORRELATED IF
YOU CAN MITIGATE THE VARIABLE IT
MAKES IT EASY TO STUDY ANOTHER.
IT DOESN'T GIVE A REPRESENTATIVE
LOOK AT A POPULATION BUT IF
THAT'S YOUR GOAL THAT CAN BE A
USEFUL STRATEGY.
THE SECOND IS A PANDEMIC.
I PANDEMIC WILL POSE ACROSS
SOCIETY AND EXPERIMENTALLY IT'S
AN INTERESTING OPPORTUNITY IN
THE SENSE THAT A LOT OF
INDIVIDUALS IN OUR SOCIETY WENT
THROUGH.
THE DUTCH HUNGER WINTER IS
ANOTHER EXAMPLE WHERE WE SAW
PART OF THE NETHERLANDS WAS CUT
OFF WITH FOOD SUPPLIES DURING
WORLD WAR II.
THESE ARE QUICK RESPONSES
BECAUSE I KNOW WE'RE AT THEN OF
THE HOUR BUT THERE ARE WAYS IN
WHICH HUMAN STUDIES IMPRECISELY
COMPARED TO ANIMAL MODELS BUT
CAN GIVE A STRATEGY TO APPROACH
THESE THINGS IF THAT'S THE
ULTIMATE GOAL.
>> VERY GOOD.
>> ONE OF THE APPROACHES WHICH
IS ALSO NOT PERFECT, THERE'S A
MULTITUDE OF ENVIRONMENTAL
EXPOSURES AT A GIVEN TIME BUT
USING AN EPIDEMIOLOGIC APPROACH
AND THERE'S A SMALLER SAMPLE WE
WOULD INVITE TO DO IMAGING AND
MAYBE SOME OF THE OTHER LASHTRY
ASSESSMENTS SO YOUR CAPTURING A
LARGER SAMPLE OF INDIVIDUALS BUT
THEN TAKING A DEEPER DIVE.
I WANTED TO ADD THAT.
>> THANK YOU.
>> WELL, WE'RE AT THE END OF THE
HOUR AND DAY BUT NOT THE END OF
THE WORKSHOP.
TO REMIND EVERYONE THERE'S
ANOTHER DAY FULL OF INTERESTING
TALKS LOOMING AHEAD WE CAN LOOK
FORWARD TO.
I'D LIKE TO THANK ALL THE
PANELIST FOR YOUR COMMENTS AND
THOUGHT IF THE DISCUSSIONS AND
THANK THE ORGANIZERS FOR PUTTING
THIS ALL TOGETHER.
IT'S BEEN A FASCINATING DAY AND
THANKS TO ALL THE ATTENDEES WHO
HAVE HELPED CONTRIBUTE TO THE
LIVELY SET OF DISCUSSIONS.
>> THANK YOU, VAN ESSEN.
>> YES, THANK YOU.
>> THANK YOU ALL FOR YOUR HARD
WORK TODAY AND WE'LL RETURN AT
NOON TOMORROW EASTERN TIME.
>> THANK YOU.