>> GOOD AFTERNOON, EVERYONE.
WONDERFUL TO BE BACK HERE IN
MASUR AUDITORIUM AFTER A COUPLE,
THREE MONTHS WHERE RENOVATIONS
WERE HAPPENING MOSTLY OF THE
A.V. SYSTEM WHICH WE HOPE NOW IS
GOING TO WORK FLAWLESSLY.
BUT IT'S ALWAYS GREAT TO HAVE
THIS LARGER AUDITORIUM FOR
PRESENTATIONS ON WEDNESDAY
AFTERNOON.
YET A LOT OF YOU HEARING MY
VOICE ARE NOT SITTING IN THE
AUDITORIUM, WE'RE LOOKING AT THE
VIDEOCAST, WELCOME TO YOU TOO.
IT'S BEEN A BIT OF A BUSY WEEK
HERE AT NIH.
WE HAD THE PRESIDENT OF THE
UNITED STATES ON CAMPUS
YESTERDAY AFTERNOON.
THIS MORNING WAS THE MAJOR HOUSE
OF REPRESENTATIVES
APPROPRIATIONS SUBCOMMITTEE
HEARING FOR THE FUTURE OF NIH IN
FY 21, WHICH INVOLVED ME AND
FIVE OF THE INSTITUTE DIRECTORS
FOR A SOLID THREE HOURS OF
QUESTIONS AND HOPEFULLY ANSWERS
WITH THE QUESTIONS BEING
PROVIDED BY THE MEMBERS OF THE
CONGRESS AND THE ANSWERS BY US.
AND I THINK IT'S FAIR TO SAY IT
WENT EXTREMELY WELL, AND WE
HEARD LOTS OF POSITIVE
STATEMENTS ABOUT NIH AND ITS
NOBLE ENTERPRISE, THINGS THAT
WOULD HAVE WARMED YOUR HEART
COMING FROM BOTH PARTIES IN THE
HOUSE.
IN FACT, I DARE TO SAY THAT IF
YOU WERE SITTING IN THE ROOM,
AND YOU CLOSED YOUR EYES SO YOU
COULDN'T SEE WHICH SIDE OF THE
DAIS THE PERSON WAS SITTING, YOU
WOULD HAVE A HARD TIME FIGURING
OUT WHICH WAS THE DEMOCRAT AND
WHICH WAS THE REPUBLICAN.
IT IS SO WONDERFUL THAT WE STILL
HAVE SOME BIPARTISAN POTENTIAL
IN THIS TOWN AND THAT MEDICAL
RESEARCH SEEMS TO BE THE PLACE
WHERE THIS IS STILL EMBRACED
ENTHUSIASTICALLY BY VIRTUALLY
EVERYBODY INVOLVED, AND THAT'S A
CREDIT TO ALL OF YOU WHO DO
AMAZING WORK HERE EVERY DAY.
WELL, I'M GLAD TO BE HERE TO BE
ABLE TO INTRODUCE TODAY'S
SPEAKER BECAUSE THIS IS A BIT OF
A WELCOME HOME FOR SOMEONE WHO
SPENT A FAIR AMOUNT OF HIS TIME
AT NIH AND FOR WHOM WE HAVE A
GREAT DEAL OF ADMIRATION AND
AFFECTION.
THIS IS KEVIN GARDNER.
KEVIN IS CURRENTLY THE SENIOR
VICE CHAIR IN THE DEPARTMENT OF
PATHOLOGY AND CELL BIOLOGY AT
COLUMBIA.
HE GOT HIS UNDERGRADUATE DEGREE
AT YALE, THEN AN M.D. PH.D. AT
HOPKINS, AND CAME TO NIH BACK IN
1989, ORIGINALLY AS A MEDICAL
STAFF FELLOW, THEN A SENIOR
STAFF FELLOW, THEN AN
INVESTIGATOR.
I WON'T GO THROUGH ALL THE OTHER
STEPS.
THERE WERE SEVERAL MORE.
AND ULTIMATELY BECAME THE ACTING
SCIENTIFIC DIRECTOR AT NIMHD AND
ITS INTRAMURAL RESEARCH PROGRAM
WHILE ALSO BEING A SENIOR
INVESTIGATOR IN THE GENETICS
BRANCH OF THE NATIONAL CANCER
INSTITUTE.
HE DID MOVE ON TO COLUMBIA IN
2017 AS A PATHOLOGIST WHO WANTED
TO GET ENGAGED IN OPPORTUNITIES
IN THAT PLACE THAT HE WAS
TELLING ME BRIEFLY ABOUT IN
TERMS OF BOTH RESEARCH AND ALSO
THE OPPORTUNITY TO MENTOR OTHER
TRAINEES WHO WERE COMING ALONG
AND ENCOURAGING THEM TO ALSO BE
SUCCESSFUL.
HIS RESEARCH WHICH I'M SURE HE'S
GOING TO TELL YOU ABOUT IS AN
INTERESTING MIX OF MOLECULAR
INSIGHTS IN ONCOLOGY AND ALSO A
FOCUS ON QUESTIONS ABOUT HEALTH
DISPARITIES.
HE'S AN ELECTED MEMBER OF THE
AMERICAN SOCIETY FOR CLINICAL
INVESTIGATION, HE'S RECEIVED THE
PHILIP J. BROWNING SCIENTIFIC
PIONEER AWARD AND A COUPLE OF
NIH DIRECTORS AWARDS AND WE ARE
HONORED INDEED TO HAVE HIM HERE
WITH US TODAY WITH THE TITLE OF
HIS TALK, "RACE IN THE MOLECULAR
BIOLOGY IN BREAST CANCER, A
PATHOLOGIST'S VIEW FROM THE
BENCH TO THE BEDSIDE."
PLEASE WELCOME DR. KEVIN
GARDNER.
[APPLAUSE]
>> IT'S GOING TO WORK GREAT,
FOLKS!
ARE WE SAFE NOW?
OKAY.
YOU GUYS CAN HEAR ME, RIGHT?
OKAY.
WELL, I WANT TO THANK
DR. COLLINS FOR THAT
INTRODUCTION.
I AM A CLINICALLY TRAINED
PATHOLOGIST THAT STUDIES IMI
NANT BASED MECHANISMS OF
TRANSCRIPTION CONTROL.
NOW, WHAT I DO IS NOT VERY
DIFFERENT FROM WHAT EVERYBODY IN
THIS ROOM DOES.
WHAT WE DO IS WE SEEK TO
UNDERSTAND DISEASE IN TERMS OF
ITS MOST BASIC COMPONENTS AND
ELEMENTS.
THEN WE TRY TO ASSEMBLE THOSE
BASIC COMPONENTS AND ELEMENTS
INTO PATHWAYS AND PROGRAMS OF
CELLULAR PHYSIOLOGY, FUNCTION
AND PHENOTYPE.
NOW, I DESIGNED THIS TALK TO BE
FOR A GENERAL AUDIENCE, BUT I
HAVE BEEN REMINDED ON SEVERAL
OCCASIONS BY MY WIFE, WHO IS AN
ARTIST, THAT I DON'T KNOW WHAT A
GENERAL AUDIENCE IS.
SO BEAR WITH ME.
SO I'LL BEGIN THE TALK WITH A
BRIEF REVIEW OF BREAST CANCER
EPIDEMIOLOGY, VERY BRIEF REVIEW
AND RACE, AND DOING A BASIC
OVERALL REVIEW OF PERSPECTIVES
ON EPIGENETIC REGULATION.
THEN I WILL DISCUSS TWO STORIES,
TWO MOLECULAR TALES OF TWO
EPIGENETIC REGULATORS, CTBP AND
KAISO AND THEIR ROLE IN BREAST
CANCER BIOLOGY AND PROGRESSION.
THEN I WILL REVIEW THE USE OF
DIGITAL PATHOLOGY AND ARTIFICIAL
INTELLIGENCE IN A -- BOTH A
BENCH TO BED SIGN APPROACH AND
LATER A BEDSIDE TO BENCH
APPROACH, TO ELUCIDATE THE
FUNCTION OF THESE DIFFERENT
PROTEINS OR OTHER FACTORS IN
BREAST CANCER BIOLOGY, AND TO
CHARACTERIZE HOW THEY MAY HAVE
DIFFERENTIAL INFLUENCE BASED ON
RACE.
THEN I'LL DISCUSS BRIEFLY SOME
NEW APPROACHES TO PIE OWE MARKER
DISCOVERY USING ARTIFICIAL
INTELLIGENCE, THEN AT THE VERY
END, I WANT TO MAKE A FEW
COMMENTS ABOUT COLLABORATIONS,
HOW TO TRY TO DO THE
MULTIDISCIPLINARY
COLLABORATIONS.
WE ALSO WILL HAVE A BRIEF
DISCUSSION ON RACE, JUST IN
GENERAL.
I HAVE NO FINANCIAL INTEREST TO
DISCLOSE.
IT'S ALWAYS A PLEASURE TO BE
REMINDED OF THAT FACT.
ALL RIGHT.
LAST YEAR THERE WERE OVER
266,000 NEW CASES OF INVASIVE
BREAST CANCER IN THE UNITED
STATES.
AND OVER 40,000 WOMEN DIED FROM
THEIR DISEASE OR FROM A
DIAGNOSIS OF BREAST CANCER.
THE INFLUENCES, THE FREQUENCIES
AND THE OUTCOME OF BREAST CANCER
ON -- EVENLY DISTRIBUTED ACROSS
POPULATIONS WHERE IT'S
WELL-KNOWN THAT WOMEN OF AFRICAN
ANCESTRY HAVE A NEAR 40% HIGHER
MORTALITY RATE THAN THEIR
EUROPEAN COUNTERPARTS.
THE REASONS FOR THIS STILL
REMAIN NOT CLEARLY DEFINED, BUT
IT'S A COMBINATION OF MULTIPLE
DIFFERENT FACTORS THAT ARE
INVOLVED OR THOUGHT TO BE
IMPORTANT HEALTH DETERMINANTS IN
BREAST CANCER.
INCLUDING TREATMENT,
PRESENTATION, TUMOR BIOLOGY,
CO-MORBID CONDITIONS,
SOCIOECONOMIC STATUS, SCREENING
AND TREATMENT.
THESE ARE ALL INTERCONNECTED AND
ALL INTERLINKED.
YOU CANNOT DISCUSS PRESENTATION
WITHOUT THINKING ABOUT
SCREENING.
YOU CANNOT DISCUSS TREATMENT
WITHOUT THINKING ABOUT TUMOR
BIOLOGY, ET CETERA, ET CETERA,
ET CETERA.
THEY'RE ALL INTERLINKED.
NOW, OUR GENERAL APPROACH OVER
THE LAST FEW YEARS HAS BEEN VERY
SIMPLE.
WE BEGIN WHICH TRYING TO
UNDERSTAND BASIC MECHANISMS OF
REGULATION, BASIC BIOLOGICAL
PROCESSES, AND THEN WE TRY TO
TRANSLATE OUR FINDINGS IN A WAY
THAT WE TRY TO UNDERSTAND THEIR
IMPLICATIONS IN BREAST CANCER
DIAGNOSIS, DISEASE DIAGNOSIS,
TREATMENT AND PREVENTION.
OKAY.
THERE ARE ESSENTIALLY TWO MAJOR
PHENOTYPIC DRIVERS OF CANCERS.
THE FIRST IS GENE MUTATION,
WHICH IS AN IRREVERSIBLE CHANGE,
THE SECOND IS EPIGENETIC
CHANGES.
UNLIKE GENE MUTATION, EPIGENETIC
CHANGES ARE REVERSIBLE.
THEY CAN BE STABLY INHERITED,
BUT THEY ALSO CAN RESPOND TO
CHANGES IN THE ENVIRONMENT.
EACH PROMOTES DISRUPTED CONTROL
OF GENE REGULATION AND CELLULAR
PHENOTYPE.
OKAY.
SO LET'S THINK ABOUT THE BEST
WAY TO DESCRIBE EPIGENETIC
REGULATION.
LET'S THINK ABOUT IT THIS WAY.
EVERY CELL IN OUR BODY THAT HAS
A NUCLEUS HAS TWO METERS OF DNA.
THAT'S 2 METERS OF DNA
COMPRESSED INTO A 10-MICRON OR
LESS NUCLEUS.
THAT'S A 10,000 FOLD COMPRESSION
RATIO.
THAT'S LIKE TAKING A 100-PAGE
BOOK AND FOLDING IT UP INTO
SOMETHING THE SIZE OF A PERIOD.
SO IT'S A PRETTY IMPRESSIVE
FEAT.
NOW, WITH THAT COMPRESSION
RATIO, YOU HAVE A NEW PROBLEM.
THE COMPRESSION RATIO THAT IS
CAUSED IS PRODUCED BY THE HIS
TOMORROW BASED NUCLEOSOMAL
STRUCTURE OF CHROMATIN.
SO NOW YOU HAVE PACKAGED DNA IN
A 10,000 FOLD COMPRESSION RATIO,
AND YOU NEED TO DO YOUR STANDARD
BIOLOGY IN THE NUCLEUS.
PROCESSES LIKE DNA REPAIR,
PROCESSES LIKE TRANSCRIPTION,
PROCESSES LIKE DNA REPLICATION.
AND SO WHAT HAS EVOLVED OVER
TIME IS A WAY TO OPEN AND CLOSE
THE CHROMATIN STRUCTURE.
AND MUCH OF THAT HAS BEEN DONE
OR CARRIED OUT BY FACTORS OR
MACHINERIES THAT ACTUALLY MODIFY
THE CHROMATIN.
MOST OF THEM CAN COVALENTLY
MODIFY IT, OTHERS CAN MOVE THE
CHROMATIN AROUND TO GAIN ACCESS
TO OPEN THE CHROMATIN AND GAIN
AND HAVE MACHINERY GAIN ACCESS
TO THE DNA SO THEY CAN CARRY OUT
THESE BASIC BIOLOGICAL PROCESSES
IN THE NUCLEUS.
THESE FACTORS ARE OFTEN REFERRED
TO AS RIDERS, THESE ARE FACTORS
THAT MODIFY COVALENT
MODIFICATIONS ON HIS TOMORROWS,
TOMORROW H
ISTONES, AND
THERE'S A THIRD COMPONENT OF
FACTORS THAT CAN USE ATP AND
ENERGY TO MOVE THE CHROMATIN
AROUND.
THE BOTTOM LINE, THE BOTTOM GOAL
IS FOR THE CHROMATIN TO BE OPEN
SO THAT THE BUSINESS IN THE
TRANSCRIPTION REGULATION, GENE
EXPRESSION, REPLICATION.
NOW, I'LL BEGIN WITH ONE
MOLECULAR STORY, ONE MOLECULAR
TALE, A PROTEIN WE'VE BEEN
STUDYING FOR A WHILE CALLED
C-TERMINAL BINDING PROTEIN.
IT'S A DIMERIC PROTEIN.
THERE'S TWO FAMILY MEMBERS SO IT
CAN FORM HET  HETERODIMERS OR
HOMO
DIMERS.
IT PLAYS A SIGNIFICANT ROLE IN
WOUND HEALING PROCESSES AND WITH
HE HAVE FOUND OVER THE YEARS
THAT IT HAS A MAJOR ROLE IN
TUMOR PROGRESSION, BREAST CANCER
PROGRESSION.
IN THE NUCLEUS, AS A DIMER, ONE
MEMBER OF THAT DIMER CAN BIND
TWO FACTORS THAT ARE DNA BINDING
FACTORS SO IT CAN ACTUALLY BE
RECRUITED TO DNA BOUND PROTEINS
AT CERTAIN LOCI THROUGHOUT THE
NUCLEUS.
AS A DIMER, THE OTHER MEMBER CAN
BIND TO OTHER CHROMATIN
MODIFYING FACTORS.
SO BECAUSE OF THIS
CONFIGURATION, CTBP ACTS AS AN
ADAPTER PROTEIN THAT CAN
ESSENTIALLY TARGET MULTIPLE
DIFFERENT CHROMATIN MODIFYING
COMPLEXES TO LOCALES THROUGHOUT
THE NUCEUS.
ESSENTIALLY IN RESPONSE TO
CHANGES IN METABOLISM, IT'S AN
NADH BINDING PROTEIN AND ITS
DIMERIZATION IS REGULATED BY
NADH, IT CAN AFFECT THE
EPIGENETIC LANDSCAPE OF THE
NUCLEUS.
OVER THE YEARS WE WERE PROFILING
WHT GENES IT MIGHT AFFECT.
WE DID CHIP SEQ STUDIES WHERE WE
CAN ACTUALLY PROFILE WHERE THE
PROTEIN BINDS THROUGHOUT THE
NUCLEUS, THESE ARE PEAKS WHERE
OTHER PROTEINS BIND USING A
PROCESS CALLED CHIP SEQ.
BOUND TO A VARIETY OF DIFFERENT
JEAN REGULATORY LOCI THROUGHOUT
THE NUCLEUS, BOTH ENHANCERS AND
PROMOTERS.
ENHANCERS ARE OTHER DNA ELEMENTS
THAT CAN ACT IN PROXIMITY OR IN
LONG-RANGE INTERACTIONS TO HELP
TURN ON OR TURN OFF THE DNA, AND
THE MAJOR EFFECT IS YOU HAVE AN
OPENING AND CLOSING OF CHROMATIN
STRUCTURE SO THIS BIOCHEMICAL
PROCESS CAN OCCUR.
NOW, IN THE LAST FEW YEARS,
WE'VE BEEN VERY PUZZLED BECAUSE
WE WERE FINDING THAT CTBP SEEMED
TO BIND OR CO-BIND WITH A
VARIETY OF DIFFERENT FACTORS.
THESE ARE JUST HEAT MAPS WHERE
WE'RE CO-ALIGNING WHERE WE CAN
SEE CTBP BINDING WITH OTHER
FACTORS LIKE BRCA, A VARIETY OF
OTHER FACTORS THAT ARE VERY
IMPORTANT IN THE WAY THAT
ESTROGEN RECEPTOR CAN BIND DNA.
WE WERE PUZZLE THE BY THE FACT
THAT CTBP SEEMED TO BE
INTERACTING IN MANY DIFFERENT
LOCALES IN BREAST CANCER CELLS
AND MAMMARY CELLS THAT SEEM
TODAY CO-ALIGN ORCO-BIND WITH
OTHER FACTORS.
A PUBLICATION IN 2014, THEY
DESCRIBED THIS COMPLEX WHERE
MULTIPLE FACTORS WERE BINDING AT
ONE COMPLEX AND THEY REFER TO IT
AS A MEGA TRANS COMPLEX THAT
COULD ACT AS ENHANCERS AND
PROMOTERS TO CONTROL CERTAIN
GENES.
MANY OF THEM ARE ESTROGEN
RECEPTOR CONTROLLED GENES.
LATER, WE FOUND ALSO THAT CTBP
CAN BIND TO OTHER MODIFYING
FACTORS SUCH AS THE SWITCH SNP
COMPLEX, THAT CAN MOVE AND SLIDE
CHROMATIN AROUND WITHIN THE
NUCLEUS.
SO AT THAT POINT, WE BEGAN
INVESTIGATING WHETHER OR NOT
THIS FACTOR COULD REALLY HAVE A
ROLE IN TARGETING MULTIPLE
DIFFERENT TRANSCRIPTIONAL
EPIGENETIC REGULATORY COMPLEXES
THROUGHOUT THE NUCLEUS.
OUR FIRST STEP WAS TO JUST
DEPLETE THE CELLS.
SO WE USE CRISPR/CAS TO KNOCK
OUT CTBP IN MCF 7 CELLS, AND
THIS WAS OUR FIRST SURPRISE.
WE SAW A MASSIVE DYSREGULATION
OF GENES THAT WERE IMPORTANT IN
CELLULAR PHENOTYPE.
THAT MASSIVE DYSREGULATION
DIDN'T MAKE SENSE TO US BECAUSE
THERE WERE SOME CELLS THAT WERE
SHOWING A MORE AGGRESSIVE BAY 
BASAL
LIKE PHENOTYPE, OTHERS GENES
WERE SHOWING A HIGH EXPRESSION
OF A LUMEN TINO TYPE.
LOSING CTBP IN A SINGLE CELL
LINE MAY BE ACTUALLY FLIPPING A
SWITCH WHICH WE'RE CHANGING ITS
EPIGENETIC PLASTICITY OR
REGULATORY PLASTICITY.
THESE ARE JUST ANOTHER EXAMPLE.
FOR EXAMPLE, MCF7 CELLS ARE
REFERRED TO AS LUMINAL CELLS,
AND THEY DON'T EXPRESS BASAL --
ALL OF A SUDDEN IN THE ABSENCE
OF CTBP 1,  -- WHILE AT THE SAME
TIME EXPRESSING HIGH LEVELS OF
ANOTHER GENE THAT'S IMPORTANT IN
THE OTHER PHENOTYPE, THE LESS
LUMINAL OR LESS
ESTROGEN-CONTROLLED PHENOTYPE.
SO WE DID SINGLE CELL ATAC-SEQ
TO SEE IF WE COULD SEE IN THE
CHANGES IN THE OPENING OR
CLOSING OF CHROMATIN BASED ON
THE LEVELS OF CTBP.
AND WE FOUND IT VERY INTERESTING
OBSERVATION THAT MANY OF THE
CELLS THAT WERE TURNING ON, THE
SPECIFIC GENES THAT ARE
IMPORTANT FOR ONE PHENOTYPIC
DIFFERENTIATION WERE ONLY BEING
EXPRESSED IN A SMALL POPULATION
OF CELLS.
SO WE STARTED TO DO AN ANALYSIS
TO CHECK ABOUT -- TO PROFILE
WHERE WE SAW ASSEMBLING OF CTBP
AT DIFFERENT LOCALES THROUGHOUT
THE NUCLEUS AND WHETHER OR NOT
THERE WAS ANY RELATIONSHIP
BETWEEN WHERE THESE COMPLEXES
BOUND AND WHERE WE SAW OPEN
CHROMATIN.
AND TO OUR SURPRISE, WE DID NOT
FIND COMPLEXES AT OPEN
CHROMATIN.
BUT IF WE TOOK ADVANTAGE OF
AVAILABLE DATA THAT BASICALLY
MAPS FROM THE DATASETS LIKE --
GENERATED BY THE 4D NUCLEOME
PROJECT THAT GENERATES MAPS OF
CHROMATIN-CHROMATIN LONG-RANGE
INTERACTIONS, WE FOUND MANY OF
THE GENES DEPENDENT ON CTBP WERE
OPEN UNDER CONDITIONS WHERE THEY
WERE FORMING LOOPS WHERE WE
COULD SEE CTBP COMPLEXES BOUND.
SO ON THE RIGHT HERE, I HAVE
WHERE WE SEE THE CTBP BOUND MEGA
COMPLEXES AND THEY'RE ALL IN
COORDINATION WITH LOOPS OF OPEN
CHROMATIN THAT ARE ONLY OPEN IN
THE ABSENCE OF CTBP.
SO THE MODEL THAT WE'RE WORKING
ON RIGHT NOW IN OUR LAB TO TRY
TO UNDERSTAND IS THAT WE THINK
THE CTBP IS ASSEMBLING AT THESE
MULTIPLE MEGA COMPLEXES IN
BRINGING IN CHROMATIN MODIFIERS
THAT CAN ACT LOCALLY, BUT ALSO
ACT AT A DISTANCE THROUGH THESE
CHROMATIN LOOPS.
WE'VE ALSO FOUND THAT CTBP IS A
MAJOR DRIVER OF METABOLISM IN
BREAST CANCER CELLS IN BOTH
TRIPLE NEGATIVE BREAST CANCER
CELLS, MORE AGGRESSIVE
PHENOTYPE, OR POSITIVE CANCER
CELLS, BY USING METABOLOMICS AND
ALSO USING SEAHORSE RESPIRATION
AND GLYCOLYSIS.
RECENTLY WE PUBLISHED A FEW
STUDIES WHERE WE'VE BEEN USING
SMALL MOLECULE INHIBITORS TO
ACTUALLY INHIBIT CTBP WHERE WE
CAN ACTUALLY PHENOCOPY GENE
EXPRESSION BOTH IN OPEN CHROME
CHROMATIN AND ALSO INFLUENCING
CHANGES IN METABOLISM.
SO THE MORAL OF THIS STORY IS WE
FEEL THAT CTBP ACTS AS A
BIDIRECTIONAL MOLECULAR SWITCH
TO REGULATE EPIGENETIC CANCER IN
RESPONSE TO CHANGES IN
METABOLISM, WE'RE FINDING NOW IT
BASICALLY BIDIRECTIONAL BECAUSE
IT BOTH RESPONDS TO AND ALSO
INCREASES METABOLIC IMBALANCE.
SO IT'S A FEED FORWARD
MECHANISM.
SO THAT'S THE SHORT STORY.
OKAY?
AND OVER THE LAST SIX OR SEVEN
YEARS, A MAJOR EFFORT IN OUR
LABORATORY HAS BEEN TRYING TO
DEFINE THE IMPLICATIONS OF WHAT
WE FIND OR SEE IN THE TEST TUBE.
WHAT DOES CTBP DO IN BREAST
CANCER, WHAT IS ITS ROLE IN
BREAST CANCER?
SO FAR ALL I'VE BEEN ABLE TO
EXPLAIN TO YOU TODAY IS THAT ALL
OUR BUSINESS SUGGESTS THAT CTBP
HAS SOMETHING TO DO WITH CANCER.
AND SO REALLY THE ONLY WAY FOR
US TO APPROACH ANSWERING THIS
QUESTION AND ASKING THE QUESTION
ABOUT THE ROLE OF CTBP IN HUMAN
BREAST CANCER IS TO GO TO THE
MOUNTAIN, GET PATIENT TISSUE.
SO OVER THE LAST SIX OR SEVEN
YEARS, WE HAVE BEEN TRYING TO
DEVELOP COHORTS SO WE CAN ASK
THESE BASIC QUESTIONS.
AND IT'S A VERY SIMPLE PROCESS
CONCEPTUALLY.
GET THE TISSUE, ANALYZE THE
TISSUE AND PROCESS THE DATA.
NOT SO EASY IN PRACTICE.
SO I'M GOING TO TELL YOU A STORY
OF A COHORT THAT WE'VE BEEN
DEVELOPING SINCE 2011.
IT'S A COHORT IN EAST NORTH
CAROLINA, 29-COUNTY AREA THAT
HAS BEEN DESIGNATED FOR YEARS AS
A CANCER HEALTH DISPARITIES
AREA.
IT HAS A POPULATION OF
1.4 MILLION, VERY RURAL, 97
PEOPLE PER SQUARE MILE, IT'S
HARD TO IMAGINE LIVING  LIVING
IN
MANHATTAN THAT THERE'S A PLACE
WHERE THERE'S ONLY 9 # 7 PEOPLE
97 PEOPLE 
IN
ONE SQUARE MILE.
27% OF THE POPULATION IS BELOW
THE POVERTY LEVEL, 31% AFRICAN
ANCESTRY, HIGH LEVEL OF
OBESITY,&
EVEN A HIGHER LEVEL OF OBESITY
IN PEOPLE OF AFRICAN ANCESTRY.
IMPORTANTLY FOR US IN THIS
STUDY, ONE SINGLE HEALTHCARE
PROVIDER, AND THE FACT THAT 80%
OF ALL THE SURGERIES DONE IN
THIS REGION ARE DONE AT ONE
HOSPITAL.
SO WE COULD ESSENTIALLY GET
ALMOST POPULATION TYPE
INFORMATION FROM A STUDY OF THIS
TYPE.
SO THIS IS WHAT THE WORK FLOW
WAS.
WE WENT DOWN TO NORTH CAROLINA,
I DID THE PATHOLOGY, WE PULLED
THE SLIDES, WE ASKED THEM TO
PULL THE BLOCK, WE SIGNED THE
IRB PERMISSIONS, AND THEN WE
WERE ABLE TO GET ABOUT 900
PATIENT SAMPLES.
FIRST THING WE DID WITH THOSE IS
TO MOVE INTO ANALYZING THE
TISSUE.
THE FIRST ROUND WAS TO MAKE
TISSUE MICRO ARRAYS.
WITH PERMISSION, WITH SOME OF
THE SAMPLES, WE WERE ABLE TO GET
SON RNA 
SOME RNA SEQ DATA, GENOME DATA,
THEN THE NEXT STEP WAS TO
CORRELATE THIS DATA WITH OUR
PHENOTYPIC DATA OVER DATA WE
COLLECTED IN COLLABORATION WITH
A SURGEON, NAZARENE BSM  BORA.
TO DATE, WE'RE STILL
COLLABORATING.
WE OFTEN TALK PROBABLY ONCE A
WEEK, SOMETIMES I CALL HER WHILE
SHE'S TAKING HER KIDS TO THE
FAIR, BUT THIS IS A LONG
COMMITTED PROCESS WHERE WE NOW
HAVE ABOUT NINE YEARS OF MEETING
FOLLOW-UP ON THE TISSUE.
THAT ALLOWS US TO ASK AND START
MAKING CORE LAYINGS BETWEEN WHAT
SEE IN THE TISSUE AND WHAT WE
SEE IN TERMS OF PATIENT
OUTCOMES.
NOW A VERY IMPORTANT STEP IN
TRYING TO ANALYZE THIS DATA AS
WE HAVE 900 PATIENTS WAS TO USE
SOMETHING THAT WOULDN'T JUST
TAKE FOREVER TO ANALYZE AND
ACTUALLY COULD GIVE US MORE
PRECISE DATA.
SO WE STARTED GETTING MORE
INVOLVED IN ARTIFICIAL
INTELLIGENCE.
SO THERE ARE ESSENTIALLY TWO
APPROACHES THAT WE'VE BEEN
MAKING TO DO THIS.
WE'RE USING MACHINE LEARNING
THAT WILL DO TWO THINGS.
IT CAN IDENTIFY TUMOR,
DIFFERENTIATE THAT FROM STROMA,
AND WE HAVE ONE THAT WITH A
LITTLE HELP FROM PATHOLOGISTS
CAN GIVE YOU A WAY TO IDENTIFY
AND SUBSEGMENT THE CELLS INTO
NUCLEI, CYTOPLASM AND MEMBRANE,
AND THEN YOU CAN USE ANY TYPE OF
STAINING PROCEDURE AND YOU CAN
BASICALLY GET A QUANTITATIVE
ASSESSMENT OF AN ANTIGEN IN ITS
SUBCELLULAR COMPARTMENT WHETHER
IT'S IN THE NUCLEUS, IN THE
CYTOPLASM OR IN THE MEMBRANES.
WE DO IT IN SUCH A WAY THAT WE
GET A WEIGHTED SCORE FOR
INTENSITY AND WE ESSENTIALLY
GENERATE A SCORE CALLED A HISTO
SCORE WHICH GOES FROM ZERO TO
300 AND REFLECTS THE PERCENTAGE
OF CELLS THAT ARE DESIGNATED AS
MOST INTENSE 3 PLUS, 2 PLUS,
1 PLUS OR 0.
SO ESSENTIALLY WE CAN GENERATE A
CONTINUOUS SCORE FOR THE ANTIGEN
EXPRESSION IN TISSUES.
AND THIS IS JUST AN EXAMPLE THAT
WE PUBLISHED MOST RECENTLY WHERE
ESSENTIALLY WE'VE COMPARED GENE
EXPRESS EGF RECEPTOR, GATA3 AND
FOX A1.
THE BOTTOM LINE IN THIS
PARTICULAR STUDY IS WE'RE ABLE
TO LOOK AT -- EACH BAR HERE IS A
SINGLE PATIENT AND THAT COLOR
SCORE IS THE ACTUAL MEASUREMENT
OF PROTEIN ABUNDANCE.
WE CAN DO UNSUPERVISED
CLUSTERING TO CLUSTER THE
ANTIGEN PROFILES OF EACH
PATIENT, THEN WE LINED THEM UP
WITH SPECIFIC PATIENT DATA.
AND IN THIS STUDY, WHICH I SAID
WE'VE ALREADY PUBLISHED, SHOWS
THAT WE COULD FIND SPECIFIC
DIFFERENCES IN THE PREDICTIVE
NATURE, PREDICTIVE VALUE OF
STANDARD ANTIGENS USED IN BREAST
CANCER DIAGNOSIS AND EVALUATION
LIKE ESTROGEN RECEPTOR.
HERE WE FOUND THAT ESTROGEN
RECEPTOR, AND LET ME REVIEW JUST
BRIEFLY, THERE ARE ESSENTIALLY
TWO MAJOR CLASSES OF BREAST
CANCER, ER POSITIVE, ER
NEGATIVE.
THE ER NEGATIVE IS MUCH MORE
AGGRESSIVE.
THERE'S A SUBTYPE OF NEGATIVE
CANCER REFERRED TO AS TRIPLE
NEGATIVE BREAST CANCER, ABSENCE
OF ESTROGEN RECEPTOR AND LACKING
EXPRESSION OF HER2.
IT'S MUCH MORE DEADLY, CRITICAL
IN SUBTYPING BREAST CANCER
TUMORS.
HERE WE'RE SHOWING THAT THERE
ARE ACTUALLY DIFFERENCES BASED
ON RACE AND HOW ESTROGEN
RECEPTOR ITSELF IS PREDICTIVE OF
BREAST CANCER SURVIVAL.
SO USING THIS METHOD, WE STARTED
TO ASK OUR QUESTION, DOES CTBP
HAVE ANYTHING TO DO WITH BREAST
CANCER?
IN THIS CASE, WE DO TWO THINGS.
WE MEASURE THE ABUNDANCE OF CTBP
1 IN THE NUCLEUS, AND WE COMPARE
TO THE ABUNDANCE OF CTBP IN 1 IN
THE
CYTOPLASM.
HIGH LEVELS OF CTBP 1 IN THE
NUCLEUS IS HIGHLY PREDICTIVE OF
POOR SURVIVAL.
CONVERSELY IF IT'S HIGH LEVELS
IN THE CYTOPLASM, IT'S
PREDICTIVE OF GOOD SURVIVAL,
SUGGING WE CAN MAKE A  WE
SEE THE SIMILAR COMPARISON,
SIMILAR RELATIONSHIP FOR CTBP 2.
SO THIS IS OUR FIRST
CONFIRMATION THAT CTBP PROBABLY
HAS SOMETHING TO DO WITH BREAST
CANCER AND ACTUALLY CAN BE
PREDICTIVE OF OVERALL BREAST
CANCER SURVIVAL.
WHAT SURPRISED US IS THAT AS WE
START TO LOOK AT TISSUES BASED
ON RACE AND IN THIS CASE, THIS
IS A COMPARISON WHERE WE LOOKED
AT TRIPLE NEGATIVE BREAST
CANCER, AS I MENTIONED BEFORE,
THE MOST AGGRESSIVE FORM, THE
MOST DEADLY FORM, THE FORM THAT
OCCURS AT A HIGHER RATE IN WOMEN
OF AFRICAN ANCESTRY.
WE FOUND THAT ALTHOUGH LOOKING
AT A TOTAL POPULATION WITH
TRIPLE NEGATIVE BREAST CANCER
CTBP 1 AND CTBP 2 PREDICTED
OVERALL BREAST CANCER OUTCOME,
IT WAS DIFFERENTIALLY PREDICTIVE
BASED ON RACE.
IT TURNS OUT FOR CTBP 1, IT WAS
MUCH MORE PREDICTIVE OF SURVIVAL
IN WOMEN OF EUROPEAN ANCESTRY
WHO HAD TRIPLE NEGATIVE BREAST
CANCER AND SO WAS CTBP 2.
IN FACT, BY COMPARISON, CTBP
2 WAS MUCH -- ALMOST TWICE AS
MUCH PREDICTIVE OF SURVIVAL IN
WOMEN OF EUROPEAN ANCESTRY.
SO THIS IS A NEW PROJECT THAT
WE'RE PURSUING IN A LABORATORY
AND WE'RE TRYING TO ASK THE
QUESTION OF WHY THAT IS.
SO OUR GENERAL THINKING NOW, THE
REAL MODEL THAT WE'RE WORKING ON
AT THE MOMENT IS THAT CTBP PLAYS
A MAJOR ROLE IN THE CONTROL OF
ENDOCRINE REGULATED ESTROGEN
RECEPTOR OR PROGESTERONE
COMPLEXES AND IT DOES THAT
THROUGH RECRUITMENT OF THESE
SPECIFIC MODIFIERS AND THE DATA
THAT WE SHOW RIGHT NOW AND THIS
IS THE BEGINNING OF OUR
INVESTIGATION, THAT COMPLEX, THE
WAY THAT COMPLEX ASSEMBLES
APPARENTLY FUNCTIONS DIFFERENTLY
BASED ON RACE.
AND IS DIFFERENTIALLY PREDICTED
BASED ON RACE.
NOW, THE SECOND MOLECULAR STORY
IS ABOUT THIS PROTEIN CALLED
KAISO.
KAISO IS A NUCLEAR PROTEIN THAT
HAS A ROLE IN TRANSCRIPTION
REGULATION.
IT CAN BOTH BE AN ACTIVATOR AND
REPRESSOR.
THIS PROTEIN SEEMED TO BE
EXPRESSED AT HIGHER LEVELS IN
WOMEN OF AFRICAN ANCESTRY AND
ALSO SEEMED TO BE PREDICTIVE OF
POORER OUT COME IN WOMEN OF
AFRICAN ANCESTRY WITH TRIPLE
NEGATIVE BREAST CANCER.
SO WE WERE TRYING TO ASK WHETHER
OR NOT WE COULD SEE SIMILAR
EFFECTS IN OUR COHORT.
SO I WANT TO POINT TO TWO
THINGS.
THIS PROTEIN, ALTHOUGH IT'S BEEN
DESCRIBED AS -- IT CAN BE FOUND
IN BOTH THE NUCLEUS AND THE
CYTOPLASM AND IN MANY CASES, A
WHOLE LOT IN CYTOPLASMIC
STAINING.
SO WE CONTACTED BOTH CLAYTON AND
WE SAID, THERE'S A LOT OF
CYTOPLASMIC STAINING IN THOSE
TUMORS, WE THINK THAT COULD MEAN
SOMETHING.
THEY SAID WE'RE ONLY PAYING
ATTENTION TO THE NUCLEAR
STAINING.
SO WE'RE ABLE TO USE MACHINE
LEARNING TO ESSENTIALLY
QUANTITATIVELY SEPARATE AND
PROFILE THE ABUNDANCE OF THIS
FACTOR IN THE NUCLEUS VERSUS THE
CYTOPLASM, WE DID THE
EXPERIMENT.
AND WE FOWPT FOUND THAT ALTHOUGH
AS CLAYTON AND JULIE HAD
PREVIOUSLY DESCRIBED THAT IT
PREDICTED POOR OUT COME,
CYTOPLASMIC KAY  KAISO WAS
HIGHLY
BREAST CANCER.
 -- ARE PREDICTIVE OF SURVIVAL
WITH A SIGNIFICANT P VALUE BUT
IN THE MULTIVARIATE SETTING
WHERE WE NORMALIZED FOR
EVERYTHING ELSE AND ASKED BHA IS
THE ACTUAL INDEPENDENT
PREDICTER, WE WERE KIND OF
SHOCKED TO FIND OUT EVEN IN THE
MULTIVARIATE SETTING, BOTH
NUCLEAR KAISO AND CYTOPLASMIC
KAISO THEMSELVES WERE
INDEPENDENT PREDICTERS OF
OVERALL BREAST CANCER SURVIVAL.
SO THIS BECAME SOMETHING THAT
REALLY PIQUED OUR INTEREST AND
WE STARTED TO ASK ABOUT WHETHER
OR NOT IT WAS OVEREXPRESSED IN
DIFFERENT SUBTYPES, AND IF WE
COMPARED NUCLEAR TO CYTOPLASMIC
KAISO, NUCLEAR ON THE LEFT,
CYTOPLASMIC ON THE RIGHT, THEY
HAD DIFFERENT DRNGSES 
DISTRIBUTIONS
BASED ON TUMOR SUBTYPE.
SIMILARLY IF WE GO ACROSS THE
VARIOUS DIFFERENT TYPES OF
BREAST CANCER, HER2 POSITIVE,
LUMINAL B WHICH IS AN ER
POSITIVE MORE AGGRESSIVE FORM
AND TRIPLE NEGATIVE CANCER, WE
FIND THAT CYTOPLASMIC KAISO WAS
MUCH MORE ASSOCIATED WITH MORE
AGRES 
AGGRESSIVE FORMS OF BREAST
CANCER.
SO THIS WAS A VERY INTRIGUING
PHENOMENON FOR US SO WE WANTED
TO ASK IF WE COULD SEE ANY
CORRELATION BETWEEN THE ANTIGENS
THAT ARE NORMALLY USED OR OFTEN
USED IN PREDICTING OUTCOME OF
BREAST CANCER AND KAISO
EXPRESSION.
AND TO SEE IF THERE'S ANY
DIFFERENCE IN THE NUCLEAR VERSUS
CYTOPLASMIC.
EACH BAR IS A PROTEIN SCORE FOR
EACH PROTEIN, THEY'VE BEEN
CLUSTERED TO SEE IF THERE'S ANY
CORRELATION BETWEEN CYTOPLASMIC
AND NUCLEAR KAISO EXPRESSION AND
PATIENT OUTCOME, PATIENT
SUBTYPE, PATIENT PARAMETERS AND
WE FOUND THAT THERE'S A
SIGNIFICANT CORRELATION OF
KAISO, CYTOPLASMIC KAISO WITH
THIS SUBTYPE HERE IN GREEN WHICH
IS TRIPLE NEGATIVE BREAST
CANCER, BUT IT WAS ALSO ABLE TO
SEPARATE TRIPLE NEGATIVE BREAST
CANCER INTO THREE DIFFERENT
SURVIVAL GROUPS WHICH I'LL SHOW
LATER.
ON TOP OF THAT, WE NOTICE THAT
THERE'S SOMETHING VERY
INTERESTING ABOUT THE
CORRELATION BETWEEN KAISO IN
THIS CLUSTER HERE AND EXPRESSION
OF THIS PROTEIN CALLED LC3.
LC3 IS A VERY INTERESTING
PROTEIN THAT'S INVOLVED IN
SECRETORY PROCESSES INVOLVED IN
AUTOPHAGY, AUTOPHAGY-RELATED
FACTORS, PROCESSES, AND IT'S
ALSO DIRECTLY INVOLVED IN A
NEWLY DEFINED SECRETORY EVENT
REFERRED TO AS LC3-DEPENDENT
EXTRACELLULAR VESICLE LOADING
AND SECRETION, A SECRETORY
PROCESS.
AUTOPHAGY, DOUBLE MEMBRANE
PROCESS, THIS SECRETORY PROCESS,
A SINGLE MEMBRANE PROCESS.
SO WE ASKED WHETHER OR NOT THERE
WAS ANY CORRELATION BETWEEN
LC3 AND SURVIVAL, AND AGAIN, WE
SEE A VERY HIGH CORRELATION
BETWEEN LC3 AND POOR SURVIVAL
AND JUST LIKE KAISO, IT SHOWS A
VERY SIMILAR DISTRIBUTION BY
SUBTYPE WITH A SLIGHT SKEW BY
RACE, A SLIGHTLY HIGHER
EXPRESSION BY RACE.
AS I MENTIONED BEFORE, LOOKING
AT THE EXPRESSION OF LC3 AND
KAISO ALLOWED US TO SEPARATE
TRIPLE NEGATIVE BREAST CANCER
INTO THREE DIFFERENT SURVIVAL
GROUPS.
MOST PARTICULAR IN THIS
AGGRESSIVE BREAST CANCER, THOSE
PATIENTS THAT HAD HIGH LEVELS OF
CYTOPLASMIC KAISO AND LOW LEVELS
OF LC3 HAD MUCH BETTER SURVIVAL.
SO THIS IS WHAT I REFERRED TO
EARLIER AS AN EXAMPLE OF US
LOOKING AT THE PATIENTS AND THEN
SEEING SOMETHING THAT COULD HAVE
GIVE US INSIGHTS INTO MECHANISM
AND FUNCTION.
SO THIS IS A POINT WHERE WE
START TO ASK A LITTLE BIT MORE
QUESTIONS.
WE SHOWED THAT CYTOPLASMIC KAISO
AND NUCLEAR KAISO, AGAIN
DESIGNATED USING ARTIFICIAL
INTELLIGENCE, WERE
DIFFERENTIALLY AND INDEPENDENTLY
INDEPENDENTLYPREDICTIVE OF
OUTCOME.
SO WE TOOK ADVANTAGE OF SOME
INFORMATION WE HAD FROM THE
PATIENT DAY A SET.
WE HAD ABOUT 140 PATIENTS SCORED
ON THESE TISSUE MICRO ARRAYS,
AND WE HAD RNA SEQ DATA.
SO WE USED A METHOD THAT MANY OF
YOU HAVE REFERRED TO THE GENE
SET ENRICHMENT ANALYSIS, A WAY
WE USE CURATED DATABASES WHERE
COLLECTIONS OF GENES ARE CURATED
BASED ON THEIR ROLE IN
BIOLOGICAL FUNCTIONS.
IT'S A WAY THAT WE CAN TAKE A
GENE EXPRESSION DATASET AND ASK
WHETHER OR NOT IT REVEALS A
BIOLOGICAL ACTIVITY ON THE CELLS
THAT ARE ASSAYED BY GENE
EXPRESSION ANALYSIS UNDER
DIFFERENT CONDITIONS.
SO WHAT WE ENDED UP DOING WAS
TAKING OUR PATIENT DATA, OUR 140
PATIENTS, RNA SEQ DATA, AND
STRATIFYING THEM BY HIGH VERSUS
LOW RNA FOR KAISO, HIGH VERSUS
LOCI TOE PLASMIC KAISO, HIGH
VERSUS LOW NUCLEAR KAISO AND
HIGH VERSUS LOW TOTAL NUMBERS.
SO THESE PATIENTS ARE STRIKE
STRATIFIED
IN THESE DIFFERENT WAYS, WE DID
GENE ENRICHMENT ANALYSIS, I WILL
ADMIT THIS WAS A FISHING
EXPEDITION BUT WE LOOKED AT
EVERY GENE EXPRESSION PUBLISHED
AND WE PROFILED IT ACROSS ALL
17,000 GENE SETS.
WE FOUND THAT OF THE GENE SETS
THAT WERE MOST INFORMATIVE OF
THE GENE ONTOLOGY GENE SET WHICH
HAD ABOUT 9,000 GENE SETS IN IT
WAS MOST INFORMATIVE.
WHAT WE DID IS WE ASKED IN TERMS
OF THE ENRICHMENT FOR THESE
DIFFERENT GENE SETS THAT WERE
BIOLOGICAL PATHWAYS, WHICH ONES
WERE AT  ENRICHED IN AT LEAST
TWO OR
MORE -- STRATIFICATION BY
CYTOPLASMIC AND TOTAL.
AND IT TURNS OUT THAT MANY OF
THE GENE SETS THAT WERE ACTUALLY
ENRICHED INCLUDED AUTOPHAGY
TERMS.
IN FACT, IF WE LOOK SPECIFICALLY
AT THE NET ENRICHMENT AND -- P
VALUE IT TURNED OUT WHEN WE
STRATIFIED PATIENTS BY THIS
HISTOLOGICAL BIOMARKER BY
NUCLEAR KAISO, ALMOST NO FOR
TOTAL KAISO, AND JUST ONE OR SO
FOR RNA STRATIFYING PATIENTS BY
RNA.
SO WE WANT TO TAKE THIS ONE STEP
FURTHER.
SO WHAT I'VE SHOWED YOU ALREADY
IS BY LOOKING SIMPLY AT
MORPHOLOGICAL DATA, COMPARING TO
BIOMARKERS FROM PATIENT SAMPLES,
WE SAW RYE LAITION SHIPS FROM
TWO ANTIGENS, USING RNA DATA
FROM THOSE PATIENTS, AND WE WERE
ABLE TO EXTRAPOLATE THAT
WHATEVER WE'RE SEEING SUGGESTING
THAT KAISO COULD BE HAVING SOME
SORT OF ROLE IN AUTOPHAGY, OR
AUTOPHAGY RELATED PROCESSES.
SO WE JUST DID THE STANDARD
EXPERIMENT, WE TOOK A TRIPLE
NEGATIVE CANCER CELL LINE AND WE
DEPLETED THEM OF KAISO AND WE
JUST DID A GENE SET ENRICHMENT
ANALYSIS AFTER DOING
DIFFERENTIAL GENE EXPRESSION AND
WE ENRICHED FOR MULTIPLE
DIFFERENT AUTOPHAGY TERMS.
IF WE LOOKED AT CELLS THAT WERE
DEPLETED OF KAISO, WE FOUND THAT
A MAJOR STEP THAT'S IMPORTANT IN
BOTH THE GENERATION OF VESSELS
THAT ARE IMPORTANT IN AUTOPHAGY
AND THE GENERATION OF VESICLES
THAT ARE IMPORTANT IN SECRETION,
IS IMPAIRED.
THIS IS A PROCESS CALLED
CONJUGATION, LC3 IS CONVERTED TO
A FASTER MOVING -- WE FOUND THE
ACTUAL CONJUGATION STEP WAS
SIGNIFICANTLY DEPLETED IN CELLS
THAT DID NOT HAVE KAISO.
THAT HAD DEPLETED LEVELS OF
KAISO.
WE ALSO JUST, AGAIN, IN A
BEDSIDE TO BENCH APPROACH, WE
JUST ASKED WHETHER THERE WAS
COLOCALIZATION, WE FOUND THAT IN
BOTH AN ER POSITIVE CELL LINE
AND TRILL  TRIPLE NEGATIVE -- IF
WE
LOOKED AT OUR PATIENT SAMPLES,
WE SAW THE SAME THING, A
COLOCALIZATION IN KAISO AND
LC3 DEPENDING ON SUBTYPE, THIS
IS A CO-LOCALIZATION MAP, RED
BEING LC3, GREEN BEING KAISO.
 KIE AND
THERE'S SIGNIFICANT LEVELS OF
KAISO THAT WE CAN QUANTITATE.
NOW, THERE WERE TWO THINGS THAT
WE LEARNED FROM THIS STUDY, WAS
THAT KAISO EXPRESSION WAS
ASSOCIATED WITH A SECRETORY
INVOLVED PROCESS, BOTH OF WHICH
COULD HAVE INFLUENCES ON TUMOR
MICROENVIRONMENT.
WE ALSO LEARNED FROM DOING OUR
GENE EXPRESSION STUDY WITH
PATIENT THAT PATIENTS WHO HAVE
HIGH LEVELS OF CYTOPLASMIC KAISO
ALSO HAD AN IMMUNE SUPPRESSED
SIGNATURE.
THEY ACTUALLY HAD A SIGNATURE
THAT'S OFTEN REFERRED TO AS AN
INTERFERON SICT.
 SIGNATURE.
SO BECAUSE WE HAD ACCESS TO THE
TISSUES WHICH WERE IN THE FORM
OF A TISSUE MICRO ARRAY, WE
STARTED TO ASK VERY BASIC
QUESTIONS ABOUT THE TUMOR
MICROENVIRONMENT, PARTICULARLY
THE IMMUNE MICROENVIRONMENT.
THIS IS A STUDY WHERE WE USE
IMMUNOFLUORESCENCE TO
IMMUNOPHENOTYPE THE TUMOR MY
CORI ENVIRONMENT IN THIS CASE
JUST ON THE TMAs.
THIS IS A SIMPLE ASSAY, WE
LOOKED AT EVERY SINGLE NUCLEI IN
THE CORES, THEY WERE STAINED FOR
TUMOR, THEY WERE STAINED FOR CD8
T-CELLS, 
IN THIS CASE -- AND
STAINED FOR MACROPHAGE, BUT
THEY'RE ALSO STAINED FOR IMMUNE
SUPPRESSIVE MOLECULE PD-1.
SO WHAT I HAVE REPRESENTED HERE
IS ESSENTIALLY A CARTESIAN DIE
GRAND CANYON OF THE
CHARACTERIZATION  CARTESIAN
DIAGRAM.
NOW USING MACHINE LEARNING AND
COMPUTATIONAL METHOD, WE DID
ANALYSIS WITH THIS TYPE OF
TISSUE.
AFTER MAPPING EVERY SINK OLE
NUCLEUS, PHENOTYPING EVERY
SINGLE NUCLEUS, WE WANTED TO ASK
HOW CLOSE THESE CELLS WERE TO
EACH OTHER ON THE CORES, HOW
CLOSE WERE TUMOR INFILTRATING
KILLER CELLS NEAR TUMOR AND IN
WHAT CASE WAS A TUMOR EXPRESSING
AN IMMUNE SUPPRESSIVE
RELATIONSHIP, EXPRESSING
PDL1 EITHER ON THE TUMOR OR ON
LYMPHOCYTES.
IT LOOKS AS IF KAISO, AS WE
FOLLOW IT AS A BIOMARKER IS
HIGHLY ASSOCIATED WITH ANOTHER
BIOMARKER THAT WE'RE USING HERE
WHERE WE'RE LOOKING AT THE
DISTRIBUTION FREQUENCY OF
DIFFERENT GENES.
SO HERE'S A PROFILE WHERE WE'RE
LOOKING AT, THE FREQUENCY OF
PDL1 POSITIVE CD8 CELLS NEAR
TUMOR ON THE X AXIS IS
ESSENTIALLY DISTANCE, PIXELS
CLOSE TO A MICRON.
WHAT WE'VE SHOWN HERE IS THAT IN
PATIENTS WHO HAD HIGHER LEVELS
OF CYTOPLASMIC KAISO HAD A
HIGHER DISTRIBUTION OF THESE --
BETWEEN TUMOR AND IMMUNE CELL.
CD8 CELLS THAT ARE PD-1 POSITIVE
THAT WERE CLOSER TO TUMOR.
SIMILARLY, IF WE LOOKED AT CD68
CELLS THAT WERE P1 POSITIVE,
THEY WERE CLOSER TO TUMOR
DEPENDING ON THE LEVEL OR
EXPRESSION OF CYTOPLASMIC KAISO.
WE SAW A SIMILAR RELATIONSHIP
WHICH WE EXPECTED TO SEE FOR
LC3.
WE DID NOT SEE THAT RELATIONSHIP
FOR NUCLEAR KAISO AND DID NOT
SEE A DIFFERENCE BASED ON RACE
FOR THIS TIME OF COUPLING.
SIMILAR CUMMING, HERE WE'RE
LOOKING AT CD8 CELLS NEAR -- WE
SEE THE SAME RELATIONSHIP.
HIGH EXPRESSION OF CYTOPLASMIC
KAISO BASED ON THIS MORPHOLOGIC
MEASUREMENT IS MORE HIGHLY
ASSOCIATED WITH IMMUNE
SUPPRESSIVE ENVIRONMENT,
CORRELATES WELL WITH LC3, WE DO
NOT SEE THAT FOR NUCLEAR KAISO,
AND IN SOME CASES WE ARE
ACTUALLY SEEING A STRATIFICATION
BASED ON RACE.
SO THE SUMMARY FROM THIS IS THAT
FROM THIS STUDY, WHERE WE'RE
USING A MORPHOLOGICAL MEASURE
USING ARTIFICIAL INTELLIGENCE TO
GET QUANTITATIVE DATA, WE CAN
SEE RELATIONSHIPS THAT COULD
HAVE SIGNIFICANT PREDICTIVE
VALUE IN PREDICTING RESPONSE TO
DIFFERENT TYPES OF THERAPIES.
OKAY.
AND IN THE CONTROL IS SIMPLY NOT
A MEASUREMENT OF WHAT PEOPLE
REFER TO AS TUMOR INFILTRATING
LYMPHOCYTES, TILs.
YOU HEARD DR. ROSENBERG WAS VERY
UNHAPPY WITH US, BUT IN ANY
CASE, WE DON'T SEE THIS, WE
DON'T SEE A CORRELATION WITH
JUST INFILTRATING CD8s OR CD
#s.
CD68s.
WE'RE SEEING IMMUNE SUPPRESSIVE
COUPLING SPECIFICALLY WHEN KAISO
IS IN THE CYTOPLASM.
SOL A NEW WAY OF BIOMARKER
PROFILING THAT ALLOWS US TO
ESSENTIALLY DEFINE WHICH
PATIENTS MAY HAVE AN IMMUNE
SUPPRESSIVE TUMOR MARKER.
WHY THAT MIGHT BE IMPORTANT,
MOST PEOPLE KNOW IMMUNE
CHECKPOINT INHIBITORS ARE MAJOR
PLAYERS IN THERAPY NOW DAYS,
PARTICULARLY IN TRIPLE NEGATIVE
BREAST CANCER.
THESE ARE ANTIBODIES THAT WILL
BIND TO ANTIBODIES LIKE PDL1 AND
BLOCK THEIR IMMUNE SUPPRESSIVE
NATURE.
WHAT WE'RE THINKING NOW IS THAT
KAISO, PARTICULARLY CYTOPLASMIC
OR LC3 COULD BE BOTH A
PROGNOSTIC MARKER OF OVERALL
SURVIVAL BUT ALSO A PREDICTIVE
MARKER OF WHO MIGHT RESPOND TO
IMMUNE CHECKPOINT INHIBITORS.
SO THIS MOLECULAR STORY ENDS
WITH THIS VERY BRIEF MODEL, WHAT
WE THINK MIGHT BE HAPPENING FOR
THIS PROTEIN BASED SIMPLY AND
MOSTLY ON JUST LOOKING AT
PROFILING ANTIGENS IN BREAST
CANCER SAMPLES.
THIS HAS ESSENTIALLY BEEN A
BEDSIDE TO BENCH APPROACH.
WE THINK THAT KAISO IN THE
NUCLEUS HAS ITS BASIC CHROMATIN
BASE TRANSCRIPTION REGULATION,
BUT WE THINK IN THE CYTOPLASM OR
CELLS THAT HAVE HIGH LEVELS OF
CYTOPLASMIC KAISO ARE ASSOCIATED
WITH A MUCH MORE SECRETORY
PHENOTYPE.
I WON'T SHOW THIS DATA, BUT IN
COLLABORATION WITH CLAYTON YATES
AT TUS  TUSKEGEE, IT SOUNDS LIKE
THAT
MIGHT BE THE EFFECT.
WE SEE A VERY DIFFERENT
SECRETORY PATTERN IN TERMS OF
EX-SOME SECRETION, WHEN CELLS
DON'T HAVE KAISO, MOREOVER, THE
VESICLES THEMSELVES ARE
DIFFERENT IN STRUCTURE.
SO IN THE ABSENCE OF KAISO,
THERE'S A DIFFERENT SECRETORY
PATTERN, IN THE ABSENCE OF
KAISO, TOTAL KAISO, WE'RE
ASSUMING MORE IN THE CYTOPLASM,
THERE'S AN ALTERATION IN THE
SECRETORY PATTERN IN THE
EXTRACELLULAR VESICLES IN BREAST
CANCER.
NOW, IN THE FUTURE, WE WANT TO
GO FROM LOOKING AT TMAs, WHICH
IS A VERY MAUL LIKE 1-MILLIMETER
CORE ON THE SLIDES, WE HAVE
PARTNERED WITH ANOTHER GROUP AT
STONY BROOK WHO HAS WORKED OUT A
WAY TO DO IMMUNE STAINING WITH
WITH -- THIS IS A TOTALLY UGLY
PICTURE, BUT YOU CAN USE DEEP
LEARNING TO SORT THIS OUT AND
PARSE OUT THE PROXIMITIES IN AND
THE PHENOTYPES AND WE CAN DO THE
SAME ASSAY, BUT IT'S GOING TO
TAKE DEEP LEARNING TO DO THIS.
WE ARE ALSO MOVING FORWARD WITH
LOOKING AT TOP LOGICAL STUDIES
LOOKING AT ANY ANTIGEN.
WE LOOKED AT PDL1, AND WE CAN
ASK QUESTIONS USING DEEP
LEARNING TO ASK OR LEARN ABOUT
HOW THERE'S DIFFERENCES IN
ACTUAL MORE CELLS VERSUS
CD8 CELLS AND HOW DOES THAT
TOPOLOGY OR THE SPATIAL
RELATIONSHIP BETWEEN THE
INTENSITY DISTRIBUTION CORRELATE
WITH TUMOR, CORRELATE WITH
THERAPY, CORRELATE WITH OUTCOME.
OKAY.
NOW I WANT TO FINISH UP WITH
KIND OF A DISCUSSION BASED ON
SOMETHING I LEARNED DURING A
MANUSCRIPT SUBMISSION.
DURING THE SUBMISSION, I GOT
SCHOOLED BY A REVIEWER WHO
OBJECTED TO THE IDEA THAT I WAS
REFERING TO DIFFERENT RACIAL
GROUPS BY ANCESTRY.
I DON'T KNOW WHO THIS PERSON
WAS, BUT I THINK IT WAS RICK
KITTLES, BUT HE WAS RIGHT.
THAT'S WHY I THINK IT WAS RICK
KITTLES.
HE'S SAYING, RACE IS A SOCIAL
CONSTRUCT.
WE WOULD ARGUE THAT WHILE
ANCESTRY HAS MORE OF A
BIOLOGICAL MEANING TO US AND AS
WE'RE LOOKING AT IT IN A MORE
OF -- THE REVIEWER WON.
BUT WHAT HE'S SAYING IS, IT
DIDN'T MAKE SENSE FOR US TO USE
THE TERM ANCESTRY WHEN WE WERE
ACTUALLY USING IT AS A BINARY
VALUE, WHERE ANCESTRY REALLY IS
A CONTINUOUS VALUE.
AND HE WAS RIGHT.
SO WE WENT BACK TO OUR SAMPLES
WE WITH HAD SOME SEQUENCING
DATA, AND WE ACTUALLY DID GO
BACK AND LOOKED AT ANCESTRAL
MARKERS, THIS WAS DONE IN
COLLABORATION WITH CLAYTON
YATES, AND WE COULD SHOW THAT
THOSE PATIENTS WHO SELF I'D SIDE
OR WHOEVER FILLED OUT THE BOX
IDENTIFIED THEM AS WHITE,
NON-HISPANIC WHITE, THEY'RE
ESSENTIALLY 99% -- .4% EUROPEAN.
THOSE WHO SELF IDENTIFIED OR
SOMEONE CHECKED IN THE BOX FOR
THEM THAT THEY WERE OF AFRICAN
ANCESTRY OR NON-HISPANIC BLACK,
ON AVERAGE, 78%, THE NEED YANK
WAS EVEN LOWER.
SO WE STARTED TO THINK MORE
ABOUT OUR DATA AND THINKING
ABOUT WHAT CLAYTON'S GROUP
FOUND, WHAT WE FOUND AND WHAT
JULIA'S GLEUP FOUND.
JULIA'S GROUP FOUND.
 -- THAT WERE ESSENTIALLY FROM
BARBADOS, WHICH IS MAINLY OF --
AND NIGERIAN ANCESTRY, SO A
HIGHER PERCENTAGE -- A LOWER
PERCENTAGE OF AD MIXTURE.
SO WE WENT BACK AND LOOKED AT
OUR DATA TO SEE IF IT MATCHED
WHAT CLAYTON HAD SEEN AND LO AND
BEHOLD IF WE START TO LOOK AT
THE HAZARD RATIOS BASED ON RACE
OPTIMIZED VALUES, WE FOUND THAT
THERE REALLY WAS A DIFFERENCE IN
THE PREDICTIVE VALUE OF KAISO,
WHETHER IT WAS CYTOPLASMIC AND
IN THE CASE OF NUCLEAR AND TNBC
BASED ON RACE.
SO THAT KIND OF REMINDS ME OF
SOMETHING THAT WE ALL KNOW, WE
ALL THINK ABOUT.
MOST OF YOU KNOW THE STORY.
I WAS FIRST TAUGHT THIS
NARRATIVE BY CHARLES MUTEEM.
MAN ORIGINATED IN AFRICA, THEN
AFTER 230,000 YEARS OF DARWINIAN
SELECTION IN RESPONSE TO
PATHOGEN EXPOSURE SHIFTS IN
NUTRIENT AVAILABILITY, HE
MIGRATED OUT OF AFRICA INTO
EUROPE AND ASIA, AND THEN 20 TO
30,000 LATER, MIGRATED ACROSS
THE BEARING STRAIT AND POPULATED
THE AMERICAS.
THOSE WERE THE THREE MAJOR
POPULATIONS FOR QUITE A WHILE
UNTIL ABOUT 500 YEARS AGO, THIS
GUY COLUMBUS SHOWS UP AND KIND
OF SETS THE WHOLE THING OFF
FOLLOWED BY OTHER MIGRATIONS,
AND YOU HAVE A VERY BROAD ADMIX
POPULATION.
SO IT REALLY HIGHLIGHTS WHAT MY
REVIEWER WHO REMAINS NAMELESS
SAID AND I WANT TO DISCUSS A
LITTLE BIT ABOUT HOW RACE IS A
SOCIAL CONSTRUCT, AND IN A REAL
BROAD AND BASIC WAY.
NOW SOME OF YOU PEOPLE MIGHT
RECOGNIZE THIS PERSON, RAISE
YOUR HAND IF YOU RECOGNIZE THIS
PERSON.
ALSO RAISE YOUR HAND IF YOU'VE
TAKEN YOUR GENETIC ANCESTRY
TEST.
ANYBODY HERE DONE THAT?
OKAY.
I'M GLAD FRANCIS IS SITTING IN
THE FRONT.
MY KIDS HAVE.
I HAVEN'T YET.
WE'LL TALK ABOUT THAT LATER ON.
OKAY?
SO THIS IS RACHEL DOLEZAL.
SHE SOMEWHERE ALONG THE WAY
DECIDED THAT SHE WANTED TO
ESSENTIALLY IDENTIFY MORE WITH
BLACK CULTURE, BLACK POPULATION
BECAUSE PRIOR TO HER MAKING THAT
DECISION, THIS IS WHAT SHE
LOOKED LIKE.
OKAY?
AND LOOK, I HAVE NOTHING AGAINST
HER, DO YOUR THING.
BUT SHE DID -- WHEN THEY FOUND
OUT THAT SHE WASN'T -- SHE HAD
ALMOST NO AFRICAN ANCESTRY, SHE
WAS IN A WORLD OF TROUBLE.
WHAT CAN I SAY, I FEEL FOR THE
SISTER.
BECAUSE IT WASN'T UNTIL SHE
DECIDED TO IDENTIFY WITH BLACK
CULTURE AND THEY FOUND OUT SHE
WAS WHITE THAT SHE REALLY
UNDERSTOOD WHAT BLACK CULTURE
WAS LIKE IN THE UNITED STATES.
NOW, RACE IS A SOCIAL CONSTRUCT.
I DON'T THINK YOU GUYS KNOW WHO
RALPH TAYLOR IS.
RALPH TAYLOR IS A GUY WHO OWNED
A BIG -- A LARGE BUSINESS, A
LARGE COMPANY, AND TOOK A DNA
TEST AND FOUND OUT THAT HE WAS
4% AFRICAN AMERICAN AND 4%
NATIVE AMERICAN AND HE'S BEEN
SUING THE GOVERNMENT EVER SINCE
TO BE QUALIFIED AS FOR SMALL
MINORITY OWNER -- MINORITY OWNED
BUSINESSES.
RACE IS A SOCIAL  AS A SOCIAL
CONSTRUCT.
WE'LL FINISH WITH THIS STORY.
THESE ARE KIDS FROM A REGION IN
THE NORTHERN PART OF NEW  NEW
JERSEY
AND SOUTHERN PART OF NEW YORK,
POPULATED WITH AN ADMIX
POPULATION OF FOLKS WHO ARE A
MIXTURE OF FREE SLAVES, DUTCH
TRAVELERS, DUTCH SETTLERS, AND
NATIVE AMERICANS.
THEY'VE BEEN OFTEN REFERRED TO
AS JACKSON WHITES.
THERE'S A WHOLE MYTHOLOGY ON WHY
THEY WERE NAMED JACKSON WHITES,
AND I'LL TELL YOU ABOUT THAT
LATER ON AT DINNER, MAYBE AFTER
A 15-YEAR-OLD SCOTCH THAT I WILL
PAY FOR.
IN ANY CASE, IN 1943, THURGOOD
MARSHALL CAME TO THE AREA TO
CHALLENGE THE PLESSY VERSUS
FERGUSON SEPARATE BUT EQUAL.
IN THIS STORY, IT TURNED OUT
THAT THE RAMIPO MOUNTAIN
CHILDREN, THE JACKSON WHITES,
WERE BEING SEGREGATED IN THE
TOWN CALLED HILLBURN IN THE
MOUNTAINS.
THERE WERE TWO SCHOOLS, THE
HILLBURN SCHOOL AND THERE WAS
THE SHAW -- THE BROOK SCHOOL.
HILLBROOK SCHOOL WAS THREE
STORIES, HAD A GYM, HAD A
LIBRARY, HAD A PLAYGROUND, AND
WAS HALF FULL.
THE SHAW SCHOOL WERE THE RAMIPO
MOUNTAIN JACKSON WHITES WHERE
THE COLORED FOLK WERE, HAD FOUR
ROOMS, SINGLE FLOOR, NO RUNNING
WATER, NO HEATING.
SO THAT'S WHERE THEY DREW THE
LINE AND THAT'S WHERE THURGOOD
MARSHALL WAS THERE 10 YEARS
BEFORE BROWN VERSUS BOARD OF
EDUCATION.
NOW, I JUST WANT TO PUT THIS
NARRATIVE IN CONTEXT.
THIS IS MY WIFE'S MOTHER.
THIS IS HER COUSIN.
SO THE NARRATIVE I'M EXPLAINING
TO YOU IS THAT THURGOOD MARSHALL
CAME TO THE RAMAPO MOUNTAINS IN
1943 SO THAT MY FUTURE
MOTHER-IN-LAW AND THIS YOUNG
STRAPPING BLUE-EYED BLOND HAIRED
COLORED BOY COULD GO TO THE SAME
SCHOOL, COULD GO TO THE SCHOOL.
SO RACE IS A SOCIAL CONSTRUCT.
FINALLY, I ASKED IF PEOPLE HAD
THEIR GENETIC ANCESTRY DONE, AND
WE GET A LOT OF HANDS RAISED AND
I HAVE TO CONFESS THAT I HAVEN'T
HAD MINE DONE BUT MY WHOLE
FAMILY HAS, AND IT WAS VERY
EXCITING FOR THEM, THEY FOUND
RELATIVES THAT -- ON MY MOTHER'S
SIDE, MY FATHER'S SIDE I DIDN'T
KNOW ABOUT.
IT WAS VERY EXCITING, BUT I
HADN'T TESTED IT.
I HADN'T TAKEN THE TEST.
AND FINALLY, THEY LOOKED AT OUR
ANCESTRY, SO MY WIFE'S SAID SHE
WAS 34% EUROPEAN ANCESTRY.
AND IN MY -- MY KIDS LOOKED AT
THEIRS, AND THEY WERE 27%
EUROPEAN ANCESTRY.
YOU KNOW, I TAKE PRIDE IN THE
FACT THAT MY KIDS CAN DO MATH.
SO YOU KNOW, THIS MAKES
INTERESTING CONVERSATION AT THE
DINNER TABLE.
THEY'RE ALL LOOKING AT ME, THEY
SAID WHO ELSE ARE WE GOING TO
LOOK AT?
SO I'LL BE TAKING THE GENETIC
ANCESTRY TEST AND WHEN I COME
BACK, I'LL LET YOU ALL KNOW
ABOUT IT.
I DOUBT IT'S GOING TO BE AS
COLORFUL AS LEZO'S GENOTYPE BUT
WE'LL TALK ABOUT IT.
NOW, I WANT TO SAY A LAST THING
ABOUT MULTIDISCIPLINARY
COLLABORATIONS.
WHAT WE'RE DOING IN OUR LAB,
WE'RE LOOKING AT DATA
SCIENTISTS, WE'RE LOOKING AT
WORKING WITH ONCOLOGISTS,
DIFFERENT STATISTICIANS, AND TWO
OF THE PEOPLE IN OUR GROUP ARE
PARTICLE PHYSICISTS.
AND A MAJOR THING WE HAVE TO
LEARN IN DOING THIS IS HOW TO
COMMUNICATE AND HOW TO RESPECT
EACH OTHER'S KNOWLEDGE IN WHAT
WE KNOW.
NOW, MY APPROACH IS VERY SIMPLE.
WE GET IN THE ROOM AND THE FIRST
THING I SAY IS, YOU KNOW,
THERE'S NOTHING ANYBODY IN THIS
ROOM IS GOING TO SAY TODAY
THAT'S -- THE ACADEMIC
ENTERPRISE IS ROBUST AND
RESILIENT.
THERE'S NOTHING YOU'RE GOING TO
SAY OR ASK OR PROPOSE THAT'S
GOING TO BRAKE IT.
 BREAK IT.
SO LEAVE YOUR EGOS AT THE DOOR,
ASK ANY QUESTION YOU WANT TO
ASK, POSE ANY QUESTION YOU WANT
TO ASK, AND LET'S DO A PROJECT
TOGETHER.
IN MOST CASES, YOU HAVE TO BE
THE REFEREE, YOU HAVE TO BE THE
CHEERLEADER AND YOU HAVE TO BE
THE COACH.
YOU HAVE TO DISRUPT ARGUMENTS.
COLLABORATOR A SAYS, I DON'T
THINK COLLABORATOR B KNOWS MUCH
ABOUT BREAST CANCER.
AND MY RESPONSE IS, THAT'S OKAY,
COLLABORATOR B IS NOT HERE FOR
BREAST CANCER.
YOU ARE.
AND WE'RE HAPPY TO HAVE YOU.
SO, THERE HAVE BEEN SOME DAYS,
THOUGH, WHEN WE'RE TALKING WITH
OWRL DATA 
OUR DATA SCIENTISTS, AND WE HAVE
THIS REALLY BRIGHT KID IN OUR
GROUP, HE DOES A LOT OF DATA
ANALYSIS, DIGITAL ANALYSIS.
HIS NAME IS ANDY, JUST
BRILLIANT, A PARTICLE PHYSICIST.
THERE WERE DAYS WHERE HE WOULD
GIVE A TALK, AND I'D SAY, ANDY,
THANKS, THAT WAS GREAT, BUT
AFTER YOU SAID "THERE IS," I
DIDN'T UNDERSTAND ANYTHING ELSE
YOU HAD TO SAY.
THAT'S ESSENTIALLY WHAT WORKING
IN A MULTIDISCIPLINARY GROUP IS,
BUT IT'S REALLY IMPORTANT, LEAVE
YOUR EGOS AT THE DOOR, AND TEACH
EACH OTHER, AND REALIZE THE GOAL
IS TO TEACH AND LEARN FROM EACH
OTHER SO YOU CAN REALIZE
SOMETHING NEW.
SO I WILL END BY SAYING MY
EXPERIENCE, WE START OUT
LEARNING TO COMMUNICATE.
AND WE BEGIN AT THIS STAGE.
AND WE END AT THIS STATE.
OKAY?
AND SO I WILL END BY THANKING
THE SEA OF DIFFERENT
COLLABORATORS WE'VE HAD.
I WANT TO MENTION THE SUPPORT
FROM THE INTRAMURAL RESEARCH
PROGRAM OF CCR, ALSO OF NIMHD
AND PRIVATE FUNDING FROM THE
ULTIVUE FOUNDATION.
I'D LIKE TO END BY TELLING
ANOTHER SMALL STORY.
ABOUT 27 YEARS AGO, I WAS A
STAFF SCIENTIST IN BUILDING 10.
AND TRYING TO SORT MY WAY&
THROUGH BECOMING AN INDEPENDENT
INVESTIGATOR.
AND I GOT AN EMAIL THAT SUMMONED
ME TO A ROOM IN BUILDING 10.
AND I WALKED IN THAT ROOM AND
THERE WAS EDDIE REED, FIRST
AFRICAN AMERICAN BRANCH CHIEF IN
NCI.
THERE WAS BILL COLEMAN, ONE OF
THE FIRST TENURED AFRICAN
AMERICANS AT NIH, SOON TO BECOME
THE FIRST SCIENTIFIC DIRECTOR AT
NIH.
AND KEN OLDEN, FIRST INSTITUTE
DIRECTOR AT NIH.
AND THEY SAT DOWN AND THEY JUST
TALKED TO ME, YOU KNOW?
AND I WAS JUST IN AWE.
I WENT HOME AND I TOLD MY WIFE,
I THINK I JUST MET THE THREE
KINGS.
BUT WHAT I WANT TO END IN SAYING
IS WHAT THEY GAVE TO ME WAS A
COMPASS.
THEY GAVE ME A REAL SENSE OF
TRUE NORTH, AND JUST AS
IMPORTANTLY, THEY GAVE ME A
SENSE THAT I WAS NOT ALONE.
SO I WILL END BY SAYING THAT,
YOU KNOW, I STAND BEFORE YOU
HERE TODAY AS A PART OF THEIR
LEGACY.
THANK YOU VERY MUCH.
I'LL TAKE QUESTIONS.
[APPLAUSE]
>> GLAD YOU TOLD THAT STORY AT
THE END.
THAT WAS INDEED INSPIRATIONAL,
AND MY GOSH, THE SWEEP OF
SCIENCE WAS PRETTY PHENOMENAL.
WE HAVE TIME FOR SOME QUESTIONS.
THERE ARE MICROPHONES IN THE
AISLES.
LET'S START RIGHT OVER HERE.
>> THANK YOU FOR THAT TALK.
I HAVE A QUELL WHERE YOU TALK
ABOUT AN IMMUNOSUPPRESSIVE
ENVIRONMENT.
THE T-CELLS, I THINK THERE MAY
HAVE BEEN A TYPO, THEY'RE PD-1
POSITIVE.
IT SAID PDL1 BSH
>> NO, PDL1.
SO WE'RE SAYING THAT THIS HAS
BEEN OBSERVED IN SEVERAL CASES
OF BREAST CANCER, SO PDL1 ON THE
TUMOR --
>> RIGHT, SO IN MOST CASES, THAT
INDUCTION REQUIRES TCR
ENGAGEMENT ON THE T-CELLS AND
THE PDL1 ON THE TUMORS,
TYPICALLY GAMMA INTERFERON
INDUCED SUGGESTING RESPONSE FROM
THE CELLS.
SO IT SAYS THERE'S AN ACTIVE
IMMUNE RESPONSE IN THE
ENVIRONMENT, SO IT'S A LITTLE
PROBLEMATIC TO CALL IT AN
IMMUNOSUPPRESSIVE ENVIRONMENT
WHEN THERE OBVIOUSLY IS EVIDENCE
FOR AN ACTIVE IMMUNE RESPONSE,
BUT NOT SUFFICIENT TO DEAL WITH
THE TUMOR BUT SETTING IT UP FOR
THE TREATMENT YOU'RE TALKING
ABOUT TO BE EFFECTIVE.
SO I'D BE INTERESTED IN WHETHER
THAT IS A REASONABLE WAY TO
CHARACTERIZE WHAT YOU SEE.
>> TO SAY MORE THAN -- TO NOT
ALREADY SAY IT'S AN
IMMUNOSUPPRESSANT ENVIRONMENT,
DEPENDING ON HOW FAR ALONG THE
WAY IT IS --
úENVIRONMENT BUT NOT SUFFICIENT
TO CLEAR THE TUMOR, WHICH IS A
LITTLE BIT DIFFERENT.
>> MM-HMM.
I WOULD NOT ARGUE WITH THAT, BUT
I WOULD ALSO SAY THAT, YOU KNOW,
WE'VE DONE A COROLLARY STUDY AND
WE HAVEN'T FINISHED THE FIRST
HALF OF IT BUT WE ALSO LOOKED AT
PDL1 AND WHETHER OR NOT THE
CELLS WERE MEMORY CELLS AND WE
SEE THAT STILL HOLDS UP IF WE
QUANTIFY THEM AS BEING MEMORY
SELLS KRELS AND WE'RE LOOKING
LOOKING AT PD-1 EXPRESSION, WE
SEE MORE QUOTE-UNQUOTE IMMUNE
EXHAUST TUMOR MICROENVIRONMENT
THAT CORRELATES WITH THE LEVELS
OF ANTIGEN.
>> THE OTHER PART OF IT IS THAT
YOU DREW THAT CONCLUSION BASED
ON SPATIAL COORDINATION, NOT
JUST PRESENCE IN THE TUMOR, AND
SO --
>> PRESENCE IN THE TUMOR DID NOT
SCORE.
SO WE WERE VERY --
>> RIGHT, SO IF THOSE T-CELLS
WERE NOT CONTACTING EITHER LOCAL
PRESENTING CELLS OR ANTIGEN ON
THE TUMOR THEMSELVES, IT WOULD
BE UNLIKELY YOU WOULD SEE THAT
PRECISE CORRELATION WITH THAT
SUBSET OF THE T-CELL, SO IT GOES
BACK TO THE ISSUE THAT THERE'S
PROBABLY ONGOING ANTIAGAIN
ENGAGEMENT UNDER THOSE
CONDITIONS.
>> I WOULD NOT ARGUE THERE ISN'T
ANTIGEN ENGAGEMENT.
OUR MEASURE IS A MEASURE OF THE
ACTUAL PROXIMITY OF CD8 CELLS
THAT ARE PD-1 POSITIVE TOWARD
TUMOR, AND WE ARE LOOKING AT A
SIMILAR ENGAGEMENT WHERE WE'RE
LOOKING AT CD8 CELLS REGARDLESS
OF THEIR PD-1 OR PDL1 STATUS AND
PDL1 POSITIVE TUMOR.
SO OUR CONCLUSION AT THIS POINT
IS BASED ON THE PREDOMINENCE OF
THE PROXIMITY OF IMMUNE CELLS
REGARDLESS OF THEIR STATUS WITH
PDL1 POSITIVE TUMOR.
AND IF WE START TAKING A LOOK AT
THE LITERATURE, THERE'S MORE
DATA SHOWING THAT PD-1 POSITIVE
STATUS, REGARDLESS OF OTHER
MARKERS IN TUMORS IS HIGHLY
CORRELATED WITH MORE AGGRESSIVE
DISEASE.
>> THANK YOU.
>> KEVIN, LET ME ASK BECAUSE IN
BOTH OF THE CASES OF THE
PROTEINS YOU STUDIED IN DETAIL,
IT SEEMS AS IF THE PARTITIONING
BETWEEN THE NUCLEUS AND THE
CYTOPLASM WAS PRETTY IMPORTANT
IN CON QENSES PARTICULARLY IN
THE ROLE OF CANCER SURVIVAL.
ONE WOULD GUESS THAT'S NOT JUST
SORT OF A RANDOM DIFFUSION, THAT
THERE'S ACTUALLY AN ACTIVE
PROCESS THAT'S INVOLVED THERE IN
TERMS OF HOW THAT PARTITIONING
HAPPENS.
MAYBE THERE'S SOMETHING THERE IN
TERMS OF A UNIFYING CONNECTION
BETWEEN NOT JUST THE TWO
PROTEINS YOU STUDIED BUT LOTS OF
OTHERS AS WELL.
WHAT DO WE KNOW ABOUT THAT IN
TERMS OF THE ROLE OF THAT KIND
OF PARTITIONING PROCESS IN
CANCER OVERALL?
>> SO THERE ARE MULTIPLE PARTS
TO THIS.
NOW, WE WERE KIND OF SURPRISED
BY THE FACT THAT WE COULD SEE
THIS DIFFERENCE IN THE
PARTITIONING.
AND IN A COUPLE EXPERIMENTS, WE
JUST ESSENTIALLY COMPARED THE
DISTRIBUTION OF NUCLEAR
CYTOPLASMIC PROTEINS TO SEE IF
WE COULD SEE A SIMILAR
DISTRIBUTION.
IN THE CASE OF KAISO, THE SITE
OF DISTRIBUTION IN THE CYTOPLASM
VERSUS THE NUCLEUS US WERE VERY
DIFFERENT.
THIS WAS IN COMPARISON TO
SOMETHING LIKE A MOLECULE THAT'S
MORE PASSIVELY TRANS LOCATED TO
THE NUCLEUS LIKE -- OR ANTIGEN
RECEPTOR WHICH SHOWED THE
SIMILAR CURVE.
NOW WHAT'S IMPORTANT TO CONSIDER
IS THAT THERE'S RECENT STUDIES
USING A METHOD CALLED APAC SEQ.
THIS IS WHERE CELLS ARE ACTUALLY
LABELED IN DIFFERENT
COMPARTMENTS, A RESIDENT PROTEIN
THAT HAS A FUSION WITH A
PEROXIDASE ON IT.
THAT PEROXIDASE CAN ACTUALLY, IN
THE PRESENCE OF BIOTIN, ACTIN
LATE WHATEVER IS NEARBY.
WE'RE FINDING THAT THE LOCATION
OF A GENE CAN BE DETERMINED BY A
SIGNATURE ON THE RNA WHICH
DICTATES WHERE IT IS HELD AND
WHERE IT BEGINS TO BE
TRANSLATED.
SO A NUCLEAR PROTEIN IS MORE
LIKELY TO BE TRANSLATED AT THE
NUCLEAR CORE.
AN ENDOPLASMIC RETICULUM IS
LIKELY TO BE TRANSLATED ON TOP
OF THE -- SO THERE'S A WHOLE --
WHERE ARE THOSE ADDRESSES ON THE
RNA.
SO ALL THE DIFFERENT TYPES THAT
WE SEE FOR DIFFERENTLY GENES,
THOSE MAY ACTUALLY ENCODE
ADDRESSES WHERE THE RNA MAY
RESIDE WHERE IT WOULD BE
SPECIFICALLY TRANSLATED --
SUBCELLULAR DISTRIBUTION.
SO WE REALLY DO THINK THERE'S A
MECHANISM ASSOCIATED WITH THAT.
>> IS THERE ANY RELATIONSHIP OF
THE FINDINGS BETWEEN THE PRIMARY
METASTASIS IN TERMS OF THE
MARKERS YOU'RE SPEAKING OF, IN
OTHER WORDS, OR A SENTINEL LYMPH
NODE MARKER THAT PEOPLE GET --
WHICH PEOPLE GET BEFORE A
MASTECTOMY IS PERFORMED?
>> I DIDN'T GET YOUR -- YOU'RE
ASKING ME IS THERE A MARKER --
>> THE MARKERS THAT YOU'RE
TALKING ABOUT, ARE THEY GOING TO
DIFFER BETWEEN THE PRIMARY SITE,
A METASTATIC SITE OR WITHIN THE
SENTINEL LYMPH NODES?
NOW DAYS WE DO SENTINEL LYMPH
NODES BEFORE THERE'S A MA STEK
TOE ME, THEY TAKE THE SENTINEL
LYMPH NODE AND SAY, IS THERE
CANCER IN THERE?
NO.
DON'T DO IT.
IS THERE?
YEAH, MAKE A DECISION.
>> HAVE WE LOOKED AT THAT?
NO.
THESE TWO GENES ARE A SET OF
BIOMARKERS THAT WERE  WE'RE
WORKING ON
NOW IN SETTINGS OF NEW ADJUVANT
THERAPY.
SO THESE NEW ADJUVANT THERAPY IS
WHEN YOU DELAY THE SURGERY AND
YOU GIVE THE PATIENT DIFFERENT
TYPES OF TREATMENT, WHERE IT
COULD BE CHEMOTHERAPY OR
CHECKPOINT INHIBITOR THERAPY OR
ENDOCRINE THERAPY.
WHAT WE'RE FINDING IS THAT WE'RE
NOT DONE, WE'RE JUST BEGINNING A
STUDY NOW, WE'RE FINDING THAT IN
THE CASE OF CYTOPLASMIC KAISO,
NOT NUCLEAR KAISO, WE WERE
SEEING A TENDENCY TO PREDICT
THOSE PATIENTS THAT MAY RESPOND
TO CHEMOTHERAPY, SO THOSE
PATIENTS THAT WILL RESULT --
WHOSE TREATMENT WILL RESULT IN A
PATHOLOGICAL COMPLETE RESONS,
WE'RE LOOKING AT WAYS THAT WE
MAY BE ABLE TO PREDICT THAT
USING A BAY OWE MARKER.
ON THE OTHER SIDE,  BIOMARKER.
ON THE OTHER SIDE, WE'RE ALSO
EUTSING DEEP LEARNING AND SO FAR
USING DEEP LEARNING, 70% OF THE
TIME WE CAN PREDICT 70% OF THE
TIME WHETHER A TUMOR WILL
RESPOND -- WILL HAVE A PCR.
THIS IS ONLY IN A VERY STRICT
SUBSET, BUT WE'RE PREDICTING
THOSE PATIENTS THAT WILL RESPOND
TO NEOADJUVANT TREATMENT IN THE
SETTING.
BUT AS FAR AS YOUR QUESTION HAVE
WE LOOKED AT METASTATIC TUMOR?
NO.
>> THANK YOU.
>> I THINK WE PROBABLY OUGHT TO
BREAK, BUT THERE WILL BE A
RECEPTION IN THE MEDICAL LIBRARY
IMMEDIATELY WITH REFRESHMENTS
AND AN OPPORTUNITY TO TALK
FURTHER TO DR. GARDNER, WHO WE
SHOULD NOW THANK AGAIN FOR A
WONDERFUL PRESENTATION.
