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>> GOOD AFTERNOON.
IT'S THAT WEEK WHERE THE TRAFFIC
GETS MUCH WORSE IN BETHESDA AND
ITS SURROUNDING AREAS.
IT'S THE WEEK WHERE KIDS GO BACK
TO SCHOOL, SOMETIMES SMILING AND
SOMETIMES COMPLAINING AND
SOMETIMES BOTH.
IT'S THE WEEK WHERE THE FIRST
NFL FOOTBALL GAME OCCURS THIS
EVENING.
I WON'T EVEN TALK ABOUT
POLITICS.
AND IT'S ALSO THE WEEK WHERE WE
KICK OFF THE WEDNESDAY AFTERNOON
LECTURE SERIES.
AND IT IS WONDERFUL TO SEE YOU
ALL HERE AND TO WELCOME YOU AS
WELL AS THOSE WHO ARE WATCHING
BY VIDEOCAST, PROBABLY IN GREAT
NUMBERS.
THAT TENDS TO BE THE CASE.
AND I HOPE YOU HAVE SEEN THE
LINE UP OF WALS LECTURES
FOR THIS ACADEMIC YEAR BECAUSE
IT'S TRULY STELLAR.
AND I WOULD ENCOURAGE YOU ALL
WHO HAVEN'T DONE SO, TO MARK
YOUR CALENDARS FOR 3:00 ON
WEDNESDAY AFTERNOONS TO TRY TO
PROTECT THAT TIME SO IT IS GOING
TO BE AN AMAZING PRACTICE RAID
OF REMARKABLE SCIENTIFIC LTD.ERS
COVERING A WIDE VIRALLY OF
TOPICS OF INTEREST TO A LOT OF
US.
A LOT OF EFFORT GOES INTO
IDENTIFYING THE SPEAKERS FOR
THIS SERIES WITH LOTS OF INPUT
FROM ALL THE INSTITUTE AND WE
ARE QUITE SUCCESSFUL IN LINING
UP THE PEOPLE WE MET WANT TO
HAVE COME AND SPEAK BECAUSE THIS
IS SEEN AS A VERY PRESTIGIOUS
PLACE TO SPEAK ABOUT YOUR
SCIENCE.
I WOULD ENCOURAGE EVERYONE TO
TRY TO BE SURE TO TAKE ADVANTAGE
OF THAT DURING THE COMING
MONTHS.
YOU WILL LEARN A LOT AND YOU
WILL GO AWAY ENRICHED AND AND
INSPIRED BY THE NATURE OF THE
TALKS THAT YOU HEAR ABOUT
CUTTING-EDGE SEARCH AND
BIOMEDICINE.
TODAY'S KICKOFF IS A GREAT
EXAMPLE OF THAT AND WE ARE
DELIGHTED TO HAVE AS OUR SPEAKER
TODAY, DR. A GARGARHE IS AN MD
AND Ph.D. -- LEVI GARRAWAY AND
HAD MOST OF HIS PROFESSIONAL
CAREER - I WOULD SAY JUST ABOUT
ALL OF IT, IN THE CITY OF
BOSTON.
HAVING RECEIVED HIS
UNDERGRADUATE DEGREE AT HARVARD,
HIS MEDICAL DEGREE AND HIS
Ph.D. FROM HARVARD, HE
FOLLOWED ON BEING A RESIDENT OF
INTERNAL MEDICINE WITH THE MASS
GENERAL A KEY RESIDENT AT MGH.
HE FOLLOWED THAT IN THE CLINICAL
FELLOWSHIPS IN MEDICAL ONCOLOGY
AT DANA FASCIAER AND BRIGHAM AND
WOMEN'S AND NOW AN ASSOCIATE
PROFESSOR AT HARVARD MEDICAL
SCHOOL AND IN THE DEPARTMENT OF
MEDICAL ONCOLOGY AT THE
DANA-FARBER CANCER INSTITUTE, AS
WELL AS SERVING AS ASSOCIATE
POSITION AT BRIGHAM AND WOMEN'S
AND SENIOR ASSOCIATE MEMBER AT
THE BOROUGH INSTITUTE KEEPING
HIMSELF CONNECTED WITH ALL THESE
AMAZING INSTITUTIONS UP THERE IN
THE CITY OF BOSTON.
HE HAS RECEIVED A NUMBER OF
IMPORTANT HONORS, I'LL MENTION
ONE BECAUSE IT'S SORT OF A NICE
NINETY-FIVE CONNECTION.
HE WAS WAS ONE OF ONE -- NIH
CONNECTION.
NEW INNOVATOR'S AWARD.
AN AWARD SPECIFICALLY DESIGNED
FOR INDIVIDUALS WOAT THAT TIME
HAD NOT PREVIOUSLY SERVED AS A
PI ON AN NIH GRAND AND HAD A
PARTICULARLY INNOVATIVE CREATIVE
APPROACH A PROBLEM THAT WAS
CONSIDERED GROUNDBREAKING AND TO
GET ONE OF THOSE WAS TO BE
EXTREMELY PELTIVE PROCESS.
SO LEVI MUST HAVE WRITTEN A
***-UP PROPOSAL TO ACHIEVE
THIS.
IT WAS ON DEFINING MELANOMA
THERAPEUTIC AVENUES WITH
FUNCTIONAL GENOMICS.
ALSO A MEMBER OF THE ASCI AND
HIS RESEARCH, AS YOU WILL HEAR,
HAS BEEN ON LEADING EDGE OF
PRECISION MEDICINE FOR CANCER.
AND SPECIFICALLY, IN THE TALK HE
IS ABOUT TO DISCUSS TODAY, GOING
BEYOND THAT FIRST LEVEL OF
IDENTIFYING WHAT KIND OF
ACTIONABLE MUTATIONS MIGHT OCCUR
IN A PARTICULAR CANCER AND ALSO
IDENTIFYING WHICH CANCERS ARE
GOING TO BE RESPONSIVE AND WHICH
ARE NOT TO TARGET THE CANCER
THERAPEUTICS.
HE HAS MADE MANY CONTRIBUTIONS
TO THAT FIELD AND PUBLISHED MORE
PAPERS THAN I CAN READ OFF TO
YOU.
JUST IN THE LAST YEAR OR TWO.
AND IT IS A GREAT PLEASURE AND
PRIVILEGE TO HAVE HIM AS OUR
KICKOFF SPEAKER AND I WOULD ASK
YOU TO GIVE A WARM WELCOME TO
DR. LEVI GARRAWAY.
[ APPLAUSE ]
>> THANK YOU DR. COLLINS FOR
THAT WONDERFUL INTRODUCTION.
MY NIH NEW INNOVATIVE AWARD IS
JUST ENDING AND I'M ALREADY
MISSING IT.
THAT'S WHAT GRANT WRITING IS ALL
ABOUT.
SO I'M VERY PLEASED TO BE HERE
AND GIVE THIS LECTURE AND HAVE A
CHANCE TO DESCRIBE TO YOU AT
LEAST FROM MY PERSPECTIVE, AND
THE PERSPECTIVE OF A LOT OF
INVESTIGATORS IN THE FIELD OF
CANCER, THE EXCITEMENT AND THE
PROMISE OF THE EMERGING ERA OF
GENOMICS-DRIVEN CANCER MEDICINE.
AND BY GENOMICS-DRIVEN CANCER
MEDICINE, ONE CAN THINK OF THAT
AS A SUB SET OF PRECISION
MEDICINE BUT IN THE FIRST
INSTANCE OF PRECISION MEDICINE
WILL BE USING GENETIC DNA-BASED
ALTERATIONS AND EXPLORING THE
EXTENT TO IMPROVE THE CARE OF
CANCER PATIENTS AND THE OTHER
POINT I THINK IS THAT IN MOVING
INTO THIS ERA, IT'S REALLY ABOUT
TESTING A HYPOTHESES THAT HAS
BUDGET BREWING REALLY FOR
DECADES AND THAT HYPOTHESES IS
SHOWN ON THIS SLIDE WHICH IS
THAT THE USE OF CANCER GENOMIC
INFORMATION TO GUIDE TREATMENT
CHOICE MAY OFFER A CATEGORICAL
MEANS TO IMPROVE THE CARE OF
CANCER PATIENTS.
THAT SUGGESTS THAT MANY, IF NOT
MOST PATIENTS WITH CANCER, WOULD
BENEFIT FROM SOME TYPE OF
SYSTEMATIC GENOMIC PROFILE AND
THE USE OF THAT RESULT TO GUIDE
TREATMENT CHOICES.
AND OF COURSE THE RATIONAL FOR
TESTING THIS HYPOTHESES IS
ROOTED IN SEVERAL KEY
OBSERVATION THAT IS HAVE BEEN
PRESENT, MANY OF WHICH HAVE BEEN
PRESENT FOR A LONG TIME BUT
OTHERS ARE MORE RECENTLY
RELEVANT.
THE FIRST IS THAT MOLECULAR
PATHWAYS INVOLVED IN TUMOR
SURVIVAL AND PROGRESSION ARE
ENACTED BY GENETIC ALTERATIONS.
WE HAVE KNOWN THIS FOR A LONG
TIME.
THE CANCER GENOME ATLAS ARE
REINFORCING THIS EVERY DAY BUT
THE SECOND AND THIRD POINTS ARE
RECENT LEHMANN FEST.
ANTICANCER AGENTS TARGETING MANY
PATHWAYS ENTERED CLINICAL
TRIALS.
THIS AT THE SCALE AND SCOPE IT
IS NOW TRUE HAS BEEN THE CASE
FOR THE PAST TWO OR THREE YEARS.
FOR THE FIRST TIME IN HISTORY,
WE CAN SAY THAT THE MAJOR
CLINICAL OR THE MAJOR SIGNALING
PATH WAYS WE HAVE KNOWN ABOUT,
MAP KINASE, MANY RECEPTOR
TYROSINE KINASES AND APOPTOSE
AND METABOLISM ARE BEING
TARGETED BY MULTIPLE DRUGS.
THAT'S A CRITICAL INGREDIENT FOR
TESTING THIS HIGH POT ASSIST.
THE FINAL POINT IS THE GENOMICS
TECHNOLOGIES HAVE GROWN TO THE
POINT WHERE THEY ENABLE
ROBUST -- ROBUST TUMOR PROFILE
THE IN THE CLINICAL ARENA.
WE HAVE KNOWN TAT CANCER GENOME
IS IN FROM FOR QUITE SOMETIME
NOW WE HAVE A REPERTOIRE OF
COMPONENTS IN PLACE TO ALLOW US
TO TEST THE GUIDING HYPOTHESES
OF THE CANCER GENOME ERA FROM A
CLINICAL PERSPECTIVE.
AND THE TESTING OF THAT ALSO
INSPIRES A FRAMEWORK, WHICH
ADMITTEDLY IN MOST CANCER
CENTRES, IS STILL LARGELY
ASPIRATIONAL BUT HAS SOME
DEFINITION TO IT IN TERMS OF
WHAT PROCESS, WHAT
INFRASTRUCTURE IS NEEDED TO PUSH
THIS HYPOTHESES.
AND IT BEGINS OF COURSE, IN A
PATIENT-CENTERED FASHION, THE
NOTION THAT WE ENCOUNTER
PATIENTS EITHER IN A FOCUSED WAY
PRIORITIZING PARTICULAR
CHARACTERISTICS OF THE PATIENTS
OR IN SOME CASES PERHAPS IN SOME
CANCER CENTRES IN
ENTERPRISE-WIDE WAY BUT
ULTIMATELY WE HOPE THAT WE WOULD
USE TISSUE IDEALLY FRESH BIOPSY
MATERIAL AND GENERATE PROFILING
USING EITHER EXISTING OR
INCREASINGLY EMERGING
TECHNOLOGIES THAT WILL THEN
GENERATE DATA THAT WE NOW APPLY
NEW ALGORITHMS AND FLAPS SOME
CASES A CORLAT OF LAB TESTING TO
INTERPRET THE DATA AND WITH
THAT, WE WILL BE EQUIPPED TO
MAKE MANAGEMENT DECISIONS.
AND THE INPUT INTO THE DECISION
MAY COME FROM REVIEW OF THE DATA
BY A COMMITTEE BY HAVING
FRAMEWORKS IN PLACE,
PATHWAY-LIKE FRAMEWORKS,
CLINICAL PATHWAY-LIKE FRAMEWORKS
TO GUIDE DECISION MAKING AND
ULTIMATELY IN THE NEAR TERM
BEING APPLIED IN
HYPOTHESES-DRIVEN PHASE I TRIALS
OR OTHER MECHANISM-BASED
CLINICAL STUDIES.
AND THEN WITH THAT DECISION, WE
WILL THEN LOOK TO SEE WHETHER OR
NOT ALL OF THIS INPUT INCREASED
THE PREVALENCE OF CLINICAL
RESPONSES AND THERE ARE A
VARIETY OF WAYS TO DO.
THAT THE OTHER HOPE WOULD BE
THAT OFTEN WE CAN GAIN ANOTHER
BIOPSY AT THIS POINT SO WE CAN
UNDERSTAND WHETHER OR NOT OUR
CLINICAL EXPERIMENT WAS
ACCOMPLISHED THERAPEUTICALLY.
DID WE INHIBIT THE TARGET THE
WAY WE HOPED?
AND THEN FINALLY, IF WE SEE
RESPONSES OR WHETHER WE DO OR
DON'T, WE NEED TO UNDERSTAND
MECHANISMS OF DRUG RESISTENCE
BECAUSE CERTAINLY PARTICULARLY
IF THESE ARE SINGLE AGENT
STUDIES, WE RECOGNIZE AND EVEN
IF WE ARE FORTUNATE TO GET
RESPONSES, THESE ARE SHORT-LIVED
IN ADVANCED CANCER.
SO WE GET ANOTHER BIOPSY AT THE
POINT OF RELAPSE COULD BE
CRUCIAL AND DISCERNING FOR US
MECHANISM RESISTANCE THEREFORE
CAN INFORM A SALVAGE THERAPY OR
PERHAPS A NOVEL THERAPEUTIC
COMBINATION THAT CAN
SUBSEQUENTLY BE TESTED AT THE
BEGINNING OF THIS PROCESS.
NOW I THINK IT'S NAIVE TO ASSUME
THAT EVERY CANCER CENTER COULD
PUT IN EVERY COMPONENT OF THIS
ENGINE BUT YET IT'S A NICE
ARK-TYPE FOR THINKING ABOUT THE
TYPES OF ACTIVITIES AND
PROCESSES AND TECHNOLOGIES AND
ALGORITHMS THAT NEED TO BE
PURSUED IN PARALLEL TO BRING
THIS NOTION OF PRECISION
MEDICINE FORWARD.
SO CLEARLY AT THE WILL BE
OCCUPYING US GREATLY FOR THE
NEXT DECADE OR MORE.
SO FOR THIS TALK I'D LIKE TO GET
A RELATIVELY HIGH LEVEL TOUCH ON
ASPECTS THAT OUR LAB HAS BEEN
PURSUING THAT REALLY GET TO
THREE UNDERLYING ACTIVITIES THAT
CAN BE INFORMED BY VARIOUS
COMPONENTS OF THIS PROCESS.
THE FIRST OF WHICH SORT OF AT
THE FRONT END WHERE ONE IS
GENERATING AND INTERPRETING
DATA, SPEAKS TO THE NEED TO
UNDERSTAND SALIENT DRIVER
MUTATIONS, PARTICULARLY THOSE
THAT COULD BE ACTIONABLE USING
THERAPEUTIC ARMAMENTARIUM.
I'LL GIVE YOU A VIGNETTE THERE.
THE SECOND IS THE CLINICAL
TESTING, HOW ARE WE GOING TO
CARRY OUT CLINICAL TESTS OF THE
PRECISION MEDICINE HYPOTHESES?
AND THE THIRD, LEVERAGING
INFORMATION AT THE BACK END BOTH
TISSUE-BASED STUDIES AND
COORDINATED SYSTEMATIC
EXPERIMENTAL STUDIES TO
UNDERSTAND MECHANISM RESISTENCE
AND INCORPORATE THE KNOWLEDGE OF
BOTH RESISTENCE AND THE SPECTRUM
OF DEPENDENCY INTO THE FUTURE
DEVELOPMENT OF NOVEL
COMBINATIONS, THE GEL OF WHICH
WOULD BE DURABLE CONTROL OF
SPECIFIC CANCERS THAT ARE DRIVEN
BY CARDINAL GENETIC ALTERATIONS.
SO TO BEGIN, I'D LIKE TO TELL
YOU A STORY OF HOW MOVING FROM
THE CATALOG OF ALTERATIONS THAT
ARE BEING GENERATED BY EFFORTS
SUCH AS TCGA TO, KNOWLEDGE OF
SALIENT DRIVER EVENTS WAS A
PROBLEM WE NEEDED TO SOLVE IN A
CANCER THAT HAS BEEN A MAJOR
FOCUS IN OUR LAB, WHICH IS
MELANOMA WE AS MANY OTHERS,
INCLUDING YOUR DENNIS SAMUALS,
WHO IS HERE, HAVE BEEN
SEQUENCING MELANOMA GENOMES
TRYING TO UNDERSTAND WHAT
BIOLOGY AND NEW DRIVERS THERE
MAY BE, AND THIS IS A FIGURE
FROM A RECENT REPORT OF WHOLE
GENOME SEQUENCING IN MELANOMA.
ONE OF THE MOST PROMINENT
FEATURES THAT LEAPS OUT IS THE
MUTATION RATE IN MELANOMA IS
RATHER HIGH.
SO, THIS IS SHOWING MUTATIONS
PER MEGABASE, THE MELANOMAS ON
THE RIGHT ARE MORE TYPICAL OF
WHAT YOU EXPECT FOR A LOT OF
EPITHELIAL MALIGNANCIES BUT A
VAST EXCESS OF MUTATIONAL LOAD
AND THAT IS ALMOST COMPLETELY
ATTRIBUTABLE TO THE MUTATIONAL
SIGNATURE THAT IS CHARACTERISTIC
OF UV LIGHT.
SO UV CAUSES MAJOR DAMAGE IN
MELANOMA WE ANYHOW THAT BUT THIS
GIVES US A CLEAR VIEW OF THIS.
AND THIS PHENOMENON POSED A HUGE
PROBLEM FROM THE STANDPOINT OF
DISCERNING DRIVER VERSUS
PASSENGER MUTATIONS.
AND THERE ARE THREE COMPONENTS
OF THAT PROBLEM THAT I'LL JUST
HIGHLIGHT BRIEFLY FOR YOU.
BUT JUST TO ILLUSTRATE THE
BREATH OF THE PROBLEM.
IF YOU LOOK AT THE MUTATIONAL
RATE OF MELANOMA, YOU CONSIDER
THE VITAL STATS OF AIR RECENT
WHOLE EXOME SEQUENCY.
WE SAW NEARLY 87,000 INDEPENDENT
CODING MUTATIONS WHICH MEANT
THAT THERE WERE 14,000 GENES
MUTATED AT LEAST ONCE,
TWO-THIRDS OF THE GENOME HAD AT
LEAST ONE SOMATIC MUTATION AND
THERE WERE 5UPON 15 GENES
MUTATED IN AT LEAST 10% OF THE
SAMPLES.
NOW IF YOU DISCOVER A GENE THAT
IS MUTATED IN 10% OF A CANCER,
THAT IS A RESPECTABLE MUTATION
FREQUENCY.
THOSE KINDS OF GENES COULD HAVE
A SUBSTANTIAL CLINICAL IMPACT IF
THEY WERE ACTIONABLE.
BUT THIS SEEMED LIKE AN AWFULLY
LARGE NUMBER OF GENES TO REALLY
BE BIOLOGICALLY RELEVANT.
AND WHEN ONE STARTED TO APPLY
STATISTICAL ALGORITHMS THAT
PREDICTED WHAT TO EXPECT BOY
CHANCE, THERE WAS CLEARLY
INFLATION.
SO THERE WERE 7GENES DEEMED
STATISTICAL SIGNIFICANT BY THEAL
GO RHYTHMMS STATE-OF-THE-ART AT
THE TIME.
THAT SEEMED TOO HIGH.
THEY TENDED TO BE ABSENT OR VERY
MINIMALLY EXPRESSED IN MELANOMA.
ANY GIVEN GENE MIGHT SHOW LOWICS
R. EXPRESSION FOR A NUMBER OF
REASONS.
TO SEE THE WHOLE CATEGORY OF
SIGNIFICANTLY MUTATED JEANS
POORLY EXPRESSED WAS A RED FLAG
AND PERHAPS THE MOST DEEPLY
CONCERNING ASPECT OF THIS
PROBLEM WAS THAT WHEN WE
CONSIDERED THE SILENT MUTATION
RATE, MEANING THE MUTATION THAT
IS DIDN'T GIVE RISE TO AMMONO
ACID SUBSTITUTIONS IN THE
RESPECTIVE GENES, ONE FOUND THAT
IN GENERAL, THE STATISTICALLY
SIGNIFICANTLY MUTATED GENES
TENDED TO HAVE A VERY HIGH RATIO
OF SILENT MUTATIONS.
SO THIS WAS A DOPE CONCERN THAT
DESPITE OUR HERETOFORE ATTEMPTS
TO APPLY ROBUST CONTROLS FOR THE
SIZE OF A GENE AND THE SAMPLES
SPECIFIC MUTATION RATES, WE WERE
STILL LEAKING IN TERMS OF LOTS
OF PASSENGER MUTATIONS COMING IN
WITH THE DRIVERS.
HOW DO WE SOLVE THAT PROBLEM?
ERAN WAS AN ASSOCIATE
COMBINATIONAL BIOLOGIST IN THE
LAB, HAD THE NOTION WE MIGHT
NEED TO DEFINE THE DEFINITION OF
BACKGROUND MUTATION RATES.
TYPICALLY WE THOUGHT AS GENOME
UNIFORM.
SO MORE OR LESS IT WOULD OCCUR
RANDOMLY WITHIN THE GENOME.
MAYBE A GIVEN SAMPLE MAY HAVE A
HIGHER MUTATION RATE THAN
OTHERS.
AT A GENOME LEVEL IT WOULD BE
RANDOM.
MAYBE THAT WAS WRONG.
WE THAN THERE ARE HETEROGENEOUS
ASPECTS OF THE BACKGROUND
MUTATION RATE, TRANSCRIBED GENES
ARE MUTATED AT A LOWER FREQUENCY
THAN UNTRANSCRIBED GENES.
THERE ARE VARIATIONS DEPENDING
ON WHETHER IT'S CODING OR
NONCODING.
PARTS OF THE GENOME INTRON THAT
IS ARE TRANSCRIBED VERSUS THOSE
THAT ARE NOT TRANSCRIBED.
SO WE KNOW THAT THIS CAN VARY
AND PERHAPS PARTICULARLY WHEN
YOU HAVE AN EXTRA LAYER OF
MUTATIONAL INSULT, THIS WAS
POSING A PROBLEM.
SO THE NOTION CAN BE SHOWN
ADDITIONALLY PICTORALY HERE
WHICH SHOWS THE HYPOTHETICAL
EXAMPLE.
THESE ARE EXONS, THIS IS
INTRONNIC SEQUENCE.
THESE ARE EXON THAT IS HAVE
EQUIVALENT MUTATION RATIOS.
IF YOU LOOK AT THE EXON MUTATION
RATIO.
HOWEVER, YOU COULD IMAGINE A
SCENARIO WHERE THERE WAS ONE
LOCUS THAT HAS A HIGH BACKGROUND
MUTATIONAL RATE IN WHICH CASE
YOU SEE HIGH INTRONNIC MUTATIONS
AND ANOTHER LOCUS THAT HAS A LOW
INTRONNIC MUTATION RATE.
IN THIS CASE, YOU MIGHT EXPECT
THESE ARE MOSTLY PASSENGER
EVENTS AND IT JUST SO HAPPENS
THAT THIS LOCUS HAS
HYDROGENERATION AND LOW REPAIR
BUT THIS MIGHT HAVE UNDERGONE
EVOLUTIONARY SELECTION.
SOCIETY QUESTION WAS, HOW COULD
YOU ENRICH FOR LOCI THAT
ACTUALLY UNDERWENT EVOLUTIONARY
SELECTION IN CANCER?
IT TURNS OUT THAT WHEN YOU
GENERATE WHOLE EXOME SEQUENCING
DATA, EVEN THOUGH YOU'RE
TARGETING PULLING DOWN THE
SEQUENCE, YOU GET A WHOLE BUNCH
OF INTRONNIC SEQUENCE AS WELL.
THE REASON FOR THIS IS BECAUSE
THE FRAGMENTS YOU PULL DOWN WITH
THE BAITS THAT ARE TARGETING THE
GENOME, TEND TO BE MORE OR LESS
RANDOMLY GENERATED SO YOU GET A
DISTRIBUTION OF SORT OF ADJACENT
INTRONNIC MATERIAL THAT COMES
FOR THE RIDE AND THAT ALLOWS US
IN THE REGIONS FLANKING THE
EXONS TO CALCULATE THE MUTATION
RATE EVEN THOUGH WE TYPICALLY
ONLY CARE ABOUT THE EXONIC
MUTATIONS THAT WILL ALLOW US TO
DEVELOP A ALGORYTHMS THAT
TALLIES THE MUTATIONAL BURDEN AT
EACH LOCUS AND ALLOWS A PER
MUTATION OF THE MUTATIONS IN A
LOCUS SPECIFIC WAY ACROSS THE
SAMPLE SET THAT GIVES US A
BACKGROUND MUTATIONAL
DISTRIBUTION AND IF THE MUTATION
BURDEN IS CONSIDERED TO FALL
OUTSIDE OF THE THAT MUTATION, WE
COULD SAY THAT THERE IS EVIDENCE
OF FOSSIL SELECTION WHEREAS IF
IT FALLS WITHIN, THERE WOULD BE
BACKGROUND EVEN IF THERE ARE
MULTIPLE RECURRENT EXONIC
MUTATIONS OF THAT WAS THE NOTION
AND WE COULD APPLY ADDITIONAL
ALGORITHMS TO ANNOTATE THESE
MUTATIONS AS PLAUSIBLY FLONGSAL
OR DAMAGING AND NOW WE CAN SORT
OF SEE HOW DID WE DO COMPARED TO
THE PRIOR APPROACHES?
AND INDEED, THIS ALGORITHM IF
ONE CONSIDERS THE CRITERIA OF
SELECTION WHERE THERE WAS A LOW
EXPRESSION AND PRIOR SIGNIFICANT
GENES SUDDENLY NOW YOU'RE IN A
SITUATION WHERE IN GENERAL, THE
MUTATIONS, THE GENES BEING
CALLED SIGNIFICANT ARE IN FACT
EXPRESSED IN MELANOMA AND NOW
WHEN YOU LOOK AT THIS QQ PLOT
WHERE THERE WAS A VAST INFLATION
EARLIER, WE NOW SEE A MUCH MORE
OF A DISTRIBUTION IN LINE WHAT
HAVE YOU EXPECT BOY CHANCE UNTIL
YOU GOAT A FEW GENES THAT ARE
CLEAR OUT LIERS AND THESE 11
GENES CAUGHT OUR ATTENTION.
THERE WERE SEVERAL VERY
INTERESTING ASPECTS OF GENES.
ONE OF WHICH MAYBE THE MOST
NOTABLE WAS A GENE CALLED RAC 1,
A MEMBER OF THE RASGTPASE SUPER
FAMILY.
THERE WAS A MUTATION AT CODON 29
AND OTHER MEMBERS OF THIS FAMILY
THAT HAD ANALOGOUS MUTATIONS AND
FUNCTIONAL STUDIES I CAN'T
DESCRIBE IN GREAT DETAIL
SUGGESTED THAT IN FACT, THIS
MUTATION, P29S DID ACTIVATE RAC
AS EVIDENCED BY A GTP LOADING
ASSAY.
SO THIS WAS A FUNCTIONAL
MUTATION AND NOW VERY
INTERESTING TO THINK ABOUT THE
RELEVANCE OF THIS GTPASE IN
MELANOMA BIOLOGY BUT THERE WERE
EARL OTHER INTERESTING MUTATION
THAT IS CAUGHT OUR ATTENTION HA
HAD NOT BEEN PREFERSLY KNOWN.
FOR EXAMPLE, THIS PROTEIN, FOOS
DAYS, WHICH HAS NOT BEEN
DESCRIBED AS A CANCER GENE BUT
IT'S KNOWN TO INTERACT WITH
PSYCHE CLIN D AND NEGATIVELY
REGULATE CYCLIN D ASK THEY WERE
LOSS OF FUNCTION EVENTS AND
THERE WERE SEVERAL STOP CODON IN
THIS PANEL.
SO THIS IS A NOVEL TUMOR
SUPPRESSOR GENE.
THIS IS ANOTHER GENE SORTING
SNX31 A GENE REPORTED TO
INTERACT WITH ACTIVATED HRAS SO
THIS MAY BE A RAS EFFECTOR
PROTEIN AND HERE IS ANOTHER
TACC1, WHICH IS AGAIN REPORTED
TO STIMULATE BOTH RAS SIGNALING
AND PI3K SIGNALING TO PATHWAYS
AND IT ALSO INTERAXE WITH AURORA
KINASE AS DOES PPP6C.
SO A NUMBER OF INTERESTING GENES
THAT ARE CLEARLY SHOWING
EVIDENCE OF POSITIVE SELECTION
DURING MELANOMA EVOLUTION AND
HAVE OR POINT A FINGER TO NOVEL
BIOLOGICAL MECHANISMS THAT WE
DID NOT PREVIOUSLY RECOGNIZE IN
THIS MALIGNANCY.
NOW YOU CAN FLIP THIS AROUND AND
ASK NOT JUST ABOUT ACTIVATING
MUTATIONS OR FUNCTIONAL
MUTATIONAL BURDENS BUT FOCUS ON
LOSS OF FUNCTION EVENTS AND WHEN
ONE DOES THAT, WE SEE SOME
INTERESTING HITS EMERGE FOR
EXAMPLE, ARID2 IS HOMOLOGUE TO
GENES SUCH AS ARID1A AND B,
MEMBERS OF THE SWITCH SNIFF
CHROMATIN MODIFYING COMPLEX,
THIS IS A COMPLEX COMPONENT OF
WHICH NOW HAVE BEEN SHOWN TO BE
MUTATED IN MANY CANCERS SO WE
CAN ADD MELANOMA TO THE LIST OF
CANCER THAT HAVE SIGNIFICANTLY
RECURRENT MUTATIONS AND CHROME
TINE MODIFYING ENZYMES.
THIS WAS A USESFUL STUD THEY CAN
FOCUS STUDIES OF CHROMATIN BILE
NEMELANOMA.
AND JUST TO KIND OF MAKE A BRIEF
POINT OF A SUBSET OF THE MEW
TALKS WE SAW BY THIS ANALYSIS,
WE HAVE
WE OF COURSE KNOW THE LARGE
FRACTION HAVE ONCOGENIC BRAS
MUTATIONS AND NRAS MUTATIONS.
BUT A SUBSTANTIAL SUBCELT OF 10
OR 15 OR SO PERCENT EVER MEL
GNOME THAT IS LACK EITHER OF
THESE MUTATIONS AND ONE OF THE
INTERESTING OBSERVATIONS WHICH
WAS CONFIRMED BY A STUD THEY
CAME OUT BY RUTH AT YALE THAT
WAS MANY OF THESE BRAS WILDTYPE
MELANOMAS HAVE NONSINCE NF1
MUTATIONS, ARRASES GAP SO IT'S
NORMAL FUNCTION IS TO INHIBIT
RAS SIGNALING SO LOSS OF
FUNCTION IN NF1 DEREGULATING RAS
WOULD BE ANOTHER MECHANISM OF
MAP KINASE PATHWAY ACTIVATION IN
MELANOMA AND WE CAN ASSIGN THIS
AS A CANCER GENE IN THAT SUB
CELT OF MELANOMA SO ALL
TOGETHER, WE CAN PUT OR TAKE THE
OUTPUT OF THIS ALGORITHM TO LOOK
FOR POSITIVE SELECTION TOGETHER
WITH BAYESIAN MINING OF THE LIST
OF KNOWN CANCER GENES AND DEFINE
A LANDSCAPE OF MELANOMA DRIVER
GENES WHICH WE WOULDN'T ARGUE TO
BE COMPLETE BUT WE HAVE
CERTAINLY LARGELY ELIMINATE THE
THE PROBLEM OF MASSIVE PASSENGER
DILUTION OF THE SIGNAL.
SO THEREFORE, GETTING BACK TO
THIS ISSUE OF SALIENT,
UNDERSTANDING SALIENT DRIVER
GENES FROM WHICH WE CAN NOW LOOK
TO UNDERSTAND ACTIONABLE
THERAPEUTIC MANIPULATIONS, THIS
WAS A NECESSARY COMPONENT OF
MELANOMA BIOLOGY AND WAS ENABLED
BY THIS KIND OF STUDY.
SO, AND THERE ARE MANY EXAMPLES
OF STUDIES LIKE THIS TAKING THE
NEXT STEP GOING FROM LIST OF
MUTATIONS TO THE SALIENT SUBSET
FOR A CLINICAL USE THAT ARE
ONGOING IN MANY DIFFERENT CANCER
TYPES OF THE SO NOW I'D LIKE TO
TURN MY ATTENTION TO ANOTHER
EFFORT THAT HAS BEEN GOING ON ON
THE OPPOSITE END OF THE POSITION
MEDICINE PROCESS WHICH IS TO
DISSECT USING BOTH SEQUENCING SEQUENCING
AND PRECLINICAL STUDIES AND
MECHANISMS OF RESISTANCE AND TO
USE THAT TO COME UP WITH NOVEL
FRAMEWORKS FOR THERAPEUTIC
COMBINATIONS AND HERE THE NOTION
IS THAT SINGLE DRUGS ARE
UNLIKELY TO CURE OR DURABLY
CONTROL MOST METASTATIC
MELANOMA.
WE NEED TO UNDERSTAND WHAT TYPES
OF COMBINATIONS, POSSIBLY 3-4
DRUG COMBINATIONS MIGHT BE GIVEN
IN VARIOUS COCKTAILS TO PATIENTS
WITH PARTICULAR GENETIC
ALTERATIONS AND IT CERTAINLY HAS
BEEN SHOWN IN HUMAN MALIGNANCIES
THAT COCKTAILS ARE NEEDED TO
ACHIEVE DURABLE CONTROL OR CURE
IN CANCER.
SO UNDERSTANDING MECHANISM
RESISTENCE MIGHT HELP WITH US
THAT PARTICULARLY IN MELANOMA
WHEN THERE ARE VARIETY OF
THERAPIES THAT ARE FDA APPROVED
SUCH AS RAS INHIBITORS OR
ADVANCED CLINICAL DEVELOPMENT
AGAINST THE MAP KINASE CASCADE
ACTIVATED MUTATIONALLY BY
MUTATIONS IN B RAS PARTICULARLY
AT CODON 600 OR B RAS.
SO THIS IS AN AREA WHERE
UNDERSTANDING RESIST SENSE
INCREDIBLY IMPORTANT BECAUSE
DESPITE THE INCREASE IN SURVIVAL
BY USING RAS INHIBITORS IN B RAS
MELANOMA, RESISTENCE IS QUITE
PREVALENT AND THIS IS PREVALENT
IN TWO WAYS.
SON IF YOU LOOK AT A WATER FALL
PLOT WHERE THE FRACTION OF
PATIENTS THAT HAVE CLINICAL
BENEFIT ARE SHOWN BELOW THE ZERO
LINE, IF WE APPLY A FORMAL
CRITERIA FOR CLINICAL RESPONSE,
A CLINICAL PARTIAL RESPONSE, YOU
SEE THAT REALLY ONLY A SUBSET OF
THESE PATIENTS ACTUALLY ACHIEVED
A PARTIAL RESPONSE.
A LARGE FRACTION OF PATIENTS
ALTHOUGH THEY ARE BENEFITING,
THERE IS A LOT OF TUMOR AROUND.
INTRINSIC RESIST SENSE A MAJOR
ISSUE.
THE MEDIAN SURVIVAL IS ABOUT 6
MONTHS WITH THE RAS INHIBITOR.
IF YOU AT A MEC TO A RAS YOU CAN
PUSH THIS OUT SOME.
SO IT IS A PERVASIVE PROBLEM OF
THE SO HOW ARE WE GOING TO SOLVE
THIS PROBLEM?
WELL, FIRST OF ALL WE CAN
BENEFIT FROM THE FACT THAT WE
KNOW A FAIR BIT ABOUT THEMES OF
RESIST TONES KINASE INHIBITORS.
SO B RAS MUTATION WHICH
ACTIVATES MELANOMA IS A
KINASE-DRIVEN, GENETICALLY AND
KINASE DRIVEN CANCER.
IF YOU TAKE A KINASE INHIBITOR
AND YOU GET A RESPONSE AND YOU
RELAPSE, IT CAN FALL INTO THREE
MAJOR CATEGORIES, TYPICALLY.
NOT UNIVERSALLY BUT TYPICALLY.
ONE MAJOR CACATEGORY
SEREACTIVATION OF THE TARGET.
OFTEN THIS OCCURS BY ACQUIRING A
SECONDARY GENETIC ALTERATION BUT
THIS CAN ALSO HAPPEN BY
ACTIVATING UP STREAM EFFECTORS
SO TO PUT THE AR GET INTO
OVERDRIVE AND THE DRUG IS NOT AS
EFFECTIVE AT A GIVEN DOSE AND
ALTERNATIVE APPROACH IS THAT A
BIPAS MECHANISM GETS ACTIVATED.
SO ESSENTIALLY YOU WORK AROUND
THE EFFECT OF THE KINASE
INHIBITOR AND ENGAGE A PARALLEL
CASCADE AND FEED INTO THE
DOWNSTREAM ONCOGENIC OUTPUT IN A
WAY THAT LEADS TO RESISTENCE.
THE THIRD MAJOR CATEGORY SEONE
CAN ACTIVATE DOWNSTREAM
EFFECTORS.
SO MEMBERS OF THE PATHWAY THAT
ACT DOWNSTREAM OF THE TARGET
ONCOPROTEIN, IF YOU TURN THEM
BACK ON, YOU CAN ACHIEVE
RESISTENCE.
AN EXAMPLE OF A BY PAS EFFECTOR
WE HAVE KNOWN ABOUT FOR SEVERAL
YEARS IS THE ACTIVATION OF THE
MET TYROSINE KINASE IN LUNG
CANCERS THAT ARE DRIVEN BY
MUTATIONS IN THE EGFR, AND
TREATED WITH INHIBITORS OF THAT
RECEPTOR.
AN EXAMPLE OF AN ACTIVATION OF A
DOWNSTREAM EFFECTOR IS RECENTLY
EXAMPLE KRAS MUTATIONS IN COLON
CANCERS TREATED WITH INHIBITORS
OF EGFR.
SO THESE ARE THREE MAJOR
CATEGORIES OF RESIST TONES
KINASE BASE THERAPEUTICS IN
CANCER.
THE TYPICAL OUTPUT, THE TYPICAL
EFFECT OF THESE, IS TO
REACTIVATE THE DOWNSTREAM
PATHWAY AND THEREFORE LEAD TO
DISEASE PROGRESSION.
IN GENERAL, WE HAVEN'T OR DON'T
HAVE A GREAT UNDERSTANDING OF
MECHANISM THAT CAN GO ALL THE
WAY AROUND THE ORIGINAL PATHWAY.
AND CAUSE DISEASE PROGRESSION.
MOST OF THE TIME, YOU TURN THE
PATHWAY BOOK DOWNSTREAM BY SOME
MECHANISM AND THAT LEADS TO
DISEASE PROGRESSION.
SO WITH THIS FRAMEWORK, WE CAN
SET OUT TO BEGIN TO UNDERSTAND
MECHANISM RESIST TONES RAS
INHIBITION IN MELANOMA.
AND THE APPROACH WE HAVE BEEN
TAKING IS TO BLEND SYSTEMATIC
EXPERIMENTAL STUDIES,
PRECLINICAL STUDIES, WHICH ARE
AIMED AT SYSTEMATIC FUNCTIONAL
SCREENS THAT DEFINE THE UNIVERSE
OF RESISTENCE MECHANISM AND I'LL
DESCRIBE THESE SHORTLY.
AND THE IDEA IS TO BLEND THESE
WITH THE RESULTS OF DEEP OMIC
SEQUENCING, DEEP CLINICAL
CHARACTERIZATION OF SAMPLES
ACQUIRED PRIOR TO TREATMENT AND
FOLLOWING RELAPSE AND THE NOTION
IS THAT INTEGRATION CAN ALLOW US
TO SEE CLINICALLY RELEVANT BOTH
THE SPECTRUM OF CANDIDATES THAT
CAN CAUSE RESISTANCE AND A
FILTER USING CLINICAL DATA TO
SEE WHICH DO CAUSE RESISTENCE
AND THE HOPE IS WE CAN LEVERAGE
THIS KNOWLEDGE TO SPEED THE
DESIGN OF RATIONAL THERAPEUTIC
COMBINATIONS AND I'LL SHOW YOU
HOW WE ARE THINKING ABOUT THIS
IN MELANOMA.
NOW ONE OF THE FIRST PATIENTS IN
UNDERWENT SEQUENCING AND IT
WASN'T WHOLE EXOME SEQUENCING.
IT WAS TARGETED.
IT WAS THIS PATIENT WHO HAD
WIDESPREAD MELANOMA REFRACTARY
TO A VARIETY OF CONVENTIONAL
THERAPEUTICS WHO HAD A B RAS
MUTATION, HAD A DRAMATIC
RESPONSE BUT UNFORTUNATELY AFTER
REALLY ONLY SEVERAL WEEKS, THREE
MONTHS OR SO, THERE WAS
WIDESPREAD TUMOR RELAPSE.
NOW THIS SPECTRUM OF PICTURES
RAISES MANY QUESTIONS, ONE IS
DID EVERY TUMOR HAVE THE SAME
MECHANISM RESISTENCE AND OF
COURSE THESE ARE NOT ANSWERABLE
WITHOUT AUTOPSY-BASED STUDIES.
WE ONLY COULD SEQUENCE A
SPECIMEN FROM ONE TUMOR BUT THAT
SPECIMEN WAS HIGHLY INFORMATIVE
BECAUSE WHAT CAME OUT OF A
MUTATION IN MEK.
SO MEK IS THE KINASE IMMEDIATELY
DOWNSTREAM OF B RAV AND THE
MUTATION WAS CONFERRED ROBUST
PHARMACOLOGIC RESISTENCE TO A
RAV INHIBITOR AS WELL AS TO A
MEK INHIBITORS WHICH HAD NOT
BEEN GIVEN BUT IF IT HAD BEEN
GIVEN IT WOULDN'T HAVE WORKED
THIS THIS SETTING SEEN
PHARMACOLOGICALLY AND
RECAPITULATED MEASURING
PHOSPHORYLATION AND THESE
WESTERN BLOTS HERE.
SO, IN PARALLEL, OUR LAB HAS
BEEN CONDUCTED RANDOM
MUTAGENESIS SCREENS TAKING CDNA
FROM MEK KINASE, MUTAGENIZING
THAT AND TRUTHING IT INTO
SENSITIVE MELANOMA CELL LINES
THAT HAVE THE B RAF MUTATION AND
ASKING ARE THERE ALLELES,
SECONDARY ALLELES TO PROMOTE
DRUG RESISTENCE IN-VITRO?
WE DID WI A MEK INHIBITOR OR A
RAF INHIBITOR AS THE SELECTIVE
AGENT AND THIS ALLOWED US TO GET
A ROBUST DISTRIBUTION OF
INDIVIDUAL MUTATIONS WITHIN MEK
ITSELF THAT COULD CONFER
RESISTANCE AND THESE FELL INTO A
COUPLE OF DIFFERENT CATEGORIES.
I'M NOT GOING TO GO THROUGH THIS
IN DETAIL BUT WHAT I'M SHOWING
YOU HERE IS THE DISTRIBUTION
WITHIN THE MEK 1CDNA OF HIGH
FREQUENCY OR ROBUST MUTATIONS
THAT WERE ASSOCIATED WITH THE
RESISTENCE.
MEK INHIBITOR OR RAF INHIBITOR.
AND A COUPLE OF THEMES THAT
EMERGED IS THERE WERE MUTATIONS
IN THE END TERMINIS WHICH
CONTAINS INHIBITORY ALPHA HELIX,
A HELIX, SUCH AS THIS Q56P
MUTATION AS WELL AS SEVERAL
OTHERS THAT WERE ASSOCIATED WITH
THE RESIST TONES ONE OR ANOTHER
INHIBITOR OF THE THERE WERE ALSO
A WHOLE CLUSTER OF MUTATIONS IN
THE C HELIX WHICH IS COMPONENT
OF THE MEK KINASE HAS TO ADOPT
THE FULLY ACTIVE CONFIRMATION
AND HAS TO BECOME A CLOSED
CONFIRMATION.
THE WHOLE SERIES OF MUTATIONS IN
THIS WERE ABLE TO CONFER RESIST
TONES ONE ANOTHER AND THE SKEP
121 I SHOWED YOU BEFORE FALLS IN
THE MIDDLE OF THIS CLUSTNER THIS
SAME REGION.
AND THEN FINALLY, WE SAW
MUTATIONS IN THE KINASE DOMAINS
SUCH AS AROUND BETWEEN CODONS
203 AND 211 THAT WERE ABLE TO
CONFER.
SO THEY FELL INTO FUNCTIONAL
CATEGORIES AND VERY RECENTLY,
WHAT WAS QUITE SATISFYING IS
THAT A STUDY BOY A CLINICAL TEAM
OF MELANOMA ONCOLOGISTS THAT WAS
PRESENTED IN ABSTRACT FORM AT AS
CO, JUST THIS PAST JUNE, HAS
SHOWN THAT IF ONE LOOKS AT
MELANOMAS OF PROGRESSION
COMPARED TO BASELINE, ONE SEES
SEVERAL INSTANCES OF MEK 1
MUTATIONS PRESENT AT PROGRESSION
AND ABSENT AT RELAPSE THAT WERE
IDENTIFIED BOY THE RANDOM
MUTAGENESIS SCREENS AND
PUBLISHED SEVERAL YOURS AGO.
THIS IS QUITE SATISFYING.
SOME OF THESE ARE
STRAIGHTFORWARD AND EASY TO
INTERPRET.
ONE, WHICH IS THE MUTATION AND
THE CODON 124, A LEUCIN OR
SYRIAN SUBSTITUTION IS CONFUSING
BECAUSE IT CAN ARISE IN
ASSOCIATION WITH THE RESISTENCE
BUT CAN BE PRESENT DINOVO AND
SOME CASES PATIENTS CAN STILL
RESPOND.
SO IT'S COMPLICATE WHAD IS
HAPPENING ALTHOUGH I'M GOING
SHOW YOU DATA TO SPEAK TO THAT
SHORTLY.
CLEARLY, THE SEVERAL OF THESE
MUTATIONS WERE KNOWN TO CAUSE
RESISTENCE.
SO ONE OF THE STUDIES WE HAD
DONE SEVERAL YEARS AGO HAD BEEN
TO TAKE A PATIENT WHO HAD BEEN
TREATED WITH A MEK INHIBITOR,
HAD A B RAF MUTATION AND RESPOND
THE TO THE MEK INHIBITOR AND WE
FOUND THE PATIENT RESPONDED BUT
WHETHER THEY DEVELOPED RELAPSE
WERE ABLE TO CULTURE CELLS FROM
THIS PATIENT.
THEY WERE STRONGLY RESISTENCE TO
THE MEK INHIBITOR.
THEY THIS ELEMENT.
WHEN YOU REINTRODUCE THAT ALLELE
YOU CAN SHIFT THE GI50 BUT THE
MAGNITUDE OF SHIFT WAS LESS THAN
WHAT ABOUT SEEN IN THE
SHORT-TERM.
NOW SIMILARLY IF YOU LOOK
INSTEAD OF A MEK INHIBITOR, YOU
LOOK AT A RAF, YOU FOUND A MORE
PROFOUND RESISTANT AFFECT IN THE
SHORT-TERM CULTURE.
IT WAS QUITE DRAMATIC.
BUT IF YOU LOOKED AT THE EFFECT
OF P124L, YOU COULD GET A SHIFT
BUT IT WAS RATHER MARGINAL.
NOW HERE IS 256P.
THIS IS SEEN CLINICALLY.
THIS WAS CAME OUT OF A RANDOM
SCREEN BUT CLEARLY A ROBUST
SHIFT.
SO P124L WAS LESS SO BUT I'LL
SHOW YOU MORE DATA SHORTLY THAT
EXPLAINS THE DICHOTOMY.
WE FOUND A MUTATION AT POSITION
203 WHEN WE DID OUR RANDOM
MUTAGENESIS SCREENS WITH THE MEK
INHIBITOR BUT USED THE RAF AS
SELECTIVE AGENT.
EACH OF THE MUTATIONS EMERGED
CLINICALLY WERE SHOWN
PRECLINICALLY TO BE RELEVANT TO
RESISTINENCE A SATISFYING WAY.
WE HAVE RECENT DATA WHERE IF YOU
LOOK AT THIS P124S, NOT L, AND
LOOK TAT NOW IN THE CONTEXT OF
INDUCIBLE SYSTEM, SO RA3
INDUCIBLE PATTERN AS OPPOSED TO
STEADY STATE.
THERE COULD BE A MEANS BY WHICH
ONE 24 CAUSES WE ASSISTANCE.
A BLEND OF TARGET-BASED
SYSTEMATIC PRECLINICAL STUDIES
TOGETHER WITH DEEP SEQUENCING OF
CLINICAL SPECIMENS ALLOWED US TO
CLEARLY NOMINATE A DISTRIBUTION
OF ALLELE THAT IS CONFER RESIST
TONES THESE INHIBITORS.
SEVERAL OF WHICH CAN BE SHOWN TO
BE RELEVANT CLINICALLY.
NOW THE OTHER APPROACH HAS BEEN
TO MOVE AWAY FROM FOCUSING
SOLELY ON A PARTICULAR TARGET
BUT TO NOW GO TO A NEAR GENOME
SCALE AND TO CARRY THIS OUT, THE
NOTION HAS BEEN TO LEVERAGE
RESOURCES THAT'S BEEN DEVELOPED
AT THE BROAD INSTITUTE IN WHICH
THE LARGE MAJORITY OF GENES FROM
THE HUMAN GENOME THAT WE KNOW OF
HAVE BEEN CLONED TO THE LENTE
VIRAL OR LIBRARIES AND SO THE
NOTION IS TO TAKE THESE
LIBRARIES, INTRODUCE THEM IN
ARRAYED FORMAT INTO SENSITIVE
MELANOMA CELLS THAT HARBOR THE
MUTATION AND DO A PHENOTYPIC
RESCUE SCREEN IF THE PRESENCE OF
INHIBITORY CONCENTRATIONS OF A
RAF INHIBITOR.
THE INITIAL STUDY WE PUBLISHED A
COUPLE YEARS AGO WAS A PILOT.
AND THE OUTPUT OF THAT WAS QUITE
REVEALING FOR SEVERAL REASONS.
ONE OF WHICH IS THAT THE MAJOR
ONE IS THAT THERE WERE SEVERAL
KINASE THAT IS SCORED AS
RESISTENCE EFFECTORS THAT
ESSENTIALLY AT LEAST DIRECT
MECHANISTIC SIMILARITIES TO WHAT
SUBSEQUENTLY HAVE BEEN SHOWN TO
BE CLINICALLY RELEVANT
RESISTENCE.
THERE WERE SEVERAL RECEPTOR
TYROSINE KINASES THAT WERE SAFES
TO CONFER RESISTANCE AND
VALIDATED IN INDEPENDENT CELL
LINES AND IT'S CLEAR THAT
RECEPTOR TYROSINE KINASES
COMPRISE A RESISTENCE.
THERE ARE A VARIETY OF THAT HAVE
BEEN DESCRIBED.
I WON'T BE ABLE TO GO THROUGH
ALL OF THEM BUT THIS CAPTURED
THAT CATEGORY QUITE NICELY.
WE ALSO FOUND THAT C RAF CONFERS
RESISTENCE.
IT IS A SISTER TO B RAF AND FUR
PUT IT INTO OVER DRIVE THERE ARE
INTERESTING MECHANISMS INVOLVING
DOIMERRIZATIONS BY WHICH LEADS
TO RESISTANCE AND I'LL SAY A
LITTLE MORE ABOUT THAT SHORTLY.
THE BIG NOVEL OBSERVATION IN THE
STUDY WAS A GENE CALLED COT, A
KINASE IS A COUSIN TO B RAF.
NOT A RAF FAMILY MEMBER BUT
PHOSPHORYLATES AND ACTIVATES MEK
SO THIS WHOLE SPECTRUM OF
KINASES CONVERGED ON TO SEVERAL
MECHANISMS THAT MADE SENSE.
EACH OF WHICH AS SHOWN BITE
WESTERN BLOT LOOKING AT
PHOSPHORYLATION COMPARED TO THE
WILDTYPE SETTING OR THE CONTROL
SETTING, LED TO SUSTAINED ERK
ACTIVATION.
SO IF YOU AGGREGATE THE RESULTS
OF THIS, BEFORE I GET TO THAT,
LET ME MAKE ONE MORE POINT.
COMING BACK IT THIS P124L
MUTATION SHOWING THIS SHORT-TERM
CULTURE THAT HAD DISCORDANCE
BETWEEN WHAT YOU SEE IF YOU JUST
PUT IN MEK P124L RATHER THAN THE
RESISTENCE PHENOTYPE.
IT OUNCE UT THE DRUG RESISTENCE
CULTURE HAD WHOPPING COD
EXPRESSION IN ADDITION TO MEK.
THIS SUGGESTS THAT MULTIPLE
MECHANISMS RESISTENCE CAN EXIST
WITHIN THE SAME TUMOR WITHIN THE
SAME CANCER CELL.
NOW, IF WE COME BACK TO THIS
NOTION OF MECHANISMS OF
RESISTENCE AND KINASE-DRIVEN
THERAPY IN CANCER.
AND YOU START TO OVERLAY WHAT WE
HAVE NOW LEARNED THUS FAR WITH
RAF INHIBITION IN MELANOMA, WHAT
WE CAN SAY IS THAT ALTHOUGH
NOBODY HAS YET SEEN SECONDARY
MUTATIONS DIRECTLY WITHIN BRA,
CLEARLY RAF DYSREGULATION HAS
BEEN OBSERVED AS A MECHANISM.
ROGER LOW'S GROUP DESCRIBED
MECHANISMS OF MUTATIONS IN N RAS
AND ESSENTIALLY PUT RAF INTO
OVER DRIVE.
THERE ARE B RAF SPLICING
VARIANTS THAT CAN DIMERIZE AND
ACTIVATE C RAF AND OUR GROUP, I
DON'T HAVE TIME TO TALK ABOUT
IT, HAS IDENTIFIED AGAIN USING
RANDOM MUTAGENESIS MUTATIONS IN
C L.A. THAT CAN PUT RAF INTO
OVERDRIVE AND THERE WAS A RECENT
PAPER SUGGESTING THAT SOME
MELANOMAS MAY HAVE B RAF
AMPLIFICATION WHICH WOULD PUT
INTO OVERDRIVE.
THESE ARE TARGET-BASED
MECHANISMS AND ALL THE
INHIBITORS IN CLINICAL USE ALSO
HIT C RAV.
SO THESE ARE TARGET-BASED RECK
FILMS OF ROW ASSISTANCE.
THE BOY PAS SHARM EXPLAINED BY
RECEPTOR TYROSINE KINASES AND
THE DOYNE STREAM EFFECTOR IS
SORT OF A MUTATION IN MEK 1.
WE CAN NEATLY POPULATE THESE
BINS OF RESISTENCE MECHANISMS BY
MULTIPLE INDIVIDUAL MEK THAT IS
HAVE BEEN DESCRIBED BOY US AND
OTHERS IN THE FIELD.
NOW, THE PROBLEM HERE AT ONE
LEVEL IS THAT THERE IS NO
EVIDENCE RIGHT NOW THAT
KNOWLEDGE OF INDIVIDUAL ROW
ASSISTANCE MUTATIONS IS
SATURATING.
WE HAVE NO NOTION THAT WE HAVE
IDENTIFIED ANYWHERE CLOSE TO THE
FULL SPECTRUM OF RESISTENCES AND
ON THE ONE HAND THAT SEEMS LIKE
A PROBLEM.
IT SEEMS LIKE IF WE'RE GOING TO
HAVE DOZENS OF INDEPENDENT
RESISTENCE MECHANISMS, DISTANT
THWART OUR ABILITY TO APPLY
PRECISION MEDICINE, HAVE MAYBE
3-4 DRUGS AS A COCKTAIL?
AND THE ANSWER COULD BE YES, BUT
THE MORE OPTIMISTIC VIEW IS THAT
IF YOU LOOK AT THIS MORE
CAREFULLY, ONE SEES THAT
ALTHOUGH THERE ARE MULTIPLE
INDIVIDUAL MECHANISMS THEY TEND
TO CONVERGE ON THESE THEMES AND
IN FACT, ONE OF THE THEMES IS
REACTIVATING MAP KINASE AND THIS
ENDS UP WORKING OUT TO BE AT THE
LEVEL OF ERK.
THERE MAY BE PARSIMONNUOUS
CONVERGENCES OF INDIVIDUAL
MECHANISMS ON TO LIMITING
CELLULAR EFFECTOR NOSED THAT
COULD BE EXPLOITED -- EXPLOITED
BY A SMALLER NUMBER OF CLINICAL
COMBINATIONS EVEN THOUGH THE
NUMBER OF INDIVIDUAL MECHANISMS
MIGHT GO INTO THE DOZENS ORREDS.
NOW THAT NOTION CAN BE TESTED
PRECLINICAL BY EXPANDING THE
SYSTEMATIC FUNCTIONAL SCREENING
APPROACH OUT OF THE CHINOME AND
NOW TO THE NEAR GENOME AND THIS
IS WHAT WE COMPLETED.
WE HAVE USED THE FULL BRODE ORF
COLLECTION TO SCREEN A QUARTER
OF A MILLION INDIVIDUAL
INSTANCES AGAIN USING OUR
WORKHORSE A375 MELANOMA CELL
LINEUP AND IT IS SENSITIVE TOW
MAP KINASE PATH WAY INHIBITORS.
IT WAS DONE IT A NEAR-GENOME
SCALE WITH NOT JUST A RAF
INHIBITOR BUT ALSO A MEK
INHIBITOR OR ERK INHIBITOR OR
THE COMBINATION OF THE RAF AND
MEK.
THE NOTION HERE IS THAT THESE
INSTANCES, THESE CONDITIONS
PHENOTYPICALLY MIMIC THE
CLINICAL TRIAL LIST THAT ARE
ONGOING IN THE FIELD RIGHT NOW.
SO AS MANY KNOW, THERE ARE
CLINICAL TRIALS THAT ARE ONGOING
TESTING THE COMBINATION OF A RAF
AND A MEK INHIBITOR WHICH LOOK
PROMISING IN TERMS OF IMPROVING
THE SCENARIO.
SO HERE THE GOAL IS TWO FOLD.
ONE IS TO BEGIN TO ANTICIPATE
THE SPECTRUM OF RESISTENCE
MECHANISMS THAT ARE LIKELY TO
EMERGE EVEN WITH DRUGS THAT ARE
ONLY JUST NOW IN CLINICAL TRIALS
WHERE THE CLINICAL STUDIES
HAVEN'T CAUGHT UP.
AND NUMBER 2 IS TO TEST THIS
HYPOTHESES THAT THERE MAY BE A
CONVERGENCE ON TO LIMITING
CELLULAR NODES THAT EVEN THOUGH
WE MIGHT SEE MANY INDIVIDUAL
HITS.
SO WHEN YOU LOOK AT WHAT COME
OUT OF THIS SCREEN THUS FAR, WE
CAN SEE WITH THIS HEAT MAP THAT
MOST OF THE GENES THAT HAVE
SCORED AND THERE ARE ABOUT 170
OR SO, ARE VALIDATING AND YOU
CAN SEE THIS BECAUSE BLUE MEANS
THAT THERE IS NO ACTIVITY.
THESE ARE A BUNCH OF CONTROLS.
BUT IF THE CELLS OR THE PICKS
ILS ARE WHITE OR RED, THAT MEANS
THAT THERE WAS A PERCENT RESCUED
THAT WAS AT A Z SCORE,
ESSENTIALLY COEFFICIENT OF
VARIATION THAT WAS HIGH IN THE
SCREEN AS A WHOLE.
YOU CAN SEE THAT MOST, NOT ALL,
BUT MOST OF THESE ARE VALIDATED
AND IN FACT, MANY OF THEM A
SUBSTANTIAL FRACTION ACTUALLY
ARE PAN RESISTANT.
THAT MEANS NO MATTER WHERE IN
THE PATH WAY YOU HIT, YOU GET
RESISTENCE.
WE CAN SEE THAT.
WE CAN ALSO BEGIN TO BEND THESE
INDIVIDUAL HITS INTO CATEGORIES
AND NOTIONS SIGNAL TRANSDUCTION
FACTORS SUCH AS KINASES WHICH WE
EXPECTED TO SEE, WE ARE SEEING
VERY INTERESTING ADDITIONAL
FAMILIES SUCH AS GTP EXCHANGE
FACTORS.
RECEPTORS AND VERY PROMINENT SET
OF TRANSCRIPTION FACTORS AND SO
ALREADY YOU CAN SEE BASED ON
THESE HIGH LEVEL VIEWS THAT WE
WE CAN BEGIN TO POPULATE NOVEL
BY PASS MECHANISMS AND NOVEL
DOWNSTREAM EFFECTORS THAT BELOW
ERK AND BEGIN TO ANNOTATE WHAT
THE SPECTRUM OF RESISTENCE MIGHT
BE.
I'M JUST GOING TO BRIEFLY POINT
OUT WE HAVE ALSO DONE THE
CONVERSE EXPERIMENT NOT WITH
OVER EXPRESSION OF ORFs BUT BY
KNOCKING DOWN GENES WITH RNA I
AND OUT PUTS OF THAT SCREEN HAS
BEEN NF1 EMERGING AS A PROMINENT
LOSS OF FUNCTIONECT, IFOR AND
THAT MAKES PERFECT SENSE FROM
THE GENETIC DATA.
WE KNOW THAT NF1 ENCODES A GTPS
GAP AND ITS LOSS WOULD DISREG
LAT SIGNALING SO IT MAKESSTANCY
LOSS WOULD CONFER RESISTENCE TO
RAF INHIBITION.
WHAT WE LIKE TO DO WITH THIS
PRECLINICAL SPECTRUM IS TO
INTEGRATE THE RESULTS OF THE
PRECLINICAL DATA WITH THE
RESULTS OF DEEP CLINICAL
CHARACTERIZATION.
WHAT I WILL TELL YOU IS THAT WE
STILL ARE NOT AT THE POINT IN
THE FIELD WHERE THERE IS A
ROBUST COLLECTION OF MANY DOZENS
OF PRETREATMENT POST RELAPSE
MELANOMA SPECIMEN THAT IS HAVE
BEEN SUBJECTED TO WHOLE EXOME
AND TRANSCRIPTOME SEQUENCING.
WE AND OTHERS ARE WORKING ON
THAT BUT WE DON'T HAVE IT YET.
IT TURNS OUT THAT EVEN IF YOU
INTERSECT THESE RESULTS WITH OUR
PRECLINICAL DATA, THE OAKS OHM
SEQUENCING PROJECT I TOLD YOU
ABOUT, ONE LEARNS INTERESTING
THINGS AND RATHER THAN WALKING
YOU THROUGH ALL OF THE STEPS OF
HOW WE DID THE INTERIGRATION,
I'M GOING SHOW YOU A PICTURE
THAT IS EMERGING AND YOU'LL HAVE
TO WAIT UNTIL WE SUBMIT OUR
PAPER TO BELIEVE THE EXPERIMENTS
THAT SUPPORT THIS.
IF YOU LOOK AT THIS PICTURE,
THIS IS THE KIND OF KERF MAP
KINASE CASCADE.
THESE ARE INHIBITORS HERE
CURRENTLY USED OR TESTED IN THE
CLINIC.
IF YOU HAVE ONE ASTERISK THAT
MEANS YOU'RE A GENE THAT WAS
SIGNIFICANTLY MUTATED IN
MELANOMA IF YOU HAVE TWO, IT
MEANS YOU HAVE BEEN IMPLICATED
IN CLINICAL RESIST TONES RAF
INHIBITIONS.
SO WE HAVE OUR CORE MODULES
HERE.
WE HAVE GENES LIKE COT AND
OTHERS AND NOW YOU CAN SEE THAT
NF1, WHICH WE HAD SEEN SHOWING
UP EN UPON RICHED IN WILDTYPE
MELANOMA, THERE ARE THOSE THAT
HAVE MUTATIONS SHOWING UP ON OUR
LIST AND ALSO YOU CAN SEE THAT
GENES AND SORT OF EFFECTORS THAT
ARE IN PINK ARE HITS THAT HAVE
COME OUT OF OUR ORF SCREEN AND
WE CAN NOW BEGIN TO NOMINATE
CLEAR MODULES THAT LOOK LIKE
THEY COULD FUNCTION AS BIPAS
EFFECTORS AND WE KNOW THERE ARE
FUNCTIONAL INTERACTIONS.
SO RECEPTOR BASED SIGNALING
ACTIVATE CERTAIN TRANSCRIPTION
FACTORS KNOWN IN THE LITERATURE.
GTPS MECHANISM OF WHICH RAF ONE
FEDS INTO THIS AS DOES P REX 2
WHICH I DON'T HAVE TIME TO
DESCRIBE BUT WE RECENTLY
PUBLISHED ON THIS.
SO THE NICE THING ABOUT THIS IS
THAT INDEED, IT SEEMS THAT WE
CAN READILY CONSTRUCT A MODEL
WHERE IN THE INDIVIDUAL HITS
FROM OUR ORF SCREENS ARE NOT
JUST SCATTERED ALL OVER THE
GENOME, THEY ARE ACTUALLY
CONVERGING FUNCTIONALLY OR THEY
READILY FIT MODELS OF SIGNALING
CASCADES THAT WE ALREADY KNOW
ABOUT THAT YOU COULD BOY PASS
EFFECTORS WE NEED TO UNDERSTAND
AND INDEED, COULD OFFER
DEPENDENCIES THAT ARE DRUGABLE
IN THEIR OWN RIGHT.
SO WE NEED TO FOLLOW THIS UP
QUITE A BIT MORE.
BUT THE BLEND OF SEQUENCING AND
PRECLINICAL STUDIES HAVE ALREADY
DONE ARE LEADING TO TO VERY
EXCITING TESTABLE MODELS.
FINALLY WHAT WE'D LIKE TO DO IS
LEVERAGE THIS KNOWLEDGE THAT WE
HAVE GLEANED FROM STUDIES OF
RESISTENCE PRECLINICAL AND
CLINICALLY, TO SPEED THE DESIGN
OF RATIONAL COMBINATIONED.
IF YOU GO FROM THIS PANEL WHICH
IS BUSY TO A MORE SCHEMATIC VIEW
WHICH IS SHOWN HERE, WE CAN
ALREADY ENVISION SOME
TANTALIZING CULMINATIONS THAT
WOULD BE WORTH TESTING.
SO, THE COMBINATION OF RAF AND
MEK INHIBITORS IN CLINICAL
TRIALS IT LOOKS LIKE IT WILL
EXTEND THE SURVIVAL BUT NOT BY
ENOUGH TO SAY THAT WE ARE DONE.
BUT GIVEN WHAT WE KNOW BEG YOUR
PARDON A NUMBER OF MECHANISM
RESISTENCE, NOT ALL, BUT MANY,
IT SEEMS REASONABLE THAT TESTING
A COMBINATION THAT WOULD INCLUDE
A RAF AND AN ERK INHIBITORS WITH
OR WITHOUT A MEK MIGHT BE OF
INTEREST.
ERK ARE IN EARLY CLINICAL TRIALS
RIGHT NOW.
OUR PRECLINICAL DATA TELLS US WE
CAN ALREADY ANTICIPATE NEW BY
PASS PATHWAY THAT IS WILL EITHER
REACTIVATE DOWNSTREAM
TRANSCRIPTIONAL EFFECTORS OR
HAVE ADDITIONAL MECHANISMS.
SO IN TERMS OF THE ONCOGENIC
TRANSCRIPTIONAL OUTPUT, THERE
ARE MANY TRANSCRIPTION FACTORS
THAT CAN LAB 38 OUTPUT.
PERHAPS WE NEED TO BEEN
SOMETHING THAT CAN SUPPRESS
THERE AND IT WOULDN'T BE
TARGETING TRANSCRIPTION FACTORS
DIRECTLY BUT PERHAPS SOMETHING
THAT MODIFIES CHROMATIN, FOR
EXAMPLE, AN HDAC INHIBITOR.
THOSE ARE CERTAINLY IN CLINICAL
TRIALS PERHAPS ONE SHOULD
CONSIDER MAYBE A RAF AND AN ERK
AND HDAC INHIBITORS AS A TRIPLE
COMBINATION.
CONVERSELY WE MAY HAVE NOT
NAILED ADDITIONAL PATH WAYS
INVOLVING RECEPTORS OR GTPS
SIGNALING THAT COULD BE
CONSIDERED AS INDEPENDENT NOSED.
SO ALREADY, FROM THESE STUDIES,
WE FEEL LIKE WE ARE GRAVITATING
TOWARDS THE KINDS OF
COMBINATIONS THAT IF WE COULD
TEST THEM CLINICALLY, WOULD BE
HIGH ON OUR PRIORITY LIST
BESIDES WHAT WE HAVE LEARNED
GENETICALLY AND EXPERIMENTALLY.
LET ME SKIP THIS SLIDE IN THE
INTEREST OF TIME.
IN THE LAST REALLY THREE-4
MINUTES, BECAUSE I WANT TO LEAVE
TIME FOR QUESTIONS, I WANT TO
COME BACK TO THE ULTIMATE TEST.
WE HAVE TALKED ABOUT KNOWLEDGE
OF SALIENT DRIVERS AND TALKED
ABOUT LEVERAGING UNDERSTANDING
THE RESIST TONES COME UP WITH
NOVEL COMBINATIONS.
WHAT ABOUT THE HERE AND NOW WITH
THE INGREDIENTS WE HAVE IN
PLACE?
THIS REALLY GETS DOWN TO
CLINICAL TESTING OF THE
PRECISION MEDICINE HYPOTHESES
AND RECENTLY AT THE DANA
FASCIAER AND THE BRODE, WE HAVE
INITIATED A PROJECT WHICH WE
CALL CAN SEQT STARTED WITH A
GRANT THAT CAME FROM THE ACRL
ALTHOUGH IT WAS THE MOAN WAS TO
FUND THIS CANCER EFFORT WAS
SUPPORTED BOY NCI SOO ARE VERY
GRATEFUL FOR THAT.
THE FOLK US THAT GRANT IS LUNG
CANCER AND COLORECTAL CANCER AND
THE NOTION IS WE WILL DO
PERSPECTIVE WHOLE EXOME
SEQUENCING AND ADD TRANSCRIPTOME
ON PATIENTS AT THE DANA FASCIAER
AND BRIGHAM AND RETURN
ACTIONABLE INFORMATION TO THE
CLINICAL CARE TEAM.
THIS IS NOW BEING ADDED AND IN
ADDITION WE ARE LAUNCH SOMETHING
STUDIES WITH ERIC IN BREAST
CANCER AND STUDIES TOGETHER WITH
GEORGE IN SARCOMA.
WE HAVE A 5-PRONGED APPROACH TO
CAN SEQ THUS FAR IN WHICH
SPECIMENS ARE RETRIEVED AT THE
DANA FARBER AND BRIGHAM AND DNA
IS EXTRACTED AND IN SOME CASES
RNA AS WELL AND THE REPORT WILL
BE MADE AVAILABLE TO THE
TREATING ONCOLOGIST.
SO, BRIEFLY WE HAVE A SERIES OF
ALGORITHMS THAT HAVE BEEN
DEVELOPED AND WE ARE REITERATING
AND BOY A COLLABORATION WITH TWO
MEDICAL ONCOLOGY FELLOWS, ELLIE
VAN ELLEN AND NICK, IN THE LAB,
AND SO THERE ARE A VARIETY OF
APPROACHES WHERE WE CAN BOTH
BEND THE SAMPLES BASED ON
ACTIONABILITY AND INVESTIGATE
THEIR RELEVANCE AND ALSO BEGIN
TO LOOK AT VARIANCE AMONG
CERTAIN SIGNIFICANTS AND MAP
THOSE AND WE HAVE DEVELOPED A
REPORT THAT IS ONLINE AND
ACTUALLY WE PLAN TO MAKE THIS
AVAILABLE BROADLY QUITE SOON
BECAUSE IT'S MORE OR LESS READY
TO GO.
BUT WE HAVE WAYS IN WHICH THE
COMMITTEE EVALUATES THIS RAPIDLY
CLICK AND SEE THE CONTENT OF
WHAT IS COMING OUT OF EXOMES.
THERE HAVE BEEN A VARIETY OF
INTERESTING EXOME THAT IS HAVE
EMERGED THUS FAR.
SOME OF WHICH HAVE MULTIPLE
DRUGABLE ALTERATIONS AND OTHERS
THAT HAVE VARIANCE OF
SIGNIFICANTS BUT THEY OCCUR IN
DRUGABLE ONCOGENES AND THERE ARE
STILL OTHERS WHERE WE SEE
PLAUSIBLY ACTIONABLE ALTERATION
THAT IS ARE OFF THE BEATEN PATH
SUCH AS BCL6 MUTATIONS WHICH WE
DIDN'T KNOW ABOUT BEFORE.
AND THIS IS A SOBERING REMIND
THEY'RE AS WE THROW THE KITCHEN
SINK AT SAMPLES GENOMICALLY, WE
FIND STILL CASE WHERE IS THERE
IS VERY THE TO DO FROM A
NATIONAL STANDPOINT.
WE SEE ONLY PEOPLE WITH
MUTATIONS AND NOTHING ELSE OR
THIS STRIKING CASE OF A SARCOMA
THAT HAD BECOME RESIST WANT TO
RADIATION.
WE SAW NO ALTERATIONS THAT WERE
ACTIONABLE.
THERE IS NOT GOING TO BE THE END
ALL BUT IT'S A GREAT WAY TO GET
US STARTED.
LET ME IN THE INTEREST OF TIME,
CLOSE BY COMING BACK TO THIS ARK
TYPE BUT PIECES OF THIS ARK TYPE
ARE CLEARLY IMPLEMENTABLE NOW
AND BEING IMPLEMENTED IN MANY
CANCER CENTRES AROUND THE
COUNTRY AND AROUND THE WORLD
WHERE WE HAVE BEGUN WITH THE
PATIENT AND WE ARE HOPING TO
BLEND BIOPSIES WITH PROFILING
AND NOVEL APPROACHES TO DATA
INTERPRETATION AND ULTIMATELY
MEASURING RESPONSE AND
RESISTENCE IN THIS APPROACH.
THE KNOWLEDGE THAT EMERGES CAN
BE BLENDED WITH PRECLINICAL
STUDIES, COMPANION PRECLINICAL
EXPERIMENTAL STUDIES TO REFINE
OUR UNDERSTANDING ON THE
BIOLOGICAL END AND ALSO TO
REFINE OUR THINKING ABOUT HIGH
PRIORITY NOVEL THERAPEUTIC
COMBINATION THAT MIGHT HAVE A
GREAT CHANCE AT ACHIEVING
DURABLE CONTROL OF MANY
DIFFERENT CANCER TYPES.
AND I LIKE TOW CLOSE BY THINKING
A NUMBER OF PEOPLE WHO HAVE BEEN
INVOLVED.
I'LL HIGHLIGHT ERAN WHO LED THE
MELANOMA LANDSCAPE STUDY
TOGETHER WITH EON WATSON AND
LINDA'S LAB AND COREY AND ELLIE
AND STEVEN WHO HAS DONE THE RNAI
SCREENING WORK.
AND WITH THAT I'LL TAKE
QUESTIONS IF THERE IS TIME.
[ APPLAUSE ]
>> YOU BEGAN YOUR TALK BY SAYING
THERE ARE A LOT OF MUTATIONS AND
PROBABLY YOU'RE NOT RESPONSIBLE
FOR MELANOMA AND ENDED BY SAYING
THERE ARE A WHOLE VARIETY OF
DIFFERENT BOY PASS ALTERATIONS
THAT WILL GO PASS SOME INITIAL
GROWTH MOW MEETING PATHWAYS AND
YOU GOT A LOT OF DATA BASED ON
TRANSFECTION EXPERIMENTS AND
KNOCKOUT EXPERIMENTS AND SO ON.
SO OBVIOUSLY IT WOULD BE GREAT
TO KNOW IN THAT PATIENT WHO HAD
HUNDREDS OF MELANOMAS AND ALL
WHICH BECAME RESISTANT, BUT
LACKING THAT INFORMATION IS
THE -- THERE ARE ANY INDICATION
THAT THE GENES THAT GIVE YOU
ALTERNATIVE PATHWAYS TO BOY PAS
RESISTENCE ARE IN ANY WAY
RELATED TO THE GENES THAT COME
UP FROM THE INITIAL MELANOMA?
ANY CORRESPONDES TO THAT?
>> THAT'S A GREAT QUESTION.
SO THE QUESTION IS WHETHER OR
NOT ARE THE MUTATIONS ASSOCIATED
WITH RESISTENCE DIFFERENT THAN
THE STEADY STATE OR OR OVERLAP?
THERE IS A LOT OF OVERLAP.
NRAS MUTATIONS ARE SEEN AT
BASELINE IN 15-20% OF MELANOMAS
AND N RAS THE SAME MUTATIONS CAN
ARISE AS A MECHANISM OF ACQUIRED
RESISTENCE.
MEK ONE MUTATIONS ARE SEEN AT
PROBABLY ABOUT 5-10% FREQUENCY
AT THE STEADY STATE BUT CLEARLY
ASSOCIATED WITH ACQUIRED
RESISTENCE TO MELANOMA THUS FAR,
WHAT WE HAVE SEEN GENETICALLY
OVERLAPS STRONGLY WITH THE
STEADY STATE WHICH SPEAKS TO
WHAT YOU'RE SAYING.
UNDOUBTEDLY A LOT OF
HETEROGENEITY WE ARE NOT
MEASURING.
SO WHAT WE SEE ACROSS MANY
INDIVIDUALS CAN BE ACTIVE AT
VARIOUS POINTS DURING THE
BIOLOGY.
SO I THINK AN IMPORTANT POINT TO
EMPHASIZE HERE IS THAT WE'RE NOT
REALLY THROWING THEM OUT.
WE ARE JUST SAYING IF YOU WANT
TO DISCOVER THE DRIVERS, YOU
HAVE TO HAVE A SCENARIO WHERE
YOU'RE NOT BEING CONFOUNDED BY
PASSENGERS.
BUT IT'S NOT TO SAY THAT ALL THE
GENES THAT WERE THROWN OUT ARE
PASSENGERS.
AT 121 SAMPLES, THIS IS A
STATISTICAL TEST SO LIMITED BY
POWER AND THE HIGHER THE
MUTATION RATE IN THE CANCER
TYPE, THE MORE SAMPLES YOU NEED
TO SEQUENCE TO BE EQUIVALENTLY
POWERED.
SOMETHING THAT MAY BE IS A
PASSENGER AT ONE POINT COULD BE
ACTED ON BOY EVOLUTION LATER IN
THE CANCER.
>> NICE TALK.
URE MENTIONED THAT THE
-- [ INDISCERNIBLE ]
>> IT'S THE ANALOGOUS RESIDUE.
SO IN RAC 1 IT'S CODON 29 AND IN
CDC42 IT'S THE ANALOGOUS CODON
OF SO IT'S EXACTLY FUNCTIONALLY
THE SAME MUTATION.
>> SOS ARE THOSE MUTATIONS
-- [ INDISCERNIBLE ]
[ INDISCERNIBLE ]
>> SO WE HAVE NOT SEEN THE
EQUIVALENT TO CODON 12 AND CODON
61 MUTATED IN MELANOMA BUT
PEOPLE HAVE MADE THE MUTATIONS
IN RAF ONE.
ONE POINT I SHOULD MAKE AND I
HAVEN'T LOOKED AT THE SPECIFIC
RESDO YOUS BUT THE L.A. ONE
MUTATION IS A CDC
TRANSITIONITION -- THE RAF 1.
AND SO YOU CAN IMAGINE THAT
MUTATIONS THAT ARE CDC
TRANSITIONED THAT ARE ACTIVATING
ARE MORE LIKELY TO BE SEEN.
I THAN CODON 12 IS NOT A CDC
TRANSITION IT'S A TRANSVERSION.
SO IT MAY BE THAT SOME OF THESE
MUTATIONS WHICH ARE ACTIVATING
IN OTHER CONTEXT ARE JUST
STATISTICALLY LES LIKELY TO
OCCUR IN MELANOMA AND GIVEN THAT
RAC ONE MUTATIONS ARE ALREADY
LOW FREQUENCY EVENTS.
JUST EVEN THOUGH THEY MAY
THEORETICALLY OCCUR, IT IS JUST
BELOW THE FREQUENCY OF DETECTION
WE HAVE 120.
>> ONE MORE QUICK QUESTION.
>> SO WHEN YOU TAKE THESE
MELANOMA CELLS WITH MUTATION IN
RAC, CAN YOU TEST IT WHETHER OR
NOT THE ACTIVITY FOR
-- [ INDISCERNIBLE ]
>> GREAT QUESTION.
WE HAVE A COUPLE OF THAT HAVE
RAF 1 MUTATIONS.
WE DON'T HAVE CD42 AS A CELL
LINE.
AND THE SHORT ANSWER IS, YOU CAN
DETECT RAF ACTIVATION BUT TO SAY
IT'S HIGH COMPARED TO OTHER
CELLS IS ACTUALLY THUS FAR MAYBE
YOU WERE JUST OUR ASSAYS ARE NOT
SENSITIVE ENOUGH.
WE CAN'T SAY IN THE STEADY STATE
IT'S GREATER THAN WHAT YOU MUTE
SEE WITHOUT THE MUTATION.
INCH DODGINESS CAN BE TRICKY --
ENDOGENOUS.
>> [ INDISCERNIBLE ]
>> SO I THINK NOW WITH THE
LATEST ALGORITHM, WE HAVEN'T
REMOVED THEM BECAUSE IF YOU'RE
COMPARING WITH WITHIN A SAMPLE
EXON TO INTRON MUTATION RATE IT
DOESN'T REALLY -- IT'S A RATIO
SO IT DOESN'T REALLY HURT YOU.
BUT THERE HAVE BEEN OTHER GENOME
PROJECTS WHERE ONE SEES A
CERTAIN DISTRIBUTION MUTATION
RATE AND THEN OUTLIERS WHERE RUE
MOVING THE OUTLIERS HAS BEEN
HELPFUL BECAUSE OTHERWISE YOU
SEE MUTATIONS ALL OVER THE
PLACE.
PARTICULARLY WHEN YOU'RE TALKING
ABOUT LOW FREQUENCY EVENTS, YOU
WORRIED IT'S BEING SKEWED BY ONE
OR TWO SAMPLES.
>> SO I WANT TO GET BACK TO
MICHAEL'S QUESTION AS IT RELATES
TO INHERENT TO ACQUIRED.
SO YOU HAVE ALL THESE UVB
MUTATIONS AND WE SEE THEM IN OUR
MOUSE MODELS AS WELL.
I DON'T KNOW IT CAUSES ALL THIS
THIS ONE SHOT OR MULTIPLE TIMES
OR WHATEVER.
THE MUTATION THANK YOU'S SEE IN
THE RECURRENT DISEASE, DID THEY
TEND TO BE UVB MUTATIONS?
ARE THEY THINGS YOU THINK ARE
LURKING AROUND IN SOME CELLS AND
THEN THEY BECOME MORE IMPORTANT
IN RESIST INNOCENCE.
>> SO, I THINK HOPEFULLY IN THE
NOT TOO DISTANT FUTURE WE WILL
HAVE ENOUGH RELAPSING SPECIMENS
WHERE I CAN GIVE YOU A ANSWER.
BUT THE SHORT ANSWER IS, YES.
THE SHORT ANSWER IS, WE HAVE NOT
GLOBALLY SEEN A DIFFERENT
DISTRIBUTION AND MUTATION.
I THINK WHAT REALLY THE KEY
THINGS IS GOING TO BE WHEN WE
HONE IN ON THE MUTATIONS THAT
ARE DIFFERENT IN THE POST
RELAPSE COMPARED TO THE
PRETREATMENT AT A EXOME LEVEL.
DOES THE DELTA, IS IT STILL HAVE
A HIGH CDT TRANSITION THAT I
CAN'T REALLY ANSWER YET.
WE HAVEN'T DONE THAT ANALYSIS.
BUT VERY SOON WE SHOULD BE ABLE
TO ANSWER THAT.
I THINK IT'S A VERY IMPORTANT
QUESTION.
>> I WANT TO LOOK AT YOUR
PROBLEM IN A VERY SIMPLE WAY.
THE LESSONS WE HAVE LEARNED THAT
IF YOU HAVE TARGETING UPSTREAM
COMPLIMENT OF PATHWAY WHICH IS
RELEVANT TO CANCER, WE SHOULD
EXPECT DOWNSTREAM ACQUIRED
MUTATION ON SOME OF
THE -- DISCERN DISEN HOPEFULLY
WE SHOULD BE ABLE TO PREDICT THE
MUTATION SO IS IT APPROPRIATE TO
SAY THAT WE HAVE DECIDED TO
TARGET UPSTREAM COMPLIMENT OR
GENE THAT WE SHOULD GET READY
FOR TARGETING DOWNSTREAM GENE
BECAUSE IN VARIABLY WE WILL GET
THAT MUTATION?
>> I THINK IT'S AN INTERESTING
GENERAL THEME THAT ONE COULD LOB
UP WOULD BE TO SAY, IF WE HAVE
EITHER PREDICTED OR
EXPERIMENTALLY THAT YES THIS
DOWNSTREAM PATHWAY IS ALWAYS A
MECHANISM RESISTENCE, WHY NOT GO
IN WITH AN UPFRONT COMBINATION
THAT HITS THE INDEX ONCOPROTEIN
AND THE DOWNSTREAM PATHWAY?
THAT'S ESSENTIALLY WHAT THE RAF
MEK COMBINATION ATTEMPTS TO DO
PARTIALLY BUT MAYBE IN LUNG
CANCER AND OTHER CANCERS ONE
SHOULD TRY THAT AS WELL.
I THINK IT'S A VERY INTERESTING
AND PEOPLE ARE CERTAINLY --
>>
WORTH TRYING.
I THINK WE ARE OUT OF TIME FOR
QUESTIONS IF I READ YOU
CORRECTLY.
>> LET'S THANK DR. LEVI GARRAWAY
FOR AN EXCITING TALK AND HELPING
US STARTED OUR SERIES THIS YEAR
SO WELL WE HAVE A RECEPTION THAT
IS SUPPORTED THROUGH THE
FOUNDATION FOR THE ADVANCED
EDUCATION OF SCIENCE IN THE
LIBRARY AND A CHANCE TO CHAT
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