TRACO 2019 – Topoisomerase and Precision medicine
Articles,  Blog

TRACO 2019 – Topoisomerase and Precision medicine


TODAY WE HAVE YVES POMMIER AS
OUR FIRST SPEAKER, M.D. AND PhD, University of
Paris then he came to NIH, he’s chief of developmental
therapeutics branch, and he plays the role in
the NCI development of therapeutics program, several
other committees as well, and he serves as an editor
in cancer research. HE ALSO HAS DONE SEVERAL GORDON
CONFERENCES, RECEIVED AWARD FROM SOCIETY OF
COMEE TALKING TODAY ABOUT TOPOISOMERASE.>>THANK YOU, TERRY. THANK YOU, EVERYBODY. THIS IS NOT RELATED TO ONE
DISEASE BECAUSE
WE’RE TALKING ABOUT ENZYME. WE’RE TALKING ABOUT UBIQUITIN
ENZYMES, DNA TOPOISOMERASES ENZYMES. THERE ARE SEVERAL REVIEWS THAT
YOU COULD G
O BACK TO AND A NUMBER OF SLIDES ARE FROM
THESE REVI
EWS. SO, THESE ARE PROBABLY MORE OF A
DRUG ORIE
NTED ASPECT OF TOPOISOMERASES. AND THE FACT THEY ARE VERY
IMPORTANT FOR M
EDICINE BECAUSE THEY USE THE
TOPOISOMERASE INHIBIT
ORS ARE USED TO TREAT CANCER AND USED TO
TREAT BAC
TERIAL INFECTIONS, INCLUDING
TUBERCULOSIS. AND I THINK THIS IS STILL AN
ONGOING PROJE
CT, STILL BEING DEVELOPED. MOST RECENT REVIEW WHICH I THINK
NOW HAS A
LARGE NUMBER OF CITATIONS, THE ONE WE
WROTE WITH
JOHN NITISS, UNIVERSITY OF CHICAGO,
JOHN AND I
WERE STARTED IN THE FIELD MANY YEARS
AGO WHEN T
HE FIELD WAS STARTED WITH THE DISCOVERIES
OF THE FI
RST TOPOISOMERASES, AND THEN SOON
AFTER THE DI
SCOVERY OF THE STRUCTURE OF DNA, IT WAS
CLEAR THE HEL
ICO RAISED THE PROBLEM, TOPOISOMERASES WERE
DISCOVERE
D. THERE’S A BOOK YOU CAN FIND IN
THE LIBRARY
, ON ALL THE TOPOISOMERASES AND CANCER,
SO THERE AR
E DIFFERENT ASPECTS OF THAT. SO THIS IS IN THE LIBRARY. I THINK IT’S ONLINE AS WELL. SO, WHY DO CELLS HAVE
TOPOISOMERASES AND W
HAT DO THEY DO? THE ISSUE WITH DNA IS BECAUSE
IT’S HELICO,
IT’S A RIGID POLYMER, AND DNA TENDS TO
MAKE SUPER
COIL, SO THE STRANDS TEND TO WRAP AROUND
EACH OTHER
, THAT’S WHAT WE CALL SUPERCOIL. AND WHEN THE DNA IS RELAXED,
SHOULD TAKE A DOUBLE-STRANDED DNA, WHEN YOU
OPEN IT UP,
YOU GENERATE ON THE FLANK OF THE
BUBBLE THAT Y
OU’RE OPENING, SUPERCOILS, SO ON ONE
SIDE YOU GE
T POSITIVE SUPERCOIL, ON THE OTHER SIDE
NEGATIVE SUPE
RCOIL. THE TOPOISOMERASES DO THAT, ALL
THE TOPOIS
OMERASES DO THAT. TOPO 1, TOPO II, TOPO II BETA
THEY DO IT E
VERYWHERE. TOPO 3S, NEGATIVE DNA, THE OTHER
IS WHEN D
NA IS REPLICATED, IF YOU REPLICATE A
CIRCLE, SUP
ERCOIL, YOU END UP WITH THE TWO CIRCLES
WILL BE IN
TERTWINED, IN BACTERIA, VIRUSES, IN HUMAN
CHROMATINS
WHEN LOOPS DUPLICATE THEY TEND TO BE
INTERTWINED, YOU
NEED TO OPEN, LET THE OTHER STRAND GOES
THROUGH, DECATINATION. THE ENZYME CAN PASS ONE DUPLEX
THROUGH THE
OTHER, UNKNOTTING, BUT COULD ALSO KNOT. IT’S NOT UNLIKELY GENOME IS
KNOWN, IT HAS
KNOTS, ON THE ROPE WHEN YOU GO SAILING THE
KNOTS ARE
USED TO MAKE PARTICULAR PULLS, MARKS,
THAT’S PROBA
BLY ALSO IN HUMAN CHROMATIN. ALSO OTHER STRUCTURES MAY EMERGE
WHEN YOU
HAVE WHAT WE CALL HOLLIDAY JUNCTIONS, TWO
DUPLEXES A
RE GETTING INTERTWINED DURING
RECOMBINATION, TOPO3 AL
PHA, AND R & D LOOPS, THIS COULD BE ALSO
WITH TOPO3,
SO TOPO3 BETA FOR EXAMPLE CAN DO THAT AND
CAN ALSO
UNKNOT& SINGLE-STRANDED RNA WHEN THE RNA
MAKES KNO
TS, THERE’S A VERY BROAD RANGE OF
ACTIVITY OF
THEY ENZYME. IF YOU TAKE A HUMAN CELL, THERE
ARE SIX EN
ZYMES, AND THE NOMENCLATURE IS GOOD TO KNOW
BECAUSE T
HE 1A ENZYME OF THE TOPO3 BETA, AND
1B, SO TYPE
1 ENZYME CLEAVES ONE STRAND, SO TOPO 1
AND TOPO 3 C
LEAVE, AT THE TIME THE TYPE 2, DUPLEX OF
DNA, SO TOP
O 2 AND TOPO 2 BETA AND HUMANS HAVE SIX. E. COLI DON’T HAVE 1B, EMERGED
FROM VIRUS
THAT INFECTED EARLY CELL AND THEN WAS
HIJACKED
TO RELAX DNA. BUT E. COLI HAS ONE. TOPO 1 AND 3, GYRASE AND TOPO4. TOPO 1 AND 1MT, ANTI-CANCER
TARGET OF WIDE
LY USED DRUGS, TARGET CAMPOTOTHECINS. GYRASE AND TOPO-IV HAD TARGETS
OF QUINOLON
ES. AND THEY DON’T CROSS OVER. SO THE ANTIBACTERIALS DO NOT
POISON THE HO
ST ENZYME. BUT THE TOPO-II INHIBITORS TO
NOT POISON T
HE BACTERIA, SO THERE ARE DIFFERENT
DRUGS. IF YOU THINK OF THE TOPO, I AND
III, ODD N
UMBERS HAD SINGLE STRAND BREAKING. IT WILL MAKE A KNICK, SINGLE
STRAND BREAK,
KNICK, AND THE NICK IS THEN USED TO
RELAX DNA. THE DRUGS ARE SPECIFIC FOR EACH
CLASS, BIN
D, WHICH IS THE CLEAVAGE COMPLEX. SO THESE ARE CLEAVAGE COMPLEXES,
THIS IS T
HE NAME GIVEN. WE AND THERE IS NO INHIBITOR FOR
TOPO 3, THER
E ARE SIX ENZYMES, MOLECULAR SIDE, TOPO 2
IS HOMODIM
ER, VERY LARGE PROTEIN, HOMODIMERS, TOPO
2 ALPHA AN
D BETA. IF YOU TAKE A HUMAN CELL THERE
ARE TWO KIN
DS OF GENOMES, NUCLEAR DNA AND
MITOCHONDRIAL DNA
. DEPENDING ON THE CELLS, THE
AMOUNT OF MITO
CHONDRIA COULD BE UP TO 5% OF THE
CELLULAR GENOME I
S MITOCHONDRIAL DNA. THE TOPO 1 IS SPECIFIC FOR
NUCLEAR TOP1MT
IS SPECIFIC FOR THE MITOCHONDRIAL
GENOME, THE
RE’S A CLEAR DIVISION OF LABOR, TOP1MT. FOR TOP 2 ALPHA AND BETA, THEY
GO IN BOTH. ALSO BOTH GENOMES HAVE THEIR OWN
REPAIR EN
ZYMES, I WILL DESCRIBE THAT AT THE END. LET’S TAKE THEM ONE AT THE TIME,
START WIT
H TOP 1 AND THE REPAIR. TOP 1, THERE ARE TWO NUCLEAR. WHEN WE DISCOVERED TOP1MT, IN
2000, WE DEC
IDED NOT TO CHANGE THE NOMENCLATURE AND
NOT TO CALL
TOP1 ALPHA AND THE BETA, WE DECIDED
TO CALL IT
MT, MITOCHONDRIAL, BECAUSE IT WAS
SPECIFIC FOR MITOCHONDRIA. SO AS I SAID, THE DIFFERENCES
BETWEEN THE
TOPO 1 AND TOPO 2 ARE MAJOR. THEY ARE BOTH TOPOISOMERASES BUT
ARE DIFFE
RENT. ONE A MONOMER, ONE A DIMER, TOPO
2 MAKES D
OUBLE STRAND BREAK STAGGERED BY FOUR
BASE PAIR. THE BREAKAGE OF THE DNA
INCUMBENT THE ENZY
ME USES TYROSINE. YOU SEE FOR TOPO 1, TARGET DNA
BACKBONE, A
ND FOR 2 IT’S ALSO TARGETING, BUT THE
POLARITY IS D
IFFERENT. IN THE TASTE OF TOPO 1 IT LINKS,
SO THIS I
S PROBABLY THE MOST CANONICAL MECHANISM FOR
TOPOISOME
RASE IN CLEAVAGE OF THE BACKBONE. IT CLEAVES THE BACKBONE, AND
ENABLING ANOT
HER STRAND TO PASS THROUGH THE BROKEN. 1 DOESN’T USE ATP, HAS ITS OWN
INHIBITORS,
TOPO 2 CONSUMES ATP, REQUIRES
MAGNESIUM AND HAS
ITS OWN SET OF INHIBITORS. TOPO 1, DNA UNTWISTING ENZYME,
IF YOU WANT
TO CALL IT THIS WAY, CRYSTAL STRUCTURE
SHOWS THE E
NZYME BINDS THE DNA AND MAKES A
COVALENT BOND TO
ONE OF THE ENDS OF THE DNA, AND THEN
THE OTHER ST
RAND ROTATES INSIDE THE ENZYME, TO
CONTROL ROTA
TION THAT DISSIPATES THE SUPERCOIL,
REALIGNS AND THE
N THE DNA RELIGATES. TOPO 1 IS ESSENTIAL FOR
TRANSCRIPTION AND REPLICATION, DISSIPATES THE
SUPERCOIL AND POTENTIALLY FOR DNA REPAIR. YET IN YEAST THE KNOCKOUT OF
TOPO 1 IS VIA
BLE, COMPENSATED BY TOPO 2 AND 3, BUT
IN MOUSE
CELLS, HUMAN CELLS, TOPO 1 IS
ESSENTIAL. SO, WHAT I DESCRIBED AT THE
BEGINNING, THI
S IDEA WHEN DNA IS BEING TRANSCRIBED OR
REPLICATE
D, TRENDS BEING SEPARATED BY HELICASE,
WHAT HAPPENS
WHEN YOU HAVE A NUCLEAR MATRIX ATTACHMENT
GENERATE
SUPERCOIL ON ONE SIDE, NEGATIVE SUPERCOIL
ON THE BAC
K. FOR THE MOVEMENT YOU NEED TO
DISSIPATE THE SUPERCOIL, OTHERWISE YOU CANNOT
MOVE ALONG
THE DNA DUPLEX. AND THIS DISSIPATION IS MOSTLY
DONE BY TOP
O 1, BINDING IN HELICO DOMAIN, ENABLE
DISTRIBUT
ING. FORMS CLEAVAGE COMPLEX NORMALLY
AS WE SPEA
K YOU’RE DOING IT ALL THE TIME, RELAXING
THE DNA, N
OTHING HAPPENS. CLEAVAGE COMPLEXES ARE
INVISIBLE. EXCEPT WHEN THERE IS A DRUG LIKE
TOPO 1 IN
HIBITOR GIVEN TO A CANCER PATIENT, THE
DNA IS DAMA
GED, THEN RELIGATION IS NOT PROPER,
CLEAVAGE COMPLEX
ES CAN FORM. THIS IS IMPORTANT BECAUSE THIS
IMAGE COMPL
EX IN ADDITION TO DRUGS CAN BE INDUCED
BY DNA LE
SIONS, SOME FREQUENT, BASIC
CARCINOGENIC ADDUCTS,
THIS IS THE REASON SOME NEUROLOGICAL
SYNDROMES WHE
N THERE ARE DNA REPAIR DEFICIENT — DNA
REPAIR IS
ALTERED, REPAIR IS ESSENTIAL. SO, THE TWO TOPO 1, NUCLEAR AND
MITOCHONDR
IA TOPO 1, DIFFERENT BY N-TERMINUS, UNCODED
IN TWO CH
ROMOSOMES, NUCLEAR TOP 1, SEQUENCE, TOP1MT
WHICH EMER
GED IN VERTEBRATES, THERE ARE TWO, AND
IT HAS A MITOCHONDRIAL TARGETING
SEQUENCE, VERY SHO
RT BUT VERY EFFICIENT IN THE
N-TERMINUS. IN THAT SENSE THE MITOCHONDRIA
IN TOP 1 LO
OKS LIKE THE VIRAL TOPO 1, IF YOU TAKE
THE VACCINIA
, IT’S A SHORT TRUNCATED VERSION OF THE
HUMAN CELL. SO TOPO 1s ARE THEIR OWN
SPECIFIC INHIBITO
RS, DISCOVERED BY NCI, OUT OF THIS
SCREEN OF P
LAN EXTRACTS IN THE 1970s, BUT THE
NCI WAS LOO
KING FOR NEW CURES FOR CANCER, NEW DRUGS,
NATURAL P
RODUCTS, AND FOUND THIS VERY ACTIVE TOXIN
FROM THIS
PLANT, CAMPTOTHECIN, THE PRESENCE OF
THE CHEMICAL
IN THE PLANS. THIS CAMPOTHECIN IS VERY
UNSTABLE. TODAY THERE ARE TWO USED
CLINICAL AT THE C
LINICAL CENTER EVERYWHERE IN THE WORLD,
CAMPTOTHEC
IN DERIVATIVES, MODIFIED TO MAKE
THEM WATER S
OLUBLE BECAUSE CAMPTOTHECIN IS WATER
SOLUBLE. THE PRO DRUG, METABOLITE, OTHER
CAMPTOTHEC
IN IN OTHER PARTS OF THE WORLD. THEY DO THEY BLOCK TOPO 1? WE DISCOVERED THAT SOME YEARS
AGO, TO DISC
OVER A PARADIGM FOR DRUG MECHANISM OF
ACTION. CAMPTOTHECIN LOOKS LIKE A BASE
PAIR, WHEN
WE LOOKED, THIS IS A TOPO CLEAVAGE COMPLEX
WHICH GOES
BACK AND FORTH, WHEN YOU PUT
CAMPTOTHECIN, YOU GET
A BREAK, BINDING AT INTERFACE HERE, BASED
ON DNA AN
ALYSIS AT THE TIME, TOOK TEN YEARS TO
CONFIRM CAMPTO
THECIN, THIS IS THE DERIVATIVE, IN GREEN
IS DNA, T
HIS IS THE BREAK, AND YOU CAN SEE THE DRUG
BEAUTIFULL
Y INSIDE THE CLEAVAGE COMPLEX. SO THIS IS WHAT WE CALL THE DRUG
DOESN’T B
IND ALONE, OR TO DNA ALONE BUT NATURE
SELECTED THAT D
RUG TO BIND ONLY IN THAT PARTICULAR
POCKET. AND WHEN IT BINDS, THE TOPO IS
SEQUESTERED
INTO CLEAVAGE COMPLEX, CAN STILL
EVENTUALLY GO
BACK BUT ONCE THE DRUG IS IN IT IT WILL
ACTUALLY PO
ISON THIS. SO WE CALL THAT THE ENTER FACIAL
INHIBITIO
N BECAUSE THE DRUG BY THE INTERFACE OF
TOPO 1 AND DN
A. ANOTHER POINT THAT CAME VERY
EARLY, VERY E
ARLY IN YOUR LIFE, 1988 WHEN THE
CAMPTOTHECINS WER
E LOOKED AT BEFORE THEY WERE APPROVED IN
2000, IT W
AS NOTED THAT IN YEAST THE CAMPTOTHECIN
WERE INACTI
VE. WHAT WAS FOUND INSTEAD OF SAYING
THAT YEAS
T COULD NOT TAKE UP CAMPTOTHECIN, IS
THAT BY DOING
MUTANTS OF RECOMBINATION, THEY WERE ALL
SENSITIVE
TO CAMPTOTHECIN. MOREOVER, IF YOU KNOCK OUT TOPO
1 IN THOSE
, THEY BECOME RESISTANT AGAIN. THIS WAS CONFIRMED IN A PAPER IN
1988, AND
CLEARLY SHOWING KEY PATHWAY FOR SURVIVAL
TO CAMPTO
THECIN, AND TO ME HISTORICALLY THIS SAYS
CAMPTOTHE
CIN WAS THE FIRST DRUG SHOWING LETHALITY
IN HOMOLO
GOUS RECOMBINATION CELL, FIRST
DISCOVERED FOR T
HE CAMPTOTHECIN, 1988, NOT 2012. NEW TOPO 1 INHIBITORS USED IN
CLINICAL CEN
TERS, BECAUSE CAMPTOTHECIN WERE
EFFECTIVE, TOP 1
WAS VALIDATED, WE KNOW AMONG DRUG
THOUGHTS IF
YOU TAKE CHEMICAL CLASS THEY HAVE
DIFFERENT ANTI-CA
NCER ACTIVITY. FOR EXAMPLE, COLCHICINE IS USED
TO TREAT G
OUT, VINBLASTINE TO TREAT CANCER,
CHEMICALLY TH
EY LOOK DIFFERENT. THE IDEA MAYBE WE SHOULD LOOK
FOR OTHER CH
EMICALS, ALSO WE KNEW CAMPTOTHECIN HAD
LIMITATIONS,
SPECIAL TOXICITY, DRUG SUBSTRATE,
CHEMICAL INSTABI
LITY IS WHAT I TOLD YOU, IN THE BLOOD IN
MINUTES C
ONVERTED TO CAROBXIATE, BINDING TO
CLEAVAGE COMPLEX
, WE DEVELOPED TOP 1 INHIBITORS, AND
DEVELOPMEN
T NOW IS BEING BETTER UNDERSTOOD IN
CONTEXT OF THE
FACT THAT CAMPTOTHECIN IS COLLECTIVE FOR
BRCA. DRUGS THAT HAVE GONE THROUGH THE
CLINIC NO
W WERE MADE AT PURDUE UNIVERSITY. WE STARTED THIS EFFORT IN 1998,
AND IT TOO
K MANY, MANY YEARS TO GET THE DRUG TO
THE CLINIC B
UT NOW THEY ARE IN THE CLINIC. ONE IS LMP400, AND LMP776 AND
LMP744. THESE DRUGS RECENTLY ABOUT A
YEAR AGO WE R
ELEASED DATA WHERE WE TESTED DRUGS IN
THE CONSORTI
UM OF NCI. SO THESE ARE CLINICS AROUND THE
UNITED STA
TES, AND THE OWNER OF DOGS WHO HAVE
CANCER CAN BRIN
G THE PETS TO THE CLINIC AND THEN GET AN
EXPERIMENTAL
TREATMENT FOR NO COST. WE DECIDED TO LOOK AT THESE
DRUGS IN DOGS
WITH TUMORS. AND WE COMPARED THREE OF OUR
INHIBITORS, A
ND WE DID LYMPHOMA. THE IDEA WAS TO COMPARE ACTIVITY
OF THE TH
REE DRUGS TO DO PHARMACOKINETICS, EASIER
IN DOGS THA
N HUMANS, LOOK AT TARGET ENGAGEMENT, WITH
JAMES DORO
SHOW, AND AMY LEBLANC, RUNNING THE
VETERINARY TRIALS
, AND IT TURNED OUT SURVIVAL TUMOR
RESPONSE PLOT IN
ALL THE DOGS, EACH BAR IS A DOG, IF IT
GOES UNDER
IT MEANS YOU GET ACTIVITY. THE COMPOUND IN MOST OF THE
DOGS, THIS ONE
WAS THE BEST COMPOUND ACTUALLY IN THE
TRIAL, WHICH
IS INITIALLY NOT PUT IN THE CLINIC. SO, AT THIS STAGE WE FOUND THAT
THE TWO CL
INICAL COMPOUNDS WERE ACTIVE IN DOGS
AND THEREFOR
E THAT PUSHES FOR PHASE 2 CLINICAL
TRIAL, AND THE
THIRD COMPOUND WAS EVEN BETTER. THE DOSE, BONE MARROW IS
EXPECTED FOR CHEM
OTHERAPY, NO DIARRHEA, A BIG DEAL BECAUSE
CAMPTOTHEC
IN HAS THIS PROBLEM, AND LONG
HALF-LIFE, SHOWS TU
MOR RETENTION, SHOW TARGET
ENGAGEMENT. SO, HAVING DONE THIS SO FAR WITH
THE TOP 1
INHIBITOR THE NEXT QUESTION BECOMES WHEN
YOU START F
ACE 2 CLINICAL TRIAL YOU HAVE TO
SELECT FOR PATI
ENT SUSCEPTIBLE TO RESPONSE AND
MEASURE SOMETH
ING THAT WILL MAKE HYPOTHESIS. THE IDEA IS TO HAVE A MOLECULAR
SIGNATURE.
& WHO WILL RESPOND? SO I’VE TOLD YOU ALREADY HRD,
BRCA PATIENT
S SHOULD RESPOND, THE OTHER THING WE
DISCOVERED IS DETRIMENTAL RESPONSE, SLFN11,
GENE EXPRESS
ION MARKER, WHICH IS IMPLEMENTED IN
THE CLINI
C. WE’RE DOING TARGETED DELIVERY TO
MINIMIZE
SIDE EFFECTS. THE NEXT PHASE DONE ALREADY FOR
CAMPTOTHEC
IN, THE PAYLOAD, COUPLED WITH
ANTIBODIES. MOST PROMISING COMPOUND FROM
JAPAN IS CAMP
TOTHECIN DERIVATIVE WITH HER-2 ANTIBODY,
RESPONSES
ARE VERY, VERY GOOD. IT’S VERY LIKELY THE DRUG IS
GOING TO BE F
DA APPROVED BY THE END OF THE YEAR,
OR VERY E
ARLY NEXT YEAR. SO WE’RE PUTTING OUR OWN DRUGS
ONTO THAT P
ARTICULAR APPROACH. SO, TOP 2, ALPHA AND BETA, I
CALL THEM TOP
2A AND TOP2B. THE DIVISION OF LABOR IS TOP2A
IS PRIMARIL
Y INVOLVED IN REPLICATION, REPLICATING DNA,
RELAXING
SUPERCOILS WHEN THEY ARISE WHEN DNA STRANDS
DUPLEX CR
OSS DURING REPLICATION. TOP2B IS MOSTLY INVOLVED IN
TRANSCRIPTION,
AND REGULATING PROMOTERS, AND
PROMOTERS ENHANC
ERS, SO THIS IS TRANSCRIPTION,
NON-REPLICATION, SO
THESE ARE THE SHAPE OF THE TWO ENZYMES,
VERY SIMILAR
. THEY ARE CATALYTIC POWER IN THE
MIDDLE, AL
PHA AND BETA ARE MOST VARIABLE IN THE
C-TERMINUS. ALL THIS PART IS VERY COMMON. IF YOU COMPARE TO BACTERIA
COUNTERPARTS, T
HEY ALSO ARE SIMILAR, EXCEPT BACTERIA,
HUMAN IS DIM
ER 2 ALPHA, TIMER 2 BETA, IN BACTERIA
YOU HAVE
A TETRIMER, BUT MACHINERY IS THE
SAME. WE KNOW ENZYMOLOGY VERY WELL. TOPO 2 TAKES TWO DUPLEXES, ONE
DUPLEX OF D
NA, ANOTHER DUPLEX OF DNA. GOES UNDER THE OTHER, NOT GOING
THROUGH, T
HIS IS GOING TO BREAK MY ARM, YOU’RE
GOING TO PUT
IT BACK, AND THEN MY OTHER ARM IS THERE. HOW DOES IT DO THIS? TWO DUPLEX, GATE AND TRANSPORT
STRAND, ENZ
YME WILL FIRST ENGAGE ONE OF THE
DUPLEXES, PUT THE
ONE ON THE TOP, CLOSE A LITTLE GATE, OPEN
THAT OTHER
STRAND, IT GOES THROUGH, ONCE IT’S THROUGH
IT RELIGA
TES AND RELEASES ATP. THIS IS THE GATE. TWO DOORS. EXACTLY WHAT YOU DO WITH
TOPOISOMERASE. YOU STAIN THE MIDDLE OF TWO
GATES AND GO T
HROUGH THE NICK, THAT’S HOW IT RELAXES DNA. IT’S A GATED SYSTEM, AT LEAST
TWO GATES, M
AYBE THREE BECAUSE IN THE MIDDLE IT BREAKS. THE DNA NEVER LETS GO, DOUBLE
STAND BREAK
IS NEVER VISIBLE INSIDE THE TOPO 2, CAN
DECATINATE
AND CATINATE, CAN RELAX SUPERCOILING
ON TWO ST
RANDS, THE STRANDS PASS ON TOP OF EACH
OTHER. IT CAN ALSO INDUCE NEGATIVE
SUPER GYRASE. THIS DOUBLE STRAND DNA LOOKING
AROUND AND
COMING TOGETHER IS VERY REMINISCENT OF
WHAT HAPPE
NS WITH TRANSCRIPTION WHEN YOU HAVE THE
ENHANCERS
WITH PROMOTERS, AND DNA MAKES A BIG
LOOP, AND W
E NOW KNOW VERY WELL TOPO2B IS CLOSE TO THE
REGIONING
NOT ONLY RELAXING DNA BUT PROBABLY RIGHT
AT THE PRO
MOTER, SO THERE’S A LOT OF ACTIVITY
ESPECIALLY IN NE
URONS, AND TO KNOW HOW GENES ARE TURNED ON
AND OFF AN
D HOW TOPO2 BETA IS PART OF THIS
PARTICULAR GYMN
ASTIC. IN REPLICATION, TOPO 1 WILL
RELAX SUPERCOI
LS. IT DOESN’T NEED DNA, JUST
TENSION, IT WOUL
D JUST RELAX. TOPO 2 NEEDS TRANSFERENCE WITH
THE OTHER. WHEN DNA IS REPLICATED,
SOMETIMES YOU GET REPLICATION, CATINASE, AND YOU
HAVE CONVER
GING, YOU HAVE THIS, I TOLD YOU ALREADY
DECATINATION
. AS FAR AS DRUGS THAT TARGET TOPO
2, FOR TH
E HUMAN THERE ARE A FLURRY OF DRUGS,
VERY WIDELY U
SED. THERE IS THE DOXORUBICIN, AND
THERE ARE A
NUMBER OF OTHER DRUGS, INHIBITORS ARE
SHOWN HERE. FOR BACTERIA TOPO2 ALL THE
ANTIBIOTICS YOU
‘VE HEARD ABOUT, YOU KNOW, THE QUINOLONES
SPECIFIC,
THEY WORK IN THE SAME WAY. BY THIS I MEAN IT’S THE THE
SAME INHIBITI
ON. THIS IS A CRYSTAL STRUCTURE,
HOMODIMER, DN
A IS HERE INSIDE THE ENZYME, AND IF YOU
LOOK FROM TH
E TOP HERE YOU SEE THROUGH THE ENZYME YOU
SEE THE DNA
. AND THE WAY THE DRUG POISONS THE
TOPO 2 IS
BINDING AT THE INTERFACE OF THE TOPO2
AND THE DNA. SO AGAIN YOU’RE GETTING THE SAME
PRINCIPLE
OF AN INTERFACIAL INHIBITION. ANTIBACTERIAL IS THE SAME
PRINCIPLE, THIS
IS GYRASE, FOUR SUBUNITS, SAME KIND OF
STRUCTURES, YO
U CAN SEE VERY SIMILAR. LOOK FROM THE TOP, AND HERE IS A
QUINOLONE
. IT’S AGAIN BOUND AT THE CLEAVAGE
SITE. WHAT DRUGS DO, THEY BIND AT
CLEAVAGE SITE,
THE LIGATION MAKES CLEAVAGE
COMPLEXES. IT’S VERY PROMINENT MECHANISM
THAT WAS I T
HINK FIRST SEEN BY TOPOISOMERASES
INHIBITORS FOR MANY MACROMOLECULES IN THE BODY,
PROTEIN INTERA
CTION COULD BY NATURAL PRODUCTS LIKE
THAT. SO THESE ARE THE TYPE OF
INTERFACIAL INHIB
ITION, THE CAMPTOTHECIN, QUINOLONE IS AT
THE CLEAVAGE
SITE, AND THE DRUG SPECIFICITY IS DRIVEN
BY SPECIFIC
HYDROGN BONDS TO THE PEPTIDE CELL. FOR TOPO 2 AS CELL. SELECTIVITY FOR THESE DRUGS FOR
THEIR PART
ICULAR ENZYME IS NOT ONLY TO THE DNA
STACKING INS
IDE THE BREAK SITE BUT ALSO TO SPECIFIC
INTERACTIO
N, PROPERLY POSITIONED FOR EACH ROW
AND FOR E
ACH ENZYME. TOPO3, SO AGAIN WE GET TWO TOPO
3s, TOPO3
ALPHA UNCODED BY A, TOPO 3 ALPHA
PRIMARILY INVOL
VED IN REPLICATION, AND IT NEEDS TO
HAVE SINGLE-S
TRANDED REGION TO FUNCTION. SO THAT HAPPENS IN ANY CATINASE,
PREVENTS RECOMBINATION, SO DEFICIENT TOPO
3A, COUPL
ED WITH HELICASE, USUALLY
HYPERRECOMEBINOGENIC, RE
MOVES THE JUNCTION. TOPO 3B IS ONGOING WORK, RESULTS
IN R LOOP
S AND D LOOPS, THE ONLY ONE IN HUMAN
CELL. THERE’S IS AN RNA
TOPOISOMERASES, WIDELY K
NOWN IN THE COMMUNITY BUT NOT TO THE
WIDE COMMUNIT
Y. THIS IS THE ONLY RNA USED FOR
HUMAN CELLS,
RODENT AND SO ON. SO, WHY WOULD YOU USE TOPO 2
VERSUS TOPO 3
DURING REPLICATION? IF YOU TAKE THE TOPO 2 PATHWAY,
YOU CAN DE
CATENINE ALL THESE TWISTED MOLECULES AND
SEPARATE T
HE TWO REPLICATED CIRCLES. BUT SOMETIMES YOU COULD GET AT
THE END A S
ORT OF — SEE THE LOOP STRUCTURE, TOPO 2
DOESN’T REC
OGNIZE THIS BECAUSE IT’S
SINGLE-STRANDED. THAT’S WHERE YOU NEED TOPO 3
ALPHA, WHICH
WORKS TOGETHER WITH BLM HELIC CASE,
AND REMINISC
ENT IN BACTERIA THE SAME SYSTEM, TOPO
1A, IN YEAS
T, SO IN REPUTATION TOPO 3 ALPHA IS
ALWAYS NEEDED. WHAT ABOUT TOPO 3 BETA, IT WAS
FORGOTTEN F
OR MANY YEARS, AND IN 2013 IT WOKE UP,
WITH TWO PA
PERS SHOWING THAT IN A GROUP OF
PATIENTS IN FIN
LAND, HIGH PREVALENCE OF NEUROLOGICAL
DISEASE, WHEN T
HEY SEQUENCED PATIENT, THE LOCUS,
TOPO 3 BETA
IS IMPORTANT FOR TRANSCRIPTION AND
VERY IMPOR
TANT AS AN RNA TOPO ISOMERASE, SO THIS WAS
DONE IN BA
LTIMORE AT THE AGING INSTITUTE AND BY
LARGER GROUP OU
TSIDE. AND THE POI NEAR — AND STILL
WORKING ON
THIS. THEY ARE VALUABLE IN SPITE OF
THE IMPORTAN
CE OF THE ENZYME. SO, HOW DOES TOPO 3 WORK? THEY USUALLY WORK IN CONJUNCTION
WITH HELI
CASE, IN TOP 3B, SCAFFOLDING PROTEIN,
RMI. THOSE WHO STUDY TRANSCRIPTION
AND RNA META
BOLISM, YOU KNOW ABOUT PROTEIN. IT’S MAKING A CONNECTION WITH
NEUROLOGICAL
DISEASE IN TOPO 3 BETA AS WE MOVE ALONG. TOPOISOMERASES GENOMIC INTEGRITY
AND HUMAN
DISEASES, OVEREXPRESSION OF OR LACK OF
REPAIR LEADS
TO GENOMIC INSTABILITY. IT’S BECOMING MORE AND MORE
OBVIOUS THIS I
S HAPPENING IN PATIENTS. WHEN I ADD CLEAVAGE COMPLEX ON
DNA AND REP
LICATION COLLIDES, YOU GENERATE DOUBLE
STRANDS. THAT’S LETHAL. IF TOP 2CC IS SEVERED, IT’S AS
IF YOU’RE T
RYING TO BREAK THE DNA, YOU’LL NEED A BIG
TRUCK TO
DO THAT, NEEDS A LOT OF ENERGY, BUT TOPO
2 BREAKS M
AY SEVER. IN SOME CASES YOU LEAVE BEHIND
SUPERCOILS,
OR KNOTS, OR CATENANESE, AND THIS IS
DISASTER AT MIT
OSIS. WE LISTED NUMBER OF CAUSES OF
ALTERATION T
HAT CREATE CLEAVAGE COMPLEXES AND LIST OF
ENZYMES THA
T DO THAT. FOR TOPO 1, YOU HAVE OXIDATIVE
DAMAGE, TOP
IS STUCK AND NOT REPAIRED, IF THERE IS
TRANSCRIPTIO
N IT WOULD COLLIDE, IT WILL FORM A HUGE
COMPLEX, IF I
T HAPPENS IN A REPLICATING CELL, THE
REPLICATION COL
LIDES, YOU MAKE DOUBLE STRAND AND
SINGLE-STRANDED DOU
BLE STRAND BREAK, AND THAT IS IRREVERSIBLE. THERE ARE DIFFERENT WAYS TO DEAL
WITH THAT
. WHEN THEY DON’T, YOU GET HUMAN
DISEASE. FOR TOPO 1, LACK OF TOP1CC, BUT
TOP2 BETA, CHROMOSOME TRANSLOCATION AS
T2BCC, SECONDA
RY LEUKEMIA, THOUGHT TO BE DUE TO
TRANSLOCATI
ON ARISING FROM COMPLEXES NOT REPAIRS. TOPO3B, NEUROLOGICAL DISORDERS. AND TWO REPAIR ENZYMES FOR
CLEAVAGE COMPLE
XES THAT LEADS TO ATAXIA AND NEUROPATHY. SO THE TOPO CLEAVAGE COMPLEXES
AS I MENTIO
NED GO THROUGH A COVALENT INTERMEDIATE,
YOU SEE F
OR THE TOPO 1, 1 AND MT, LINKAGE, FOR 2
AND 3 YOU
GET A FIVE PRIME LINKAGE, NORMALLY
REVERSIBLE, E
LIMINATE THE PHOSPATE AND GET THREE
PRIME, BUT IF I
T GETS STUCK YOU GET CLEAVAGE
COMPLEXES, WITH A C
OVALENT TOPO CLEAVERRAGE COMPLEX, BREAK
AND DNA PR
EPPING CROSSLINK. HOW IS THIS REMOVED? THIS IS THE SCHEME OF THIS DRAWN
IN DIFFER
ENT WAYS. THIS IS TOPO 1 FOR INSTANCE,
COVALENT CROS
S-LINK FOR DNA BACKBONE, YOU CAN SEE
COVALENT LINKAGE
, LET’S ASSUME THIS IS NOT REVERSIBLE. WE KNOW CELL HAS TWO MAIN
PATHWAYS, REMOVE
LESIONS, ONE IS SURGICAL PATHWAY,
DIESTERASE, PHOSPHO-DIESTERASE, TDP1 CAN
EXCISE THEM. FOR TOPO2, THE POLARITY IS
OPPOSITE, FIVE
PRIME LINKAGE. TYROSINE DNA, ESTERASE, PDP2,
AND THEN IT
WILL RELEASE THE TOPO AND DNA REPAIR
CAN TAKE P
LACE. THERE’S BACKUP. BECAUSE THIS IS PROBABLY AT
LEAST SO OFTEN
THAT MANY WAYS TO DEAL WITH IT BEYOND THE
PDPs, THEY
USE NUCLEASE. AND THE NUCLEASE WILL CHOP THE
DNA WITH TH
E TOPO AND RELEASE THE THING AND DO A
LITTLE GAP CLEA
NING. SO, THAT’S TRUE FOR TOPO 1 AND
TOPO 2, AND
THESE NUCLEASES YOU’VE HEARD VERY
PROMINENT LIKE
MRE11, OR 81, AND WE KNOW IN BRCA
DEFICIENT TUMORS M
R 11 IS VERY DEFICIENT, SO THERE’S LACK
OF REPAIR
OFTY TOPO2 LESION, HYPOTHESIS MADE THAT IN
BREAST CAN
CER THE PREVALENCE OF BRCA DEFICIENCY IS
BECAUSE B
RCA IS NOT HELPING MR 11 TO REMOVE TOPO 2
CLEAVAGE CO
MPLEX. THE IDEA OF PROMOTERS DRIVEN BY
ESTROGEN,
HE GET A LOT OF TOPO 2 CLEAVAGE
COMPLEXES, MEMORY C
ELLS DURING THE MENSTRUAL CYCLE OR
LACTATION, I
F THEY ARE NOT REMOVED AND BRCA NEEDS TO
HELP TO BRIN
G THE NUCLEASE TO THIS LESION, AND ONE
OF THE ME
CHANISMS PROPOSED ARE SELECTIVITY FOR
OVARIAN AND B
REAST CANCER IS BRCA CANNOT DRIVE THE
REPAIR OF
TOP 2. SCHEMATICALLY, YOU COULD THINK
OF IT THIS
WAY, TWO MAIN WAYS TO DEAL WITH THIS IS
PHOSPHO-DIE
STERASE, TDP1, ENZYMES ARE NOT EFFICIENT,
THAT LEAD
S TO NEUROLOGICAL SYNDROME, MOSTLY. IF NOT EFFICIENT, YOU ALSO GET
(INDISCERNI
BLE). SO TWO TDPS HAVE DIFFERENT
ACTIVITY, DISCO
VERED BECAUSE OF TOPOISOMERASES, BUT 1
HAS A GRE
ATER RANGE OF DNA REPAIR FUNCTION, THIS IS
ALSO NOT S
O WELL ESTABLISHED, NOT SO WELL
ACKNOWLEDGED, I W
OULD SAY, IN THE DNA REPAIR FIELD BUT THIS
REPAIR A
LOT OF LESIONS BY ACTIVATING AGENT,
BLOCKING LESI
ON, THREE PRIME REPLICATING DNA, IT WORKS
IN MITOCHO
NDRIA, NUCLEASE, AS I’VE TOLD YOU TDP1
DEFICIENCY
IS FOUND IN PATIENTS WHO HAVE NERVOUS
SYSTEM STABIL
ITY. IT IS ALSO INVOLVED PRESUMABLY
DURING PROT
EOVIRUS REPLICATION TO EXCITE THE
TYROSINE OF THE
END OF THE NUCLEIC ACIDS. SO NORMAL CELLS, TWO PATHWAYS TO
REPAIR CO
MPLEXES, COUPLED WITH PARP1, ALTERNATIVE
PATHWAY IS XPF-ERCC1. IF ONE IS DEFICIENT, CELLS RELY
ON THE SEC
OND. THERE’S LETHALITY HERE, IF YOU
BLOCK THE P
ATHWAY WITH PARP INHIBITOR, THE CELLS
BECOME EXCL
USIVELY DEPENDENT ON THE MR 11 XPF
PATHWAY, AND MA
Y BE PROVIDING AN OPPORTUNITY TO GIVE
PARP INHI
BITORS WITH TOPO 1 INHIBITORS IN MRE11,
AND MUTAT
IONS ARE NOT RARE, THEY ARE FOUND IN
MISMATCH REPAI
R COLON CANCER, IT’S BEEN
UNDERAPPRECIATED BUT IF
WE TOOK THOSE PARTICULAR PATIENTS’
TUMORS, MRE11 D
EFICIENT, AND GAVE A TOPO1 INHIBITOR PLUS
PARP INHIB
ITOR MAYBE WE WOULD SEE RESPONSES WHERE WE
DON’T SEE
THEM NOW. SO I’D LIKE TO MAKE
ACKNOWLEDGMENT, A LOT
OF DRUG WORK IS DEVELOPING
INDENOISOREQUESTSQUINOL
INE. I’D BE HAPPY TO QUESTIONS OR IF
YOU WANT T
O SEND ME AN E-MAIL IT’S EASY TO FIND MY
E-MAIL.>>THANK YOU. [APPLAUSE] ANY QUESTIONS? SO HOW FAST DO THE
TOPOISOMERASESES UNWIND
THE DNA?>>THE SPEED WE CALCULATED WITH
NEWMAN IN
THIS BUILDING, DOING SINGLE MOLECULE
ANALYSIS,
AND MY APPROXIMATION, ROTATION IS ABOUT
6,000 RPM
. SO GIVES YOU –>>PRETTY FAST.>>PRETTY FAST. THESE THINGS WORK IN A SECOND, A
MILLISECO
ND, WHEN WE DO BIOLOGICAL EXPERIMENTS IN
HOURS AND
MINUTES,& IT’S NOT AT THE SCALE OF WHAT
CELLS DO. CELLS WORK IN THE MILLISECOND. AND THE PASSAGE, I DON’T KNOW
QUICKLY PASS
AGE, GOING THROUGH NIH, I THINK — I DON’T
KNOW THE S
PEED ACTUALLY.>>THESE THINGS WORK VERY, VERY
EFFICIENTL
Y AND CONTINUOUSLY. YOUR CELLS, MY CELLS, WORKING
ALL THE TIME
. WHETHER WE TRANSCRIBE OR
REPLICATE OR WHAT
EVER WE DO. A VERY ESSENTIAL MACHINE.>>AND DO THEY CAUSE — ALTER
THE CELL CYC
LE? DO CANCEL CELLS BUILD UP IN.>>USUALLY CANCER CELLS
OVEREXPRESS THE TOPOISOMERASES BECAUSE THEY
REPLICATE FAST
, TRANSCRIBE A LOT, VERY COMMON
OVEREXPRESSI
ON OF TOPO1, IN BREAST CANCER
AMPLIFICATION WITH
HER-2 OF TOPO 2 ALPHA WHICH IS NEAR, AND
THAT PROBA
BLY ENABLES TO REPLICATE AND
TRANSCRIBE QUICKL
Y ONCE YOU PUT TOPO POISON, THEY ARE
SENSITIVE TO POI
SON, SO BECAUSE THEN YOU POISON THE
ENZYME THAT TH
E ENZYME IS USING, SO IT GOES BOTH WAYS. A LOT OF TOPO, SHOULD BE MORE
SENSITIVE, T
HAT’S THE CASE, USUALLY. SO, YEAH, CANCER CELLS TEND TO
PUT A LOT O
F THESE ENZYMES UP. >>I WAS WONDERING IF YOU CAN
EXPAND ON TH
E RELATIONSHIP BETWEEN THE BRCA
MUTANT, BREA
ST AND OVARIAN CANCERS, AND THE
SYNTHETIC YEAST (INDISCERNIBLE) AND
TOPOISOMERASES INHIBIT
ORS, IN MY UNDERSTANDING AT LEAST
RESISTANCE TO PARP
INHIBITORS EMERGES QUICKLY, THEY ARE NOT AS
GREAT IN
THE CLINIC WHEN TREATING PATIENTS AS THEY
ARE IN TISS
UE CULTURE, WONDERING IF YOU
SUGGEST WE CAN U
SE THEM LIKE SEQUENTIALLY OR ONCE
RESISTANCE EMERG
ES OR IF IT’S LIKE — BECAUSE I THINK
ALSO ONE OF T
HE MECHANISMS THROUGH RAB 51 LOSS,
WHICH RESC
UES THE WHOLE DEFECT, TOPOISOMERASES
INHIBITORS WO
ULD MAYBE NOT WORK AS WELL.>>YEAH, I THINK YOU’RE BRINGING
A NUMBER
OF QUESTIONS, SO CONNECTION WITH
BRCA AND TOP
O2 HAS BEEN WORKED ON LAST YEAR AND THE
YEAR BEFO
RE, IN KYOTO, (INDISCERNIBLE), AND THE
CONCEPT AS
I SAID IS THAT WHEN THE CELLS THROUGH
ESTROGEN OR PR
OSTATE CELLS THROUGH ANDROGEN, ANDROGEN
RESPONSE, RESPONSIVE ELEMENT, THEY HAVE TO
RETRIEVE
TOPO 2 ON PROMOTER TO FACILITATE
TRANSCRIPTION. NOW, THESE BREAKS OF THE
PROMOTERS TEND TO
BE PRETTY STABLE, AND TOPO CLEAVAGE
COMPLEX IS THOUG
HT TO (INDISCERNIBLE), AND IT’S A
MYSTERY WHY TH
EY ARE SO STICKY BECAUSE USUALLY TOP WILL
GO AWAY, I
N THOSE CASES THEY DON’T GO AWAY
QUICKLY. THE IDEA IS CELLS USE THE
NUCLEUS PATHWAY
TO TAKE THEM OFF. THEY HAVE TO TAKE IT OFF. AND THE IDEA IS THE BRCA
PROTEINS ARE RECR
UITED TO FACILITATE RECRUITMENT OF THE
NUCLEASE FOR
THAT. SO IF YOU HAVE A BRCA
DEFICIENCY, THEY ARE
NOT REPAIRED. HORMONE DEPENDENT TUMORS, YOU
GET THE MUTA
TIONS, AND THEN YOU GET EVENTUALLY
TRANSLOCATION AND
ALL THE BAD THINGS. MAYBE THAT’S ONE EFFECT OF YOUR
QUESTION. THE OTHER ASPECT OF THE PARP
INHIBITOR, WH
EN I FIRST LOOKED AT PARP INHIBITORS THE
MOST STRIKIN
G FINDING IS WHEN WE TOOK THE NCI 60 CELL
LINE, ABOU
T ONE HALF DO NOT RESPOND, EVEN TO 100
MICROMOLAR. SO WHAT IS IT? SOME RESPONDED AT 10 NANOMOLAR. SOME CELLS ARE BLACK AND WHITE,
OTHERS RES
POND AND NOT RESPOND. THE DETERMINANT OF RESPONSE WHEN
WE LOOKED
CAREFULLY WAS NOT THE BRCANESS TURNED OUT
WHEN WE LO
OKED AT UNRELATED, UNKNOWN, THIS IS
ANOTHER STORY. IN THE CASE WHERE THE PARP
INHIBITORS DON’
T WORK, EVEN IF TUMOR IS BRCA DEFICIENT
BECAUSE TH
AT HAPPENS, BECAUSE AS YOU SAID,
THE TOPO 1 I
NHIBITORS MAY BE A WAY TO GO. THAT’S WHAT WE’RE PROPOSING. OR MAYBE YOU ADD TO PARP
INHIBITOR THAT MA
Y LIMIT THE RESPONSE. THAT’S WHAT WE’RE GOING TO BE
TESTING WHET
HER ADDING TOPO 1 TO PARP WILL LIMIT
FRACTION OF PATI
ENTS, FOR THE MOMENT IT’S MORE
HYPOTHETICAL BUT CLEA
RLY TOPO 1 INHIBITORS, THREE DRUGS, BRCA,
HR DEPENDEN
T, PARP INHIBITOR, YES. CISPLATIN, IN PART, BECAUSE
PLATIN IS ALSO
NER, WE ALL WANT TO SAY HR BUT MORE
COMPLICATED, T
HESE ARE ARE THREE CLASS BUT OTHERS DON’T
DEPEND. NO HR, MANY DRUGS, THESE ARE THE
THREE CLA
SSES I KNOW, PARP INHIBITOR, PLATINUMS,
TOPO 1 IN
HIBITORS, BRCA DEFICIENT, HR DEFICIENT
PATIENTS, FRO
M THE PRE-CLINICAL MOLECULES THAT’S
CLEAR.>>OKAY. IF THERE’S NO FURTHER QUESTIONS
WE’LL TAKE 5 MINUTE BREAK SO CURT HARRIS, NEXT SPEAKER,
CHIEF OF THE LABORATORY OF HUMAN
CARCINOGENESIS, M.D. F
ROM KANSAS UNIVERSITY, AND STUDIED INTERNAL
MEDICINE
AT UCLA, WASHINGTON VETERANS
ADMINISTRATION HOSPITA
L, AND NCI. AND THEN CAME TO NCI AND ADJUNCT
PROFESSOR
THE MEDICINE AT GEORGETOWN
UNIVERSITY. HE’S WON SEVERAL AWARDS,
INCLUDING THE ACR
AWARD, AND HE’S CHIEF OF THE JOURNAL
CARCINOGENES
IS, AND HE’S GOING TO TALK TO US TODAY
ABOUT LUNG
CANCER, PRECISION MEDICINE STRATEGY.>>OKAY. ALL RIGHT, TERRY. SO, ALL OF YOU DIE-HARDS STILL
HERE AFTER
5:00, ACTUALLY I FOUND MANY OF MY
POSTDOCS ARE S
TAYING AFTER 5:00 NOW. I DON’T KNOW WHY. THERE WAS A TIME I — FORGET
ABOUT THAT. LET’S TALK ABOUT SCIENCE, LUNG
CANCER AND PRECISION MEDICINE SO WHAT IS PRECISION MEDICINE
AND WHEN DID
IT START? STARTED HERE AT THE NCI. AND HAROLD VARMUS AND FRANCIS
COLLINS HAD
AN INSTITUTE OF MEDICINE GROUP GET
TOGETHER,
AND COME UP WITH WHAT THEY CALLED
PRECISION MEDICIN
E. IT’S ESSENTIALLY AN UPDATE OF
THE KIND OF
MEDICINE THAT IS ONGOING AND WAS ONGOING. SO TRADITIONAL MEDICINE AT THAT
TIME WAS T
O — THERE WE GO — TO GET FAMILY HISTORY
AND DO SIGN
S AND SYMPTOMS, GET SOME LABORATORY
TESTS, AND T
HAT’S HOW IT WENT FOR MANY, MANY, MANY
DECADES, IF N
OT CENTURIES. SO WHAT’S PRECISION MEDICINE? IT’S MULTI-LAYERED. IT’S INDIVIDUAL CENTRIC, IT’S
INTERCONNECT
ED. AND ONE OF THE KEYS IS AN
INFORMATION COMM
ONS, WHICH HAS THESE OMICS, AND I’VE ADDED
CLINICAL INFORMATION, EPIDEMIOLOGICAL
DATA. AND THIS GETS PUT TOGETHER TO
FORM A KNOWL
EDGE NETWORK, AND A NEW MOLECULAR
TAXONOMIC CLASSIFICATION OF INDIVIDUAL
PATIENTS, TO
GUIDE CLINICAL STUDIES, TO IMPROVE
CLINICAL INVESTIGATIONS, TO PREVENT,
EXCUSE ME, TO
GUIDE PREVENTION RESEARCH, I ADDED
THAT, THAT WA
SN’T IN THE ORIGINAL, TO INFORM
BIOMEDICAL RESEARC
H. THESE ARE FEEDBACK LOOPS THAT
ENRICH AND E
XPAND THE INFORMATION COMMONS. SO, LUNG CANCER I THINK YOU
HEARD ABOUT A
SESSION ON LUNG CANCER, FAIRLY RECENTLY
ACTUALLY. IT’S ONE OF THE THINGS WE
STUDIED IN THE L
ABORATORY OF HUMAN CARCINOGENESIS. THIS IS A — AT THE TIME OF THE
50th ANNIV
ERSARY OF THE SURGEON GENERAL REPORT,
THEY DID A CALCULATION OF THE NUMBER OF
CANCER-RELATE
D DEATHS, AND DISEASE-RELATED DEATHS, AND
CAME UP WI
TH ABOUT, OH, OVER 20 MILLION PEOPLE DIED
FROM TOBAC
CO USE. AND OF COURSE THAT’S STILL
ONGOING. IN THE UNITED STATES, THE
INCIDENCE IS GOI
NG DOWN, IN MALES, AND STILL PRETTY
PLATEAUED IN FE
MALES. LET’S SEE IF THIS WORKS ANY
BETTER. YEAH, THAT WORKS BETTER. OKAY. THE DATA IN 2019, OR 2020,
PROBABLY UPDATE
OF THIS, AND THERE MAY BE A SLIGHT
DECREASE IN FEMA
LE LUNG CANCER BY THAT TIME. AND EVENTUALLY, MALE WILL
COINCIDE WITH TH
E FEMALE. SO, WHAT CAUSES LUNG CANCER? OBVIOUSLY TOBACCO SMOKE. WHY IS IT GOING DOWN IN THE
UNITED STATES? THE UNITED STATES WE USED TO
LOOK LIKE THI
S. THAT’S 35 TO 60 SMOKE PACK
YEARS, OR FREQU
ENCY OF SMOKING I SHOULD SAY, STILL
QUITE COMMON I
N RUSSIA, ASIA, A NUMBER OF OTHER
COUNTRIES. AND WE USED TO LOOK LIKE THIS,
AND THAT’S
WHY LUNG CANCER WAS SO — HAS BEEN SO
PREVALENT IN
THE UNITED STATES. SO, THE VARIOUS PEOPLE IN
LABORATORY OF HU
MAN CARCINOGENESIS, THERE ARE FIVE
P.I.s, INCL
UDING MYSELF. WE FOCUS ON STUDYING THE MAJOR
LETHAL TYPE
S OF HUMAN CANCER. LUNG CANCER. SORRY ABOUT THAT. LUNG CANCER AND REID RYAN AND
MYSELF. BREAST CANCER AND PROSTATE
CANCER, STEPHAN
, PANCREATIC CANCER, HUSSAIN. SO THAT’S — AND WE’RE TALKING
ABOUT, OH,
PROBABLY CLOSER TO FIVE TO SIX MILLION
DEATHS A YEA
R FROM JUST THIS GROUP OF CANCERS. SO, A NUMBER OF YEARS AGO,
ACTUALLY IN 198
1, I PARTICIPATED IN A MEETING IN
GREECE. AND THIS IS CAPE SUNION, THIS IS
A WATERCO
LOR FROM PROFESSOR HIRAYAMA. PROFESSOR HIRAYAMA REPORTED THE
VERY FIRST
EVIDENCE OF PASSIVE SMOKING IN INDUCTION
OF LUNG CA
NCER. I WILL TELL YOU OF ABOUT, OH,
FOUR OR FIVE
HUNDRED PEOPLE AT THIS MEETING, AT LEAST
HALF OF T
HEM DIDN’T BELIEVE IT. BUT HE PROVED TO BE RIGHT. SO, THERE ARE PROBABLY OVER 100
PAPERS NOW
IN THE LITERATURE SHOWING PASSIVE
SMOKING, YOU GE
T IN YOUR WORKPLACE, OR FROM YOUR SPOUSE,
IS ASSOCIA
TED WITH INCREASED RISK OF LUNG CANCER. AND I’M RATHER FOND OF THESE OLD
KINDS OF
QUOTES. THIS IS FROM HIPPOCRATES, SOME
MEN/WOMEN H
AVE CONSTITUTIONS LIKE WOODED
MOUNTAINS RUNNIN
G THE STREAMS, OTHERS LIKE THOSE WITH
POOR SOIL
AND LITTLE WATER, STILL OTHERS LIKE LAND,
RICH IN PAS
TURES AND MARSHES, OTHERS LIKE THE BARE,
DRY EARTH O
F THE PLAIN, PEOPLE DIFFER FROM ONE
OTHER, EVEN
OBVIOUS THOUSANDS OF YEARS AGO IN RISK
OF DISEASE
AND OTHER THINGS. SO I WAS SITTING AT THIS
MEETING, I SAID,
WELL, IS THERE ANY EVIDENCE OR COULD I
FIND SOME EV
IDENCE TO INVESTIGATE WHETHER OR NOT
SMOKING OF YOUR
PARENTS INCREASES YOUR RISK OF
DEVELOPING LUNG CAN
CER. SO THIS IS IN THE LATE ’80s, OR
EARLY ’80s
I SHOULD SAY. AND WOMEN DIDN’T START SMOKING
IN THE UNIT
ED STATES HEAVILY UNTIL SECOND WORLD WAR. AND THEN YOU DON’T GET CANCER
UNTIL 50, 60
, 70 YEARS OF AGE. I FIGURED IT WOULD TAKE ABOUT 35
YEARS BEF
ORE I COULD DO THAT STUDY. BUT IN FACT WE DID DO THE STUDY,
OF 38 YEA
RS LATER. AND THE HYPOTHESIS WAS THAT
CHILDHOOD EXPO
SURE TO SECONDHAND SMOKE AND GENETIC
ALTERATIONS I
N INNATE IMMUNITY INCREASED LUNG CANCER
RISK IN NEV
ER SMOKING ADULTS. SUSAN WAS INVOLVED WITH THIS. WE COLLABORATED, ONE OF THE
COHORTS CAME F
ROM THE MAYO CLINIC, ONE FROM OUR COHORT
AT THE UN
IVERSITY OF MARYLAND. AND WE IN FACT DID FIND THAT
PARENTAL SECO
NDHAND SMOKE EXPOSURE IN CHILDHOOD IS
ASSOCIATED
WITH DOSE DEPENDENT INCREASE IN LUNG
CANCER RISK AMO
NG NEVER SMOKERS, TWO DIFFERENT COHORTS. WHETHER IT WAS THE MOM OR THE
DAD OR BOTH,
MOM AND DAD BOTH IT WAS ADDITIVE. IT WAS EVEN SOME EVIDENCE THAT
GRANDPARENT
S TAKING CARE OF THE KIDS AT AN EARLY AGE
INCREASED
THEIR RISK. IT WAS ESPECIALLY TRUE IN
MANNOSE BINDING
LECTIN TYPE 2 HAPLOTYPE REFLECTIVE OF
HIGH ACTIVE
INNATE IMMUNE SYSTEM, AND SURPRISINGLY
THESE CASE
S DEVELOPED CANCER PRIMARILY IN
THEIR 50s AN
D 60s INSTEAD OF 60s AND 70s LIKE MOST
OF US WOU
LD. SO, THAT LED ME TO THINK ABOUT
THE EXPOSES
OME, SOMETHING THAT WAS DEFINED BY
CHRIS WILD,
WHO WAS DIRECTOR OF THE INTERNATIONAL
AGENCY FOR R
ESEARCH ON CANCER, AND IT INVOLVED NOT ONLY
EXTERNAL ENVIRONMENT, TOBACCO SMOKE,
INFECTION, DIE
T, TOXINS, RADIATION, BUT ALSO THE INTERNAL
ENVIRONME
NT RELATED TO THAT. WE ADDED OBESITY, CHRONIC
INFLAMMATION, LA
TER ON THE GENOME CHANGES, AND EPIGENOME
CHANGES, AND DEVELOPMENT OF CANCER BIOMARKERS
OF RISK,
DIAGNOSIS, FOR PREVENTION AND SCREENING,
UNDERSTANDIN
G CARCINOGENESIS FEEDS INTO THIS
AND ALSO LE
ADS TO CANCER THERAPY, AS I’M SURE ALL
OF YOU KNO
W. SO GENE OLD, WELL, HOW ABOUT
LUNG CANCER I
N THE GENOME? THE TRADITIONAL VIEW OF LUNG
CANCER WHEN I
WAS A RESIDENT AND MEDICAL ONCOLOGY
FELLOW WAS S
MALL CELL ADENO, AND SQUAMOUS, IN 1987
KRAS MUTATION
WAS FOUNDS. P53 MUTATIONS WERE FOUND MUCH
BEFORE THIS. FOLLOWING KRAS, EGFR MUTATIONS,
AND FINALL
Y IN 2014, THERE HAVE BEEN A COUPLE MORE
THAT HAVE BE
EN FOUND, PRIMARILY FUSIONS AND A FEW
OTHER THINGS A
SSOCIATED SUCH AS BRF WITH LUNG CANCER. SO, WHAT CAUSES LUNG CANCER? AND CAUSES CANCER IN MANY
SITUATIONS? THERE WAS A PERIOD OF TIME WHICH
PEOPLE WE
RE STUDYING CHEMICAL
CARCINOGENESIS, INCLUDIN
G MYSELF. AND YOU COULD GO EPIDEMIOLOGICAL
BACK INTO
THE 18th CENTURY AND CHIMNEY SMOKE
SWEEPERS DE
VELOPED CANCER, ASPERGILLUS FLAVUS
CAUSES FORMATIO
N, LIVER CANCER, SMOKING, 66 DIFFERENT
CHEMICAL CAR
CINOGENS IN IT, SO IT’S A WITCH’S BREW OF
CARCINOGE
NS, ANDS THAT WHY IT’S SO CARCINOGENIC. THREE DECADES OR THREE ERAS
LISTED HERE, E
XAMPLES OF INITIAL SEMINAL ADVANCES IN
EXPOSURE OF ENVIRONMENTAL CARCINOGENS, BEING
MOLECULAR
LY LINKED TO MUTAGENESIS AND TO
EPIDEMIOLOGY FOR THA
T POINT. AND SO BACK IN THE ’70s, THEY
WERE FINDING CARCINOGENS, CHEMICAL
CARCINOGENS ARE MUTA
GEN, SO THAT WAS ALL VERY EXCITING, BUT
IT SORT OF
TIED CARCINOGENS WITH DNA DAMAGE. AND THEN DISCOVERY OF P53
MUTATIONS LINKED ENVIRONMENTAL CARCINOGEN
EXPOSURE. AND THE ADDITIONAL STUDIES DONE
BY OUR GRO
UP AND ABOUT THAT THAT I WON’T HAVE
TIME TO TELL
YOU ABOUT THAT. AND THERE’S ALSO REVIEW THAT WE
WROTE FOR
MULTIPLE KINDS OF CARCINOGENS THAT CAUSED
P53 MUTAT
IONS. THIS IS THE START OF MOLECULAR
EPIDEMIOLOG
Y, AND WHICH I AND OTHER PEOPLE
CONTRIBUTED TO. THEN MORE RECENTLY, IN 2013,
LUDMIL ALEXAN
DER AND MIKE STRATTON PUBLISHED
SEQUENCES, TRINUCL
EOTIDE SEQUENCES INSTEAD OF LOOKING AT
ONE GENE,
LOOKING AT THE WHOLE GENOME. AND PUBLISHED IN “NATURE” AS
ESSENTIALLY A
LINK BETWEEN LOOKING AT A SINGLE GENE
AND LOOKI
NG AT THE ENTIRE GENOME. BEFORE THAT, IT WAS FOUND THAT
AFLATOXIN,
AS I MENTIONED, G TO T CONVERSIONS
PARTICULARLY
AT CODON, SMOKING AT VARIOUS HOT SPOTS,
AGAIN G TO T
WITH STRAND BIAS, AND STRAND BIAS IN
THIS CASE
MEANS ONE OF THE ALLELES, THE WILDTYPE
ALLELE, SINCE
THERE ARE TWO ALLELES, IS LOST. AND YOU HAVE MUTATION OF THE
OTHER. ULTRAVIOLET LIGHT HAS A
CHARACTERISTIC CC
TO TT TRANSITION, WHICH IS NOT FOUND
WITH ANY OT
HER CARCINOGEN THAT’S KNOWN. ARISTOLOCHIC ACID CAUSES KIDNEY
TUMORS, A
TO T TRANSITION, THAT WAS SORT OF THE
STATUS OF
THINGS BACK IN THE EARLY ’90s AND WENT
FURTHER TH
AN THAT. BUT P53 GOES BACK 40 YEARS NOW,
WHEN IT WA
S FIRST DISCOVERED. AND THEN FINDING MUTATIONS IN IT
WAS DISCO
VERED AFTER THAT. AND THERE’S SOME CANCER TYPES
SUCH AS OVAR
IAN CANCER P53 MUTATIONS ARE ALMOST OVER
90%. SOME ARE LOSS OF FUNCTION AS
TUMOR SUPPRES
SOR, AND OTHERS ARE GAIN OF FUNCTION. SO IT SWITCHES FROM A TUMOR
SUPPRESSOR TO
AN ONCOGENE, JEKYLL AND HYDE
SWITCH, IF YOU W
ANT TO THINK IT OF THAT WAY. NOT ALL MUTATIONS ARE EQUAL. SOME ARE PURELY LOSS OF
MUTATIONS. SOME WITH LESS AND LESS WILDTYPE
ACTIVITY
SUCH AS THESE. OTHERS GAIN ONCOGENIC ACTIVITY,
AND THESE
ARE JUST EXAMPLES OF THAT. SO DEVELOPING THERAPIES AGAINST
THE ONCOGE
NIC FORMS OF P53 IS SOMETHING THAT THE
FIELD HAS BEE
N INVOLVED WITH FOR TEN YEARS NOW, AND
PROGRESS ACTUA
LLY IS BEING MADE, WE’RE LEARNING MORE
ABOUT THAT
IN MAY IN ISRAEL, WHEN THE NEXT P53
MEETING IS HELD. BUT P53 AND ITS FUNCTIONS AFFECT
MULTIPLE
LEVELS OF OMICS DATA, AND THIS IS JUST A
NICE CARTOO
N THAT WE’VE PUT TOGETHER, ANNA ROBLES
AND MYSELF
A FEW YEARS AGO. AND THERE’S — WHY PEOPLE ARE
STILL INTERE
STED IN P53, IT JUST DOES LOTS OF
THINGS. ALL RIGHT. NOW LET’S GO BACK TO
COMPUTATIONAL ANALYSI
S THAT LUDMIL AND MIKE STRATTON DID. THIS WAS THEIR INITIAL PAPER IN
WHICH THEY
DESCRIBED 21 DIFFERENT SIGNATURES, AND
LOOKING AT MU
LTIPLE CANCERS, INCLUDING LUNG CANCER,
HEAD AND N
ECK CANCER, AND IN THOSE SMOKING
THERE WAS SPE
CIFIC SIGNATURE THAT WAS ASSOCIATED
WITH SMOKING
, AND THOSE KINDS OF CANCERS. THERE ARE SIGNATURES THAT ARE
ASSOCIATED W
ITH AGE, THOUGH THIS REPLICATION OF
CELLS, THAT’S A
N INTERESTING ASPECT OF CANCER IN
AGING. AND THESE ARE JUST SOME OTHER
EXAMPLES. AND THIS HAS BEEN MARKEDLY
EXPANDED SO THE
RE ARE AT LEAST I THINK OVER 35 DIFFERENT
SIGNATURES
NOW THAT THEY CHARACTERIZE, AND THE THE
AFLOTOXIN
IS SIGNATURE 35, AS I RECALL. THERE WE GO. SO, ONE OF THE KINDS OF THINGS
THAT THEY H
AVE DONE IS COMPARE SMOKERS VERSUS
NONSMOKERS, SO S
IGNATURE 4, THAT’S THE BLUE LINES, MUCH
MORE COMMON
IN SMOKERS THAN IN NEVER SMOKERS,
OR NONSMOKE
RS. AND THAT’S — THOSE ARE THE
KINDS OF CORRE
LATIONS THAT ARE — THAT HAVE BEEN MADE,
AND THEY
ACTUALLY MAKE SENSE FROM KNOWING THE
VARIOUS CARCIN
OGENS THAT ARE INVOLVED. SO THIS IS AN EXAMPLE OF THE
KINDS OF DATA
THAT THEY SEE, C TO A TRANSITIONS THAT I
MENTIONED,
FOR EXAMPLE, WHICH IS SIGNATURE
NUMBER 4. IF THEY TOOK HUMANIZED MICE, IN
WHICH HUMA
NIZED WITH HUMAN P53 AND EXPOSED THOSE MICE
TO BENZOP
YRENE, A PRIMARY CARCINOGEN IN TOBACCO
SMOKE AND PO
LLUTED AIR THEY GET THE SAME SIGNATURE OR
TAKE HUMAN
EMBRYONIC CELLS THEY GET THE SAME
SIGNATURE WITH EXP
OSURE, THE LINKS THEY ARE MAKING BETWEEN
EXPOSURE TO
VARIOUS CARCINOGENS AND MUTAGENS AND
HUMAN CANCER. THIS SHOWS GAIN OF FUNCTION
MUTATIONS PATI
ENTS HAVE A SLOWER — A POOR PROGNOSIS
THAN THOSE WI
LD TYPE VERSUS THOSE THAT ARE JUST LOSS
OF MUTATIO
N. AND IF YOU LOOKED AT CODON 249
IN LIVER CA
NCER IT’S A GAIN OF FUNCTION BUT IT’S LIKE
THIS. SO THAT ONE MUTATION IN LIVER
CANCER IS HI
GHLY DEADLY. IT’S CAUSED BY AFLOTOXIN. CHRONIC INFLAMMATION IS TIED TO
HUMAN CANC
ER, BACK TO AT LEAST THE 1800s. AND THESE ARE EXAMPLES OF
PRIMARILY INHERI
TED VERSUS ACQUIRED HUMAN CHROMATOSIS,
APPARENT OVERL
OAD, CROHN’S DISEASE, YOU CAN PUT
OTHER DISEASE
S, FAMILIAR PANCREATITIS, FOUND IN
CERTAIN FA
MILIES, SUCH AS CARTER’S FAMILY, HE’S
ONE OF THE F
EW MEMBERS OF THAT FAMILY, STILL ALIVE,
DIDN’T GET PA
NCREATIC CANCER. ALTHOUGH HE HAS METASTATIC
MELANOMA NOW AT
AGE 99 I THINK. MORE COMMON ARE ACQUIRED VERSUS
INHERITED,
VIRUS, BACTERIA. AND PARASITIC INFECTIONS. GLOBAL IMPACT IS TWO MILLION
CANCERS PER Y
EAR, CALCULATED OR RELATED TO
INFECTION. OTHER CAUSES OF INFLAMMATION ARE
ASSOCIATE
D WITH MANY MORE CANCERS PER YEAR, FOR
EXAMPLE IN
ADDITION TO 66 CHEMICAL CARCINOGENS,
SMOKING IS A V
ERY POTENT INFLAMMATORY AGENT, AND IF YOU
TOOK A DRAW
OF CIGARETTES, IN YOUR EARLY AGE,
HOPEFULLY N
OT LATER, PROBABLY STARTED TO COUGH
BECAUSE IT’S REA
LLY TOXIC, AND IF IT WASN’T FOR NICOTINE,
KIDS ARE BE
ING HOOKED WITH NICOTINE WITH THESE
CIGARETTES RIGHT
NOW, NO ONE WOULD BE SMOKING. IN MY OPINION. VARIOUS AGENTS HAVE BEEN
INVESTIGATED. WE FOUND IL-8 AND C-REACTIVE
PROTEIN IS FOUND IN EUROPEAN-AMERICANS AND
IN A STUDY THAT COLLECTED SAMPLES 20,
30, 40 YEARS AGO AT SHADY GROVE. WE FOUND THOSE WERE PREDICTORS
OF DEVELOPING CANCER, ACTUALLY
YEARS PRIOR TO DEVELOPING LUNG CANCER. AND AT THE TIME TIME CANCER WAS
FOUND, IL-8 AND IL-6, VERY FEW AFRICAN-AMERICANS IN THAT
INITIAL STUDY BUT AFRICAN-AMERICANS ALSO HAVE
INCREASE IN IL-1 BETA AND IL-10, COMPARED
TO EUROPEAN-AMERICANS SO THERE’S
SOME HEALTH DISPARITY DIFFERENCES
THAT WE AND REID RYAN AND OTHERS ARE INVESTIGATING. FOR SURVIVAL, SO THIS IS PRIMARILY AT STAGE 1 LUNG CANCER. STAGE 1 LUNG CANCER IS ABOUT THAT BIG. AND THERE’S NO METASTASES. OR NO DETECTABLE METASTASES. AND IF THE CASE OR YOUR PATIENT OR IF YOU’RE ON THE OUTSIDE YOUR CLIENT HAS ELEVATED THESE DIFFERENT CYTOKINES, OR MANNOSE BINDING LECTIN, WHICH I MENTIONED EARLIER, YOU HAVE INCREASE THE PROBABILITY OF DYING, OF RECURRENCE. NOW LOOK AT TRANSCRIPTOME. THIS WILL TAKE US BACK ABOUT TWO OR THREE DECADES NOW. VICTOR AND GARY DISCOVERED THERE WERE NON-CODING RNAs, THERE’S A NON-CODING RNA LECTURE AS PART OF THE SERIES, ISN’T THERE, TERRY? YOU KNOW ABOUT ALL OF THAT. AND THAT WAS QUITE INTERESTING AT THE TIME, AND CARLO CROCE DECIDED TO LOOK AT HUMAN CANCERS, AND HE FOUND THAT microRNAs ARE DIFFERENT, THEY EXPRESSED IN HUMAN CANCERS, AND THAT THEY CAN PREDICT RISK DIAGNOSIS OR PROGNOSIS, MOST STUDIES WERE DONE WITH ARTHUR. AS YOU LEARNED FROM NON-CODING RNA GROUP LESSONS, THE microRNAs CAN INHIBIT TRANSLATION, OR IF THERE’S SOME BIT OF A MISMATCH THEY CAN CAUSE MESSAGE TO CLEAVE. BUT THEY CAN ALSO BIND TO PROTEINS AND AFFECT PROTEIN FUNCTION. THEY CAN BIND TO RECEPTORS AND INCREASE IL-6 AND TNF ALPHA. THAT’S PRETTY INTERESTING IN TERMS OF INFLAMMATION. THIS IS NOZUMO WHEN HE WAS A YOUNG FELLOW IN THE LAB. AND WE FOUND microRNA PROFILES WERE SIGNIFICANTLY DIFFERENT BETWEEN PRIMARY LUNG CANCERS AND AMONG HISTOLOGICAL TYPES. AND MIR-21 AND THESE OTHER TWO WERE OVEREXPRESSED, LET-7 WAS UNDEREXPRESSEDDED, STAGE 1 LUNG CANCER, PRIMARILY INTERESTED IN STAGE 1 LUNG CANCER, WHY THEY RECUR. ANOTHER STUDY WE DID WITH CARLO, LOOKED AT SIX CANCER TYPES, AT THAT POINT THERE WAS I THINK 190, MAYBE 200, AND SO microRNAs THAT HAVE BEEN DISCOVERED, NOW OVER 2,000. BUT OF THOSE THAT WERE DISCOVERED AT THAT TIME, WE LOOKED AT THESE SIX CANCER TYPES, MIR-21 WAS OVEREXPRESSED IN ALL. WHEN WE LOOKED AT CANCERS IN THE FIELD UPREGULATED IN 18 MAJOR CANCERS, BIOMARKER OF POOR PROGNOSIS IN 14. SO WE FIGURED THAT WAS PROBABLY PRETTY INTERESTING AND IMPORTANT, OUR GROUP LOOKED AT THREE COHORTS, ONE IN MARYLAND, ONE NORWAY, ONE JAPANESE COHORT. THERE’S SOME DIFFERENCE HERE. WE USE CANCER SPECIFIC MORTALITY WHICH I MUCH PREFER, THE JAPANESE PREFER THE RELAPSE-FREE SURVIVAL. SO, THEIR DATA LOOKS BETTER THAN OUR DATA. AND THE REST OF THE WORLD. BUT NEVERTHELESS, IF MIR-21 IS HIGH, THAT’S THE RED, POOR PROGNOSIS, IN ALL THREE OF THESE COHORTS. AND THEN THE SAME IS TRUE IN LARGE NUMBER OF DIFFERENT KINDS OF COHORTS, SO HIGH LEVELS OF MIR-21 POOR PROGNOSIS, IN MULTIPLE TYPES OF CANCERS. WHAT’S THE MECHANISTIC UNDERPINNING OF THIS? WELL, ONE IS THAT MIR-21 IS AMPLIFIED IN THE GENOME, FAIRLY FREQUENTLY, ESPECIALLY IN LUNG CANCER. IT LEADS TO DECREASED TRANSCRIPTIONAL SILENCING. WE FOUND EGRF MUTATIONS YOU DON’T FIND KRAS MUTATIONS BUT YOU FIND INCREASE IN MIR-21, YOU FIND KRAS, DON’T FIND EGFR MUTATIONS, YOU FIND INCREASE IN MIR-21. SO THEY ARE IN THE SAME PATHWAY OR SIMILAR PATHWAY. DAVID BALTIMORE FOUND VARIOUS CYTOKINES INCREASE STAT3 IN ONE OF THE GENES STAT3 INCREASES IS MIR-21 AND DIFFERENT KINDS OF STRESS KINASE AND FREE RADICALS INCREASE MIR-21. HOW DOES IT WORK? INHIBITS A VARIETY OF DIFFERENT GENE EXPRESSION OF DIFFERENT GENES, AND MOST OF THOSE ARE ONES THAT ARE INVOLVED IN INHIBITING CANCER IN VARIOUS WAYS. OR IN INHIBITING MISMATCH REPAIR, SO YOU HAVE LESS MISMATCH WE PAIR WITH INCREASED EXPRESSION OF MIR-21. SO, THERE’S A LOT MORE DATA THAT’S BEEN COLLECTED SINCE I PREPARED THIS SLIDE A NUMBER OF YEARS AGO. SO, THEN WE WENT AND THERE WAS A TIME IN WHICH THERE WERE PEOPLE LOOKING AT EXPRESSION OF LARGE NUMBERS OF PROTEIN CODING GENES, WE TOOK A DIFFERENT APPROACH, DECIDED WE WANT TO LOOK AT MINIMUM NUMBER OF LARGE EXPRESSION OF CODING GENES, INCLUDING WE FOUND IN THESE STUDIES AND ANALYSIS, SOME OF THE WAYS INCREASE IN XPO 1, INVOLVED IN TRANSPORT OF microRNAs, BRCA 1 EXPRESSION HIGH LEVEL WHICH IS PREVIOUSLY SHOWN BY OTHERS TO CAUSE NEUROMIC INSTABILITY, HEP 1 ALPHA NOBEL PRIZE, THAT WAS WON THIS YEAR BY THREE DIFFERENT GROUPS. AND ALSO DECREASE DCL 1, TUMOR EXPRESSER GENE DISCOVERED HERE AT THE NCI. SO WE FOUND THIS FOUR-GENE CLASSIFIER IS QUITE REASONABLE IN IDENTIFYING AGAIN STAGE 1 ADENOCARCINOMA IN ORIGINAL FIVE COHORTS, AS YOU CAN SEE, SO 100% SURVIVAL, 0% SURVIVAL, AND THIS IS TIME IN YEARS. SO WHEN WE UPDATED THAT WITH SEVEN MORE COHORTS, STAGE 1 ADENOCARCINOMA OF THE LUNG, ESSENTIALLY THE SAME THING WAS FOUND. AND EVEN STAGE 1A, CHANGES IN THOSE THREE GENES, WAS ASSOCIATED WITH POOR PROGNOSIS, AND BOTH STAGE 1A AND STAGE 1B, THREE TO FIVE CENTIMETERS IN SIZE. AND THIS IS JUST LOOKING AT ALL THOSE DATA PUT TOGETHER. SO, WE DECIDED WE WANTED TO ASK COULD WE COMBINE PROTEIN-CODING GENES MECHANISTICALLY RELATED TO LUNG ADENOCARCINOMA AND MIR-21 TO FIND A BETTER CLASSIFIER THAN EITHER ALONE. THIS IS RELAPSE-FREE SURVIVAL VERSUS — THIS IS A 4-GENE, MIR-21, 4-GENE, MIR-21, HIGH, POOR SURVIVAL, AND IF YOU PUT THE TWO TOGETHER, POOR SURVIVAL, AND ESPECIALLY IN PRIMARILY 1B VERSUS 1A. SO, HOW DID WE THINK ABOUT THAT AT THE TIME? AND THE — WHAT WE CAME UP WITH WAS NON-CODING RNA AND CODING RNAs, PUT THEM TOGETHER, THEY ARE BOTH LOW, IF EITHER ONE IS HIGH, OR IF BOTH ARE HIGH, AGAIN THESE ARE SURVIVAL CURVES. BOTH CAN IDENTIFY PEOPLE WHO ARE AT RISK, BUT EACH MISCLASSIFIES SOME PATIENTS, BUT THEY MISCLASSIFIED OTHER PATIENTS. SO THE COMBINATION OF THE TWO IS BETTER THAN JUST ONE. WE FOUND THAT NOT ONLY IN LUNG CANCER BUT IN COLON CANCER, ESOPHAGEAL CANCER, BOTH ADENO, SQUAMOUS, LUNG CANCER WHICH YOU’VE SEEN, AND OTHER GROUP FOUND THAT TO BE IN BREAST SO THAT HYPOTHESIS ACTUALLY OR PRINCIPLE FOUND HAS BEEN MULTIPLE KIND OF CANCER CELLS. LET’S LOOK AT THE THIRD OMICS, THE EPIGENOME. AGAIN, WE’RE LOOKING AT LUNG CANCER. AND THIS IS DONE BY ANNA ROBLES, HYPOTHESIS WAS INTEGRATED BIOMARKER CLASSIFICATION STAGE 1 LUNG CANCER, ADENOCARCINOMA BASED ON INDEPENDENT MESSAGE, microRNA AND DEMETHYLATION MARKERS WILL IMPROVE THE CLASSIFIER. IT’S GOING FROM ONE TO TWO, NOW THREE. ONE OF OUR MANEL ESTELR STUDIED DNA MET LAYINGS, CAME UP WITH A SIGNATURE WITH ALL OF THESE MARKS, DNA METHYLATION MARKS, AND I LOOKED AT THAT AND I SAID, WELL, MAYBE ALL OF THOSE ARE DEPENDENT ON EACH OTHER, OR MAYBE THEY ARE INDEPENDENT OF EACH OTHER. WE ANALYZED THAT. WE FOUND THAT THEY ARE ALL DEPENDENT ON EACH OTHER. SO WE DECIDED, WELL, LET’S LOOK AT THE ONE THAT’S MOST HIGHLY EXPOSED, EXPRESSED, NOT EXPRESSED, FOUND, AND THAT’S HOXA 9. WE WENT FROM FIVE OR SIX DOWN TO ONE AGAIN. THE OBJECTIVE IS TO GET SMALLER AND SMALLER, THAT GIVES YOU BETTER AND BETTER RESULTS. WE PUT ALL THREE TOGETHER IN STAGE 1 LUNG CANCER. THESE ARE KAPLAN-MEIER PLOTS AGAIN, THIS IS A FIVE, THIS IS MONTHS, THIS IS FIVE-YEAR POINT. SO IF ALL THREE ARE POSITIVE, CLASSIFICATION OMICS ARE POSITIVE, VERY POOR PROGNOSIS. STAGE 1A IS A LITTLE BIT BETTER THAN STAGE 1B. SO, TAT WAS SOMETHING THAT IMPRESSED US, AND NCI HAS PATENTS ON ALL THIS STUFF. SO, NOW SOMETHING NEWER. THAT’S MICROBIOME. AND WAS THERE A LECTURE ON THE MICROBIOME? OKAY. SO, SHOULD BE FAMILIAR WITH THIS. AND MICROBIOME IS ABOUT TEN TIMES, 100 TIMES MORE BACTERIA AND FUNGI ON OUR BODY, IN OUR GUT AND ELSEWHERE, THAN THERE ARE HUMAN CELLS. AND THE MICROBIOME VARIES DEPENDING ON THE SURFACE THEY ARE ON, OR THE INTERIOR THEY ARE ON, AND SO JUDY SEGRAY AND OTHERS MADE IMPORTANT DISCOVERIES IN VARIATION, WE COLLABORATED WITH HER. IT WAS KNOWN A FEW YEARS AGO NOW THAT THERE WERE BACTERIA ASSOCIATED WITH INCREASED CANCER RISK, A PYLORI AND COLON CANCER, DYSBIOSIS, THAT MEANS A CHANGE IN THE FREQUENCY OF DIFFERENT CLASSES OF BACTERIA IN CANCER THERAPY. DOUG LOWY AND JOHN SCHNEIDER FOUND HUMAN PAPILLOMAVIRUS, VACCINE, RECENTLY PUBLISHED DATA ON ACIDOVORAX. ALL OF THESE HAVE DIFFERENT EFFECTS ON CELLS. EITHER ON THE SURFACE OF EPITHELIUM, FOR EXAMPLE, OR VIRUSES CAN CAUSE MUTATIONS, THEY CAN CAUSE PROBLEMS WITH THE MU COASTA BARRIER, ESPECIALLY CIGARETTES WILL CAUSE THIS, BACTERIA GET IN, AND CAUSE INFLAMMATION. AND SOME OF THE BACTERIA PRODUCE ACTUALLY PROTEINS WHICH ARE MUTAGENS, WHICH IS ANOTHER INTERESTING WAY OF CAUSING MUTATIONS IN HUMAN CANCERS, IN HUMAN CELLS, CAUSING CANCER. SO IN THE STUDY THAT WE RECENTLY PUBLISHED, I GUESS SOMETIME LAST YEAR, WE FOUND THERE WAS INTERACTION BETWEEN THE MICROBIOME AND SMOKING, P53 MUTATIONS, AND HUMAN LUNG CANCER, AND WE FOUND SEVERAL PACKS INCLUDING ACIDOVORAX WERE HIGHER IN SMOKERS VERSUS FORMER SMOKERS VERSUS NONSMOKERS, SO FORMER SMOKERS AND PEOPLE WHO WERE CURRENT SMOKERS ARE INCREASED FREQUENCY OF ACIDOVORAX. A GROUP OF FACTS ASSOCIATED WITH SQUAMOUS CELL CARCINOMA, AND AS I SAID ENRICHED IN SMOKERS. AND THAT THESE WERE ASSOCIATED WITH P53 MUTATIONS. SO, IT WAS P53 MUTATIONS ACTUALLY PLAYING A ROLE OR WAS IT A CONSEQUENCE OF THE FACT THAT THESE WERE SMOKERS? AND THAT’S AN INTERESTING KIND OF QUESTION. THIS CAME TO A CONCLUSION THAT THE SQUAMOUS CELL CARCINOMA ATTACKS IN PEOPLE WERE TP53 MUTATIONS, ESTABLISHING A MICROBIOME-GENE INTERACTION IN LUNG CANCER. NEXT QUESTION ARE BACTERIA PASSENGERS? OR ARE THEY PLAYING A ROLE IN THE DEVELOPMENT OF THE CANCER? WE’RE DOING A LARGE NUMBER OF ANIMAL STUDIES AND OTHER KINDS OF STUDIES RIGHT NOW, I’LL JUST SHOW YOU ONE SLIDE MAYBE. THAT GOT DELAYED. I GUESS IT DIDN’T GET TRANSFERRED, WHEN HE TRANSFERRED MY USB STICK. WE FOUND INDEED THAT ACIDOVORAX INCREASES THE SIZE OF THE TUMORS IN A MOUSE MODEL, KRAS AND P53 MUTATION AND THEY GOT TUMORS QUICKER THAN IF IT WAS ACIDOVORAX OR IF THEY WERE EXPOSED TO SHAM OR INTRANASAL OR LACTOBACILLUS, AN ANTI-INFLAMMATORY AGENT. SO, LOOKS LIKE IT’S RELATED TO INFLAMMATION, AND SO WE HAVE EXPERIMENTS NOW LOOKING WHETHER OR NOT INFLAMMATORY AGENTS EITHER CHEMICALS OR DRUGS OR LACTOBACILLUS WILL DECREASE FREQUENCY OF LUNG CANCER CAUSED BY ACIDOVORAX IN THE ANIMAL MODEL. SO LET’S — WE’RE READY TO END UP, LOOKING AT THE METABOLOME, IN THE PREVIOUS SLIDE. AND HYPOTHESIS THAT THESE TWO POSTDOCS, MAJDA AND EWY, EWY HAS JUST TAKEN A HIGH LEVEL POSITION AT NCATS, AND MAJDA HAS A HIGH LEVEL POSITION AT FDA NOW. UNBIASED METABOLOMICS WILL DISCOVER BIOMARMERS ASSOCIATED WITH RISK, DIAGNOSIS, PROGNOSIS OF THERAPEUTIC OUTCOME OF LUNG CANCER. LET’S GO BACK TO PREVIOUS SLIDE, HIPPOCRATES AGAIN. SO HIPPOCRATES, IT’S SAID, TASTED URINE FOR DIAGNOSIS OF DISEASE IN HIS PATIENTS. NOW, I’M NOT AS OLD AS HIPPOCRATES, ALTHOUGH MY KIDS MIGHT THINK I AM. BUT I NEVER TASTED URINE, EXCEPT WHEN WE HAD SMALL KIDS. I WAS CHANGING DIAPERS. SO, BUT — SO THAT WAS ONE OF THE THINGS THAT PHYSICIANS DID AT THIS STAGE. AND THEN A PHYSIOLOGIST, ARMSTRONG, IN EUROPE, THIS IS A PICTURE OF ALL THIS, WRITES FROM A LIQUID WINDOW THROUGH WHICH PHYSICIANS FELT THEY COULD VIEW THE BODY’S INNER WORKINGS, URINE BECAME THE BEGINNINGS OF LABORATORY MEDICINE. WE’RE NOT ALLOWED TO WRITE THIS KIND OF FLOWERY LANGUAGE BUT I THINK IT MAKES A POINT, AND THIS DUTCH PAINTING IS A GOOD EXAMPLE OF THAT. OKAY. SO WE DID BIASED SCREEN IN EUROPE, CHROMATOGRAPHY, MASS SPEC ANALYSIS, AND FOUND THERE WERE FOUR DIFFERENT METABOLITES, ONE CREATININE RIBOSIDE, ONE N-ACETYLNEUROAMINNIC ACID, CORTISOL SULFATE. PUT THEM TOGETHER, PROGNOSIS IS VERY POOR, THREE OUT OF THE FOUR ALSO POOR, AND GETS BETTER IF ONLY TWO, OR ONLY ONE. AND ALSO DIAGNOSIS, THESE ARE — THIS IS A ROCK CURVE. SO THIS IS LOOKING AT SPECIFICITY AND SENSITIVITY, AND SO THE AREA IN THE CURVE HERE IS, OH, LET’S SEE IF I CAN READ IT HERE. IT’S ACTUALLY — YEAH, IT’S DOWN THERE. IT’S ABOUT .9, WHICH IS ACTUALLY QUITE GOOD. AND PREDICTIVE VALUE, POSITIVE PREDICTIVE VALUE, NEGATIVE PREDICTIVE VALUE, PHYSICIANS INCLUDING MYSELF LOOK AT THE NEGATIVE PREDICTIVE VALUE BECAUSE YOU HAVE SOMEONE WHO HAS LOW DOSE CT SCANNING AND THERE’S A LESION THERE, THE NEGATIVE PREDICTIVE VALUE MIGHT ALLOW YOU TO SAY, WELL, WHY DON’T WE WAIT THREE MONTHS AND SEE IF THE LESION INCREASES OR NOT. BECAUSE MOST OF THEM ARE NOT CANCER. I’LL SHOW YOU THAT IN JUST A MOMENT. WE FOUND THE AMOUNT IN THE URINE WAS ASSOCIATED WITH THE AMOUNT IN THE TUMOR, AND THIS IS A CORRELATION CURVE, PRETTY GOOD. HIGH LEVELS IN THE URINE. IT’S ALSO THE CORRELATION HERE BETWEEN URINE AND TUMOR, ALSO HOLDS UP IF YOU LOOK AT SERUM, PLASMA. A CLINICAL TEST IS BEING MADE OF THIS, CLIA-BASED CLINICAL TEST FOR LICENSING AND HOPEFULLY PUT IN CLINICAL PRACTICE. LET’S GO TO LOW DOSE CT. THE TURNING POINT HERE WAS IN OLD DAYS THAT WASN’T SUCH A LONG TIME AGO CHEST X-RAY WAS THE SCREEN, YOU DIDN’T SEE ANYTHING UNTIL THEY GOT STAGE 2 OR 3 OR 4 CANCER. LOW DOSE CT DECREASED THE MORTALITY ABOUT 20%, IN THIS ORIGINAL STUDY, IN THE STUDY DONE IN ENGLAND IT WAS CLOSER TO 30%. AND WOMEN WITH BETTER PREDICTING CANCER, DECREASING MORTALITY IN WOMEN THAN MEN. SO THIS WAS A CASE-CONTROLLED STUDY, I SHOULD SAY, COMPARING X-RAY VERSUS LOW DOSE CT. AND THE FALSE POSITIVE RATE WAS PRETTY HIGH. I’LL MAKE A POINT OF THAT. BUT IT DID DETECT PRIMARILY EARLY STAGE, STAGE 1A AND 1B LUNG CANCER, IN WHICH THE CURE RATES ARE THE BEST WITH SURGERY. BUT THE HIGH FALSE POSITIVE RATE VERSUS THOSE THAT WERE DETECTED, YOU JUST LOOK AT THIS CARTOON OF — I DON’T KNOW WHERE YOU GO FOR YOUR CONCERTS, BUT THIS IS THE STAGE, AND THIS IS THE BALCONY. THESE ARE THE SEATS. SO, LOW DOSE CT WILL DETECT 3 1/2 PEOPLE SCREENED IN THE WHOLE AUDIENCE, BUT FALSE POSITIVE RATE IS MUCH HIGHER. SO THAT’S A PROBLEM. AND THE PROBLEM IS THE FINANCIAL PROBLEM, IT’S A PROBLEM OF MORBIDITY. IT’S A PROBLEM OF ANXIETY. AND THIS ISN’T ONLY TRUE OF LUNG CANCER AND SCREENING, IT’S TRUE OF MAMMOGRAMS, A HIGH FREQUENCY OF FALSE POSITIVE MAMMOGRAMS, MY WIFE HAD FIVE NOW, ALL NEGATIVE, SHE REFUSES TO TAKE MORE BECAUSE GOING THROUGH BIOPSY, PSYCHOLOGY OF ALL THAT, SHE DECIDED THAT SHE HAD ENOUGH. THAT’S BETWEEN HER AND HER PHYSICIAN. SO LOW DOSE CT NOW IS FUNDED BY THE U.S. GOVERNMENT. SO THERE’S NO REASON THAT PEOPLE WHO FIT CRITERIA, AND THIS IS THE CURRENT CRITERIA, CAN’T GET LOW DOSE CT. BUT THERE’S ABOUT 10 MILLION OF THOSE FOLKS OUT THERE. AND THE CAPACITY FOR DOING LOW DOSE CT MAY BE 100,000 TO 200,000, IT’S INCREASING. BUT OBAMACARE, AFFORDABLE CARE, AND ALSO OTHER MEDICARE WILL PAY FOR IT, SO THERE IS A NEED TO IDENTIFY HIGH RISK INDIVIDUALS OUTSIDE CRITERIA, NEVER SPOK SMOKERS, 13% COMING IN ARE NEVER SMOKERS, FROM PASSIVE OR PARENTAL EXPOSURE OR IS IT JUST BAD LUCK? OR THEIR JOB? SO WE NEED CRITERIA TO IDENTIFY INDIVIDUALS, AND ALSO PRIORITIZE THESE INDIVIDUALS AND TO THOSE AT GREATEST RISK. SO THEY DON’T HAVE TO STAND IN LINE FOR SIX MONTHS OR A YEAR OR TWO OR THREE YEARS. AS I SAID, AT THE TIME IN 2010 THERE WERE ABOUT OVER 8 MILLION, THERE ARE OVER 10 MILLION NOW. SO I’M ABOUT READY TO END. SO WHAT’S OUR STRATEGY FOR EARLY STAGE LUNG CANCER, UNMET NEEDS? ONE OF COURSE IS IDENTIFY PEOPLE WHO ARE AT RISK, AND INCLUDING THOSE WHO ARE SMOKERS, OR NONSMOKERS, AND FOR PRIORITY SCREENING, AND LOOKING AT VARIOUS CYTOKINES, URINARY, TUMOR METABOLITES AS A QUICK ASSAY, AND ALSO NASAL EPITHELIUM IS BEING EXPLORED AND CLIA-BASED ASSAYS ARE IN PROGRESS. YOU FIND SOMEONE, DECIDE, WELL, THIS PERSON NEEDS A SCAN, THEN YOU NEED TO DETERMINE WHETHER OR NOT THE LESION IS A CANCER OR NOT. I WAS TELLING YOU EARLIER, MOST OF THEM ARE NOT CANCER. SO, YOU NEED EARLY DIAGNOSTIC MARKERS, AGAIN SERUM CYTOKINES, URINARY TUMOR METABOLITES, AND INDEED NASAL EPITHELIUM, AND OTHER BIOMARKERS ARE BEING DEVELOPED NOW. THIS IS A BIG AREA, LET’S SAY MORE ABOUT THAT. AND THEN THE NEXT QUESTION IS, WELL, IT’S CANCER, BUT YOU DO SURGERY ON THAT PERSON, AND YOU REMOVE THAT CANCER, DO THEY HAVE METASTASIS GOING ON? AND ABOUT 25, 30% WILL HAVE METASTASES, EVEN THOUGH YOU CAN’T SEE THEM. SO PATHOLOGIST MISSES THEM. THEY ARE MICROMETASTASES. SO IF YOU COULD IDENTIFY THOSE PEOPLE, MAYBE YOU COULD OFFER THEM ADJUVANT THERAPY. EITHER IMMUNOTHERAPY OR CHEMOTHERAPY. AND ONE RATIONALE MIGHT BE MICRO METASTASES MAY BE MORE SUSCEPTIBLE THAN A LESION THAT’S 4 OR 5 CENTIMETERS, WHAT KILLS THE PATIENT IS RECURRENCE OF ORIGINAL TUMOR SO THERE ARE SEVERAL WAYS PEOPLE ARE FOCUSING ON THIS. WHAT WAS I PREACHING ABOUT? STAGE 1 LUNG CANCER, CURATIVE SURGERY, 25% RECUR AND DIE, STAGE 1A OR 1B, SURGERY IN BOTH. SOME PEOPLE ARE LOW RISK, SOME ARE HIGH RISK, HOW DO YOU IDENTIFY THOSE PEOPLE AT HIGH RISK? AND PRECISION MEDICINE IS THE STRATEGY THAT PEOPLE ARE USING NOW, INCLUDING TO DECREASE FALSE POSITIVE RATE, DECREASE FINANCIAL COST, IMPROVE PATIENT CARE, AND GUIDE FURTHER MECHANISTIC STUDIES. AND THESE PEOPLE, YOU CAN OBSERVE TO SEE IF THEY CHANGE. THESE PEOPLE ADJUVANT THERAPY IS WHAT WE WOULD RECOMMEND. THESE ARE JUST SOME FELLOWS IN THE LABORATORY, SOME CURRENT PEOPLE, MANY COLLABORATORS, I THINK I’VE TRAINED OVER 130 POST DOCS. THEY ARE CHAIRMEN OF DEPARTMENTS, DEANS OF THIS, THAT AND THE OTHER, SO I’M VERY PROUD OF ALL OF THEM. WE GET TOGETHER ONCE IN A WHILE, THERE’S LIKE 60 OF THEM IN JAPAN, SO WE PARTY, YOU KNOW, SO I THANK THEM AND I THANK YOU FOR PUTTING UP WITH ME AFTER 5:00. [APPLAUSE] HAPPY TO ANSWER ANY QUESTIONS. YES? WHAT’S YOUR NAME? JOANNA? HI. SECOND FLOOR.>>[OFF MICROPHONE].>>I HOPE IT’S NOT OVERHEATED LIKE OUR LAB IS.>>[OFF MICROPHONE].>>GO AHEAD, WHAT’S YOUR QUESTION?>>(OFF MIC.).>>SO, YEAH. SO THAT’S REALLY A VERY INTERESTING QUESTION. SO PEOPLE HAVE BEEN THINKING ABOUT TUMOR MUTATIONAL BURDEN FOR VARIOUS REASONS, INCLUDING — WELL, MAYBE MORE NEOANTIGEN, SO YOU’D HAVE YOUR IMMUNOTHERAPY MIGHT BE MORE SUCCESSFUL, IT’S CONTROVERSIAL. INITIAL RESULTS SUGGEST MAYBE THAT WAS GOING TO BE A CASE BUT THERE ARE LOTS OF RESULTS THAT DON’T FIND THAT TO BE THE CASE. AND TUMOR MUTATIONAL BURDEN VERSUS BIOMARKERS, THAT’S NOT BEEN WELL STUDIED YET. AND BUT THAT’S SOMETHING THAT CAN BE DONE, INCLUDING WITH PCGA DATA, OR WITH DATA THAT WE’VE COLLECTED, AND THAT’S ACTUALLY SOMETHING THAT WE’RE QUITE INTERESTED IN AND ITS RELATIONSHIP TO MICROBIOME, METABOLOME, SO THAT’S A SOPHISTICATED QUESTION AND A VERY GOOD ONE. THANK YOU. YEAH?>>[OFF MICROPHONE].>>OKAY. SO, THERE MAY BE ANOTHER CONNECTION. SO, SOME BACTERIA ACTUALLY PRODUCE A PROTEIN THAT IS A MUTAGEN. AND SO THAT’S SOMETHING THAT WE’RE SEARCHING FOR, IN ADDITION TO ACIDOVORAX, PLASELLA IS ALSO ASSOCIATED WITH LUNG CANCER, THERE’S FIVE OR SIX SPECIES OF KLEBSIELLA IN ACIDOVORAX, THERE A 60 BASE PAIR SEQUENCE THAT USUALLY CAN TELL YOU MAYBE THIS PROTEIN IS THERE. AND SO THAT’S A BIOINFORMATIC KIND OF EXAMPLE, AND YOU HAVE TO ASK THE QUESTION, CAN YOU BIND THE PROTEIN AND THEN IS THERE A WAY OF INHIBITING THE PROTEIN, AND ONE OF OUR NEW COLLABORATORS FOUND A SIGNATURE FOR THAT PROTEIN IN ONE OF THESE SPECIES THAT LIKE THE SIGNATURES I WAS TALKING ABOUT WITH CHEMICAL CARCINOGENS, THEY WERE SIGNATURES ASSOCIATED WITH THESE PROTEINS, SMALL PROTEINS PRODUCED BY BACTERIA. AND SO THAT MIGHT BE ANOTHER CLUE TO WHO GETS CANCER AND WHO DOESN’T GET CANCER AND WHAT KIND OF CANCER AND SO ON AND SO FORTH. VERY GOOD QUESTION. TWO VERY GOOD QUESTIONS. WANT TO TRY A THIRD ONE? WANT TO GO HOME? OKAY.
01:45:21.782,00:00:00.000
THANK YOU.

One Comment

  • Edward Branca

    I am 68 years old and I have been disabled for all of my life. I don't pay anything for the many medications that I must take. I don't pay anything for any of my healthcare. I don't pay any Medicare premiums because New York state's Medicaid program pays my premiums for me. My healthcare is paid by Medicare and Medicaid. My income is SSDI. and SSI. Because I have many serious medical issues, I see doctors about once a week, and I take many medications. I needed to be hospitalized three times this year alone. I know that I am costing you taxpayers a heck of a lot of money, but what can I do? I am not going to commit suicide and I want to remain alive for as long as I possibly can. By the way, on the infrequent occasions that I receive a medical bill, I toss it into the garbage can and then I forget that I received it.

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