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TRACO 2018 – Non-small cell lung cancer and Genomics

TODAY WE HAVE EVA SZABO GIVING HER FIRST TALK, M.D. DURING UNIVERSITY, INTERNAL MEDICINE RESIDENCY AT BELLEVUE NEW YORK UNIVERSITY MEDICAL CENTER, AND SHE DID MEDICAL ONCOLOGY FELLOWSHIP AT NCI, SHE’S DOING PREVENTION RESEARCH EVER SINCE. THE TITLE IS CHIEF LUNG AND UPPER AIR DIGESTIVE CANCER RESEARCH GROUP. EVA? >> THANK YOU. OKAY. THIS WORKS. FANTASTIC. SO, THANK YOU FOR MY, WHAT, 15th YEAR AT TRACO, OR WHATEVER IT IS. THAT’S ABOUT RIGHT. SO TODAY WE’RE GOING TO BE TALK BE ABOUT NON-SMALL CELL LUNG CANCER, DIVIDED INTO HALF AND HALF, A LITTLE BIT ABOUT BIOLOGY, NOT VERY MUCH, A LITTLE BIT ABOUT THERAPEUTICS, AND THEN ABOUT HALF ABOUT PREVENTION AND TEENY TINY ABOUT EARLY DETECTION. SO, THIS IS A COMPLICATED SLIDE, BUT THERE’S SOMETHING VERY EASY TO SEE. THIS GREEN THING THAT SAYS GLOBAL INCIDENCE AND MORTALITY OF LUNG CANCER, THIS GREEN AREA HERE SHOWS THAT GLOBALLY ACROSS THE ENTIRE WORLD, LUNG CANCER INCIDENCE IS A SIGNIFICANT PART OF ALL CANCER INCIDENCE, MAYBE A TENTH, MAYBE A LITTLE BIT LESS, BUT IN TERMS OF MORTALITY IT’S REALLY AN OUTSIDE CONTRIBUTION TO GLOBAL MORTALITY, YOU KNOW, ON THE ORDER OF ABOUT A FIFTH TO A QUARTER OF ALL CANCER DEATHS.

IT’S A MAJOR, MAJOR PROBLEM ACROSS THE WORLD. HERE IN THE UNITED STATES, I’VE BEEN DOING THIS ACTUALLY WE WERE TALKING ABOUT — A FORMER COLLEAGUE, SHE AND I USED TO TRADE OFF THESE STATISTICS SLIDES, AND THEY HAVE GONE UP AND UP, EVEN AS SMOKING PREVALENCE HAS GONE DOWN BECAUSE IT TAKES REALLY A LONG TIME TO UNDO THAT DAMAGE. SO FOR THIS YEAR THE ESTIMATE IS ABOUT 234,000 NEW CASES, 154,000 ESTIMATED DEATHS, AND THIS IS THE LEADING CAUSE OF CANCER DEATH IN THE UNITED STATES, WHICH IS GREATER THAN THE NEXT THREE CAUSES OF CANCER DEATH ADDED TOGETHER. NOW, THE GOOD NEWS IS THAT THE DEATH RATES ARE DECREASING. THIS IS MEN. THIS IS WOMEN. WITH REALLY THE TOBACCO CONTROL INITIATIVE THAT HAVE BEEN PUT IN PLACE SINCE THE 1960s, IT TAKES A LONG TIME. THE SURVIVAL HAS IMPROVED OVER TIME. THIS IS NOW THERAPEUTICS, THAT WE’RE TALKING ABOUT, AND MAYBE SOME EARLIER DETECTION. I PUT THAT IN QUOTES. USED TO BE ABOUT 5% IN THE 1950s, NOW 18% FIVE-YEAR SURVIVAL. THE REASON SURVIVAL IS SO POOR IS BECAUSE MOST LUNG CANCER IS NOT DISCOVERED EARLY BUT ACTUALLY DISCOVERED WHEN IT’S ALREADY METASTATIC OR AT LEAST LOCALLY ADVANCED, GETTING SYMPTOMS, AND THAT’S OFTEN USUALLY ALMOST ALWAYS NOT A CURABLE SITUATION.

OKAY. SO, THE RISK FACTORS ARE ACTUALLY PRETTY WELL KNOWN. IT’S TOBACCO FOR 85% OF ALL LUNG CANCER. THAT INCLUDES PASSIVE SMOKING SO IF YOU’RE A CHILD IN A HOUSEHOLD THAT HAS HEAVY SMOKING GOING ON, YOU WILL HAVE THAT EXPOSURE. SPOUSES, WORKPLACE. A PRIOR AERODIGESTIVE MALIGNANCY DUE TO TOBACCO EXPOSURE IS ALSO INDEPENDENT RISK FACTOR, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, A TOBACCO-RELATED PROBLEM THAT’S COPD, A LITTLE BIT DIFFERENT FROM ASTHMA, BUT EVEN COPD NOT ASSOCIATED WITH TOBACCO, THERE IS SUCH A THING, EVEN THAT IS ASSOCIATED WITH LUNG CANCER. SO IT GIVES YOU INCREASED RISK INDEPENDENT OF JUST THE TOBACCO EXPOSURE. NOW, MOST OF THE OTHER EXPOSURES ARE — DUE TO WORKPLACE EXPOSURE, WITH THE EXCEPTION OF ASBESTOS, THAT’S BEEN GOING ON, KNOWN FOR A LONG TIME, WE THINK ABOUT ASBESTOS AND MESOTHELIOMA, THE MORE COMMON IS NON-SMALL CELL LUNG CANCER. RADON, INDOOR RADON EXPOSURE IS A RISK FACTOR. THAT’S WHY WE ALL NEED TO GET OUR HOUSES TESTED BEFORE WE BUY THEM, AT LEAST HERE IN MONTGOMERY COUNTY, MANY PLACES. AND THEN A WHOLE VARIETY OF OTHER WORKPLACE EXPOSURE. NICKEL, INORGANIC ARSENIC FOUND IN WELL WATER, IN SOME THIRD WORLD COUNTRIES, AND SUCH.

THERE’S ALSO A GENETIC PREDISPOSITION. THIS IS ACTUALLY FAIRLY HARD TO STUDY BECAUSE OF TOBACCO. SO SEPARATE THAT FROM TOBACCO EXPOSURE, BUT THERE ARE ACTUALLY NOW WELL DOCUMENTED CASES OF FAMILIAL LUNG CANCER AND SOME OF WHICH — FOR SOME OF THESE CASES WE KNOW WHAT THE ABNORMALITY IS. IT’S THE GROWTH FACTOR RECEPTOR WHICH I’LL TALK ABOUT BUT THE P 790M MUTATION IN PARTICULAR, OCCURS IN FEMMES, AND IS ASSOCIATED WITH ADENOCARCINOMA, EVEN IN NEVER SMOKERS. THE NICOTINEOID ACETYLCHOLINE RECEPTOR, SUBUNITS, POLYMORPHISMS ARE ASSOCIATED WITH LUNG CANCER INCIDENCE AS WELL AS COPD INCIDENCE. AND SO THESE ARE SOME OF THE BETTER CHARACTERIZED LUNG CANCER SUSCEPTIBILITY LOCI. THERE ARE LOTS OF STUDIES ABOUT HOW PEOPLE METABOLIZE CARCINOGENS, AND THERE ARE RELATIVE RISKS OF 1.3, 1.2, ASSOCIATED WITH VARIOUS GENE POLYMORPHISMS, BUT THIS IS A VERY HIGH LEVEL OVERVIEW. IN TERMS OF WHAT LUNG CANCER ACTUALLY IS, PATHOLOGICALLY, IT IS NOT LUNG DISEASE, MOLECULARLY, IT’S EVEN MORE DISEASES BUT PATHOLOGICALLY WE TEND TO DIVIDE IT INTO WHAT WE SEE UNDER THE MICROSCOPE. SO NON-SMALL CELL LUNG CANCER IS PRIMARILY ADENOCARCINOMA, WHICH IS ABOUT 40% OF CASES AND THOSE TEND TO BE PERIPHERAL.

THOSE ARE THE ONES ALSO ASSOCIATED WITH NEVER SMOKING, BUT VERY HIGHLY ASSOCIATED WITH SMOKING AS WELL. SQUAMOUS CELL ARE 20%, MORE CENTRALLY LOCATED REFLECTING THE CELL OF ORIGIN. LARGE CELL CARCINOMA, A FAIRLY UNCOMMON, 10 TO 15% OF CASES, AGAIN TEND TO BE MORE PERIPHERAL AND THERE’S A SMATTERING OF OTHER CANCERS, BENIGN OR MALIGNANT, SARCOMATOID, NON-SMALL CELLS, RELATIVELY UNCOMMON CANCERS. THE OTHER 20% OF LUNG CANCER IS SMALL CELL, I THINK THAT’S A SEPARATE LECTURE. SO, LUNG CANCER, BECAUSE IT IS OFTEN USUALLY DUE TO EXPOSURES, ACTUALLY THE PROCESS OCCURS OVER A LONG PERIOD OF TIME. YOU START SMOKING WHEN YOU’RE A KID, TEENAGER, YOU DEVELOP YOUR LUNG CANCER WHEN YOU’RE IN YOUR 50s, ’60s, 70s. IT’S A LONG PROCESS. AND DURING THIS PROCESS THERE’S A PROGRESSIVE DEVELOPMENT OF HISTOLOGIC CHANGES IN THE BRONCHIOLE EPITHELIUM. METAPLASIA, DYSPLASIA, ACCUMULATION OF MOLECULAR ABNORMALITIES, BUT THIS GIVES US THE OPPORTUNITY TO REALLY INTERVENE ALONG THIS ENTIRE CONTINUUM. NOW, TREATMENT IS THE IDEAL INTERVENTION. YOU KNOW WHO YOU’RE TREATING, RIGHT? BECAUSE SOMEBODY COMES TO YOU, THEY HAVE LUNG CANCER. THE PROBLEM IS THAT OFTEN IT’S TOO LATE TO HAVE A CURE, EXEMPT FOR THE VERY EARLY LOCALIZED CANCERS. EARLY DETECTION WOULD BE ANOTHER OPTION WHICH WE’LL TALK ABOUT A LITTLE BIT LATER.

THERE YOU CAN START TO — YOU HOPE TO DETECT EARLY ENOUGH THAT AN INTERVENTION SUCH AS SURGERY WILL RESULT IN CURE. BUT IT’S REALLY THE WHOLE PROCESS, 20, 30, 40 YEARS OF TOBACCO EXPOSURE THAT GIVES US THE OPPORTUNITY FOR PREVENTIVE APPROACHES AND THAT IS WHAT I WILL REALLY TALK ABOUT MAINLY. BUT BEFORE I DO, LET’S TALK ABOUT — MY SLIDES LOOK A LITTLE WEIRD. I DON’T KNOW WHETHER IT’S ME OR SOMETHING ABOUT IT. BUT ANYWAY, OKAY. LET’S TALK ABOUT TREATMENT STRATEGIES FOR LUNG CANCER. SO, TREATMENT IS BASED ON STAGE. LIKE ALL CANCERS, IF IT’S EARLY LOCALIZED, WE’RE TALKING ABOUT SURGERY. IF IT’S SLIGHTLY NOR SPREAD, SO IT’S A BIGGER CANCER OR DEVELOPS LYMPH NODES, WE ADD SOME CHEMOTHERAPY TO GET A LITTLE BIT OF BENEFIT. IF IT’S ALREADY SPREAD TO LOTS OF LYMPH NODES OR CROSSES TO THE OTHER SIDE OF THE MEDIA STEINUM WE’RE TALKING ABOUT RADIATION TOGETHER WITH CHEMOTHERAPY, SOMETIMES WITH SOME SURGERY AS WELL, A MUCH LESS CURABLE SITUATION FROM 5 TO 20% FIVE-YEAR SURVIVAL. AND ONCE YOU’RE OUT OF THE CENTRAL MEDIASTINAL AREA, WHEREVER THE CANCER ORIGINATED, IF YOU INVOLVE THE PLEURAL SURFACE OR DISTANT SITES, THEN YOU’RE TALKING ABOUT METASTATIC DISEASE EVEN TODAY IS CONSIDERED AN INCURABLE SITUATION.

AND THERE WE USE CHEMOTHERAPY, IMMUNOTHERAPY, TARGETED THERAPIES, RADIATION IS NEEDED FOR LOCAL CONTROL, SOMETIMES WE TAKE OUT SOME ISOLATED METASTASES, BUT IT’S REALLY A SYSTEMIC APPROACH. FOR SMALL CELL IT’S SYSTEMIC FROM THE GET-GO PLUS OR MINUS RADIATION. SO, THE HALLMARK, THE STANDARD FOR METASTATIC TREATMENT OF METASTATIC DISEASE, I HAVE TO SAY, HAVE INCREASED AND CHANGED DRASTICALLY DURING MY 29 YEARS IN MEDICAL ONCOLOGY. CHEMOTHERAPY IS STILL SOMETHING THAT THE VAST MAJORITY OF PATIENTS WILL SEE. WE USE PLATINUM, CISPLATIN, CARBOPLATIN, WITH ADDITIONAL DRUGS, INTRAVENOUS TREATMENT GOES TO THE WHOLE BODY THEORETICALLY. IT’S USED IN ADJUVANT TREATMENT, BUT MAINLY FOR METASTATIC DISEASE. WE HAVE TARGETED THERAPIES FOR TARGETED MUTATIONS AND DRUGS THAT TARGET THOSE SPECIFIC MUTATIONS HAVE VERY GOOD RESPONSE RATES, BUT NOT CURE. THESE ARE GENERALLY ORAL THERAPIES, THEY ARE BETTER TOLERATED, AND THEY DO EXTEND SURVIVAL. THERE’S A NUMBER OF THEM WHICH I’LL DESCRIBE.

AND NOW OVER THE LAST FEW YEARS WE HAVE IMMUNOTHERAPY, WHICH NOW HAS A DEFINITIVE ROLE, FRONT LINE AND SECOND LINE TREATMENT. SO PERSONALIZED THERAPY, THE SAME GRAPH HERE, BUT ADDED TO THE SIDE. SO ALSO, WE’VE BEEN WITH THE TCGA AND MANY — LOTS OF HARD WORK, WE NOW KNOW THAT IN ADENOCARCINOMAS, 40% OF LUNG CANCERS, THERE ARE A NUMBER OF DIFFERENT DRIVER MUTATIONS WHICH ARE RESPONSIBLE FOR THIS SUBTYPE. AND A NUMBER OF THESE ARE ACTUALLY TARGETABLE. SO I’LL TALK ABOUT EGFR, ALK, REARRANGEMENTS, ROS1 REARRANGEMENTS, THERE’S A WHOLE LIST NOW OF MOLECULAR ABNORMALITIES THAT WE LOOK FOR WHEN A PERSON IS DIAGNOSED WITH METASTATIC LUNG CANCER, BECAUSE IN FACT THE RESPONSE RATES, IF YOU TREAT THEM WITH TARGETED THERAPIES, ARE ON THE ORDER OF 50 TO 80%, SO ABOUT 20% OF ALL NON-SMALL CELL LUNG CANCER PATIENTS ARE ACTUALLY APPROPRIATE FOR TREATMENT WITH TARGETED THERAPIES.

AND THIS IS REALLY — IT’S THE EPIDURAL GROWTH FACTOR RECEPTOR STORY THAT PUT NON-SMALL CELL LUNG CANCER INTO THE PRECISION MEDICINE BASKET, SO TO SPEAK. AND IT’S A GOOD STORY BECAUSE IT WAS FOUND THAT THERE WAS A SPECIFIC DRUG, GA FIT NAB, ERLOTINIB, 10% RESPONSE RATE WITH THE NEW AGENTS, HIGH IF PEOPLE HAVE A SPECIFIC MUTATION, EGFR MUTATION, LEADING TO PROGRESSION-FREE SURVIVAL, ON THE ORDER OF 10 TO 14 MONTHS WITH FIRST GENERATION THERAPIES WHICH IS VERY DIFFERENT FROM THE FOUR TO SIX MONTHS YOU GET WITH STANDARD CHEMOTHERAPY. AND MEDIAN SURVIVAL WHICH IS NOW ON THE ORDER OF 2 TO 2 1/2 YEARS. SO WE HAVE MULTIPLE DRUGS, ERLOTINIB WAS ONE OF THE MOST SUCCESSFUL FIRST GENERATION AGENTS, APPROVED FOR FIRST, SECOND, THIRD LINE TREATMENT.

THERE ARE OTHERS, AFATINIB, GEFITINIB, NOW OSIMERTINIB, TARGETS NOT USUAL SENSITIZING, BUT ALSO RESISTANCE MUTATION, T7 90M MUTATION, WHICH OCCURS IN 50% OF PEOPLE TREATED WITH ERLOTINIB. OSIMERTINIB IS THE NEW FRONT LINE WINNER, AND THIS MUTATION IF YOU LISTEN HARD IS ONE OF THE RARE FAMILIAL LUNG CANCER MUTATIONS. SO WHERE IT CAME FROM, WHO KNOWS, BUT IT’S AN INTERESTING STORY. AND SO THIS IS NOW A MUCH BETTER PATH TO GO INTO, IF YOU HAVE TO HAVE NON-SMALL CELL LUNG CANCER, YOUR PROGNOSIS IS BETTER AND THERE ARE MULTIPLE DIFFERENT TREATMENTS AVAILABLE IF YOU HAVE AN EGFR MUTATION. THE ELK IS ANOTHER EXAMPLE, ONE OF THE I WOULD SAY, WINNERS IN TERMS OF GOING FROM IDENTIFICATION OF THE ABNORMALITY TO AN APPROVED THERAPY. THIS WAS IDENTIFIED IN 2007, SO 11 YEARS AGO. IT ACTUALLY OCCURS IN 5% OF PEOPLE. JUST LIKE EGFR, IT’S MAINLY IN NEVER SMOKERS, AND THERE’S STRIKING RESPONSE TO TARGET KINASE INHIBITORS, ON THE ORDER OF 60% OR SO, AND NOW WE HAVE MULTIPLE AGENTS WHICH ARE APPROVED FOR FRONTLINE TREATMENT, SOME OF WHICH ARE EFFECTIVE IF YOU’VE HAD CRIZOTINIB FIRST, YOU CAN NOW GET CERITINIB, BRIGATINIB, STILL NOT A CURE.

ROS 1 IS A THIRD REARRANGEMENT, IT IS ANOTHER TYROSINE KINASE, HIGHLY RESPONSIVE TO ORAL TREATMENT, IN THIS CASE CRIZOTINIB, 70% RESPONSE RATE, A LONG DURATION OF RESPONSE. NOT CURABLE. SO THOSE ARE THE THREE MOST COMMON ABNORMALITIES THAT ARE FOUND. SO, THE WHOLE TREATMENT PARADIGM HAS BEEN SORT OF TURNED UPSIDE DOWN, WITH THE ADVENT OF IMMUNOTHERAPY AND I’M SURE THAT THAT’S WHAT YOU’RE HEARING ABOUT IN JUST ABOUT EVERY DISEASE THAT THERE ARE LECTURES ABOUT. IN PARTICULAR, THE PD-1, PD-L1 PATHWAY IS THE ONE THAT IS VERY IMPORTANT IN THE TREATMENT OF NON-SMALL CELL LUNG CANCER, AND EVEN ACTUALLY APPROVED. IT REGULATES T CELL ACTIVATION, AND THE GOAL OF INHIBITING THIS PATHWAY IS TO REV UP THE PATIENT’S OWN IMMUNE SYSTEM AND SO YOU GET A BETTER IMMUNE RESPONSE.

AND THERE ARE SEVERAL ANTIBODIES NOW THAT ARE USED AND THAT ARE APPROVED, PEMBROLIZUMAB IS APPROVEDFOR FRONT LINE TREATMENT IN PEOPLE WHO HAVE HIGH PD-L1, SO THE LIGAND EXPRESSION IN TUMOR CELLS, IT’S A LITTLE BIT HARD TO SEE HERE BUT THIS IS OVERALL RESPONSE WITH CHEMOTHERAPY, AS OPPOSED TO PEMBROLIZUMAB. WHAT YOU’RE SEEING AT THE TAIL END IS THERE SEEMS TO BE A LITTLE BIT OF A FLATTENING OF THE CURVE, AND A SEPARATION THAT IS QUITE STRIKING OF ABOUT 20% BETWEEN THOSE WHO GET PEMBROLIZUMAB, FRONTLINE VERSUS THOSE WHO GET CHEMOTHERAPY ONLY. PEMBRO CAN BE GIVEN WITH CHEMOTHERAPY FOR THOSE WHO DON’T HAVE SUCH HIGH PD-L1 EXPRESSION, AND IT TOO SHOWS A VERY SIGNIFICANT SURVIVAL ADVANTAGE.

YOU KNOW, AS WITH ALL TREATMENTS, IMMUNOTHERAPY CAME INTO USE IN SECOND LINE AND THIRD LINE TREATMENT. SO WE NOW HAVE FAIRLY LONG FOLLOW-UP OF PEOPLE, AND THE REASON WHY IT IS SO EXCITING IS THAT THIS IS ONE OF THE OTHER PD-1 ANTIBODIES, NIVOLUMAB, OR OPDIVO, COMPARE TO STANDARD SECOND LINE TREMENDOUS WITH CHEMO DOCETAXEL, AGAIN WHAT YOU SEE OUT HERE OUT TO TWO YEARS IS THE FLATTENING OF THE CURVE AND SO PEOPLE ARE ASKING IS IT POSSIBLE THAT SOME OF THE PATIENTS ARE ACTUALLY CURED? THERE ARE PEOPLE OUT THERE FOR FIVE YEARS OR MORE AFTER IMMUNOTHERAPY TREATMENT. AND HOW CAN WE MOVE THIS CURVE UP? AND KEEP IT FLAT LIKE THIS. SO NOW THE MULTIPLE ANTIBODIES, PD-1, PD-L1, THEY ALL HAVE A FAIRLY SIMILAR EFFICACY. SO, EXCITEMENT, BUT WE HAVE ALL SEEN THESE FOLKS HERE, TWO, THREE YEARS OUT, THEN GET RECURRENT LUNG CANCER. SO AS EXCITING AS IT IS, I THINK THE C WORD, THE CURE WORD, NEEDS TO BE USED JUDICIOUSLY AND A LOT OF WORK NEEDS TO BE DONE FOR TREATMENT.

AND I SHOULD MENTION THAT THESE THERAPIES COST OVER $100,000 A YEAR. THEY ARE NOT COMPLETELY BENIGN. THEY ARE VERY WELL TOLERATED, FOR THE MOST PART, EXCEPT FOR THOSE PEOPLE WHO GET ENDOCRINE SIDE EFFECTS, AUTOIMMUNE SIDE EFFECTS, AND THOSE CAN BE QUITE SIGNIFICANT AND DEADLY. SO, YOU KNOW, IT’S NOT — IT’S NOT A TEA PARTY, BUT VERY EFFECTIVE THERAPY THAT A LOT OF PEOPLE ARE GETTING. SO, IF WE CAN’T CURE OR CAN’T CURE YET, HOW ELSE CAN WE REDUCE CANCER MORBIDITY AND MORTALITY? AND SO THIS IS WHERE WE NOW START TO TALK ABOUT PREVENTION AND EARLY DETECTIONS. IF 85% OF LUNG CANCER IS CAUSED BY SMOKING, WHAT’S THE BEST WAY TO REDUCE DEATH FROM LUNG CANCER? IF YOU COULD STOP PEOPLE FROM EVER SMOKING, STOP THE YOUNG KIDS FROM SMOKING, OR GETTING THEM TO QUIT VERY EARLY ON, THAT WOULD BE GREAT. BUT IN FACT SMOKING CESSATION, AS IMPORTANT AS IT IS FOR OVERALL HEALTH AND LUNG CANCER HEALTH, IS STILL NOT — FIRST, IT’S NOT EASY, BUT IT DOESN’T GET RID OF ALL THE LUNG CANCER.

SO THIS 15-YEAR FOLLOW-UP OF A STUDY DONE, YOU KNOW, 25 YEARS AGO, 20 YEARS AGO, THE LUNG HEALTH STUDY WHICH WAS DONE IN PEOPLE ITH COPD LOOKED AT RATES OF DEATH PER THOUSAND PEOPLE A YEAR, FROM LUNG CANCER, IF YOU CONTINUED TO SMOKE, IF YOU INTERMITTENTLY, OCCASIONALLY QUIT AND THEN WENT BACK TO SMOKING, OR IF YOU QUIT FOR GOOD. AND YOU SEE THAT WITH A 15-YEAR FOLLOW-UP, YOU CAN HAVE THE RATE OF LUNG CANCER DEATH BY COMPLETELY QUITTING SMOKING. WHAT’S INTERESTING IS THE SAME CURVES, AT FIVE YEARS OF FOLLOW-UP, SHOWED NOTHING. IN OTHER WORDS, IF YOU QUIT, FIVE YEARS FROM NOW YOUR RISK OF LUNG CANCER IS NOT — YOUR RISK OF DEATH FROM LUNG CANCER IS NOT APPRECIABLY DIFFERENT THAN THE PEOPLE WHO CONTINUE TO SMOKE. IT TAKES A LONG TIME TO SEE THAT BENEFIT, WHICH IS NOT TO SAY YOU SHOULDN’T QUIT AND YOU SHOULDN’T TELL PEOPLE TO QUIT BUT IT’S TAKES A LONG TIME.

AND SO WHAT IS GOING ON HERE? AND HOW CAN WE TAKE ADVANTAGE OF THIS LONG TIME TO DEVELOP LUNG CANCER SO THAT WE CAN ACTUALLY UNDO THE DAMAGE? AND THIS WAS WHERE CANCER CHEMOPREVENTION, WHAT I DO FOR A DAY JOB, IS ALL ABOUT, THE USE OF NATURAL OR SYNTHETIC AGENTS OR STRATEGIES, INCLUDING VACCINES TO SUPPRESS OR REVERSE OF PROCESS OF CARCINOGENESIS, SO NOT TO TREAT THE CANCER ITSELF BUT TO UNDO THE EFFECTS OF THE PROCESS AND TO REGRESS THOSE EXISTING EARLY PRECURSOR LESIONS TO PREVENT THE DEVELOPMENT OF NEW ONES, SUPPRESS RECURRENCE OF PRIOR NEOPLASTIC LESIONS. THIS REALLY WAS CODIFIED BY THE WORK OF MICHAEL SPORN, WHO WAS HERE MANY YEARS AGO, AND IN MANY RESPECTS IS ONE OF THE LEADERS IN THIS FIELD. SO WITH REGARD TO LUNG CANCER, WHY WOULD WE WANT TO GO THIS APPROACH AS OPPOSED TO TREAT? WELL, AS EXCITING AS THE CURRENT THERAPEUTICS ARE, METASTATIC LUNG CANCER IS RARELY CURABLE. I NEED TO UPDATE THIS SLIDE, WE’RE TALKING ABOUT 18% FIVE-YEAR SURVIVAL SAID OF 15% WHICH FRANKLY IS STILL DISMAL. WE KNOW FROM OTHER DISEASES CANCER IS PREVENTIBLE.

THE P1 BREAST CANCER PREVENTION P1 TRIALS, THE STAR TRIAL, THE SHOW WITH TAMOXIFEN, GIVEN TO WOMEN WHO ARE AT RISK, AND RALOXIFENE AND AROMATOSE INHIBITORS, GIVE TO WOMEN AT RISK BUT DO NOT HAVE BREAST CANCER YET YOU CAN PREVENT THE OCCURRENCE OF HALF OR SO OF BREAST CANCERS. AND WE HAVE LOTS OF ANIMAL STUDIES WITH MULTIPLE AGENTS WHERE WE CAN MODEL THIS. AND THAT PRE-CLINICAL PHASE WITH INCREASING ABNORMALITIES IN SOME IDENTIFIABLE POPULATIONS, SMOKERS MORE IDENTIFIABLE AND JUST SMOKERS. THIS GIVES US THE TOOLS WE NEED TO TRY PREVENTION. SO HOW DO WE APPROACH THIS? HOW DO WE IDENTIFY NEW AGENTS? IDEALLY KNOWLEDGE OF MECHANISMS. AND THIS IS WHERE LUNG CANCER PREVENTION IS ACTUALLY NOT THAT FAR ALONG. IN THE SETTING OF CERVICAL CANCER WE KNOW HPV IS THE REQUISITE MOLECULAR ABNORMALITY, AND THEREFORE THE HPV VACCINE IS — WAS EXPECTED TO BE HIGHLY EFFECTIVE, AND IN FACT WE’VE SEEN THAT WITH THE ALMOST ERADICATION OF PRE-CANCER AFTER VACCINATION.

BUT WITH LUNG CANCER YOU HAVE MANY WAYS TO DEVELOP LUNG CANCER, EVEN IN SMOKERS, AND OF COURSE IN NEVER SMOKERS. AND SO WE REALLY NEED A BETTER UNDERSTANDING OF THE MOLECULAR PATHOGENESIS OF THIS PROCESS. WE OFTEN GO TO PRE-CLINICAL STUDIES TO FIND — TO TEST WHETHER AGENTS AND PATHWAYS ARE WORTHWHILE. AND OFTEN THESE ARE CARCINOGEN TREATED ANIMAL MODELS OR WE ALSO USE TRANSGENIC MODELS THAT DEVELOP LUNG CANCER. AND, YOU KNOW, AGAIN, THIS IS A GOOD INTERMEDIATE STEP BUT ALL OF HUMAN LUNG CANCER IS NEVER MODELED IN ONE ANIMAL MODEL. AND SO THERE ARE ISSUES IN TRANSLATION, HOW TO GET THE RIGHT ANIMAL MODELS AND TREATMENTS, TRANSLATED TO THE APPROPRIATE HUMAN COHORTS AT RISK FOR DISEASE FROM THAT PARTICULAR PATHWAY DEREGULATION. WE ALSO GO TO OBSERVATIONAL EPIDEMIOLOGY, VARIOUS STUDIES. THIS IS HOW ASPIRIN AND NONSTEROIDALS WERE IDENTIFIED FOR COLON CANCER, ONE OF THE WAYS FOR REDUCING INCIDENCE OF MORTALITY, AND THEN WE ALSO LOOK AT OTHER CLINICAL TRIALS, AND SAY WHAT’S THE EFFECT ON LUNG CANCER. AGAIN THIS IS PART OF HOW THE BREAST CANCER PREVENTION STORY CAME TO BE.

SO, IN LUNG CANCER WE’RE AT A DISADVANTAGE BECAUSE THERE ARE MULTIPLE WAYS TO GET TO THE DEVELOPMENT OF THE PROCESS. AND WE HAVE DIFFERENT PROGENITOR CELL LINEAGES, SO I TOLD THAT YOU SQUAMOUS CELL TENDS TO BE CENTRAL, PROBABLY ARISING FROM BASAL CELLS. ADENOCARCINOMAS ARE PERIPHERAL, OFTEN ARISING FROM TYPE 2 PNEUMOCITES. YOU NEVER KNOW WHO IS GOING TO DEVELOP WHAT CANCER AND WHY WOULD WE THINK THAT A CANCER ARISING FROM A BASAL CELL WOULD RESPOND TO A CANCER ARISING FROM A TYPE 2 PNEUMOCYTE? WE ALSO HAVE TO REMEMBER THAT IT’S A LONG PROCESS, YOU HAVE TO TAKE INTO ACCOUNT THINGS CHANGE OVER TIME SO INITIAL CHANGES WHICH MAY GIVE A PROLIFERATION ADVANTAGE MAY NOT BE AS IMPORTANT ONCE YOU HAVE ADDITIONAL MOLECULAR CHANGES THAT NOW MAKE IT METASTATIC AND MODAL METASTATIC, ET CETERA. SO IT MAY BE THAT WE HAVE TO DELIVER DIFFERENT STRATEGIES TO ACCOUNT FOR THE DIFFERENT PATHOGENESIS OF LUNG CANCER AND DIFFERENT ACCORDING TO WHERE ALONG THAT CARCINOGENESIS PROCESS A SPECIFIC PERSON IS. THAT’S A CHALLENGE. THAT’S A CHALLENGE. WE TEND TO SELECT OUR COHORTS FOR STUDY BASED ON THE TYPE OF CANCER THAT WE THINK THEY ARE GOING TO GET.

SO FOR THE SQUAMOUS CENTRAL CANCERS, WE OFTEN STUDY BRONCHIAL DYSPLASIA FOR ADENOCARCINOMA, WHICH ARE PERIPHERAL. THEY DON’T ARISE FROM BRONCHIAL EPITHELIUM. WE LONG AT NODULES. WE DON’T KNOW THOUSAND STUDY PREVENTION OF LARGE CELL LUNG CANCER OR SMALL CELL LUNG CANCER BECAUSE WE DON’T KNOW HOW TO FIND THOSE PEOPLE WHO ARE AT RISK. AND OF COURSE NONSMOKERS WHICH IS THE MAJORITY OF THE POPULATION, THERE’S NO WAY TO IDENTIFY WHO IS GOING TO GET LUNG CANCER UNLESS YOU HAPPEN TO BE IN ONE OF THOSE UNUSUAL FAMILIES THAT HAS A LOT EVER LUNG CANCER IN IT LIKE THE EGFR TC 79M FAMILIES.

AN ADDITIONAL ISSUE TO KEEP IN MIND FOR PREVENTION IS RISK/BENEFIT, FOR ANY KIND OF PREVENTION. YOU’RE TALKING ABOUT PEOPLE HEALTHY NOW, AT RISK FOR DEVELOPMENT OF CANCER LATER, SO EFFICACY NEEDS TO BE BALANCED VERY WELL WITH TOLERABILITY, SO PEOPLE WILL TAKE THE MEDICINES, AND WITH MAJOR ADVERSE SIDE EFFECTS THAT COULD LEAD TO PROBLEMS FROM OTHER DISEASES. SO ONE OF THE STORIES IN CANCER PREVENTION IS THE VIOXX STORY. THIS IS A SELECTIVE COX2 INHIBITOR. IT WAS A BLOCKBUSTER DRUG FOR PFIZER, FOR PAIN RELIEF. IT WAS STUDY FOR COLON CANCER PREVENTION, IN PEOPLE WHO HAD COLON POLYPS. QUITE EFFECTIVE, 30% DECREASE IN NEW COLON POLYPS, BUT TWO TO THREE-FOLD INCREASE IN HEART ATTACKS.

THOSE COME EARLY. THE BENEFIT FROM COLON CANCER PREVENTION COMES MUCH LATER. ACTUALLY IT CAME OFF THE MARKET BECAUSE OF THAT STUDY. NOW SHOULD IT HAVE COME OFF THE MARKET ANYWAY, BECAUSE OF THE SIDE EFFECT THAT WAS NOT RECOGNIZED IN THE INITIAL SHORTER DURATION STUDIES, BUT THE POINT IS THAT THIS IS A VERY IMPORTANT ISSUE FOR CANCER PREVENTION. A FOURTH ISSUE TO CONSIDER IS FOR PHASE 3 STUDIES WE LOOK AT DEVELOPMENT OF CANCER. BUT FOR THOSE INTERMEDIATE EFFICACY STUDIES HOW DO WE KNOW THAT WE’RE BEING EFFECTIVE? CANCER TREATMENT WE DO CAT SCANS AND LOOK AT THE LESIONS AND MEASURE, ARE THEY GETTING BIGGER, SMALLER, IS THERE A RESPONSE. THERE’S A REASONABLE CORRELATION BETWEEN RESPONSE RATE AND ACTUAL SURVIVAL THAT’S NOT AS STRONG ANYMORE IN THE AGE OF IMMUNOTHERAPY, SO THERE’S LOTS OF ONCs IN THE FIELD BUT THERE’S SOMETHING YOU CAN MEASURE.

CANCER PRE-ESSENTIAL YOU’RE LOOKING TO MEASURE SOMETHING THAT’S NOT THERE YET. WE DON’T HAVE A CANCER YOU CAN MEASURE. HOW DO YOU FIND THE PRE-MALIGNANT LESION? YOU DON’T DO IT BY IMAGE, CERTAINLY NOT FOR LUNG CANCER PREVENTION. SO WE’RE STILL IN THE PROCESS OF TRYING TO FIGURE OUT WHAT ARE SOME OF THESE INTERMEDIATE MARKERS THAT CAN GIVE A SENSE OF PRELIMINARY EFFICACY THAT COULD GIVE US ENOUGH INFORMATION TO MOVE TO PHASE 3. IT’S A CHALLENGING FIELD. I’LL SHOW YOU HOW WE’VE BEEN APPROACHING IT. AND MAYBE THE DISCLAIMER UP FRONT THAT WE DON’T HAVE ANY APPROVED DRUGS FOR LUNG CANCER PREVENTION, ALTHOUGH WE DO FOR OTHER RISK REDUCTION IN OTHER CANCERS. ASPIRIN NOW RECOMMENDED FOR COLON CANCER IN PEOPLE WHO ARE HIGH ENOUGH RISK, IN TERMS OF CARDIOVASCULAR DISEASE TO WARRANT TREATMENT FOR THAT AS WELL. TAMOXIFEN, RALOXIFENE ARE APPROVED FOR RISK REDUCTION FOR BREAST CANCER. SO INFLAMMATION IS PERHAPS THE SINGLE MOST COMPELLING STORY, IF I MAY CALL IT SUCH, FOR LUNG CANCER PREVENTION.

IT IS WELL KNOWN THAT THE INFLAMMATION THAT YOU GET FROM TOBACCO EXPOSURE IS IMPORTANT IN THE GENESIS, ACTUALLY OF MANY CANCERS, LUNG CANCER IN PARTICULAR, AND WE HAVE A LARGE BODY OF DATA SHOWING THAT INTERVENING IN ANIMAL MODELS THAT ARE PRIME TO DEVELOP LUNG CANCER WITH ORAL OR INHALED STEROIDS CAN TO A GREAT EXTENT REDUCE THE NUMBER OF TUMORS, THE SIZE OF THE TUMORS, EXTEND ANIMAL LIFE. THERE IS SOME EPIDEMIOLOGY FROM SOME STUDIES IN COHORTS THAT HAVE COPD AND WERE TAKING INHALED STEROIDS TO THOSE THOSE PEOPLE WHO TAKE INHALED STEROIDS COMPARED TO THOSE WHO DO NOT HAVE DECREASED INCIDENCE OF LUNG CANCER.

THIS IS AN EXAMPLE OF AN ANIMAL STUDY, AND WHAT YOU SEE IS THIS IS STEROID GIVEN ORALLY, BUDESONIDE, 80% DECREASE IN NUMBER OF TUMORS, ANIMALS EXPOSED TO A CARCINOGEN WILL GET. AND NOT ONLY DO YOU HAVE FEWER TUMORS BUT YOU HAVE LESS ADVANCED TUMORS. SO THIS BLACK IS A LONG DURATION OF TREATMENT, AND THE NUMBER OF PERCENTAGE OF TUMORS THAT ARE CARCINOMAS GOES DOWN, PERCENTAGE OF ADENOMAS, SO NOT YET AS ADVANCED, GOES WAY UP.

SO YOU DECREASE TOTAL NUMBER AND SHIFT TO A LESS ADVANCED HISTOLOGY. HOW DO WE TRANSLATE THIS TO HUMAN BEINGS? SO, BACK IN THE LAID 90s, EARLY 2000s WHEN THIS FIELD CAME TO BE IN ITS OWN, THE ONLY WAY TO TRANSLATE ANIMAL STUDIES IS LOOK AT BRONCHIAL DYSPLASIA, PRECURSOR FOR LUNG CANCER, NORMAL EPITHELIUM TO INCREASING GRADES OF DYSPLASIA, AS YOU CAN SEE IT’S LOOKING WORSE AND WORSE UNTIL YOU GET CARCINOMA IN SITU. AND TO MAKE A LONG STORY SHORT, JUST FOCUS HERE, I’LL GIVE YOU LOTS OF NUMBERS HERE BUT PEOPLE WITH LOW OR HIGH GRADE LESIONS WHO ARE FOLLOWED UP OVER AN EXTENDED PERIOD OF TIME, ABOUT A THIRD OF THEM DEVELOPED INVASIVE CANCER. ABOUT 40% OF WHICH WERE FROM THE ABNORMAL SITE THAT WAS BEING FOLLOWED, VERSUS THE OTHER 60% BEING ELSEWHERE, EITHER IN THE BRONCHIAL EPITHELIUM OR PERIPHERY. SO, THE PRESENCE OF BRONCHIAL DYSPLASIA IDENTIFIES A VERY HIGH RISK COHORT, AND SOME OF THOSE LESIONS WILL PROGRESS TO CANCER EVEN IN A RELATIVELY, RELATIVELY SHORT PERIOD OF TIME. SO THE WAY THE STUDIES WERE DONE THEREFORE, AND THIS IS A TRIAL OF INHALED BUDESONIDE BASED ON ANIMAL MODELS WAS TO LOOK AT PEOPLE WITH BRONCHIAL DYSPLASIA, DO A BRONCHOSCOPY, BIOPSY, COUNT LESION, LOOK UNDER THE MICROSCOPE, GIVE BUDESONIDE OR PLACEBO FOR SIX MONTHS, LOOK AT SITES, GRADE OF DYSPLASIA AND A NUMBER OF OTHER MARKERS.

THESE ARE HARD STUDIES TO DO. STEPHEN LAM AT BRITISH COLUMBIA IS AN INCREDIBLE INVESTIGATOR WHO IS ABLE TO DO A NUMBER OF THESE. AND SO IN OUR INHALED BUDESONIDE STUDY, WHICH WAS AGAIN A DIRECT TRANSLATION, WE SCREENED ABOUT A THOUSAND PEOPLE WITH SPUTUM PSYCHOLOGY, IDENTIFIED ABNORMALITIES, HALF OF THE INDIVIDUALS UNDERWENT BRONCHOSCOPY, ULTIMATELY 112 SMOKERS WITH DYSPLASIA WERE RANDOMIZED TO BUDESONIDE OR PLACEBO. THE STUDY UNFORTUNATELY WAS NEGATIVE. HARD TO DO. SIX-MONTH INTERVENTION MAY OR MAY NOT BE ENOUGH. BUT THE COMPLETE RESPONSE RATE VERSUS PROGRESSIVE DISEASE RESPONSE RATE WERE NOT ANY DIFFERENT. SO THE ANIMAL STUDIES I DESCRIBED LOOKED AT ADENOMAS IN THE PERIPHERAL LUNG. THIS WAS LOOKING AT SQUAMOUS CELL PRECURSOR BRONCHIAL DYSPLASIA. CT STARTED BEING USED FOR — STUDIED FOR EARLY DETECTION OF LUNG CANCER, AND AS PART OF THE STUDY PEOPLE ALSO UNDERWENT CT AND THERE WAS THIS SLIGHTLY STATISTICALLY SIGNIFICANT — WELL, STATISTICALLY SIGNIFICANT BUT SOME DECREASE IN THE NUMBER OF LUNG NODULES THAT RESOLVED.

THAT WOULD BE THE PART OF THE LUNG THAT WOULD BE MORE RELEVANT TO WHAT THE ANIMAL STUDIES ACTUALLY SHOWED. AND SO OUR SECOND STUDY, AND THIS IS AGAIN THE TRIAL MODEL IS UNDER EVOLUTION, THE SECOND STUDY THAT WE DID WITH INHALED BUDESONIDE WAS LOOK AT PEOPLE WITH CT-DETECTED LUNG NODULES, ONES THAT WERE PERSISTENT BECAUSE NODULES CAN COME AND GO. THEY WERE BEING STUDIED FOR EARLY DETECTION OF LUNG CANCER WITH OUR COLLEAGUES AT THE EUROPEAN INSTITUTE OF ONCOLOGY IN ITALY, AND SO WE RANDOMIZED 202 PARTICIPANTS WITH THESE NODULES TO INHALED BUDESONIDE AND PLACEBO NOW FOR A YEAR, BECAUSE THAT’S THE INTERVAL BETWEEN THEIR CT SCREENINGS.

AND THIS STUDY IS GIVING US A HINT AS TO HOW MAYBE WE SHOULD DO THE TRIAL. SO I TOLD YOU THERE ARE 200 PARTICIPANTS. 70% OF THEM HAD SMALL SOLID NODULES, WHETHER YOU GAVE THEM BUDESONIDE OR PLACEBO, NO CHANGE. SO THESE WERE PROBABLY LITTLE AREAS OF FIBROSIS OR WHEREVER AND WERE SMALL, UNDER A CENTIMETER. ON THE OTHER HAND, THE ONES THAT WERE NOT SOLID, THERE SEEMED TO BE A DIFFERENCE WITH A BIGGER CHANGE IN THOSE WHO GOT BUDESONIDE AND THE SAME WITH THE PARTIALLY SOLID NODULES, COMPARED BUDESONIDE VERSUS PLACEBO. BUT THIS WAS CLEARLY NOT STATISTICALLY SIGNIFICANT. THIS IS 30%, 60 PEOPLE ALTOGETHER OUT OF THE WHOLE COHORT. WHEN WE FOLLOWED THESE PEOPLE OVER TIME BECAUSE THEY WERE PART OF THE CT SCREENING PROJECT THEY GOT ONE YEAR OF TREATMENT AND THEN THEY WERE OFF TREATMENT. INTERESTINGLY, THE BUDESONIDE TREATED PARTICIPANTS, THE NODULES CONTINUED TO GET A LITTLE BIT SMALLER TO THE POINT THAT FIVE YEARS THIS WAS STATISTICALLY SIGNIFICANT.

WHAT TO DO WITH THAT? OUR TAKEHOME WAS DON’T STUDY THESE SOLID NODULES, STUDY THESE OTHER NODULES. NOW, WHAT ARE THESE OTHER NODULES? THEY LOOK LIKE THIS. THESE ARE THE GROUND GLASS OPACITY, OVER TIME STARTING TO GET A BETTER UNDERSTANDING OF THE NATURAL HISTORY ALTHOUGH ONLY FROM THE ONES THAT ARE LARGE ENOUGH TO BE TAKEN OUT. INDETERMINATE NODULES, SOME STUDIED AND TAKEN OUT, SHOWED 1/4 TO 1/2 OF THEM ARE THIS LESION HERE, CALLED ATYPICAL ADENOMA HYPERPLASIA, WHICH IS A PRECURSOR ADENOMA. THERE’S A REASON TO THINK THAT SOME OF THEM ARE PRECURSORS TO ADD KNOW CARCINOMAS. HERE IS ONE RECENT STUDY OF THE NATURAL HISTORY OF THESE NODULES. 795 PATIENTS, THAT’S A PRETTY LARGE STUDY. 1229 SUBSOLID NODULES, GROUND GLASS OPACITIES, EITHER WITH COMPLETELY GROUND GLASSY OR SMALL COMPONENT THAT IS SOLID, AND THESE WERE FOLLOWED OVER TIME, OKAY? AND BOTTOM LINE IS THAT OVER THIS FOUR-YEAR OR SO PERIOD, AVERAGE PERIOD OF FOLLOW-UP, ABOUT 1% OF THEM ACTUALLY BECAME INVASIVE CANCER, ANOTHER 3, 4, 5, 6% WERE MINIMALLY INVASIVE OR CARCINOMA IN SITU, A SMALL NUMBER WERED A ADENOMATOUS HYPERPLASIA.

SOME PROGRESS OVER TIME. THERE IS AN EXAMPLE FROM OUR PRACTICE, OUR CLINIC. THIS IS A FAMILY FRIEND WHO CAME TO US IN 2011. SHE WENT TO THE EMERGENCY ROOM BECAUSE SHE HAD SHORTNESS OF BREATH, THEY DID A CAT SCAN, TRIED TO MAKE SURE SHE DIDN’T HAVE A PULMONARY EMBOLUS AND FOUND THIS NODULE RIGHT HERE, ACTUALLY THERE WERE THREE OR FOUR ELSEWHERE AS WELL. THEY TOLD HER COME BACK IN THREE MONTHS. HERE IT IS AGAIN, NOT MUCH DIFFERENT, A LITTLE LESS PROMINENT BUT REALLY THE SAME. COME BACK IN A YEAR, LIKE ALL GOOD PEOPLE WHO FEEL GOOD SHE SAID, YEAH, I WILL, AND FORGOT ABOUT IT UNTIL 2010 WHEN SHE AGAIN HAD SHORTNESS OF BREATH, WENT TO THE EMERGENCY ROOM, HAD A CAT SCAN, AND THIS TIME IT LOOKS LIKE THIS.

STILL LOOKS — STILL GROUND GLASSY IN APPEARANCE, BUT NOW BIGGER. SO THIS TIME AROUND SHE DID COME BACK A YEAR LATER, AND NOW IT’S GOT A SOLID CORE AND TURNS OUT TO BE A STAGE 1 INVASIVE ADENOCARCINOMA, WITH AREAS OF ADJACENT ATYPICAL ADENOMATOUS HYPERPLASIA. SO IT TAKES A LONG TIME. I PUT IT HERE. I SHOW THIS HERE BECAUSE THIS CAN HAPPEN OVER A LONG TIME, AND THESE GROUND GLASS OPACITIES NEED TO BE FOLLOWED LONG TERM. WE LOOK BACK AT THE NATIONAL LUNG SCREENING TRIAL, AS TO WHAT HAPPENS TO PEOPLE WHO HAVE ONLY THESE GROUND GLASS OPACITIES, AND WE FOUND THAT EARLY ON VERY LOW RISK OF CANCER COMPARED TO THOSE WHO HAVE SOLID NODULES, BUT FIVE YEARS OUT AND MORE THERE’S ABOUT A THREE-FOLD INCREASED RISK OF CANCER SO SOME OF THESE NODULES ARE CLEARLY PRECURSORS AND IT TAKES A WHILE FOR THEM TO DEVELOP INTO INVASIVE CANCER.

STUDIES ARE NOW BEING DONE LOOKING AT THE MOLECULAR PROFILE OF THESE LESIONS, THESE ADENOCARCINOMA PRECURSORS AND THESE EARLY NON-INVASIVE OR MINIMALLY INVASIVE ADENOCARCINOMAS. AND LIKE EVERYTHING ELSE, THEY ARE COMPLEX. THEY ARE NOT SIMPLE GENETICALLY, SO EVEN EARLY ON THESE PRECURSOR LESIONS HAVE MULTIPLE ABNORMALITIES. ONE THING THAT’S INTERESTING IN THIS HUGE EFFORT BUT WOUND UP BEING SIX PATIENTS WITH AH ONLY, FIVE HAD A SMOKING HISTORY. AAH PRECURSORS HAD LESIONS OFTEN NOT SHARED, ABNORMALITIES NOT SHARED WITH THE TUMOR. NOW, IT’S NOT THE PRECURSOR TO THAT TUMOR THAT IS IN THE PATIENT FROM WHOM IT WAS RESECTED, BUT MAYBE IN SOME CASES THEY ARE RELATED. AND WHAT’S PARTICULARLY INTERESTED IS THAT A LOT OF THESE AAHs, IN THIS PARTICULAR STUDY, AND IN OTHER STUDIES AS WELL, HAD BRAF MUTATIONS. BRAF IS ONE OF THE KNOWN DRIVERS. IT IS ONE OF OUR TARGETED THERAPIES BUT QUITE UNCOMMON AND SO THIS SUGGESTS THAT BRAF ALONE IS FAR FROM SUFFICIENT, IN FACT IT’S NOT WHAT LEADS TO LUNG CANCER IN MOST CASES.

SO THERE’S A LOT OF HETEROGENEITY IN PRE-MALIGNANT LESIONS, AND THE REASON I STRESS THIS IS THAT WE NEED TO UNDERSTND WHAT’S GOING ON. AND THAT IS HOW WE WILL MAKE PROGRESS AND IDENTIFYING TARGETS FOR LUNG CANCER PREVENTION. I’M GOING TO TELL YOU A COUPLE OTHER STORIES, MOVING ALONG QUICKLY. A NUMBER OF YEARS AGO, A METANALYSIS WAS DONE, ACTUALLY IT WAS FOLLOW-UP OF A NUMBER OF STUDIES USING ASPIRIN MAINLY FOR CARDIOVASCULAR REASONS AND LOOKING AT THE LONG-TERM FOLLOW-UP. THIS IS BY SIR PETER ROTHWELL, ET AL., A WHOLE SERIES OF PAPERS ABOUT A 20% DECREASED RISK OF CANCER DEATHS WHICH YOU SEE REALLY STARTS TO HAPPEN AFTER FIVE YEARS OR MORE OF ASPIRIN.

AND OF PARTICULAR INTEREST IS LUNG ADENOCARCINOMAS, WHERE THESE TWO CURVES REALLY START TO DIVERGE FAIRLY QUICKLY WITHIN ABOUT TWO YEARS, AND QUITE SIGNIFICANT DECREASE IN LUNG ADENOCARCINOMA BUT NOT SQUAMOUS CELL CARCINOMA DEATHS. AND SO THIS BECAME THE SOURCE OF OUR NEXT CT SCREENING NODULE TRIAL, WHICH WE’RE WAITING FOR THE FINAL ANALYSIS NOW. SO, I TOLD YOU THAT WE LOOKED AT ALL CT NODULES, GAVE PEOPLE INHALED BUDESONIDE, NOW WE FOCUS ONLY ON THE NON-SOLID AND PART SOLID NODULES, THE ONES THAT SEEM TO MODULATE WITH INHALED BUDESONIDE, AND SO WE TOOK ASYMPTOMATIC FORMER AROUND CURRENT SMOKERS, PERSISTENT SOLID AND NON-SOLID MODULES, LOW DOSE OF ASPIRIN VERSUS PLACEBO FOR A YEAR BEFORE THE NEXT CT SCAN, NEXT YEAR I’LL HAVE THE RESULTS OF THIS TRIAL.

BUT THIS IS OUR CURRENT MODEL FOR STUDYING LUNG ADENOCARCINOMA PREVENTION. I’M GOING TO TELL YOU ONE LAST STORY VERY QUICK BECAUSE IT SHOWS HOW WE TRY TO GET INTO USING THE CURRENT OMIC TECHNOLOGIES TO REALLY LEARN A LOT MORE. SO MONOSOTOL IS A SUBSTANCE, A DRUG, WHICH IS REALLY AN ISOMERIC GLUCOSE, AN ACTIVE SIGNALING MOLECULE, COMES FROM DIET. IT’S BEEN STUDIED IN A NUMBER OF DIFFERENT CONDITIONS. AND THERE HAVE BEEN A NUMBER OF STUDIES STUDIES LOOKING AT MYO-iNOSITOL IN ANIMAL MODELS, SHOWING A SIGNIFICANT INHIBITION OF CARCINOGENESIS, INCLUDING A MODEL OF SMOKE EXPOSURE, VERY DIFFICULT TO DO AND GENERALLY NEGATIVE FOR MOST OTHER AGENTS. SO THIS DRUG HAS BEEN USED IN MULTIPLE STUDIES, IT’S WHAT WE CALL GRAS, GENERALLY REGARDED AS SAFE BY FDA TECHNOLOGY, YOU DON’T HAVE TO HAVE A NEW DRUG APPLICATION, CAN YOU JUST GIVE IT. AND IT MAKES YOU FEEL GOOD, IT WILL BE TOLERABLE WITHOUT THE LONG-TERM SIDE EFFECTS. WITH STEPHEN LAM PERFORMED PHASE 1 STUDY LOOKING AT THE MAXIMUM TOLERATED DOSE IN 26 PARTICIPANTS WHO HAD BRONCHIAL DYSPLASIA, FOUND A DOSE, THIS WAS AN UNCONTROLLED STUDY BUT THERE WAS A 90% DECREASED REGRESSION OF DYSPLASIA COMPARED TO 50% IN HISTORICAL CONTROLS.

NOT THE WAY TO DO A STUDY BUT FOR PHASE 1 GAVE US A SENSE THAT PERHAPS THIS COULD BE EFFECTIVE. AND SIGNIFICANTLY, WE TEAMED UP WITH BOSTON UNIVERSITY, AVI SPIRA, STUDYING ABNORMAL PATHWAYS THAT GET ACTIVATED IN THE AIRWAYS IN THE FIELD OF SMOKERS, AND HE FOUND THAT THE PI3 KINASE PATHWAY IS ACTIVATED NOT JUST IN PEOPLE WITH A CONCURRENT CANCER, ONE THAT DOESN’T NECESSARILY HAVE PI3 KINASE MUTATIONS BUT ALSO IN PEOPLE WITH DYSPLASIA WITH THE BRONCHIAL EPITHELIUM.

FURTHERMORE IN THAT SMALL NUMBER OF PEOPLE WHO WE TREATED WITH MYO-iNOSITOL, THEY ALSO HAD REVERSION OF THE KINASE ACTIVATION SIGNATURE. WHAT DOES THIS MEAN? IS THIS A WAY TO IDENTIFY THE SMOKERS AT INCREASED RISK FOR LUNG CANCER? BECAUSE WE KNOW THAT THOSE WITH DYSPLASIA ARE AT INCREASED RISK? CERTAINLY EASIER TO GET NORMAL BRUSHINGS THAN IDENTIFY DYSPLASIA FROM BIOPSIES WHICH ARE VERY DISCRETE LESIONS, YOU DON’T REMOVE THE BIOMARKER WITH YOUR BRUSHING. SO, THIS IS POTENTIALLY A GOOD COHORT TO STUDY, AND POTENTIALLY A NEW CLINICAL TRIALS MODEL. SO WHAT DO WE DO? WE WENT TO A PHASE 2 STUDY USING MYO-iNOSITOL, SAME WAY AS WHAT I DESCRIBED WITH BRONCHIAL — WITH INHALED BUDESONIDE. THE BOTTOM LINE IS THAT ABOUT 40 PEOPLE WERE TREATED WITH MYO-iNOSITOL OR PLACEBO, ALL HAD DYSPLASIA AT BASELINE, LOOKING DYSPLASIA AT FOLLOW-UP. A NON-STATISTICALLY SIGNIFICANT, SO NO STATISTICAL SIGNIFICANCE IN ANY OF THIS, SLIGHT INCREASED INCIDENCE EVER COMPLETE REGRESSION WITH MYO-iNOSITOL, ALSO PROGRESSION. THAT’S PROBABLY TOO FINE A LIGHT ON ALL OF THIS. BOTTOM LINE THERE WAS NO STATISTICAL SIGNIFICANCE.

WHAT ABOUT OUR BIOMARKER, PI3 KINASE AKT PATHWAY? STILL A CORRELATION WITH RESPONSE. I DON’T KNOW WHAT TO DO WITH THAT BECAUSE THAT DOESN’T TELL ME ANYTHING. RESPONDERS HAVE THIS BUT IT DOESN’T TELL ME WHO IS GOING TO RESPOND. IT’S ONLY AN UNDERSTANDING OF THE EFFECTS OF THE DRUG. IT DOESN’T HELP US MOVE THIS DRUG FORWARD. ALTOGETHER THIS WAS ANOTHER NEGATIVE STUDY BUT SHOWED US THE POWER OF USING OMIC TECHNOLOGIES, AND THAT’S WHERE WE NEED TO BE MOVING FORWARD WITH.

OKAY. I’M GOING TO SPEND FIVE MINUTES, WHAT WE HAVE LEFT, ON A HUGE FIELD, EARLY DETECTION. YOU NEED TO KNOW ONLY A FEW THINGS RIGHT NOW. ISSUES IN EARLY DETECTION. THERE ARE BIASES, SOUNDS EASY, RIGHT? WE FIND IT, YOU GET IT OUT EARLY, ALL IS GOOD. NOT THAT EASY. THERE’S LEAD TIME BIAS, YOU ARE SCREENING, YOU FIND CANCERS EARLIER, IF YOU HADN’T FOUND THEM THE PERSON WOULD DIE AT THE SAME TIME. SURVIVAL WILL APPEAR LONGER BUT IN FACT THE PERSON DIES WHEN THEY WERE SUPPOSED TO DIE NO MATTER WHAT. THIS IS WHY YOU DON’T LOOK AT LUNG CANCER SPECIFIC MORTALITY. YOU LOOK AT OVERALL MORTALITY.

LENGTH BIAS, YOU’RE MORE LIKELY TO FIND INDOLENT DISEASE THAN THOSE AGGRESSIVE TUMORS THAT DEVELOP BETWEEN SCREENINGS, THESE ARE THE BETTER PROGNOSIS TUMORS, THEY HAVE A BETTER OUTCOME. BUT, AGAIN, IN THE BIG PICTURE YOU’RE NOT HELPING THE POPULATION OVERALL. FINALLY OVERDIAGNOSES, WHERE YOU IDENTIFY CLINICALLY UNIMPORTANT LESIONS, THEY LOOK LIKE LUNG CANCER, WOULD HAVE NEVER LED TO DEATH FROM LUNG CANCER. THIS IS PARTICULARLY AN ISSUE IN PROSTATE CANCER SCREENING BUT ACTUALLY OCCURS IN LUNG CANCER TOO. OF COURSE ONCE YOU PUT PEOPLE INTO THE MEDICAL SYSTEM, YOU’RE GOING HAVE MORBIDITY, MORTALITY FROM THE SCREENINGS, THE FOLLOW-UPS OF THE SCREENINGS, THE COST OF THE SCREENINGS, ET CETERA. SO A FEW THINGS TO KNOW. CHEST X-RAY HAS BEEN STUDIED MANY TIMES, UNCLEAR ANSWERS.

THIS IS THE DEFINITIVE STUDY, THE PLCO, 154,000 PARTICIPANTS, CHEST X-RAY VERSUS USUAL CARE, NO DIFFERENCE IN SURVIVAL. CHEST X-RAY ALONE HAS BEEN NOT USED FOR A LONG TIME, USED TO BE USED IN THE ’70s, ’80s. IT IS NOT THE THING TO DO FOR EARLY DETECTION. NATIONAL LUNG SCREENING TRIAL, AGAIN, HUGE, 53,000 SMOKERS, 30 PACK YEARS. UNDERWENT TC SCREENING VERSUS CHEST X-RAY. THREE TIMES ALTOGETHER. AND THIS WAS A VERY SIGNIFICANT POSITIVE. LOTS OF PEOPLE HAD POSITIVE TEST. MANY MORE THAN WITH CHEST X-RAY BUT 20% REDUCTION IN LUNG CANCER MORTALITY, NOT JUST INCIDENCE BUT MORTALITY. AND ACTUALLY A SIGNIFICANT REDUCTION IN ALL-CAUSE MORTALITY, REFLECTING LUNG CANCER IS A MAJOR CAUSE OF ALL MORTALITY. THIS IS JUST A COUPLE OF THE GRAPHS SHOWING THIS IS CUMULATIVE NUMBER OF LUNG CANCER CASES. SO THIS IS X-RAY. THIS IS CT.

OF COURSE YOU IDENTIFY MORE CASES BUT WHAT’S REALLY IMPORTANT IS THE DEATHS FROM LUNG CANCER, LOW DOSE CT VERSUS CHEST X-RAY, 20% FEWER. AND ALTHOUGH THERE HAVE BEEN A NUMBER OF STUDIES IN EUROPE, THE MOST RECENT DATA FROM THE NELSON TRIAL IN THE NETHERLANDS IS THE FIRST LARGE STUDY OTHER THAN NLSD THAT WAS ONCE — NLST THAT WAS HIGHLY POSITIVE. IT WAS PRESENTED AT A MEETING IN SEPTEMBER. I DON’T DON’T HAVE THE GRAPH. LUNG CANCER SCREENING IS LEER — HERE TO STAY. HOW DO WE MAKE IT BETTER? LOTS OF NODULES, MOST PEOPLE DON’T HAVE LUNG CANCER. CAN WE USE THAT, HOW DO WE BETTER USE IT TO FEED INTO OUR CHEMOPREVENTION TRIALS? SO THIS IS ONE STUDY, STEPHEN LAM, COLLABORATORS, SHOWING USING VARIETY OF FACTORS, AGE, SEX, FAMILY HISTORY, EMPHYSEMA, COPD, YOU CAN IDENTIFY A HIGHER RISK COHORT MOST LIKELY TO DEVELOP CANCER. THESE ARE THE PEOPLE WE NEED TO TARGET FOR PREVENTIVE APPROACHES.

HOW DO WE MOVE FORWARD? WE NEED TO UNDERSTAND BIOLOGY. I SHOWED YOU A LOT OF NEGATIVE STUDIES, PART OF THAT IS BECAUSE WE DON’T UNDERSTAND THE BIOLOGY AND THE NATURAL HISTORY. WE ARE WORKING ON MOVING FORWARD, PRE-MALIGNANT — PRE-CANCER ATLAS, LIKE THE LARGE TCGA EFFORT BUT NOW FOCUSING ON THOSE EARLIER STAGES OF CARCINOGENESIS. WE NEED TO USE AGENTS THAT ARE APPROPRIATE FOR THE PATHWAYS THAT ARE LIKELY TO BE DEREGULATED, DRUGS THAT ARE SAFE, FOR INSTANCE, REPURPOSED DRUGS, WE NOW STARTING TO MOVE INTO HARNESSING THE IMMUNE RESPONSE AS WELL.

IT’S IMPORTANT TO KNOW WHICH OF THESE PRE-MALIGNANT LESIONS WILL PROGRESS. WHO WILL PROGRESS, WHY? AND THAT WILL TELL US HOW TO INTERVENE. SO, INNOVATIVE TRIAL DESIGNS, USING OMIC TECHNOLOGIES LIKES WHAT WE DISCUSSED, FOCUSED ON MOLECULARLY HOMOGENOUS COHORTS WHICH WE HAVEN’T DONE BEFORE, IT’S A CHALLENGE. AND USING — GETTING MULTIPLE TRIALS TO ACTUALLY BUILD A BODY OF EVIDENCE THAT WILL GET US TO PHASE 3. SUMMARY, LAST SLIDE, WE HAVE MADE A LOT OF PROGRESS IN UNDERSTANDING LUNG CARCINOGEN IS.

PRECISION MEDICINE IS APPLICABLE TO A SIGNIFICANT BUT SMALL SUBSET OF ADVANCED STAGE PATIENTS. WE NEED OTHER APPROACHES. THESE ARE THE EARLY DAYS OF IMMUNOTHERAPY. PROLONGED SURVIVAL AGAIN IN A SMALL SUBSET AND WE NEED TO LEARN HOW TO APPLY THIS TO PREVENTION, IT’S NOT CLEAR HOW TO DO THAT. EARLY DETECTION WITH HELICAL CT IS HERE TO STAY. DECREASED LUNG CANCER AND OVERALL MORTALITY. AND THESE NEW TARGETS AND TOOLS ARE NOW AVAILABLE FOR STUDYING EARLY DISEASE AND SO OVER THE NEXT FIVE TO TEN YEARS MAYBE WE’LL HAVE SOME STUDIES THAT WILL BE POSITIVE TO PRESENT TO THIS FORUM.

ALL RIGHT. I’M DONE. I DON’T KNOW WHETHER THERE ARE ANY QUESTIONS. JUN WEI, GIVING THE NEXT LECTURE, HE GOT HIS Ph.D. IN BAYLOR COLLEGE OF MEDICINE, DID POSTDOCTORAL TRAINING IN PAUL MELCH’S LAB, CANCER GENETICS BRANCH, AND THEN JOINED THE ONCOGENOMIC SECTION, STAFF SCIENTIST IN 2009, ASSISTED KAHN, TODAY APPLYING GENOMICS TO PRECISION MEDICINE. JUN? >> CAN YOU HEAR ME? GOOD. OKAY. THANK YOU, TERRY, FOR ALLOWING ME TO GIVE THIS LECTURE. AND HERE IS THE OUTLINE FOR WHAT I’M GOING TO DO FOR THIS HOUR. I’M GOING TO GIVE YOU SOME REVIEW OF THE SUCCESS AND THE CHALLENGES OF TREATING PEDIATRIC CANCER. THE REASON I’M GOING THIS PEDIATRIC CANCER IS OUR SECTION HAS A LONG-TERM INTEREST IN THE PEDIATRIC CANCER. BUT THE TREND OF THE PEDIATRIC CANCER ACTUALLY THE SAME AS THE ADULT CANCER. THE CHALLENGES AND SOME SUCCESS. AND THE NEXT SECTION I’M GOING TO TALK TO YOU ABOUT, GENOMICS AND ESPECIALLY A TECHNOLOGY CALLED NEXT GENERATION SEQUENCING, WHICH IS THE MAN WORKING FOR THE GENOMICS NOW, I’M GOING TO INTRODUCE YOU TO THAT TECHNOLOGY, AND THEN GIVE YOU A STUDY THAT ILLUSTRATES HOW TO USE THESE GENOMIC TOOLS AND GENOMICS TO DO PRECISION MEDICINE. OKAY. THIS IS A SLIDE THAT SHOWS OVER THE PAST SEVERAL DECADES, AND ACTUALLY THERE IS A VERY SUCCESSFUL STORY TO TREATING PEDIATRIC CANCER.

YOU CAN SEE THE GRAPH, THE SURVIVAL RATE IS DRASTICALLY IMPROVED IN ALL SORTS OF CANCERS IN PEDIATRIC FROM THE ’60s TO ’90s. HOWEVER, THE CHALLENGES SEEMS THESE KIND OF IMPROVEMENTS IN TREATMENT HAS REACHED PLATEAU, THIS IS MORTALITY RATE OVER THE SEVERAL DECADES. YOU CAN SEE IT’S DECREASING UNTIL AROUND 2000, AND THESE LEVEL OFF. WE’RE REACHING TO TREATMENT OF PLATEAU, SO ALL THE EXISTING TREATMENT SEEMS TO NOT REDUCE FURTHER THE MORTALITY RATE, SO THAT’S THE CHALLENGE OF THE TREATING THE PEDIATRIC CANCERS. AND REALLY THE CHALLENGE ACTUALLY TO SPECIFIC DISEASE, SPECIFICALLY METASTATIC AND RECURRENT DISEASE, AND TO REFRACTORY CANCERS THAT IT’S RESISTANT TO CURRENT THERAPY. YOU CAN SEE ALL DIFFERENT KIND OF CANCER. IT’S ALL THIS HIGH RISK METASTATIC DISEASE, STAGE 4 DISEASE. THAT HAS VERY POOR SURVIVAL FOR ALL THE CANCERS. AND THIS IS TRUE IF YOU HAVE A LOCAL DISEASE, THE CHANCE OF BEING CURED IS RELATIVE HIGH, BUT IF HAVE YOU METASTATIC DISEASE OR DISEASE COME BACK, RELAPSE SETTING, THIS USUALLY IS TRUE FOR ALL THE CANCERS. SO LET’S THINK ABOUT THE BIOLOGY OF CANCER, OKAY? AND THIS SLIDE JUST GAVE YOU ILLUSTRATION HOW IMPORTANT THE GENE EXPRESSION IS IN THE BIOLOGY.

SO THIS IS A VERY DRAMATIC CONSEQUENCE OF GENE EXPRESSION. YOU CAN SEE THE CATERPILLAR, AND THIS BUTTERFLY, ALL SHARE THE SAME EXACT GENOME. HOWEVER, IT’S BECAUSE OF THE GENE EXPRESSION AND THE SUPPRESSION PATTERN RESULTING IN THE DIFFERENT PROGRAM AND DIFFERENT RESULT IN TISSUE, AND THEN HAVE DIFFERENT PHYSIOLOGY, AND THEN TOTALLY DIFFERENT PHENOTYPE. THIS IS TRUE FOR HUMAN BEING TOO, RIGHT? AND THE WAY WE KNOW THAT ALL CELLS SHARE THE SAME GENOME, SAME DNA.

HOWEVER, BECAUSE OF THIS EXPRESSION DIFFERENT PATTERN, THE TIMING, THE LOCATION, RESULT ALL SORTS OF DIFFERENT KIND OF TISSUES TO FORM A BODY AND THEY ALL HAVE SPECIFIC FUNCTION. SO, THIS IS THE CENTRAL DOGMA OF THE BIOLOGY, I’M PRETTY SURE YOU’RE FAMILIAR LIKE MIDDLE SCHOOL OR COLLEGE TEXT BOOK. SO THE INFORMATION FLOW IN ANY BIOLOGICAL SYSTEM IS FROM THE DNA TO APPROACHES, THIS IS GENOMIC DNA AND THROUGH THE TRANSCRIPTION WE MAKE THE MESSENGER RNA, AND THEN MESSENGER RNA TRANSLATES INTO THE PROTEIN, AND THE PROTEIN IS THE ONE TO GIVE THE PHENOTYPE, AND THIS IS INCLUDING CANCER PHENOTYPE, DIAGNOSTICAL CANCER AND RESPONSE TO TREATMENT. THIS IS ALL RESULT OF THE PROTEIN. HOWEVER, THE SYSTEM IS NOT THAT SIMPLE. IT’S VERY COMPLICATED. YOU CAN SEE A LOT OF FEEDBACK LOOPS TO THE PROTEIN WHERE REGULATED mRNA, MESSENGER RNA, ALSO THE PROTEIN REGULATE THE DNA. AND THESE ARE ANOTHER GROUP OF RNA CALLED microRNA, DISCOVERED FAIRLY RECENTLY, ABOUT LIKE 20 YEARS AGO. AND WE FOUND THESE microRNA, ONLY ABOUT A COUPLE THOUSAND IN A NUMBER OF THOUSAND BUT THEY HAVE VERY CRUCIAL REGULATORY FUNCTIONS FOR THE TRANSLATION PROCESS, AND THE MRNA STABILITY AND TRANSCRIPTION PROCESS FROM THE DNA TO THE MESSENGER RNA.

SO, THIS IS A VERY COMPLICATED SYSTEM, PROBABLY THE SURFACE WE KNOW. A LOT OF THINGS WE DON’T KNOW YET. IN TERMS OF NUMBERS, 3 BILLION BASE PAIR OF DNA IN OUR GENOME, AND THESE WERE TRANSCRIBED INTO 20 TO 30,000 GENES. BUT ON THE TOP OF THAT BECAUSE THE GENES WHERE YOU COULD HAVE THE SYSTEM, SO IT GOT SPLICED, ALTERNATIVE SPLICE FORM. SO THEY ONLY HAVE 25 TO 30,000 GENES, BUT THE RESULTING ALTERNATIVE SPLICING OF THE TRANSCRIPT CAN BE MORE THAN LIKE 150,000. AND AS I’VE TOLD YOU THERE’S ABOUT LIKE A THOUSAND. I THINK THIS NUMBER IS PROBABLY NOT ACCURATE. IT’S A COUPLE THOUSAND microRNA. AND ALSO THERE’S AN ENCODING RNA. IT’S LARGER THAN 20 BASE PAIR. microRNA IS 20 TO 22 NUCLEOTIDE RNA, BUT THERE’S LONGER COATING — CODING RNA, THERE’S A LOT. IT’S STILL IN THE STAGE OF BEING DISCOVERED. AND THEN THE TOP OF THAT, THERE’S ABOUT A HALF MILLION PROTEINS MADE DURING THIS PROCESS. SO YOU CAN SEE THIS IS THE NUMBERS WE’RE TALKING ABOUT. ALSO IN THE FIELD USUALLY THIS IS THE BOUNDARY, A STUDY OF THIS CATEGORY, THE DNA, MESSENGER RNA AND microRNA IS CALLED GENOMICS.

AND THIS DEMAND TO STUDY THE PROTEIN AND ITS MODIFICATION IS CALLED PROTEOMICS. WE’RE USING GENOMIC TOOLS, SO MY TALK BASICALLY IS CONCENTRATED ON THIS KIND OF — THIS SIDE OF THE DOMAIN. AND THE REASON THE STUDY SHOWS ABOUT 80% OF THE GENOME ACTUALLY TRANSCRIBED, SO THEY ARE FUNCTIONAL. BEFORE WE THINK THE CODING GENE IS THE MAJOR IMPORTANT COMPONENT OF THE GENOME, BUT IT’S ONLY CONSISTS OF 1 TO 2% OF THE WHOLE GENOME. HOWEVER, RECENTLY DATA SHOWS 80% OF GENOME IS FUNCTIONAL. THEY ARE TRANSCRIBED. SO THE MAJORITY OF GENOME ACTUALLY IS DEVOTED TO REGULATION OF WHEN AND WHERE GENES ARE MADE AND PROTEIN EXPRESSED. SO THE CHALLENGE OF GENOMICS, HOW TO MEASURE THE GENES AND PRODUCTS IN MASSIVELY PARALLEL WAY, RIGHT? BECAUSE WE HAVE SUCH A BIG NUMBER OF GENES WE NEED TO MEASURE OR DETECT.

SO THE REQUIREMENT FOR THIS KIND OF PROCESS IS USING THE HIGH THROUGHPUT TECHNOLOGY. AND IF WE HAVE A HIGH THROUGHPUT TECHNOLOGY WE HAVE TO HAVE COMPUTATIONAL POWER. SO THIS TWO COMBINATION THAT RESULT IN VERY LANDMARK SCIENTIFIC PROJECT WHICH IS HUMAN GENOME AT THE TURN OF THE CENTURY, ACTUALLY END OF THE LAST CENTURY, FROM 1990 TO 2003, NIH LEAD SEQUENCING OF THE FIRST HUMAN GENOME, SPANNED 13 YEARS, A COUPLE BILLION DOLLAR, SEQUENCE ONE GENOME. THIS IS VERY IMPORTANT SCIENTIFIC DISCOVERY, BECAUSE IT’S MAP OUT THE GENES ON THE CHROMOSOMES SO GIVE US A MAP THAT WE CAN DO A LOT OF COOL THINGS EASILY AND FAST WITH THE TECHNOLOGY, IN THIS TALK. THIS IS THE FIRST GENERATION GENOMIC TOOLS. IT’S CALLED MICROARRAY. I DON’T KNOW HOW MANY PEOPLE HEAR ABOUT IT. AND THE MICROARRAY BASICALLY IS USING ALL DIFFERENT TECHNOLOGIES TO PRINT THIS PROBE ONTO SOLID SURFACE SO THAT YOU CAN USE MICRO (INDISCERNIBLE) TO DETECT GENE EXPRESSION, THAT’S A CONCEPT BEHIND IT.

IT IS A DIFFERENT WAY TO MAKE microRNA, YOU CAN USE MECHANICAL (INDISCERNIBLE) DIP INTO THE DNA SOLUTIONS AND PRINT ON THE SURFACE OF THE GLASS. OR YOU CAN USE INK JET TECHNOLOGY, ELECTRONIC PIEZO, PRINTING HEAD LIKE THE INK JET PRINTER. INSTEAD OF PRINTING INK YOU USE THE PROBE TO PRINT ON THE SLIDES. LATER THEY HAVE TECHNOLOGY TO USE LITHOGRAPH MAKING, BASICALLY USE SEMI CONDUCTOR PRODUCTION METHOD TO GROW THE NUCLEOTIDE ON THE SURFACE OF THE SILICON WAFER. AND THE LATEST — ACTUALLY USING THE TECHNOLOGY CALLED DIGITAL MICROMIRROR DEVICE, IT’S THE SAME DEVICE IN THE PROJECTOR, IT CAN — IT DOESN’T NEED THE PHYSICAL — THE LIGHT MASK TO MAKE THE CHIP. INSTEAD THEY USE THE MICROMIRROR DEVICE TO SYNTHESIZE NUCLEOSIDE ON THE SURFACE OF GLASS. THE MICROARRAY, WE CAN EXTRACT BIOLOGIC SAMPLES, FOR EXAMPLE RNAs FROM HEALTHY INDIVIDUAL AND CANCEROUS TISSUE, AND WE CAN LABEL THEM WITH FLUORESCENT LABEL, AND PUT INTO THE CHAMBER THIS IS THE microRNA CHIP, YOU PUT THIS IN, THIS HAPPENS AND USE SCANNING MICROSCOPE TO SCAN THE SLIDES SO THAT YOU CAN DETECT THE SIGNALS ON EACH SPOT.

FOR EXAMPLE, THIS SPOT, THERE’S MORE CANCEROUS SIGNALS BIND TO THIS SPOT. THIS PROBE. THIS GRAY SPOT MEANS FOR HEALTHY MESSENGERS BIND TO THAT SPOT, OKAY? AND CAN YOU QUANTIFY IT TO MEASURE THE SIGNAL OF THE — IN THIS ORIGIN OF SAMPLES. HERE I GIVE YOU ONE EXAMPLE TO USE SUCH TECHNOLOGY TO DO THIS KIND OF GENOMIC. NOWADAYS, THIS IS KIND OF A CRUDE WAY. BUT AT THAT TIME IT WAS STATE-OF-THE-ART WAY TO DO THINGS. SO, IN THIS CASE, THERE IS A CURE THAT WAS REFERRED TO THE PEDIATRIC ONCOLOGY GROUP, THE BRANCH, TO HAVE A SECOND OPINION OF THIS TUMOR. SO IT’S A PRETTY BIG MASS, UPPER LEVEL KIDNEY HERE, ALSO HAVE MASS IN THE INTERIOR VENA CAVA. SO AT THAT TIME THE DIAGNOSIS OF THE INITIAL DIAGNOSIS THEY THINK IS A KIDNEY TUMOR, IN THIS CASE. HOWEVER, WHEN WE — OH, THE TREAT BUT THE RESPONSE WAS NOT THAT GOOD. THAT’S THE REASON COME TO ASK FOR THE SECOND OPINION.

WE TOOK THE BIOPSY SAMPLE, EXTRACT RNA FROM IT, AND PUT IT INTO THE MICROARRAY AND DID GENE EXPRESSION PROFILE. THIS TUMOR AND WE DID PRINCIPLE COMPONENT ANALYSIS WITH THE OTHER TUMORS, YOU CAN SEE THIS TUMOR HERE (INDISCERNIBLE) INSTEAD OF THIS YELLOW, THE WILM’S TUMOR. FROM THE GENE EXPRESSION PROFILE, IT’S — IT CAN DIAGNOSE THIS IS NOT A WILM’S TUMOR. INSTEAD IT’S A NEUROBLASTOMA. LATER THIS KID TRANSFERRED, PUT ON TREATMENT FOR NEUROBLASTOMA, RESPONSE WELL FOR THIS TREATMENT. THIS IS THE FIRST TIME WE’VE DEMONSTRATED THIS, VERY POWERFUL TECHNOLOGY WE CAN USE FOR THE CLINIC. NOW, GENOMIC TOO MAJOR USING IN THE LAB USING THIS TECHNIQUE CALLED NEXT GENERATION SEQUENCING. AND SO THIS IS THE WAY HOW IT WORKS BASICALLY TO SHOW CONSEQUENCING. TAKE THE DNA, RNA, DO FRAGMENTATION, AND PUT ADAPTER ON IT, PUT IT ON SEQUENCER TO SEQUENCE EVERY BIT OF THE DNA ON THE SEQUENCER.

AND THEN WE CAN USE THE MAP GENOME WHICH IS THE MAP GENERATED FROM THE HUMAN GENOME PROJECT AS A MAP, MAP ALL THE FRAGMENTS TO THE GENOME, AND SO THAT WE CAN KNOW WHERE THIS DNA OR RNA COMES FROM. AND WE CAN PUT BACK THE ORIGINAL SEQUENCE OF THIS SAMPLE. SO THAT’S BASICALLY THE PRINCIPLE BEHIND THIS TECHNOLOGY. SO THIS IS A PICTURE SHOWING YOU THIS IS A REALLY PICTURE FROM THE SEQUENCER. AND THIS IS A FIELD, A PICTURE FROM THE SEQUENCER. YOU CAN SEE EACH DOT REPRESENT ONE SEQUENCING SO EACH DOT IS A LITTLE BIT UNIQUE DNA FRAGMENTS. YOU CAN SEE THE DOTS ON THIS FIELD. AND THIS IS THE SCALE, OKAY? YOU SAW IT’S JUST A LITTLE SQUARE ON THIS BIG CHIP, AND IT IS THE FLOW CELLS AND CHEMISTRY HAPPENING IN THOSE FLOW CELLS.

SO THIS IS A MASSIVE PARALLEL SEQUENCE. WHEN SQUANDED YOU CAN SEQUENCE HUNDREDS, MILLIONS OF DNA FRAGMENTS. CAN YOU RAPIDLY SEQUENCE HUMAN GENOME. NOWADAYS CAN SEQUENCE HUMAN GENOME OVERNIGHT INSTEAD OF 13 YEARS LIKE THE FIRST HUMAN GENOME. SO WHAT INFORMATION CAN WE GET FROM THIS KIND OF EXPERIMENT? OKAY. IF WE DO GENOMIC DNA, WE CAN DETECT QUANTUM MUTATION, CAN DETECT HOMOZYGOUS DELETION. IF YOU HAVE DELETION OF THE MATERIAL, YOU JUST DON’T SEE IT. YOU CAN SEE SOME, BUT THE COVERAGE IS LOWER THAN IT SHOULD BE. AND THE COPY NUMBER AGAIN AND IF WE DO THE WHOLE GENOME DNA SEQUENCING WE CAN DETECT THE TRANSLOCATION BREAK POINTS.

THIS IS ALREADY IN THE BASE PAIR RESOLUTION CAN DETECT. AND SOME CASES THE TUMOR IS CAUSED BY THE VIRUS OR WHATEVER, WE CAN DETECT THE PATHOGEN DNAs IN THESE KIND OF EXPERIMENTS. AND WE CAN ALSO SEQUENCE IN THE RNA, THIS IS CALLED WHOLE TRANSCRIPTOME RNA SEQUENCING. THE INFORMATION WE CAN GET IS DIGITAL GENE EXPRESSION. WE CAN GET EXPRESSION OF MUTATION, DETECT THE MUTATION IN THE SAMPLE. AND WE CAN DETECT THE TRANSCRIPT, THAT’S VERY IMPORTANT ASPECT OF THIS TYPE OF EXPERIMENT, I WILL SHOW YOU SOME EXAMPLE LATER. AND WE ALSO CAN DETECT ALTERNATIVE SPLICING EVENT AND RNA EDITING, NOVEL TRANSCRIPT AND ALSO NON-CODING RNA. SO WHAT IS THE ADVANTAGE OF THIS SEQUENCING TECHNOLOGY? FIRST IT IS — IT DOESN’T — NOT NEEDED TO PREPARE CLONES FOR DNA FRAGMENTS, WHICH microRNA NEEDS THAT. AND THEN ANOTHER THING IS NO NEED OF PRIOR KNOWLEDGE FOR PROBE DESIGN BECAUSE IF YOU DO THE microRNA — MICROARRAY TECHNOLOGY, YOU USE CONTROL, YOU NEED TO HAVE PRIOR KNOWLEDGE TO DESIGN A PROBE.

IF YOU HAVE A FUSION GENE YOU WANT TO DETECT IF YOU DON’T KNOW THE FUSION CAN YOU NOT JUST DESIGN THE PROBE EASILY. BUT IN THE SEQUENCING EXPERIMENT YOU DON’T NEED THAT PRIOR KNOWLEDGE. AND WE CAN ALSO DETECT THE GENOMIC STRUCTURE CHANGE, THAT IS ABLE TO DO IT IN THE MICROARRAY. AND PARALLEL SEQUENCING AT BASEPAIR RESOLUTION IMMEDIATELY CAN TELL YOU ALL THE DETAILED CHANGE, AND BETTER HIGH THROUGHPUT. AND ANOTHER ADVANTAGE OF NEXT GENERATION SEQUENCING THIS PLATFORM CAN ACQUIRE ALL DIFFERENT GENOMIC AND EPIGENOMIC INFORMATION.

SHOWN IN THIS SLIDE, OKAY, WE CAN SEQUENCE DNA, RNA, AND WE CAN HAVE WHOLE GENOME SEQUENCING OR THE WHOLE EXOME SEQUENCING WHICH ONLY DUE TO GENOME PARTITION PULLS OUT COATING REGION TO SEQUENCE IT. OR WE CAN PUT — PULL OUT THE PROTEIN BINDING PLACES, THE DNA, THIS IS CALLED THE — WE CAN USE IT TO DETECT METHYLATION OR SPECIFICALLY TRANSCRIPTION FACTOR BINDING SITE, CALLED ChIP-SEQ. ALL THIS KIND OF THING, OKAY, HAVING THE INFORMATION OF THE COPY NUMBER CHANGE, GENE ARRANGEMENTS, REARRANGEMENT AND ALL THIS INFORMATION WITH THE SAME KIND OF PLATFORM. RNA, ON THE RNA SIDE, WE CAN DETECT MESSENGER RNA, NON-CODING RNA, AND ALL GENE EXPRESSION, ALL THIS INFORMATION WE CAN HAVE. AND WITH THE SAME PLATFORM CAN DETECT BIOMARKERS FOR DIAGNOSIS AND PROGNOSIS, AND ALSO WE CAN STUDY BIOLOGY WITH THAT TO FIND OUT WHAT IS (INDISCERNIBLE) FOR THE CANCERS AND HOPEFULLY USE THIS INFORMATION TO DEVELOP THERAPEUTIC TARGETS. SO, THIS SLIDE SHOWS ANOTHER CHALLENGE OF PEDIATRIC CANCER. BECAUSE NEXT GENERATION SEQUENCING TECHNOLOGY IS WIDELY AVAILABLE, AND A LOT OF — IN THE PAST 10 TO 15 YEARS THERE’S SO MANY STUDIES TO STUDY ALL DIFFERENT CANCERS, BUT WE SEE THERE IS VERY PECULIAR THINGS ABOUT PEDIATRIC CANCER.

THIS IS ALL THE ADULT CANCER, MEASURING SOMATIC MUTATION BURDEN. THAT MEANS HOW MANY SOMATIC MUTATION PER MEGABASE, HOW MANY SOMATIC MUTATION ARE THERE IN EACH CANCER. YOU CAN SEE ADULT CANCER GENERALLY HAVE MORE MUTATIONS THAN PEDIATRIC CANCERS. PEDIATRIC CANCER VERY FEW MUTATIONS PER CANCER. SO GIVE US CHALLENGES HOW THIS GENOMIC CAN HELP THE CRITICAL CARE FOR THIS PEDIATRIC CANCER. BECAUSE WE DON’T HAVE TOO MUCH TARGET WE CAN DO FOR THE PEDIATRIC CANCER.

SO IN ORDER TO FIND OUT IF THIS IS USEFUL TECHNOLOGY THAT WE DID EXPERIMENT, A STUDY TO USE GENOMICS TO STUDY PEDIATRIC CANCERS, FOR THE PATIENT COMING TO THE CCR, ALL THE PATIENTS COME TO THE CCR. IN THIS CASE WE USE THE STATE OF ART MULTI-DIMENSIONAL INTEGRATED OMIC STUDY PLATFORM. SO THIS IS A STUDY DESIGN. AND THIS IS A PILOT TO DETERMINE UTILITY AND FEASIBILITY OF PERFORMING COMPREHENSIVE GENOMIC ANALYSIS IDENTIFIED CLINICALLY ACTIONABLE MUTATION IN PEDIATRIC AND IN YOUNG PATIENT WITH METASTATIC REFRACTORY OR RELAPSED SOLID TUMOR COMING TO NIH. SO IN THIS STUDY WE RECRUIT 59 PATIENTS, AND THEY ARE AGE RANGE FROM 7 MONTHS ALL THE WAY TO 25 YEARS. AND IT IS 20 DIAGNOSIS CATEGORY, INCLUDING MOST OF THEM SOLID TUMORS, THAT IS NOT CENTRAL NERVE SYSTEM TUMOR.

AND WE PERFORM THE MULTI-OMICS BASICALLY WE USE EXOME BASICALLY SEQUENCE ALL THE CODING REGION OF THE GENOME, GERMLINE DNA, ALSO COMBINE WITH RNA SEQUENCING OF THE TUMOR, AND (INDISCERNIBLE) SNP ARRAY TO STUDY COPY NUMBER OF THE TUMOR. SO FIRST WE HAVE TO DEFINE WHAT IS CONSIDERED ACTIONABLE. THERE’S A SIDE OF THINGS WHAT IS THE ACTIONABLE GERMLINE MUTATION, MEANS THIS IS HEREDITY PART OF THE PATIENT. SO THE GERMLINE ACTIONABLE GERMLINE MUTATION IS LOSS OF FUNCTION MUTATION ON NO HOT SPOT ACTIVATING MUTATION OF CANCER CONSENSUS GENE WHICH THIS IS A COLLECTION OF THE SANGER DATABASE. OR THE PATHOGENIC OR LIKELY PATHOGENIC MUTATIONS OF AMERICAN COLLEGE OF MEDICAL GENETICS GENE. SO THERE’S A LIST MAINTAINED BY THE AMERICAN COLLEGE OF MEDICAL GENETICS. THEY HAVE A GENE SAYING IF YOU FIND ANY MUTATION FROM THESE GENES YOU’RE OBLIGATED TO REPORT, OKAY? BECAUSE THOSE ARE VERY SERIOUS MUTATION, LIKE BRCA1, BRCA2, P53, HAVE VERY DIRE CONSEQUENCE FOR THE PATIENT AND THE FAMILY.

THAT’S THE REASON YOU NEED TO REPORT. THEY HAVE GUIDELINES FOR THAT. THAT’S WHAT OUR DEFINITION OF WHAT THE GERMLINE MUTATION IS. ALSO WE ALSO FROM THE STUDY WANT TO IDENTIFY WHAT IS THE SOMATIC MUTATION, THAT MEANS SPECIFICALLY FOR THE TUMOR. IT’S NOT SOMATIC CELLS. SO, OUR DEFINITION IS GENOMIC ALTERATIONS BUT CHANGE THE PATIENT’S DIAGNOSIS, OR MAY TARGET BY FDA DRUGS OR SAFETY AND CLINICAL TRIALS ACCORDING TO NCI-ADULT MATCH-CRITERIA, DOING THE SAME THING, USING GENOMIC TOOLS TO IDENTIFY SPECIFIC MUTATIONS IN TUMORS, AND THEN PUT INTO THE RIGHT CATEGORY FOR THESE TRIALS. I THINK THE PREVIOUS SPEAKER ALSO NOWADAYS CANCER, RIGHT? THE PREVIOUS SPEAKER TALK ABOUT THE LUNG CANCER.

YOU WANT TO KNOW WHAT SPECIFIC MOLECULAR PROFILE OF THIS CANCER SO YOU CAN TREAT WITH THE RIGHT DRUG OR METHOD. SO THAT’S THE IDEA BEHIND THIS. SO THIS IS AN OVERVIEW. THIS IS A BUSY SLIDE. IT’S NOT MEANT FOR YOU TO SEE THE DETAIL BUT I GAVE YOU OVERVIEW OF THE THING. AND THIS CATEGORY IS IDENTIFIED BY RNA-SEQ, BASICALLY ALL THE FUSION GENES DETECTED IN THE TUMORS, YOU CAN SEE THERE’S A LOT OF FUSION. IT’S DIAGNOSTIC FOR THE TUMOR, OKAY? ESPECIALLY WITH PEDIATRIC CANCER, FOR EXAMPLE, EWING SARCOMA, EITHER ERK FUSION, EWING SARCOMA, FOX 4, THE EWING-LIKE SARCOMA, SO I’M NOT GOING THROUGH EACH ONE BUT THIS IS VERY DIAGNOSTIC MARKER FOR THE TUMOR. ALSO THERE ARE DRIVERS. THIS PART IS THE DNA SEQUENCING FROM THE DNA SEQUENCING AND RNA SEQUENCING, BASICALLY SOMATIC MUTATIONS WE’RE DETECTING ON THE TUMORS, AND THOSE ARE THE DRIVER TUMORS AND SOME ARE ACTIONABLE.

HERE IS THE COPY NUMBER CHANGE DETECTED BY SNP ARRAY, AND SOME COPY NUMBER CHANGE GENES, IT’S ALSO ACTIONABLE. AND FROM THE DNA GERMLINE SEQUENCING WE CAN DETECT THE DISEASE CAUSING OR ACTIONABLE AND ALSO HAVE CONSEQUENCES WITH THE FAMILY MEMBERS. AND THIS SLIDE SHOWS THAT USING THIS KIND OF PLATFORM WE CAN ACCURATELY DIAGNOSE THE CANCER. WITH THESE FOUR CANCERS, BECAUSE OF THE GENOMIC STUDY WE CHANGE THE DIAGNOSIS. FOR EXAMPLE, THERE’S ORIGINAL EWING SARCOMA, THEY THINK TYPICAL EWING SARCOMA, BUT WE DETECT FUSE GENE THAT IS NOT TYPICAL EWING, SO IT’S DETECTED — IT’S CHANGE THE DIAGNOSIS AS EWING-LIKE SARCOMA. AND THE SAME WITH THE OTHER CASES THAT EITHER THE EXPRESSION PROFILE IS NOT AS ORIGINAL TUMOR OR THE HALLMARK FUSION IS NOT THERE SO YOU HAVE — WE HAVE TO CHANGE THE DIAGNOSIS.

AND YOU TURN OFF THE GERMLINE MUTATION, DETECT 10% OF PATIENTS IN THIS COHORT HAS ACTIONABLE GERMLINE MUTATION. YOU CAN SEE SOME GERMLINE MUTATION IS PRETTY SERIOUS. YOU HAVE BRCA1 MUTATIONS, YOU HAVE TP 53, DISPOSED FOR OTHER CANCERS, NOT ONLY FOR THE PATIENT BUT FOR THE FAMILY AS WELL. THIS IS IMPORTANT INFORMATION FOR A PATIENT TO KNOW AND FOR THE TREATING PHYSICIAN TO KNOW. SOMATIC SIDE DETECT 50% OF THE CASE HAVE ACTIONABLE SOMATIC MUTATION. AND YOU CAN SEE THIS IS THE MUTATION WE DETECTED, HERE IS THE DRUG POTENTIALLY WE CAN USE THIS DRUG FDA APPROVED DRUG TO TREAT THOSE MUTATIONS. THIS IS VERY IMPORTANT THING, ALL THIS DISCOVERY IS TO BE USED FOR THESE PATIENTS.

SO WE DEMONSTRATE WITH THIS STUDY THE IMPORTANCE AND FEASIBILITY OF PERFORMING MULTI-DIMENSIONAL CLINICAL IN THE CLINIC SETTING IN REAL TIME. AND 50% OF CHILDREN HAVING THIS ACTIONABLE SOMATIC MUTATION, 10% HAS ACTIONABLE GERMLINE MUTATION. SO, OF THE FEASIBILITY STUDY, THIS IS THE MODEL WE THINK HOW TO USE GENOMICS IN PRECISION MEDICINE. METASTATIC DISEASE, ALL COMERS MIGHT HAVE DIFFERENT MOLECULAR PROFILE, BUT BY USING GENOMICS TO IDENTIFY BIOMARKERS, WE CAN SEPARATE THEM INTO SOME PEOPLE HAVE GOOD SIGNAL, SOME PATIENTS HAVE POOR SIGNATURES BUT A GOOD SIGNATURE CAN USE STANDARD THERAPY WHICH WOULD KNOW THEY ARE GOING TO RESPOND TO STANDARD THERAPY SO WE GIVE THEM THE STAND AROUND THERAPY. BUT FOR THE PEOPLE WHO HAD POOR SIGNATURE, WE CAN FURTHER DETECT THEIR TRUE DRIVER MUTATION AND USE TARGETED THERAPIES TO TREAT THOSE PATIENTS, HOPEFULLY THAT’S WAIT WE CAN IMPROVE SURVIVABILITY OF THOSE PATIENTS.

AND ESTABLISHING CLINICAL PROGRAM BASED ON OUR STUDY, AND THIS KIND OF HYPOTHESIS, AND WHEN THE PATIENT COME INTO THE CCR, THE CENTER OF CANCER RESEARCH, USUALLY PEOPLE COMING TO THE CAN — THE CANCER PATIENTS COMING TO CCR ARE NOT REGULAR PATIENTS, THEY ARE RELAPSED, EXHAUSTED STANDARD THERAPY ARCHIVES, RIGHT? THERE’S NOTHING THEY CAN DO ABOUT IT. THAT’S THE REASON THEY COME FOR CLINICAL TRIALS. THIS IS ALL HIGH-RISK PATIENT THAT COME TO THE CCR, THE P.I., DEPENDS WHAT KIND OF CANCER, LOAD THEM INTO DIFFERENT CLINICAL PROGRAM PROTOCOL, THEY CAN ORDER THE NEXT GENERATION SEQUENCING TEST AND BIOPSY WILL SEND PATHOLOGY, THEY DO THE NUCLEAR ACID EXTRACTION, AND DO THE INITIAL Q.C. AND SEND TO US TO SEQUENCE. THIS IS ALL CLEAR CERTIFIED PROCESS, AND FROM THAT, THAT DNA, RNA MATERIAL, WE CAN GET GERMLINE DATA AND SOMATIC DATA.

AND CAN HAVE THE TUMOR BOARD TO DISCUSS WHAT IS THE IMPORTANT MUTATION FOUND IN THIS TUMOR. AND GENETIC TO IDENTIFY GERMLINE MUTATION IDENTIFIED IN THE STUDY AND EVENTUALLY THOSE RECORD WILL PUT INTO THE CLINICAL MEDICAL RECORD. AND ALSO THE DATA IS AVAILABLE FOR THE CLINICAL RESEARCH, WHICH IS STORED IN DATABASE AT NIH. SO THE WHOLE PROCESS TAKES ABOUT — FROM OUR PILOT STUDY IS ABOUT A FOUR-WEEK TURNAROUND, PRETTY FAST IN TERMS OF THESE KIND OF THINGS SO WE CAN USE THIS PROGRAM TO REALLY BENEFIT THE PATIENT. AND THIS IS THE PROGRAM, THE INSTRUMENT WE USE IN THE PROGRAM. WE HAVE TWO NEXT Seq 500, HIGH SPEED, CAN SEQUENCE 65 GIG A BASE IN 24 HOURS, VERY FAST, OVERNIGHT YOU CAN SEQUENCE THE SAME COUPLE PATIENTS USING THIS INSTRUMENT. SOMETIMES WE HAVE HiSEQ, 2500, WHICH HAS MUCH HIGHER THROUGHPUT, ABOUT A THOUSAND GIGABYTES, PER RUN, TAKES TWO WEEKS TO RUN ONE RUN. AND THIS PIECHART SHOWS UP TO I THINK END OF AUGUST WE HAVE SEQUENCED 255 PATIENTS, OF 81 DIFFERENT DIAGNOSES OF THE DIFFERENT CANCERS.

ANOTHER IMPORTANT THING, A TOOL WE DEVELOPED IS THIS DATA PORTAL. YOU CAN IMAGINE THIS IS A TECHNOLOGY GENERATE A LOT OF DATA, IT’S NOT EASY TO LOOK AT THOSE BECAUSE THOSE ARE JUST LIKE SHORT WAITS, RIGHT? IT’S BIOINFORMATICALLY LIKE TERABYTES OF DATA BUT IF YOU’RE A BIOLOGIST OR CLINICIAN, IT’S NO WAY FOR US TO SEE THE RESULT EASILY. OKAY? THAT’S THE REASON WE DID THIS TOO, TO VISUALIZE THE DATA FROM THE WEBSITE. AND FRONT END OF THE WEBSITE, THIS IS THE PATIENT SUMMARY PAGE AND YOU CAN SEE THIS PATIENT WILL HAVE A CASE WHICH IS A BIOPSY, THE CODE, WE HAVE LIKE FIVE EXPERIMENTS FOR THIS BIOPSY. DID EXOME GENERALSING, SEQUENCING FOR THE NORMAL BLOOD SAMPLE, AND T FOR THE TUMOR, TUMOR SEQUENCING, THIS REPRESENTS RNA SEQUENCING. WE HAVE EXOME PANEL SEQUENCING FOR BOTH GERMLINE, TUMOR DNA, AS WELL AS RNA SEQUENCING. AND THIS IS THE COVERAGE PLOT, HOW GOOD THE SEQUENCING IS AND THE SUMMARY. AND WE ALSO DEVELOPED THIS Q.C. REPORT, WE WANT TO SEE HOW GOOD THE EXPERIMENT WE DID, RIGHT? THIS ONE GAVE YOU OVERVIEW OF THE Q.C., HOW MANY READS WE GENERATED PER LIBRARY, WHAT’S THE COVERAGE FOR THE SAMPLE.

AND ANOTHER IMPORTANT THING, WE PERFORMED GENOTYPING EVERY TIME FOR EVERY PATIENT. ENSURE THERE’S NO MESSED UP IN THE LAB TO SWAP SAMPLES. SO THIS IS OUR GENOME PATTERN USING THE BASE PAIR RESOLUTION SEQUENCING DATA. AND THIS IS FURTHER Q.C., WE CAN SEE WE PLOTTED ALLELE FREQUENCY. YOU CAN SEE THIS TUMOR, A LOT OF ZYGOSITY, YOU BECOME HOMOZYGOCITY. THIS JUST GIVES OVERVIEW OF GENOME. THIS TUMOR HAS A LOT OF AMI PLOITY.

IN THIS CASE THE TUMOR IS 45, 50% TUMOR, THE REST IS NORMAL CELLS, IN RNA SEQUENCING CAN DETECT HOW GOOD THE RNA QUALITY IS, WHAT’S THE COVERAGE. HERE IS HOTSPOT COVERAGE, MOST IMPORTANT DISEASE-CAUSING VARIANT THAT WE NEED TO KNOW, HOW GOOD DETECTION IS. GERM LINE AND SOMATIC MUTATION, YOU CAN SEE THE DIFFERENT INFORMATION, AND HERE THIS SLIDE SHOWS YOU EXAMPLE OF SOMATIC MUTATION WE DETECT IN ONE NON-SMALL CELL LUNG CANCER PATIENT, IN THE TUMOR. THIS IS THEIR CLASSIC T7 90 TO N MUTATION, IN THE EGFR GENE. THIS MUTATION IS CONFIRMED TO THE EGFR INHIBITOR RESISTANCE. SO IF WE KNOW THIS PATIENT, THIS MUTATION, WE WILL PREDICT EGFR INHIBITOR IS NOT GOING TO BE A FACTOR FOR THIS PATIENT SO THEY IMMEDIATELY — THE CLINICIAN WILL KNOW THAT THINGS THEY SHOULD BE USED TO TREAT, WHAT DRUGS THEY SHOULD NOT USE TO TREAT THIS PATIENT.

AND THIS ONE IS TO SHOW YOU THE COPY NUMBER OF THE TUMOR. AND THIS IS THE TWO COPY. THE GENOME, DIPLOID GENOME TWO COPY, ANYTHING ABOVE IT IS GAIN, ANYTHING BELOW IS LOSS. YOU CAN SEE THIS TUMOR HAS A LOT OF COPY NUMBER CHANGES IN THE TUMOR. AND ANOTHER THING WE DEVELOPED IS THE MUTATION SIGNATURES. THIS IS DEVELOPED BY THE SANGER, THE CONTEXT OF THE MUTATION, HOW THE SOMATIC MUTATION HAS IN THE CONTEXT, BECAUSE THIS WILL GIVE US A HINT HOW THIS MUTATION ARISE, BECAUSE EACH — BECAUSE DUE TO THE CHEMISTRY OF THE MUTATION, SOMETIMES BECAUSE OF THE REPAIRING MECHANISM, AND SOMETIMES THESE BECOME THE UV OR OTHER THINGS, CARCINOGEN, THE SIGNATURE IS GOING TO BE DIFFERENT.

IN THIS CASE, IN THIS TUMOR WE DETECTED THERE’S ENRICHMENT OF SIGNATURE 7. LOOK AT THE SANGER COSMC WEBSITE, THE SIGNATURE 7 IS UV SIGNATURE, SO THIS IS A MEDICAL — MELANOMA, TYPICAL UV SIGNATURE. WE ALSO HAVE A TWO FOR THE MUTATION BURDEN, TACKLE IT, HOW MANY SOMATIC MUTATIONS PER MEGABASE, VERY IMPORTANT FOR NEW THERAPY BECAUSE ALL THIS NEW THERAPY, THERE’S ONE MARKER, BIOMARKER, THIS MUTATION BURDEN. IF HAVE YOU HIGHER MUTATION BURDEN USUALLY THERE ARE MORE LIKELY TO RESPOND TO THE IMMUNE CHECKING — CHECK POINT INHIBITOR THERAPY. BUT OTHERWISE YOU HAVE LOW MUTATION BURDEN LIKELY YOU’RE NOT GOING TO RESPOND TO THAT.

AND DEVELOP TOOL TO VISUALIZE THE FUSION GENES, YOU CAN SEE THIS ONE IS EWS, WT1 FUSION, AND THIS IS A FUSION, WSR, THE FRONT PART, FUSED WITH WT1, THE LATER PART, CREATED THIS FUSION GENE, AND THIS GIVE YOU EXACTLY THE PROTEIN SEQUENCE AS WELL AS NUCLEAR ACID SEQUENCE. THAT’S VERY EASY USING THIS TOOL TO DESIGN PRIMER TO VALIDATE THIS FUSION. OTHER TOOLS WE DEVELOPED ON THE WEBSITE INCLUDING TISSUE TYPING, HGRA, NEW ANTIGEN PREDICTION, GENE EXPRESSION, AND GSA ANALYSIS AND ALSO IF WE HAVE THE SURVIVAL DATA ASSOCIATED WITH THE SAMPLES, WE CAN PERFORM SALIVA ANALYSIS. SO IN CONCLUSION, THE NEXT GENERATION SEQUENCING INCLUDING WHOLE GENOME, EXOME, TRANSCRIPTOME AND DETERMINANT DETERMINES THE GENOMIC PORTRAIT OF THE CANCER AT BASE LEVEL, BASE PAIR LEVEL, VERY HIGH RESOLUTION INFORMATION. INTEGRAL ANALYSIS CAN IDENTIFY BIOLOGICAL RELEVANT DIAGNOSIS, PROGNOSIS, BIOMARKER AND ALSO NOVEL TARGETS FOR THE PRECISION MEDICINE.

SO THIS IS A HUGE TEAM WORK, AND CLINICAL PROJECT BASICALLY IT’S THE COLLABORATION BETWEEN THE GENETIC BRANCH AND LABORATORY PATHOLOGY. AND THERE IS A LOT OF INDIVIDUAL INTO THIS PROGRAM, THERE’S A LOT OF BIOLOGISTS, BIOINFORMATICS, HIGHLY RELY ON TOOLS, DEVELOP NEW TOOLS AND SHOW YOU THOSE, ALSO PEOPLE’S DEDICATION TO MAKE THIS HAPPENING. AND ALSO I WANT TO ACKNOWLEDGE THE CTR LEADERSHIP TO — CCR LEADERSHIP TO MAKE THIS PROGRAM POSSIBLE.

>> QUESTIONS? >> . >> IT’S REALLY DEPENDS. IN THE CCR THEY ARE COMING — ALL THE PATIENTS ARE HIGH RISK, AND METASTATIC. THEY DON’T HAVE ANY WAY TO CREATE THEM. IN THE PAST BEFORE THE GENOMIC ERA, PEOPLE JUST GUESSED UP. YOU TRY THIS, DOESN’T WORK, YOU TRY THE OTHER ONE. SHOOTING A BLANK, OKAY? NOW WE HAVE THESE TWO. THEY HAVE SOME RATIONAL EDUCATED GUESS, OKAY? IF THEY HAVE THE MUTATION, MAYBE INHIBITOR OR SOMETHING.

SO THAT’S THE UTILITY. BUT THE QUESTION IS, NOW THIS KIND OF STUDY IS STILL PRETTY EXPENSIVE, YOU KNOW. WE SPEND LIKE — I THINK ANYWHERE BETWEEN 3,000 TO 5,000 PER PATIENT FOR THIS KIND OF THING. SO I THINK THE SEQUENCING, THE PRICE EVENTUALLY COMING DOWN OR IF IT’S CHEAP, IT’S OKAY, YOU CAN ORDER IT TO DO IT. BUT CURRENTLY, WITHIN THE CCR, THE IDEA IS STILL USING THIS, BECAUSE THESE PATIENT ARE HIGH RISK THE IDEA IS WAIT TO SEQUENCE EVERYONE. OUTSIDE OF THE NIH I’M NOT SURE, YOU KNOW. I KNOW SOME PEDIATRIC CANCER, THE INSURANCE EVEN COVER THIS KIND OF STUDY, YOU KNOW, BUT I’M NOT SURE IT’S LOCALIZED THE DISEASE OR THAT KIND OF THING, I’M NOT SURE INSURANCE — HOW COMMON THEY USE THIS TOOL. EVENTUALLY THEY WILL USE IT BECAUSE IT’S ALL ABOUT COST. YEAH. >> PRECISION MEDICINE IS PRETTY WELL DEFINED FOR ADULTS. FOR THE CHILDREN, IF YOU IDENTIFY MUTATION, YOU CAN’T NECESSARILY EFFECTIVELY USE THE ADULT DRUGS.

>> WELL, THAT IS TRUE. I THINK NOW THE BOTTOM LINE IS THE DRUG AVAILABILITY TO THOSE MUTATIONS, OTHER MUTATIONS FOUND IN THE PHYSICAL SENSE WE JUST DON’T SEE — WE KNOW THE DRIVER BUT DON’T HAVE ANY EFFECTIVE DRUG. ANOTHER THING IS THIS KIND OF ADULT DRUG HOW DO YOU USE IN THE PEDIATRIC CASE, I’M NOT A CLINICIAN, BUT I THINK THEY ARE WORKING ON THESE THINGS. THEY HAVE CLINICAL TRIALS TO TRY THE DRUG OR REPURPOSE SOME DRUGS FOR THIS KIND OF USE, YEAH. >> OKAY. 01:51:17.137,00:00:00.000 THAT WILL DO IT. .