Paolo Vineis University of Torino and ISI Foundation, Torino, Italy address: GENE-ENVIRONMENT INTERACTIONS IN CANCER

LIMITATIONS OF GENETIC DETERMINISM 1. HUMANS AND MICE HAVE THE SAME ESTIMATED NUMBER OF EXPRESSED GENES 2. HUMANS AND CHIMPANZEES SHARE 98% OF THE GENOME 3. THE SEQUENCE INFORMATION IN DNA IS INSUFFICIENT TO DETERMINE HOW GENE PRODUCTS INTERACT TO PRODUCE AN ORGANISM

4. GENETIC PATHWAYS COMPLETELY SPECIFY ORGANISMAL FUNCTION ONLY IN RARE CASES, I.E. MONOGENIC DISEASES (SICKLE CELL ANEMIA, MUSCULAR DISTROPHY), WHEN THE CELL HAS NO COMPENSATORY MECHANISM AND ENVIRONMENTAL INFLUENCES ARE NIL – “ONE MUTANT GENE – ONE DISEASE PARADIGM” STROHMAN: “THE CELL IS STARTING TO LOOK MORE LIKE A COMPLETE ADAPTIVE SYSTEM RATHER THAN A FACTORY FLOOR OF ROBOTIC MACHINE GENES”

SOME FIGURES LIFETIME RISK OF BREAST CANCER IS 12.6% IN WOMEN, OF PROSTATE CANCER IS 15.9% IN MEN, AND OF COLON CANCER IS 5.6% IN BOTH SEXES BRCA1 AND BRCA2 CONFER A RELATIVE RISK OF BREAST CANCER OF 5-10 GENOTYPES AT MISMATCH REPAIR LOCI CONFER A RR OF COLON CANCER OF 9.3 METABOLIC POLYMORPHISMS CONFER A RR FOR SEVERAL TYPES OF CANCER OF LESS THAN 2

ABOUT 0.25% OF WOMEN CARRY BRCA1 OR BRCA2 SUSCEPTIBLE VARIANTS, AND 0.1% OF PEOPLE HAVE SUSCEPTIBLE VARIANTS FOR MISMATCH REPAIR LOCI THESE GENOTYPES ACCOUNT FOR LESS THAN 5% OF BREAST OR COLON CANCERS 20% OF THE GENERAL POPULATION HAVE THE APOLIPOPROTEIN E4 ALLELE, WITH A RR OF ALZHEIMER’S DISEASE OF ABOUT 2; THIS GENE ACCOUNTS FOR 16.7% OF ALL CASES OF AD

HOW MANY CANCERS ARE ATTRIBUTABLE TO GENETIC PREDISPOSITION? LICHENSTEIN ET AL, N ENGL J MED 343: 78-85, ,788 PAIRS OF TWINS STUDIED IN SCANDINAVIAN COUNTRIES ESTIMATES: PROSTATE 42% (95% CI 29-55) COLORECTAL 35% (10-48) BREAST 27% (4-54) EDITORIAL BY R. HOOVER: GENE-ENVIRONMENT INTERACTIONS ARE NOT ACCOUNTED FOR (THESE ARE PROBABLY OVERESTIMATES)

ATTENTION TO DIFFERENT RISK MEASURES: ABSOLUTE RISK, E.G. LIFE-TIME CUMULATIVE RISK (50-70% OF BREAST CANCERS FROM BRCA1 MUTATIONS IN MUTATION CARRIERS) RELATIVE RISK (PENETRANCE)=5-10 TIMES ARe =PROPORTION AMONG CARRIERS= 80% OF BREAST CANCERS IN CARRIERS OF BRCA1 MUTATIONS ARE DUE TO THIS GENE ARp = PROPORTION IN THE POPULATION=5-10% OF ALL BREAST CANCERS ARE ATTRIBUTABLE TO BRCA1 MUTATIONS

WHEN ESTIMATING THE EFFECTIVENESS OF “SCREENING” WE HAVE TO CONSIDER: (A) PREDICTIVE VALUE, THAT DEPENDS ON THE PREVALENCE OF MUTATIONS (B) PENETRANCE OF THE GENE (NNT) (C) MOST IMPORTANT, THE AVAILABILITY OF PREVENTIVE OR CURATIVE MEASURES

EXAMPLE: MUTATION YESNO TEST POSITIVE1510 NEGATIVE5115 PREVALENCE=20/145=13.8% SENSITIVITY=15/20=0.75 SPECIFICITY=115/125=0.92 POSITIVE PREDICTIVE VALUE=15/25=0.60 I.E. OUT OF 100 POSITIVE TESTS 60 HAVE THE MUTATION

EXAMPLE: MUTATION YESNO TEST POSITIVE NEGATIVE PREVALENCE=20/12520=0.16% SENSITIVITY=15/20=0.75 SPECIFICITY=11500/12500=0.92 POSITIVE PREDICTIVE VALUE=15/1015=0.015 I.E. OUT OF 1015 POSITIVE TESTS ONLY 15 HAVE THE MUTATION

WHAT IS THE EFFECT OF PENETRANCE? IMAGINE WE HAVE AN EFFECTIVE PREVENTIVE MEASURE THAT REDUCES THE RISK OF DISEASE IN THE SCREENEES BY 58% LET US IMAGINE THAT THE RISK OF DISEASE IS 1.4% FOR A LOW PENETRANT MUTATION AND 37% FOR A HIGHLY PENETRANT MUTATION (REALISTIC FIGURES FOR A METABOLIC POLYMORPHISM AND BRCA1, RESPECTIVELY)

WE COMPUTE THE NUMBER NEEDED TO TREAT (SCREEN), I.E. THE NUMBER OF MUTATIONS CARRIERS WHO NEED TO UNDERGO SCREENING TO PREVENT A SINGLE CANCER THE NNT(S) DEPENDS ON PENETRANCE PLUS THE EFFECTIVENESS OF PREVENTIVE MEASURES

WITH 58% SUCCESSES AND A RISK OF DISEASE OF 37%, THE NUMBER OF CASES DECREASES BY 22%. THE RECIPROCAL OF 0.22 IS APPROXIMATELY 4.5 WITH A RISK OF DISEASE OF 1.4% AND 58% SUCCESSES, THE RISK DECREASES BY AND ITS RECIPROCAL IS 1/0.008=125 I.E. WE NEED TO TREAT 4.5 SUBJECTS IN THE FIRST CASE AND 125 IN THE SECOND (NNT)

NOW WE CAN COMBINE THE NNT AND PREVALENCE TO OBTAIN THE NNS CASE 1 IF WE SCREEN THE GENERAL POPULATION FOR A LOW PENETRANT GENE (NNT=125, PREVALENCE=13.8%, PPV=60%), IN ORDER TO PREVENT A CANCER WE HAVE TO MULTIPLY THE NNT BY THE RECIPROCAL OF PREVALENCE 125 X (1/0.138) = 906 SUBJECTS (WITHOUT CONSIDERING SENSITIVITY AND SPECIFICITY)

CASE 2 IF WE SCREEN THE GENERAL POPULATION FOR A RARE, HIGHLY PENETRANT GENE (NNT=4.5, PREVALENCE=0.16%, PPV=1.5%), IN ORDER TO PREVENT A CANCER WE HAVE TO MULTIPLY THE NNT BY THE RECIPROCAL OF PREVALENCE 4.5 X (1/0.0016) = 2813 SUBJECTS (WITHOUT CONSIDERING SENSITIVITY AND SPECIFICITY)

CASE 3 IF WE SCREEN FAMILIES FOR A RARE, HIGHLY PENETRANT GENE (NNT=4.5, PREVALENCE IN THE FAMILIES=0.50), IN ORDER TO PREVENT A CANCER WE HAVE TO MULTIPLY THE NNT BY THE RECIPROCAL OF PREVALENCE 4.5 X (1/0.50) = 90 SUBJECTS (WITHOUT CONSIDERING SENSITIVITY AND SPECIFICITY)

Calculation of the Number Needed to Screen in the case of screening for a low penetrant gene (GSTM1 in smokers), and a highly penetrant gene (BRCA1), respectively in the general population or in families (from Vineis et al, The Lancet, 357: , 2001) Lung cancerBreast cancer in workers exposed to PAH BRCA1 BRCA1 GSTM1 nullGSTM1 wildgeneral population families Relative risk1.34 ( ) 1.0 (a)5 10 Cumulative risk13%10%40% (b) 80 % Risk reduction 50% 50% (c)50% (Tamoxifen 50% or Raloxifene) (d) Cumulative risk after intervention6.5%5%20% 40% Absolute risk reduction6.5%5%20% 40%

Lung cancerBreast cancer BRCA1 GSTM1 null GSTM1 wildgeneral BRCA1 population families NNS in mutation carriers Prevalence 50%50%0.2% (e) 50% NNS in whole target population30402,500 5 NNS in all occupationally exposed35 (a) from Vineis et al, IARC Scie. Publ. No. 148, (b) from Hopper et al, 1999 (c) theoretical maximum reduction in risk of lung cancer due to preventive action (d) theoretical benefit, based on the BCPT trial with a 45% benefit, and the Raloxifene trial with a 76% benefit (e) Coughlin et al, 1999

An illustration of the principle of “one exposure - many diseases, one disease - many low penetrant genes”. ExposureProportion attributable Tobacco smokeLung cancer90% Bladder cancer70% men 30% women Larynx cancer90% CHD12.5% Chronic bronchitis80% OccupationalLung cancer4-20% (a) exposure Bladder cancer1-10% (a) to PAH (a) depending on the areas

DiseaseLow penetrant genes Odds Ratio (a) Lung cancerCYP1A1 MspI (asians)1.73 CYP1A1 MspI (caucasians)1.04 CYP1A1 Exon 7 (asians)2.25 CYP1A1 Exon 7 (caucasians)1.30 CYP2D61.26 GSTM11.34 Bladder cancerNAT - 2 slow1.37 GSTM11.57 Colon cancerNAT - 2 rapid1.19 (a) meta - analisys from Vineis et al, IARC Scie. Publ. No. 148, 1999

MANY GENES CONTRIBUTE TO MODULATE THE RISK, AND THE CONTRIBUTION OF EACH IS MODEST ( EXCEPT IN HIGH RISK FAMILIES) ADOPTING PREVENTIVE MEASURES ONLY IN THE HIGHLY SUSCEPTIBLE WOULD IMPLY VERY LITTLE ADVANTAGES OVER PREVENTION FOR ALL