Susceptibility Markers

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Susceptibility Markers
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Susceptibility Markers

• Susceptibility markers represent a group of
  biological markers, which may make an individual
  susceptible to cancer.
• These markers may be genetically inherited or
  determined or acquired.
• They are independent of environmental exposures.

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Biomarker of Genetic Susceptibility

• High risk genes
• Low risk genes

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Genetic Susceptibility to Cancer
010205
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Frequency Distribution of Breast Cancer
Hereditary
Familial
10
20
70
Unexplained by Family History or Inherited
Predisposition
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BRCA1 and BRCA2 Mutations in the Ashkenazi Jewish
Population
An estimated 1 in 40 Ashkenazi Jews carries a
BRCA1 or BRCA2 mutation
BRCA1
185delAG Prevalence 1
5382insC Prevalence 0.15
BRCA2
6174delT Prevalence 1.5
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Hereditary Breast and Ovarian Cancer
BRCA2 (32)
Predisposing factor in 15-45 of hereditary
breast cancer
Sporadic
Am J Hum Genet 1998 62676-89
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BRCA1-2 Mutations Increase the Risk
ofEarly-Onset Breast Cancer
By age 70
By age 50
By age 40
45-87
33-50
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BRCA1-2 Mutations Increase the Risk of Ovarian
and Related Cancer
By age 70
Population risk
Hereditary risk
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DNA damage repaired
Defected DNA repair gene
If DNA damage not repaired
G0
If loose cell cycle control
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Susceptibility Markers Metabolic Genes

• Tumor susceptibility markers such as P450s, GSTs,
  and NATs, act in enzymatic pathways related to
  metabolizing and eliminating carcinogens.

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Phase I Enzymes

• The phase I enzymes such as p450 enzyme
  superfamily metabolize exogenous or endogenous
  agents or carcinogens to intermediates, which can
  result in DNA damages and act as risk factors for
  cancer.

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Phase I Genes

• The phase I genes encode detoxifying enzymes that
  recognize a large variety of substrates.
• Many drugs, poisons, and other exogenous
  chemicals, as well as a number of natural
  endogenous compounds are metabolized by these
  enzymes.

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Phase II Genes

• The major function is to detoxify carcinogens
• Including GSTs, NATs

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14 13 12 11 10 9 8 7 6
5 4 3 2 1
PCR P450 2E1 after Using Pst1 RFLP
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Case 1 Case 2 Case 3 Case 4 Case 5
Case 6 Case 7 Case 8
ile/val ile/val ile/ile
val/val ile/val ile/ile
ile/val ile/ile
Figure. GSTP1 polymorphism
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Case 1 Case 2 Case 3 Case 4 Case 5
Arg/Arg Arg/Arg Pro/Pro Arg/Arg
Arg/Pro
Figure. P53 polymorphism at codon 72 from buccal
cell DNA.
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DNA Repair Genes
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Polymorphism of DNA repair genes

• DNA repair system maintains the intergrity of the
  genome by
• Reducing the mutation frequency of cancer-related
  genes,
• minimizing replication errors,
• removing DNA damage
• Minimizing deleterious rearrangement arising via
  aberrant recombination
• Four pathways for repairing DNA damage
• Base excision repair (BER)
• Excision of a damaged region ? fill-in repair
  synthesis using opposite strand as template
• Nucleotide excisions repair (NER)
• Remove photoproducts from UV radiation and bulky
  adducts
• Recombination repair
• When both strands are damaged ? acts on
  double-strand breaks and inter-strand links
• Mismatch repair
• On base mismatches that arise during replication
  by misincoporation or slippage on the template
  strand

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DNA Repair
Genetic Variation in Repair Genes ?
DNA Repair Capacity ORs
1.4-75.3 Cancer Occurrence
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Base Excision Repair
hOGG1
LIG1
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hOGG1

• Often deleted in a variety of cancers
• Somatically mutated in some cancer cells
• Ser326Cys, exon 7 highly polymorphic
• 0.2 Caucasian0.4-0.6 Chinese
• Ser326 protein 7-fold greater repair activity
• ORs Lung 2.2-3.4, Orolaryngeal 4.1-6.9

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LIG1

• Encodes DNA ligase I, a DNA joining enzyme
• Participates in BER, NER, MMR, and HRR
• Exon 6, codon 170 polymorphism
• 0.5 allele frequency in Caucasians
• No studies in esophageal, stomach, liver cancers
• No studies in Chinese

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Nucleotide Excision Repair

• Removes bulky adducts caused by environmental
  agents
• UV radiation
• Chemical carcinogens

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XPD/ERCC2
ERCC1
LIG1
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XPD/ERCC2

• Involved in DNA unwinding during NER
• Helps repair genetic damage induced by tobacco
  and other carcinogens
• Exon 10, codon 312
• Exon 23, codon 751
• Most studies of both polymorphisms have been done
  in lung cancer (most ORs 1.5-3.5)

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Homologous Recombinational Repair

• One mechanism for repairing double-strand breaks
  in DNA
• Accurately replaces sequence information by
  physically exchanging a segment from an
  homologous intact DNA molecule

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XRCC3
LIG1
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Adjusted Odds Ratios of Selected DNA Repair Genes
for Stomach Cancer
Genes Adjusted ORs 95 CIs
XRCC1-399 (AA GG vs. GA) 1.38 0.9-2.1
XRCC3 (TT TM vs. MM) 0.57 0.3-1.2
XPD10 (GG GA vs. AA) 0.77 0.5-1.2
XPD23 (LL LG vs. GG) 0.82 0.5-1.5
HOGG1 (SS SC vs. CC 1.20 0.7-2.1
LIG1 (AA AC vs. CC) 0.71 0.5-1.1
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Interactions between smoking and GST M1(odds
ratios and 95 confidence intervals)
5.29 (1.81, 15.4)
2.79 (0.97, 7.99)
1.13 (0.32, 3.95)
1.00
Adjusted for age, sex, race, and level of
education
More than multiplicative interaction
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Polymorphism of DNA repair genes

• DNA repair system maintains the intergrity of the
  genome by
• Reducing the mutation frequency of cancer-related
  genes,
• minimizing replication errors,
• removing DNA damage
• Minimizing deleterious rearrangement arising via
  aberrant recombination
• Four pathways for repairing DNA damage
• Base excision repair (BER)
• Excision of a damaged region ? fill-in repair
  synthesis using opposite strand as template
• Nucleotide excisions repair (NER)
• Remove photoproducts from UV radiation and bulky
  adducts
• Recombination repair
• When both strands are damaged ? acts on
  double-strand breaks and inter-strand links
• Mismatch repair
• On base mismatches that arise during replication
  by misincoporation or slippage on the template
  strand

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Lung Cancer Study
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Associations between Cigarette Smoking, Selected
Susceptibility Genes and Lung Cancer
Adjusted ORs 95 CIs
Smoking (Yes/No) 3.70 2.70-4.90
P53 (P/P vs. A/A or A/P) 1.00 0.76-1.32
GSTP1 (Val/Val Val/Ile vs. Ile/Ile) 1.01 0.76-1.33
Adjusted for age(continuous),sex and
race(white/non-white)
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P53 Codon 72 Polymorphism, Smoking, and Lung
Cancer
Smoke P53 Cases Controls OR(95CI) adjusted
Never Arg/Arg 28 125 1.0
Never Arg/Pro Pro/Pro 38 139 1.13 (0.65-1.97)
Yes Arg/Arg 133 132 4.32 (2.65-7.04)
Yes P/P 170 170 4.03 (2.50-6.49)
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GSTP1 Polymorphism, Smoking and Lung Cancer
Smoke GSTP1 Cases Controls OR(95CI) adjusted
Never Ile/Ile 31 111 1.0
Never Any Val 28 140 0.69 (0.39-1.24)
Yes Ile/Ile 125 135 3.16 (1.95-5.11)
Yes Any Val 164 152 3.64 (2.27-5.82)
OR int 1.66 (0.85-3.24)
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PCR primers and enzymes
Genes Primers 5 to 3 Enzyme
ALDH2 Sense CAA ATT ACA GGG TCA AGG GCT Mbo II
ALDH2 Anti-sense CCA CAC TCA CAG TTT TCT CTT Mbo II
ADH2 Sense GAAGGGGGGTCACCAGGTTG Mae III
ADH2 Anti-sense AATCTTTTCTGAATCTGAACAG Mae III
ADH3 Sense AAT AAT TAT TTT TCA GGC TTT AAG AGT AAA TAT TCT GT Ssa I
ADH3 Anti-sense AAT CTA CCT CTT TCC AGA GC Ssa I
CYP 2E1 Sense TTCATTCTGTCTTCTAACTGG Rsa I
CYP 2E1 Anti-sense CCAGTCGAGTC GAGTCTACATTG TCA Rsa I
NQO1 Sense TAT CAG AGT GTC TTA CTG AGA
NQO1 Anti-sense AAT GCT ATA TGT CAG TTG AGG
NQO1 Sense GTG GCT TCC AAG TCT TAG AAT
NQO1 Anti-sense TTT CTA GCT TTG ATC TGG TTG
XRCC1 399 Sense CCC CAA GTA CAG CCA GGT C Msp I
XRCC1 399 Anti-sense TGT CCC GCT CCT CTC AGT AG Msp I
XRCC1 194 Sense GTT CCG TGT GAA GGA GGA GGA Pvu II
XRCC1 194 Anti-sense CGA GTC TAG GTC TCA ACC CTA CTC ACT Pvu II
P53 Intron 3 Sense TGGGACTGACTTTCTGCTCTT
P53 Intron 3 Anti-sense TCAAATCATCCATTGCTTGG
P53 Intron 6 Sense TGGCCATCTACAAGCAGTCA Msp I
P53 Intron 6 Anti-sense TTGCACATCTCATGGGGTTA Msp I
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Stomach Cancer Study
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Adjusted Odds Ratios of Selected Metabolic and
Cell-Cycle Genes for Stomach Cancer
Genes Adjusted ORs 95 CIs
GSTM1 (null vs. non-null) 1.15 0.8-1.8
GSTT1 (null vs. non-null) 0.93 0.6-1.4
GSTP1 (Val/Val Val/Ile vs. Ile/Ile) 1.01 0.7-1.5
ALDH2 (AG/AA vs. GG) 1.00 0.4-2.4
CYP2E1 (c1c1 c1c2 vs. c2c2) 0.82 0.6-1.2
NQO1 (CC/CT vs. TT) 1.5 0.9-2.3
MTHFR (CC/CT vs. TT) 2.0 1.3-3.2
p53 (AA/AP vs. PP) 1.2 0.7-1.9
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Polymorphism of Susceptibility Genes
Methylenetetrahydrofolate Reductase (MTHFR)

• MTHFR gene deals with folate metabolism.
• Folate metabolism may play an important role in
  carcinogenesis through its involvement in both
  DNA methylation and nucleotide synthesis
• A common Ala(222)/Val variant in the
  methylenetetrahydrofolate reductase (MTHFR) gene
  leads to a disturbed folate metabolism and is
  associated with decreased genomic DNA methylation.

Heijmans et al. Cancer Res. 2003 Mar
1563(6)1249-53
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Effects of MTHFR and Green Tea Drinking on the
Risk of Stomach Cancer
2.94 (1.3-6.6)
1.48 (0.6-3.5)
2.27 (1.0-4.9)
MTHFR CC CT/TT
CC CT/TT Green
tea Drinker Drinker
Non-Drinker Non-Drinker
OR for interaction 0.88 ( 0.3-2.3)
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2-3 Results. Gene-Gene interactions

• APEX is involved in the restoration phase of
  BER it removes the abasic site after DNA
  cleavage by OGG1
• Small number
• Biologically plausible

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2-3. Results Multigenetic analyses by pathway
Metabolic genestrend p0.50
DNA repairtrend p0.83
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2-3. Results Multigenetic analyses for all
genes, and genes with suggestive evidence of
effect
All genes trend p0.01
Genes with suggestive effects trend p0.02

• (Genes with suggestive effects NQO1 Pro187Ser,
  XRCC1 Arg194Trp, OGG1 Ser326Cys, CCND1 G870A)
• Suggests that genetic susceptibility depends on
  multiple loci
• Considering variants in different pathways might
  give a more complete picture of carcinogenesis

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2-3 Results multigenetic factors by smoking
status and packyear ( all genes)
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2-3 Results multigenetic factors by smoking
status and packyear ( genes with suggestive
effects)


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2-3. Results Interaction with ETS among never
smokers
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