Cancer Genetics

From Iusmgenetics

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===Loss of heterozygosity===
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====Loss of heterozygosity====
 +
*Loss of heterozygosity: "loss of a normal allele from a region of one chromosome of a pair, allowing a defective allele on the homologous chromosome to be clinically manifest. A feature of many cases of retinoblastoma, breast cancer, and other tumors due to mutation in a tumor-suppressor gene."
 +
*That is, when a tumor suppressor gene is mutated, the organism is then relying on the second copy of the gene to maintain proper function; when a second loss occurs ("loss of heterozygosity") the deficiency is finally manifested since, now, neither copy works sufficiently well to maintain normal cellular function.
 +
*LOH occurs when the second, functional allele (that is allowing for proper function) is overwritten by the non-functional copy (perhaps because of complexity of DNA replication or because of repair at the allele that used the other allele as a template).
 +
*LOH can result from several mechanisms: somatic recombination, loss / duplication, chromosomal atresia.
 +
**'''Note that a very small lesion directly at the site of the (second, still functional) allele <u>will not change flanking / intragenic markers</u> and is <u>therefore not considered a loss of heterogeneity</u>'''
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Loss of Heterozygosity
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*LOH (loss of heterozygosity) can also refer to a laboratory analysis technique that identifies the mechanism of the second hit.
 +
*LOH can lead to the loss of an intragenic or flanking marker for a given tumor suppressor gene / product.
 +
*LOH is a way to identify the existence of tumor suppressor genes.
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•
 
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(Definition from text) Loss of a normal allele from a region of one chromosome of a pair, allowing a defective allele on the homologous chromosome to be clinically manifest. A feature of many cases of retinoblastoma, breast cancer, and other tumors due to mutation in a tumor-suppressor gene. 
 
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•
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===Breast cancer===
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Represents the mutation, inactivation or loss of the remaining wild-type allele tumor suppressor gene.  
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*Breast cancer is common (#1 in incidence for women, #2 in deaths for women).
 +
*Lifetime risk of breast cancer is 1/8.
 +
*180k new cases each year.
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•
 
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Also used to refer to a laboratory analysis of the mechanism of the “second hit”.
 
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•
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*Most breast cancer is sporadic.
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Loss of heterozygosity (or reduction to homozygosity) results in loss of a flanking or intragenic marker.
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*'''5% of breast cancer is considered hereditary'''
 +
*'''15-20% of breast cancer is considered family-clustered'''
 +
*'''10% of ''ovarian cancer'' is considered hereditary'''
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•
 
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A way to identify the existence of tumor-suppressor genes.
 
 +
*Susceptibility genes for breast cancer include brca1 and brca2.
 +
*Mutations in these genes '''account for 3-5% of all breast cancers'''
 +
*brca1 and brca2 were cloned in 1994/5.
 +
*brca1 and brca2 have '''autosomal dominant effects'''
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Types of Second Hits
 
-
Modified text fig 16-7
 
 +
*Inheriting a '''mutated brca1 gene allele increases one's lifetime risk of developing cancer''':
 +
**One '''primary breast cancer risk: 50-85%''' (compared to 12% population risk)
 +
**Second primary breast cancer risk: 40-60% (compared to 2% population risk)
 +
**'''Ovarian cancer risk: 15-45%'''
 +
**''Potentially elevated risk for other cancers'' like prostate and colon, too.
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Not LOH for distal Loss of Heterozygosity (LOH) for rb and also for marker(s) distal marker(s)
 
-
Breast Cancer
 
-
•
 
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Breast cancer is a common disorder
 
 +
*Inheriting a '''mutated brca2 gene allele increases one's lifetime risk of developing cancer''':
 +
**Breast cancer risk (female): 50-85% (same as brca1 mutation risk)
 +
**Breast cancer risk (male): 6% (no increased risk with brca1 mutation)
 +
**Ovarian cancer risk: 10-20% (compared to 15-45% with brca1 mutation)
 +
**'''Increased risk of prostate, laryngeal, and pancreatic cancers, too.''
 +
***Magnitude unknown.
-
•
 
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Lifetime risk is ~ 1 in 8.
 
-
•
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===Colon Cancer===
-
180,000 new case each year  
+
*150k new cases each year
 +
*57k deaths each year (#3 cancer killer in both men and women)
 +
*2-5% lifetime risk
 +
*The vast majority of colorectal cancer is sporadic in etiology.
 +
*About 25% of colorectal cancer is familial or HNPCC in etiology.
 +
*A small proportion of colorectal cancer is due to '''Familial adenomatous polyposis (FAP)''' and a '''subvariant called Gardner syndrome'''.
 +
====Familial adenomatous polyposis (FAP)====
 +
*Familial adenomatous polyposis is '''also known as adenomatous polyposis coli'''.
 +
**Hence the causative gene is called APC.
 +
*Inheritance of FAP is '''autosomal dominant'''.
 +
*Offspring with FAP are heterozygous at the APC locus for function.
 +
*Heterozygotes develop many polyps within the first two decades of life.
 +
**These polyps are benign.
 +
*Because there are so many polyps (hundreds, thousands), there is always transformation to malignancy.
 +
*Treatment is by surgical removal of the colon.
 +
*Carriers and relatives of pts should be screened with regular colonoscopy.
 +
*'''70% of sporadic colon cancer cases have loss of APC at both alleles''' despite not having inherited a defunct copy as with FAP cases.
-
How Much Breast and
 
-
Ovarian Cancer Is Hereditary?
 
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15%-20%
+
*APC is a tumor suppressor gene.
-
-10%
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*Beta-catenin is a pro-proliferation transcription factor.
 +
*APC acts to inhibit cell proliferation by maintaining low beta-catenin levels.
 +
**APC is a kinase that phosphorylates beta-catenin, thus targeting it for destruction.
 +
*When APC becomes non-functional, beta-catenin accumulates, migrates to the nucleus, and '''induces transcription of myc and other pro-proliferation genes'''.
-
Breast cancer Ovarian cancer
 
-
•
 
-
Sporadic
 
 +
*As colon cancer develops, mutations accumulate in common sites:
 +
**APC
 +
**Mismatch repair genes
 +
**RAS
 +
**DCC (a tumor suppressor gene)
 +
**SMAD4
 +
**p53 (a tumor suppressor gene)
 +
**TGF-beta receptor 2
-
•
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====HNPCC: Hereditary non-polyposis colon cancer====
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Family clusters
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*HNPCC was first describe in 1913 by Alfred Warthin.
 +
*Warthin noticed that his seemstress's family had a string of stomach and endometrial cancers
 +
*Lynch (Henry) then characterized hereditary non-polyposis colorectal cancer
-
•
 
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Hereditary
 
 +
*HNPCC is '''autosomal dominant'''
 +
*HNPCC usually results in a '''proximal colon cancers'''.
 +
*'''HNPCC increases risk for endometrial cancer and ovarian cancer in women.'''
 +
*HNPCC increases urinary tract cancers (in the kidneys and ureter).
 +
*HNPCC also gives rise to cancers in non-colon areas of the GI tract: '''stomach, biliary tract, small intestine.'''
 +
*Finally, HNPCC is associated with increased brain cancer.
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ASC®"
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*Average age of colorectal onset in HNPCC is 44 years old (as compared to the general population average age of 64).
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Breast Cancer
+
=====Amsterdam criteria=====
 +
*The Amsterdam criteria identifies HNPCC families
 +
**These are high risk individuals who are candidates for confirmatory molecular testing for APC mutations.
 +
*The criteria has '''a series of 3-2-1 requirements''':
 +
**'''3''' relatives with CRC (2 of them must be first degree relatives to the proband)
 +
**'''2''' successive generations with CRC
 +
**'''1''' case of CRC before 50 yo
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•
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=====MMR Defects in HNPCC and MSI=====
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Two major susceptibility genes, BRCA1 and BRCA2 have been identified.  
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*'''HNPCC is caused by a defect in mismatch repair.'''
 +
*There are 5 genes related to mismatch repair, each of which can cause HNPCC if mutated:
 +
**'''hMLH 1/2/6'''
 +
**'''hPMS 1/2'''
 +
*Mutations in these genes cause ineffective DNA repair and therefore '''microsatellite instability''' (MSI) and therefore HNPCC.
-
•
 
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Mutations in these genes account for 3-5% of all breast cancers.
 
 +
*'''MSI (microsatellite instability) is the expansion or contraction of short, repeated segments of DNA secondary to MMR defects.'''
 +
*MSI is not normally found in properly functioning cells.
 +
*'''MSI is found in 90% of HNPCC tumors.'''
 +
*MSI is found in only 15% of sporadic colorectal cancers.
 +
*What is the significance of MSI?  Diagnosis?
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BRCA 1 and BRCA2: An Overview
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====HNPCC Take-home Points====
 +
*Mutations in MLH1 and MSH2 result in defective mismatch repair and thus cause HNPCC.
 +
*Mutations in MLH1 and MSH2 raise the risk of CRC (colorectal cancer) by the age of 70 to 70-85%.
 +
**The general population risk is 2-5%.
 +
*Mutations in MLH1 and MSH2 raise the risk of endometrial cancer by the age of 70 to 42-60%.
 +
**The general population is ''much lower''.
-
BRCAl  BRCA2 
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===Cancer cells and Epigenetics===
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Year cloned  1994  1995 
+
*Cancer cells demonstrate several epigenetic changes: hypo / hyper methylation.
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Chromosome location  17q21  13q12 
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*Recall that '''methylation closes DNA off from expression'''.
-
Genomic DNA I coding exons  5.6 kb I 22 exons  10.2 kb I 26 exons 
+
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Number of amino acids  1,863  3,418 
+
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Number of mutations  > 1,230  > 1,380 
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reported 
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Inheritance  pattern  Autosomal dominant  Autosomal dominant 
+
-
Breast Information Core. Available at: http://research.nhgri.nih.gov/bic/. Accessed October 17, 2003.
 
-
ASC®~
 
 +
*Hypomethylation:
 +
**Recall that hypomethylation will generally allow more expression of the DNA.
 +
**Hypomethylation can be seen in both '''benign and malignant neoplasms'''.
 +
**Hypomethylation usually '''occurs at repetitive sequences'''.
 +
**Hypomethylation may have several effects:
 +
***'''genomic instability'''
 +
***'''activation of oncogenes'''
 +
***'''activation of retrotransposons'''
 +
***'''loss of imprinting'''
 +
**For example, loss of imprinting on the IGF2 gene is seen in 40% of colorectal cancers.
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BRCA1-Associated Cancers:
 
-
Lifetime Risk
 
 +
*Hypermethylation:
 +
**Recall that hypermethylation will generally inhibit expression of the DNA.
 +
**Hypermethylation is '''usually at CpG islands.'''
 +
**Hypermethylation may contribute to cancer via '''promotor silencing of tumor suppressor genes'''.
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BRCA2-Associated Cancers:
 
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Lifetime Risk
 
-
 
+
==Indiana Familial Cancer Clinic==
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Breast ca. risk by age 70 (Pop risk 10-12%)  Ovarian ca. risk by age 70 (Pop risk 1-2%) 
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*Genetic Services for Familial Cancer
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BRCA1  In AD families 50-85% Not . male risk  In AD families 15-45% 
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*Referral
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BRCA2  In families 50-85%  In families 10-20% 
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*Intake Information
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*Family History Questionnaire
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Male carriers, 6% risk
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BRCA2 – ca. 10-20% of all male breast ca.
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In population screen for BRCA1 or BRCA2 carriers, the risk for breast cancer by age 70 is 45-60%.
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Ashkenazi Jews (1/40 carriers): BRCA1: 185del AG, 5382insC -BRCA2: 6174delT
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COLON CANCER
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•
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150,000 new cases a year.
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57,000 deaths a year.
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•
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All Americans have a 2-5% life-time
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risk for Colorectal Cancer (CRC).
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Etiology of Colorectal Cancer
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Familial
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+
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A small proportion of colorectal cancer is due to Familial adenomatous polyposis (FAP) and a subvariant Gardner syndrome.
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Familial adenomatous polyposis (FAP)
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(Clincal case # 13)
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–
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Also known as Adenomatous polyposis coli (APC).
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– Gene is named APC
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–
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Autosomal dominant.
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–
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Heterozygotes develop numerous adenomatous (benign)polyps in the first two decades of life.
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–
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In almost all cases, one or more polyps becomes malignant.
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–
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Treat by surgical removal of colon.
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–
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Relatives/carriers examined by periodic colonoscopy.
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Text Clinical
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Case Study
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APC gene
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Tumor suppressor
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Individuals without FAP but with adenomatous polyps (sporadic)
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Nearly 70% have loss of both APC genes in tumor
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See text fig 16-13
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HNPCC
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Hereditary Non-polyposis Colon Cancer
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•
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First describe in 1913 by Alfred Warthin, who identified a clustering of predominantly stomach and endometrial cancers in the family of his seamstress (family G).
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Fifty years later, HNPCC was characterized further by Henry Lynch, as Lynch syndrome.
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HNPCC
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Autosomal dominant
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Colon Cancer (proximal location)
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Endometrial Cancer
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Ovarian Cancer
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Urinary Tract (Kidney/Ureter)
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Stomach
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Biliary Tract
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Brain
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Small Intestine
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Average age of CRC in HNPCC:
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• 44 years old
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Average age of CRC in general population:
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HNPCC
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• 64 years old
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Amsterdam Criteria
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For identifying HNPCC families
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(high-risk candidates for molecular genetic testing)
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3 relatives with CRC.
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– 2 of the relatives are first degree
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Two successive generations
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1 case of CRC before 50 years of age.
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Mismatch Repair Defect (MMR) Genes
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Mutations in 5 genes lead to a MMR phenotype in HNPCC.
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hMLH1
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hMSH2
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hMSH6
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hPMS1
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hPMS2
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Mutations lead to ineffective DNA repair and microsatellite instability (MSI).
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Microsatellite Instability (MSI)
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Found in tumors, not normal tissue.
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Characterized by expansion or contraction of short, repeated DNA sequences.
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Found in >90% of tumors of patients with HNPCC.
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Found in approximately 15% of sporadiccolorectal cancers.
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BAT-25 BAT-26 D2S123 D5S346
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HNPCC Key Points
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Mutations in the MLH1 and MSH2 genes increase the risk of CRC to 70-82% before the age of 70, as compared to the general population risk of 2-5%.
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Mutations in the MLH1 and MSH2 genes are associated with an approximately 42­60% risk of endometrial cancer before the age of 70.
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Cancer cells show changes of epigenetic
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marks in their genome
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•
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Global DNA hypomethylation
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–
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In both benign and malignant neoplasms
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–
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Typically at repetitive sequences (satellite or pericentromeric)
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May add to genomic instability
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May lead to activation of oncogenes or retrotransposons
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May lead to loss of imprinting (LOI)
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– E.g., LOI of the IGF2/H19 region seen in about 40% ofcolorectal cancer
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Hypermethylation
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–
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Tends to be focal at CpG islands
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–
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E.g., Promoter silencing of tumor suppressor genes byhypermethylation
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DNA and epigenetic changes that inactivate tumor-suppressor genes
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Norma
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Indiana Familial Cancer Clinic  
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•
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Genetic Services for Familial Cancer  
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•
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Referral  
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•
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Intake Information  
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•
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Family History Questionnaire  
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END
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Revision as of 17:23, 30 November 2011

Contents

Cancer Genetics

Objectives

  • Understand that cancer is a genetic disease and a multistep process.
  • Know the types of genes associated with cancer.
  • Know fundamentals about cancer pathogenesis, including the concepts of:
    • oncogene action / activation;
    • modes of disease pathogenesis associated with tumor suppressor genes (e.g., two hit);
    • microsatellite instability
    • potential role of epigenetics in cancer
  • Know features of the specific disorders discussed in class.

Cancer

  • Cancer is a heterogeneous disease that will claim more than 560,000 lives in our country this year.
  • Cancer INCIDENCE
Cancer % of all cancers cases Gender Gender % of all cancer cases Cancer
Prostate 29% Male Female 26% Breast
Lung / Bronchus 15% Male Female 15% Lung / Bronchus
Colon / Rectum 10% Male Female 11% Colon / Rectum
Bladder 7% Male Female 6% Uterine


  • Cancer DEATHS
Cancer % of all cancers cases Male Female % of all cancer cases Cancer
Lung / Bronchus 31% Male Female 26% Lung / Bronchus
Prostate 9% Male Female 15% Breast
Colon / Rectum 9% Male Female 10% Colon / Rectum
Pancreas 6% Male Female 6% Pancreas


  • 1999: estimated that a general practioner would see 1-2 pts / month who require genetic services.
  • 2007: estimated 2-4 pts / month require genetic services.
  • More patients becoming (will be) aware of genetic considerations.
  • In order to study possible hereditary pattern of disease.
    • Take at least three generations of family history into account.

Hereditary Predisposition for Cancer

  • Cancer inheritance is not necessarily straight forward.
    • Autosomal or sex chromosomes inheritance
    • Incomplete penetrance
    • Gender specific penetrance
    • Variable expressivity
    • Early-onset diagnosis
    • Multiple primary cancers manifested
    • Multiple cases of cancer
    • Unclear ages of onset
    • Commonality of cancers

Features suggesting an inherited predisposition to cancer

  • Two or more close relatives affected.
  • Early age of onset.
  • Cancers of a specific type occurring together (e.g., breast and ovary).
  • Multiple or bilateral cancers occurring in one person.

Cancer is a genetic disease

  • All cancers involve genetic changes in somatic cells, the germ line, or both.
  • In addition to genes, there are other predisposing factors such as:
    • Infection (virus)
    • Radiation
    • Carcinogens
    • Immunological defects


  • Cancer is a multistep process and clonal
  • Cancer is a multistep process and is clonal in nature.
  • Hits might be inherited or acquired mutations or environmental factors.
  • "Hits" (mutations in a cell's genome) accumulate over time, potentially lending it neoplastic features like auto-regulation.
  • There is increasing aneuploidy as the cell accumulates lesions.
  • Recall that lesions to DNA repair genes can accelerate the rate of lesion accumulation.


  • Genes controlling cell proliferation and death are important in the natural history of cancer development.

Cell Proliferation and Cell Death Genes

  • Genes involved in proliferation and death are important regulators of cancer.
  • There are several categories of these genes:
    • Oncogenes
    • Tumor suppressor genes
    • DNA repair/metabolism genes
    • Other

Oncogenes

  • To understand oncogenes, first understand that proto-oncogenes are normal genes that have something to do with the cell cycle or proliferation.
    • Proto-oncogenes are found in the normal genome and are an important part of cellular function and organism development.
    • Proto-oncogenes have many regulations upon them that cause them to function at the right time and place in the organism and in development.
    • Examples of proto-oncogenes include:
      • Growth factors / receptors
      • Signal transduction molecules (nuclear proteins)
      • Transcriptional regulators (which affect the cell cycle)


  • An oncogene, then, is a proto-oncogene that is out of control--acting aberrantly in time or space.
  • Oncogenes are "dominantly acting" because only one copy of the gene need be turned on to induce it's pro-growth, pro-proliferation effect. 
*Oncogenes are "dominant at the cellular level"
  • Oncogenes have been identified by their ability to convert non-neoplastic cells into neoplastic cells--that is they promote tumors / cancers.


  • Activation of a proto-oncogene (into an oncogene):
    • Activation of a proto-oncogene generally requires a gain of function mutation.
    • A gain of function occurs either through a change in protein structure or a change in expression.
    • Proteins structure changes can occur in many ways, including point mutations and hybrid proteins:
      • Ras is commonly point mutated to gain function.
      • CML has the t9:22 to generate the function-gained bcr-abl gene.
    • Protein expression changes can manifest as a change in expression level or a change in expression location (as in tissue):
      • Viral insertion can cause expression in a new location or a new level.
      • Gene amplification causes increased expression.
      • Translocation can cause increased or decreased expression depending on the promotor relavant to the translocation.


  • Common oncogenes incluede:
    • ret, met, and ras: kinases and signaling genes
    • fas: pro-apoptotic (in wildtype form)

Burkitt lymphoma

  • Burkitt lymphoma is the most common tumor in children of equatorial Africa (but is rare, elsewhere).
  • Burkitt lymphoma is a B-cell tumor of the jaw.
  • Burkitt lymphoma is characterized by translocations that convert proto-oncogenes to oncogenes.
  • myc conversion
    • t(8;14) is the primary translocation associated with Burkitt lymphoma
    • Converts myc to an oncogene.
    • t(8;22) and t(2;8) are also common translocations that convert myc to an oncogene.
  • Immunoglobulin genes
    • Chromosomes 2, 15, and 22 carry genes required for immunoglobulin formation.
    • Ch 2: kappa light chain
    • Ch 14: heavy chain
    • Ch 22: lambda light chain

Inherited mutations in oncogenes

  • It is rare to inherit a mutation in an oncogene, but it does happen; MEN2 and HPRC are two examples.


  • MEN2 is associated with an inherited RET mutation
    • MEN2 presents as an autosomal dominant cancer predilection syndrome.
      • This makes sense as we previously mentioned the dominant activity of oncogenes (only one has to be mutated to cause cancer).
    • Thyroid carcinoma is usually the primary tumor culprit.
    • RET is a tyrosine kinase receptor
    • Gain-of-function mutations in RET (inherited, remember) lead to constitutive kinase activity.
    • NB: loss-of-function mutations in RET lead to Hirschsprung disease


  • Hereditary papillary renal carcinoma (HPRC):
    • HPRC, like MEN2, is inherited in an autosomal dominant fashion.
    • HPRC is associated with gain-of-function mutations in MET.
    • MET is a tyrosine kinase receptor.
    • Gain-of-function mutation in MET lead to constitutive activation of the kinases to which MET is bound (even when the proper ligand isn't present).

Tumor suppressor genes

  • Tumor suppressor genes are those that normally serve to discourage growth and replication.
  • Tumor suppressor gene mutations act in a recessive manner because though one copy of the gene may become defective, the other copy can usually maintain the proper cell cycle.
  • Because tumor suppressor gene mutations act in a recessive mannner, the two hit hypothesis suggests that at least two hits (genetic lesions) are required to "knock-out" the function of a tumor suppressor gene.
    • The two hit hypothesis was developed by Knudson. 
*Loss-of-function lesions on tumor suppressor genes can act dominantly at the organismal level.
  • Mutation of only one copy of a tumor suppressor gene leads to loss of heterozygosity: the state of having two of the same allele for a gene (or having only one functional copy of the allele and therefore no hetergeneity in gene product).


  • Common tumor suppressor genes are:
    • rb, p53: cell cycle regulators
    • msh2, mlh1: DNA repair / inspection regulators
    • bcl2, telomerase: antiapoptotic

Text fig 16-1

Cancer genes

  • Most mutations related to cancer occur in somatic cells that are not passed on to off-spring.
  • However, some mutations do occur in the germ line and can be passed to off-spring.
  • Inherited mutations can come from the egg, the sperm, or the zygote.
  • Inherited mutations are usually / often found in the genome of every cell of the body.


  • Alfred Knudson was the first to describe the phenotypic difference between somatic and inherited mutations in cancer.
  • Knudson observed that cases of retinoblastoma had distinct characteristics when there was a family history of retinoblastoma:
    • tumors occurred earlier in life,
    • tumors were more likely to be bilateral, and
    • tumors were mutlifocal (have more than one site of origin).
  • So he reasoned that a family history suggests that the germline contains a "hit" or lesion against the rb gene and that offspring had earlier tumors that were more likely to be bilateral and multifocal because they had only to receive one more "hit" to develop retinoblastoma.
  • In comparison, with no family history, two independent "hits" had to occur to develop retinoblastoma and therefore the tumors occurred later in life and were less likely to be bilateral or multifocal.


Retinoblastoma

  • Rb is the most common eye tumor in early childhood.
  • Retinoblastoma is a tumor of the retina.
  • Retinoblastomas may actually begin forming in utero.
  • Average age of Rb onset is 18 months.
  • Treatment for retinoblastoma is to remove the entire orbit.


  • 1/23k live births have retinoblastomas.
  • Retinoblastoma can be inherited as an autosomal dominant trait.
  • 40% of retinoblastomas are inherited.
    • Parent may be a carrier or there may have been a germline mutation.
    • Bilateral state suggests inheritance.
    • 15% of inherited retinoblastomas are unilateral.
  • 60% of retinoblastomas are sporadic.


  • Retinoblastoma pts have elevated risk for other cancers, too.
    • Including osteosarcoma


Loss of heterozygosity

  • Loss of heterozygosity: "loss of a normal allele from a region of one chromosome of a pair, allowing a defective allele on the homologous chromosome to be clinically manifest. A feature of many cases of retinoblastoma, breast cancer, and other tumors due to mutation in a tumor-suppressor gene."
  • That is, when a tumor suppressor gene is mutated, the organism is then relying on the second copy of the gene to maintain proper function; when a second loss occurs ("loss of heterozygosity") the deficiency is finally manifested since, now, neither copy works sufficiently well to maintain normal cellular function.
  • LOH occurs when the second, functional allele (that is allowing for proper function) is overwritten by the non-functional copy (perhaps because of complexity of DNA replication or because of repair at the allele that used the other allele as a template).
  • LOH can result from several mechanisms: somatic recombination, loss / duplication, chromosomal atresia.
    • Note that a very small lesion directly at the site of the (second, still functional) allele will not change flanking / intragenic markers and is therefore not considered a loss of heterogeneity 


*LOH (loss of heterozygosity) can also refer to a laboratory analysis technique that identifies the mechanism of the second hit.
*LOH can lead to the loss of an intragenic or flanking marker for a given tumor suppressor gene / product.
*LOH is a way to identify the existence of tumor suppressor genes.


Breast cancer

  • Breast cancer is common (#1 in incidence for women, #2 in deaths for women).
  • Lifetime risk of breast cancer is 1/8.
  • 180k new cases each year.


  • Most breast cancer is sporadic.
  • 5% of breast cancer is considered hereditary
  • 15-20% of breast cancer is considered family-clustered
  • 10% of ovarian cancer is considered hereditary


  • Susceptibility genes for breast cancer include brca1 and brca2.
  • Mutations in these genes account for 3-5% of all breast cancers
  • brca1 and brca2 were cloned in 1994/5.
  • brca1 and brca2 have autosomal dominant effects


  • Inheriting a mutated brca1 gene allele increases one's lifetime risk of developing cancer:
    • One primary breast cancer risk: 50-85% (compared to 12% population risk)
    • Second primary breast cancer risk: 40-60% (compared to 2% population risk)
    • Ovarian cancer risk: 15-45%
    • Potentially elevated risk for other cancers like prostate and colon, too.


  • Inheriting a mutated brca2 gene allele increases one's lifetime risk of developing cancer:
    • Breast cancer risk (female): 50-85% (same as brca1 mutation risk)
    • Breast cancer risk (male): 6% (no increased risk with brca1 mutation)
    • Ovarian cancer risk: 10-20% (compared to 15-45% with brca1 mutation)
    • 'Increased risk of prostate, laryngeal, and pancreatic cancers, too.
      • Magnitude unknown.


Colon Cancer

  • 150k new cases each year
  • 57k deaths each year (#3 cancer killer in both men and women)
  • 2-5% lifetime risk
  • The vast majority of colorectal cancer is sporadic in etiology.
  • About 25% of colorectal cancer is familial or HNPCC in etiology.
  • A small proportion of colorectal cancer is due to Familial adenomatous polyposis (FAP) and a subvariant called Gardner syndrome.

Familial adenomatous polyposis (FAP)

  • Familial adenomatous polyposis is also known as adenomatous polyposis coli.
    • Hence the causative gene is called APC.
  • Inheritance of FAP is autosomal dominant.
  • Offspring with FAP are heterozygous at the APC locus for function.
  • Heterozygotes develop many polyps within the first two decades of life.
    • These polyps are benign.
  • Because there are so many polyps (hundreds, thousands), there is always transformation to malignancy.
  • Treatment is by surgical removal of the colon.
  • Carriers and relatives of pts should be screened with regular colonoscopy.
  • 70% of sporadic colon cancer cases have loss of APC at both alleles despite not having inherited a defunct copy as with FAP cases.


  • APC is a tumor suppressor gene.
  • Beta-catenin is a pro-proliferation transcription factor.
  • APC acts to inhibit cell proliferation by maintaining low beta-catenin levels.
    • APC is a kinase that phosphorylates beta-catenin, thus targeting it for destruction.
  • When APC becomes non-functional, beta-catenin accumulates, migrates to the nucleus, and induces transcription of myc and other pro-proliferation genes.


  • As colon cancer develops, mutations accumulate in common sites:
    • APC
    • Mismatch repair genes
    • RAS
    • DCC (a tumor suppressor gene)
    • SMAD4
    • p53 (a tumor suppressor gene)
    • TGF-beta receptor 2

HNPCC: Hereditary non-polyposis colon cancer

  • HNPCC was first describe in 1913 by Alfred Warthin.
  • Warthin noticed that his seemstress's family had a string of stomach and endometrial cancers
  • Lynch (Henry) then characterized hereditary non-polyposis colorectal cancer


  • HNPCC is autosomal dominant
  • HNPCC usually results in a proximal colon cancers.
  • HNPCC increases risk for endometrial cancer and ovarian cancer in women.
  • HNPCC increases urinary tract cancers (in the kidneys and ureter).
  • HNPCC also gives rise to cancers in non-colon areas of the GI tract: stomach, biliary tract, small intestine.
  • Finally, HNPCC is associated with increased brain cancer.


  • Average age of colorectal onset in HNPCC is 44 years old (as compared to the general population average age of 64).
Amsterdam criteria
  • The Amsterdam criteria identifies HNPCC families
    • These are high risk individuals who are candidates for confirmatory molecular testing for APC mutations.
  • The criteria has a series of 3-2-1 requirements:
    • 3 relatives with CRC (2 of them must be first degree relatives to the proband)
    • 2 successive generations with CRC
    • 1 case of CRC before 50 yo
MMR Defects in HNPCC and MSI
  • HNPCC is caused by a defect in mismatch repair.
  • There are 5 genes related to mismatch repair, each of which can cause HNPCC if mutated:
    • hMLH 1/2/6
    • hPMS 1/2
  • Mutations in these genes cause ineffective DNA repair and therefore microsatellite instability (MSI) and therefore HNPCC.


  • MSI (microsatellite instability) is the expansion or contraction of short, repeated segments of DNA secondary to MMR defects.
  • MSI is not normally found in properly functioning cells.
  • MSI is found in 90% of HNPCC tumors.
  • MSI is found in only 15% of sporadic colorectal cancers. 
*What is the significance of MSI?  Diagnosis?

HNPCC Take-home Points

  • Mutations in MLH1 and MSH2 result in defective mismatch repair and thus cause HNPCC.
  • Mutations in MLH1 and MSH2 raise the risk of CRC (colorectal cancer) by the age of 70 to 70-85%.
    • The general population risk is 2-5%.
  • Mutations in MLH1 and MSH2 raise the risk of endometrial cancer by the age of 70 to 42-60%.
    • The general population is much lower.

Cancer cells and Epigenetics

  • Cancer cells demonstrate several epigenetic changes: hypo / hyper methylation.
  • Recall that methylation closes DNA off from expression.


  • Hypomethylation:
    • Recall that hypomethylation will generally allow more expression of the DNA.
    • Hypomethylation can be seen in both benign and malignant neoplasms.
    • Hypomethylation usually occurs at repetitive sequences.
    • Hypomethylation may have several effects:
      • genomic instability
      • activation of oncogenes
      • activation of retrotransposons
      • loss of imprinting
    • For example, loss of imprinting on the IGF2 gene is seen in 40% of colorectal cancers.


  • Hypermethylation:
    • Recall that hypermethylation will generally inhibit expression of the DNA.
    • Hypermethylation is usually at CpG islands.
    • Hypermethylation may contribute to cancer via promotor silencing of tumor suppressor genes.


Indiana Familial Cancer Clinic

  • Genetic Services for Familial Cancer
  • Referral
  • Intake Information
  • Family History Questionnaire
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