Cancer Genetics Flashcards Preview

MS 1 Unit 7 MCP > Cancer Genetics > Flashcards

Flashcards in Cancer Genetics Deck (57):

Cancer Info

-25 years ago they thought it was random
-now we know it is the result of environmental events combined with an individuals genetic make-up
-malignant tumor of potentially unlimited growth that expands locally by invasion and systemically by metastasis
-overgrowth of cell material



-overgrowth of cell material
-solid vs dispersed
-clonal: start as a single cell with a mutation which proliferates to form a group of similarly abnormal cells
-some can be benign some malignant



-uncontrolled cell growth characteriszed by a change in the normal organizational pattern of tissues or cells
-karyotype changes- chromosomes are useful in establishing clonality
-malignant tumors tend to be deleterious, and may metastasize
-metastasis is when cells become invasive or migrate to another site. When they move they retain the original cell morphology


Types of Cancer

-Sarcoma- mesenchymal tissue (bone, cartilage, muscle, fat)
-Carinoma- epitheloid tissues
-Hematopoietic/lymphoid- leukemias (WBC from bone marrow) and lymphomas (WBC from spleen and lymph nodes)
-a primary cancer in a secondary location is known by the primary classification



-Environmental mutagens: UV light, absestos, cigarette smoke, plastics, red dye #3
-effect changes in normal cell regulation and/or development
-additional element in cancer induction


Hallmarks of Cancer

-mutation or loss of genes involved in cell control including growth/division, proliferation, metabolism
-environmental elements may influence mutation
-mutations may be inherited or acquired
-chromosome instability (CIN)- gain loss or rearrangement of chromosomes


Types of Genes Associated with Cancer

-tumor suppressors



-a dominantly acting gene involved in unregulated cell growth and proliferation
-carried by viruses
-associated with disease in animals:
H-ras- Harvey rate sarcoma virus
sis- Simian sarcoma virus
abl-Abelson murine leukemia virus


Viral oncogenes in humans

-HPV-cervical cancer
-EBV-nasopharyngeal cancer, Hodgkin and Burkitt lymphoma
-HHV-8 (herpes virus) - Kaposi sarcoma
-HTLV-1- T cell leukemia
-HTLV-2- various leukemias
-mutation of proto-oncogenes (humans and other mammals)



-structurally important housekeeping genes involved in cell proliferation and development
-growth factors
-cell surface receptors
-intracellular signal transduction
-DNA binding proteins (transcription)
-regulation of cell cycle


Proto-oncogene to cancer

-mutation (translocation, amplification, point mutation) can result in activation of a proto-oncogene
-this may cause a change in gene regulation, transcription, or a protein product generating alterations to cell growth, proliferation, or differentiation
-this can lead to tumorigenesis
-gain of function mutation
-dominant- only one mutation required


Chronic Myelogenous Leukemia

-relatively common form of leukemia
-first leukemia associated with a genetic marker [t(9;22 -> Ph' (Philidephia) chromosome]
-juxtaposition of 2 genes that generates a chimeric protein produce with a new function associated with disease
-the outcome is the loss of proper regulatory controls and overproduction of tyrosine kinase, a protein involved in cell cycle regulation


Treatment of CML

-delineation of the genetic abnormality led to better understanding of proto-oncogenes
-allowed development of a new class of drug: those targeted to the genetic lesion: STI-571 [Gleevec]: bcr/abl specific
-molecular analysis led to new ideas about treatment of disease


Acute promyelocytic leukemia

-another proto-oncogene related disease which is characterized by a 15;17 translocation breaking the PML gene on chromosome 15 and the RARA gene on chromosome 17
-again the disease is the result of a translocation that gives rise to chimeric protein product
-this is a dual fusion probe
-the translocation splits the probe recognition site so that half of each probe is moved to the reciprocal chromosome
-no rearrangment is detected by two red and two green signals. The translocation is seen if there is 1 red, 1 green and two fusion yellow signals
-the t(15;17) is clinically diagnostic of APL and is required for a positive diagnosis of the disease
-the translocation results in a fusion signal that can be detected using FISH technology
-this aids in diagnosis of the disease and monitoring of the patient during treatment
-if the normal signal pattern returns after treatment, the patient has responded to therapy (gone into remission)
-if the fusion pattern subsequently returns, the patient has relapsed


Tumor Suppressor

-genetic element whose loss or inactivation allows the cell to display an alternate phenotype leading to neoplastic growth
-oncogenic potential when gene activity is lost
-recessive- requires mutation of both alleles, so the tumor suppressor functions are recessive


Normal Gene Function of Tumor Suppressor

-gate keepers- suppress tumors by regulating cell cycle or growth inhibition
-caretakers- repair DNA damage and maintain genomic integrity- effect is indirect- accumulation of errors in cells
-cell to cell interactions
-regulation of growth inhibitory substances
-cell proliferation
-cell differentiation
-chromosome repair


Important Tumor Suppressors

-RB1 was the first
Two important:
-p53 on the short arm of chromosome 17. nearly all cancer types
-MTS1 (multiple tumor suppressor 1)- another very common finding in cancers


Solid Tumors

-mutation of tumor suppressors are often expressed as solid tumors
-although these are difficult to culture, karyotype analysis can be useful, though chromosomal changes are not always found
-a number of diseases are known to have specific chromosomal changes, so this information can be used in classification. It is also interesting to note that most tumor suppressors are tissue specific. E.g. mutations will only cause disease in one or a few cell types


Karyotype of Malignant tumor

-one with exceedingly abnormal with few identifiable normal chromosomes.
-benign tumors can have many chromosome abnormalities and malignant tumors may have none
-those solid tumors present a challenge and determining what changes are directly related to the disease if difficult
-new technology looking at the patterns of expression of the genes is becoming more important for diagnosis


Rb1- Classic Gatekeeper Mutation

-functions in regulation of cell cycle
-controls progression from G1 to S
-loss of function eliminates an important mitotic checkpoint resulting in uncontrolled growth



-this disease is directly related to mutations of the gene, RB1 which is located on chromosome 13 at band 13q14.2
-a classic example of a tumor suppressor is seen in the disease retinoblastoma which is a tumor of the retinoblasts (immature retinal cells) of the eye
-once the retinoblasts mature to retinal cells (around 5 years of age) the target tissue of the disease is gone and the disease does not occur
-onset is prenatal to 5
-can be unilateral or bilateral
-if untreated the tumor can grow both forward out of the skull and back into the brain
-some may be treated by laser surgery
-severe cases require enucleation
-sporadic-usually unilateral
-inherited-often bilateral
-secondary cancer:osteosarcoma


Mechanism of Retinoblastoma

-it one mutation is inherited, then all the cells of the body will have that mutation
-however the disease is tissue specific, so it will only be a problem in the retinoblast cells. If a second mutation in the RB1 locus occurs in any retinoblast cell, the probability of a tumor is extremely high
-it is possible that more than one mutation may occur, so that several tumors in one or both may occur
-hard to get the two mutations randomly without having inheriting one


Knudson's Two Hit Hypothesis

-two mutations in the same cell
-sporadic usually unilateral
-inherited usually bilateral
-appearance of dominance
-most cases of sporadic disease had only a single tumor in one eye, but there were multiple tumors in both eyes for inherited disease


Tumor suppressor

-primary mutation-specific tissue target
-can be secondary to another cancer gene
-somatic-usually older age of onset
-familial-usually younger onset


Familial Cancers

-breast and ovarian cancer
-familial polyposis coli
-von Recklinghausen neurofibromatosis
-Wilm's tumor
-von Hippel Lindae/ Renal cell cancer


Li Fraumeni

-familial cancer syndrome
-multiple neoplasia
-increased risk of cancer- 50% at age 30, 90% at age 70
-inherited mutation of p53 (loss of checkpoint control of DNA damage)
-tumors include: soft tissue sarcoma, breast cancer, adenocortical cancer, leukemic, brain tumors, osteosarcoma, melanoma, gonadal germ cell tumor, lung cancer, prostate cancer


Breast Cancer

-lifetime risk: 1/8 to 1/10
-familial or sporadic
-mutations: errors in homologous recombination, DNA repair defects
-2 known genes
-BRCA 1- chromosome 17 (near NF1 and p53)
-BRCA 2- chromosome 13 (near Rb1)


Survival Guilt

-psychological damage possible
-neg for inherited mutation but still at risk for sporadic form


Affected Males

-morality in males can be quite high because they don't seek help early enough
-can also carry to mutation and pass it on to their daughters


BRCA1 and BRCA 2

-80-90% of familial breast cancer- review of pedigrees to assess risk followed by testing when appropriate
-approximately 5-9% of all breast cancer
-multiple mutations
-increased risk of male breast cancer
-increased risk of Ashkenazi Jewish population
-counseling of patients critical


Caretaker Mutations

-inability to repair DNA defects/mutations
-accumulation of abnormal DNA/genes
-increase ingenome instability
-may lead to mutation of proto-oncogenes or tumor suppressor genes
-inherited or acquired: Fanconi anemia, ataxia telangiectasia, Breast cancer, NHPCC, bladder cancer


Breakage Syndromes

-Fanconi anema
-Bloom syndrome
-Ataxia telangiectasia
-Xeroderma pigmentosum
-Cockayne syndome
-chromosomal breakage syndromes are a diverse group of diseases, all with very different clinical phenotypes and caused by genes on different chromosomes
-recessive inheritance
-chromosome instability
-defective DNA repair mechanisms
-susceptibility to cancer


Commonality of Chromosome Instability

-the diseases were originally linked because of the common finding of chromosome instability or fragility- thus the name, breakage syndromes
-sister chromatid exchange: exchange of gene regions between sister chromatids. Normal cells it results in a swap of identical pieces of DNA. If errors occur there is unequal exchange resulting in the duplication of sequences on one chromatid and deletion on the other. In normal cells, these errors would be detected and repaired, but repair may not happen in cells with mutations in a DNA repair gene
-triradials- instead of the normal linear chromosome, a replication error has resulted in a Y-shaped or forked structure
-excessive breakage of the chromosomes that can lead to chromosome deletion and genomic defects


DNA Repair Defects in Chromosome Breakage Syndromes

-chromosomes are unstable because the patients lack the fundamental process of DNA repair
-DNA repair is handled by a number of different enzymes, and for each breakage syndrome, the gene hat is mutant is different
-failure to be able to repair the chromosomes leads to instability. It also increases the risk of cancer


Defects in DNA Repair Genes

-inability to repair DNA defects/mutations
-accumulation of abnormal DNA/ genes
-increase in genome instability
-may lead to mutation of proto-oncogenes or tumor suppressor genes
-inherited or acquired: Fanconi anemia, ataxia telangiectasia, Breast cancer, NHPCC, bladder cancer


Hereditary Nonpolyposis Colon Cancer (HNPCC)

-2-4% of hereditary colon cancer
-90% lifetime risk for males who inherit one mutation
-70% lifetime risk for females who inherit one mutation
-40% risk of endometrial cancer
-10-20% risk of urinary tract cancer
-10-20% risk of ovarian cancer
-mutations of MSH2 and MLH1 acount for 70-80% and MSH6 accounts for another 7-10%
-TGFBR2 is not mismatch repair gene but is a growth factor receptor involved in cell growth
-HNPCC7 has been reported in only a single case report so is still under investigation
-microsatellite analysis suggests the presence of a defect in mismatch repair
-this finding is consistent with a mutation in one of the 5 genes associated with HNPCC
-the test is indirect
-DNA instability leads to additional mutations throughout the genome- possibly affecting tumor suppressor genes
-is NOT: gene mutation -> aberrant protein -> disease; is: malfunction in a normal cellular process that in and of itself is not deleterious, the accumulation of errors eventually results in system dysfunction


Mismatch Repair

-one type of DNA repair
-if an error occurs during replication it is detected by the appropriate error checking enzyme, the defect is excised along with adjacent bases, the missing bases are filled in, and the fragment is ligated back to the existing DNA
-Defect: the error is not detected it will not be repaired. During the next DNA replication cycle, both strands will be replicated, but since they are different, the resulting DNAs will be different. 2 cell populations: 1 with the correct sequence and 1 with mutation- 2 cell lines



-Repeats of 2,3,4 nucleotides: ATATAT or CGGCGGCGG
-highly polymorphic in the population
-can detect DNA repair defects
-subject to replication error due to slippage
-mutations in mismatch repair can alter total number of repeats
-presence of extra bands in putative HNPCC tumor tissue is consistent with disease diagnosis


Proto-oncogene vs Tumpr Suppressor gene mutations

-Proto-oncogene mutations:
-dominantly acting
-chromosome translocation, amplification, point mutation
-primary target: leukemias/lymphomas
-gain or change of function

Tumor Suppressor mutations:
-1 mutation may be inherited
-deletions,chromosome gain/loss, gene mutation
-primary target: solid tumors
-loss of function
-gate keeper or caretaker functions


Chromosome Instability

-De novo:
-breakage or recombination
-chromosome rearrangment
duplication or deletions, translocations or inversions, tandem duplication of genes, generation of supernumerary chromosome
-gain or loss of whole chromosome
-karyotype analysis that have been done confirm the involvement of a variety of different mechanism
-proto-oncogene mutations- chromosome translocation, amplification, point mutation
-tumor suppressor mutations- deletions, chromosome loss, gene mutation
-error accumulation (DNA repair defects)- increased breakage and rearrangement in some diseases


Cancer Evolution

-cancer is a complex disease that requires more than one step
-progression from normal to cancer cell requires a combination of environmental and gene effects
-this can be demonstrated by a classic pathwa
-many different mutations arise but the key principle is that these mutations must occur within a single cell, they dont have to be sequential
-a person with an inherited mutation has a jump state on the process, passing the first checkpoint quickly



-a normal cell may have a single mutation which proliferates and generates an abnormal clone
-this is an aquired change in a limited number of cells
-further chromosomal changes may modify the karyotype and produce additional clones
-karyotype analysis can be used to monitor the presence and evolution of clones


Karyotype evolution

-the change over time in the karyotype due to acquisition different mutations
-generally, increasing complexity and numbers of chromosome abnormalities are associated with poorer prognosis
-it is possible to use the chromosome abnormalities to follow the patient from diagnosis to remission and relapse


Clinical Testing

-detection of molecular and chromosomal anomalies associated with disease: diagnosis, prognosis, monitor remission and relapse, must have basleine, molecular diagnosis, cytogenetics: karyotype and FISH


Constitutional findings

-original DNA and chromosome complement that is the foundation for the genetic constitution in all cells of the body
-originated in zygote
-acquired anomalies
-a change which has occured in the constitutional DNA or karyotype
-usually present in a single cell line (clone)



-karyotype analysis is a key element in oncology
-it yields very valuable information about chromosome abnormalities associated with a patient's disease
-the range of possible findings:
-loss of genetic material- deletion, monosomy
-gain of genetic material- duplication, trisomy, gene amplification
-relocation of genetic material- translocation
-molecular level changes may not be detected here, though deletions or duplications may be picked up FISH or microarray


Chromosome rearrangements with leukemia

-some chromosome rearrangements have been shown to be uniquely associated with only one disease
-in these instances, the presence of the anomaly will provide a diagnosis
-in other cases, a particular chromosome rearrangement or anomaly may be reported in more than one disease
-its presence would then not give a specific diagnosis,but would confirm the presence of disease and could narrow the possible diagnosis to a few disorders
-some chromosome abnormalities are associated with a better outcome than others, so it is important to know the specific findings for best patient care
-Down syndrome patients have an increased risk for leukemia
-Trisomy 21 is also an acquired change in a leukemic cell line in a non-DS patient


Loss of Heterozygosity

-one molecular tool in determining the presence or absence of mutation (normal vs. abnormal) is detection of loss of heterozygosity
-using markers that are known to be heterozygous in unaffected tissues, the state of those markers in the tumor DNA can be evaluated
-if the test reveals homozygosity this is probably due to disease and is in reality "loss of heterozygosity"
-1 locus, 1 chromosome arm, entire chromosome
-LOH does not mean there is only a single allele present
-karyotype analysis has shown tumors with multiple copies of the target chromosome but only a single band on DNA analysis
-DNA from this tumor showed LOH for chromosome 17- but there are clearly 3 copies of 17 present
-this means there must have been loss of one of the original 17s then duplication of the remaining 17 to a final total of 3 copies of the same chromosome


Prognosis for Loss of Heterozygosity

-in some instances, there is a direct correlation between a particular chromosomal finding and the course of the disease
-knowing that information may aid in determining the type of treatment utilized
-a more resistant disease may be treated more aggressively


Monitoring the disease-

-at diagnosis, both normal and cancer cells are present
-the treatment will hopefully cure the patient
-often the treatment suppresses the disease -> remission
-the patient may then relapse, and the chromosomal abnormalities will reappear


FISH and Acute Leukemia

-FISH has broadened the amount of information that can be obtained by cytogenetic analysis
-it can be very tedious to score slides looking at standard banded chromosomes
-FISH probes have been developed that can quickly identify the presence of specific abnormalities
-this allows more cells to be scored, increasing the level of significance of the study, but only those abnormalities specifically being tested will be assessed
-FISH is useful in monitoring bone marrow transplant patients- mixed sex transplants score X and Y
-after transplant there can be some recipiant cell line but it should die off over time and the donor should become dominant



-gene amplification is another type of anomaly seen in some cancer
-it has been well documented that one type of breast cancer with gene amplification will respond to the drug herceptin, but the drug is not effective in other types without amplification
-the FDA has approved aFISH assay to detect this amplification
-the target, HER2-neu, is labeled in red and the control locus is gene
-normal cells have 2 red and 2 green cells, tumor cells should have only the 2 green control signals per cells, but multiple red signals indiciating gene amplification


Detect cancer mutations with PCR

-although 95% of BCR-ABL rearrangements can be detected by karyotype analysis or FISH, PCR can also be used and often is able to detect the remaining 5% of cases
-comparison of bands of known sizes to bands obtained in patient samples is the key to this technology



-sequencing has been introduce as a new technology to identify known disease related mutations in specific genes


Expression Arrays

-one type of array, expression arrays, is providing valuable information on genes and proteins specific to particular cancer
-this type of study also allows use to determine relatedness between difference diseases
-example with 50 markers for prostate cancer- a comparison should allow you to discriminate between a normal or cancer pattern


Mutational signatures of human cancer

-unique subsets that can be used for identification purposes
-the next step was to take all the unique signatures that were catalogued and connect them with specific tumors
-the gial was to achieve a unique pattern, similar to a DNA fingerprint
-if this study can be standardized it could be used worldwide a a direct identification panel


Genetics and Cancer

-mutations may be inherited and/or acqured
-somatic mutation is usually required for disease expression
-disease is due to multi-step process at somatic cell level
-carrier parents has a 50% chance of passing on a mutation
-second mutation occurs at the somatic level
-risk is correlated to number and degree of affected relatives
-inherited mutation-> increased risk of acquiring the disease
-primary genetic causes of cancer can be linked to oncogenes, tumor suppressor genes (gatekeepers and caretakers)
-many diseases now have clinical testing avaible
-new technologies are providing new diagnostic methods and new treatments