FINALS LEC 1: CANCER GENETICS AND GENOMICS Flashcards
- type of disease in which certain cells become able to DIVIDE MORE OFTEN, leading to an abnormal growth (a tumor) or disruption of a proportion of blood cell types (a “liquid” tumor).
- may be inherited or due to environmental factors such as UV radiation or toxic
CANCER
One researcher calls the accumulating DNA changes that lie behind cancer is what we called?
GENOMIC SCARS
WHOLE-BODY LEVEL
DIAGNOSIS:
SYMPTOM TESTS
TEST TO UNDERGO:
BIOMARKERS
IMAGING
MUTATION DETECTION
CELLULAR LEVEL
-skin cancer cells divide faster than surrounding cells
DISRUPTED PATHWAYS:
CELL FATE
CELL SURVIVAL
GENOME MAINTENANCE
study of how our behaviors or environmental factors make cause changes that can affect our genes
- REVERSIBLE
- does not change our DNA sequences, but it can change/affect our DNA sequences by changing how the body reads or interprets it
EPIGENETICS
GENOME LEVEL
- If there are altertions:
POINT MUTATION
COPY NUMBER VARIANTS
CHROMOSOME REARRANGEMENT
ANEUPLOIDY
CHANGES IN GENE EXPRESSION
CANCER AFFECTS 3 BASIC CELLULAR
PATHWAYS:
Differentiation (specialization)
A. CELL FATE
B. GENOME SURVIVAL
C. GENOME MAINTENANCE
CELL FATE
CANCER AFFECTS 3 BASIC CELLULAR
PATHWAYS:
Ability of cells to WITHSTAND VARIOUS STRESSES and maintain their viability
A. CELL FATE
B. GENOME SURVIVAL
C. GENOME MAINTENANCE
GENOME SURVIVAL
CANCER AFFECTS 3 BASIC CELLULAR
PATHWAYS:
Abilities to survive in the presence
of reactive oxygen species (ROS) & toxins, to repair DNA, to maintain chromosome integrity & structure, & to correctly splice mRNA molecules.
A. CELL FATE
B. GENOME SURVIVAL
C. GENOME MAINTENANCE
GENOME MAINTENANCE
- Growth of tissue that exceeds and is not coordinated with normal tissue
- They are formed as a result of abnormal cell growth and division
TUMORS (NEOPLASMS)
TYPES OF TUMORS
- Grows in place but DOES NOT SPREAD into, or “INVADE” surrounding tissue
BENIGN TUMOR
TYPES OF TUMORS
- Infiltrates nearby tissue, invasive & tending to RECUR AT MULTIPLE SITES
(cancer)
MALIGNANT (CANCEROUS) TUMOR)
A tumor is cancerous, or malignant, if it infiltrates nearby tissue. Pieces of a malignant tumor can enter the bloodstream or lymphatic vessels and travel to other areas of the body, where the cancer cells “_______” the formation of new tumors.
SEED
TYPES OF TUMORS
- Means “NOT STANDING STILL” process of spreading
- can make a cancer DEADLY, because the new growth may be in an inaccessible part of the body, or genetically distinct enough from the original, or primary, tumor that drugs that were effective early in the illness no longer work.
METASTASIS
Abnormal growth of melanocytes (pigment-producing cells) in the skin
CUTANEOUS MELANOMA
CUTANEOUS MELANOMA
- ___________ is often used as a guideline to recognize potential signs
ABCDE rule
Asymmetry
Border irregularity
Color variations
Diameter (>5mm)
Elevation (raised/elevated area)
GENES (when mutated) CAN CAUSE CANCER:
>100, cause cancer when they are expressed when it wouldn’t being healthy cells/is over expressed (dominant)
ONCOGENES
Genes that normally trigger cell division are called
PROTO-ONCOGENES
GENES (when mutated) CAN CAUSE CANCER:
>30, cause cancer when they are deleted/inactivated (dominant)
TUMOR- SUPPRESSOR GENES
GENES (when mutated) CAN CAUSE CANCER:
MISMATCH MUTATIONS, allowing other mutations to persist activating oncogenes/ inactivating tumor suppressor genes
DNA REPAIR GENES
Most fundamental characteristic of cancer
Cancer begins when a cell divides more frequently, or more times
Example: A mutation in a gene that
normally halts/slows the cell cycle can lead to
LOSS OF CELL CYCLE CONTROL
May also contribute to cancer by affecting the cell cycle
LOSS OF CONTROL OVER TELOMERE LENGTH
Protect chromosomes from breaking
In humans, they consist TTAGGG repeats & normally lost from the telomere ends as a cell matures
TELOMERES (chromosome tips)
Enzyme responsible for maintenance of the length of telomeres
TELOMERASE
TELOMERASE IN NORMAL CELLS:
IS TURNED OFF
TELOMERASE IN CANCER CELLS:
IS TURNED BACK ON
TYPES OF PREDISPOSITION OF CANCER
Rare, every cell has 1 GENE VARIANT that increases cancer susceptibility & a somatic mutation occurs in the cells of the affected tissue
GERMLINE CANCER or SPORADIC CANCER?
GERMLINE CANCER
TYPES OF PREDISPOSITION OF CANCER
Common, caused by SOMATIC MUTATIONS, affecting only NON-SEX CELLS. May result from a single dominant/2 recessive mutations in copies of the same gene
GERMLINE CANCER or SPORADIC CANCER?
SPORADIC CANCER
CANCER AT THE CELLULAR LEVEL
CHARACTERISTICS OF CANCER CELLS
Oilier, less adherent
Loss of cell cycle control
Heritable
Transplantable
Dedifferentiated
Lack contact inhibition
Induce local blood vessel
formation (angiogenesis)
Invasive
Increased mutation rate
Can spread (metastasize)
ORIGIN OF CANCER CELLS
Small population of cells within a tumor that possess stem cell-like properties
Have the ability to self-renewand differentiate into various cell types within the tumor, similar to normal stem cells in healthy tissues
Found in cancers of the brain, blood, and epithelium (breast, colon, and prostate)
ACTIVATION OF STEM CELLS THAT PRODUCE CANCER CELLS (cancer
stem cells)
ORIGIN OF CANCER CELLS
Cells lose some of their distinguishing characteristics as mutations occur when they divide
May begin to express“stemness” genes that override signals to remain specialized
DEDIFFERENTIATION
ORIGIN OF CANCER CELLS
If a mutation renders a differentiated cell able to divide to yield other cells that frequently divide, then over time these cells may takeover, forming an abnormal growth
INCREASE IN THE PROPORTION OF A TISSUE THAT CONSISTS A STEM/PROGENITOR CELLS
ORIGIN OF CANCER CELLS
Too much repair may trigger tumor formation
If too much cells divide to fill in the space left by injured tissue, & those cells keep dividing, an abnormal growth may result
FAULTY TISSUE REPAIR
2 TYPES OF GENETIC ALTERATIONS THAT OCCUR WITHIN CANCER CELLS
Provides the selective growth advantage to a cell that defines the cancerous state
Directly contribute to the development & progression of cancer
Typically found in oncogenes/tumor suppressor genes (about 200)
DRIVER MUTATION
2 TYPES OF GENETIC ALTERATIONS THAT OCCUR WITHIN CANCER CELLS
Occurs in cancer cell, but does not directly contribute to the development/progression of cancer
Considered incidental and may arise as a consequence of the genetic instability commonly observed in cancer
cells
Thousands of genes can harbor passenger mutations
Example: silent
PASSENGER MUTATION
3 STRIKES DRIVE CANCER
Breakthrough: BRAF
Expansion: TERT
Invasion: CDK2NA, TP53, PIK3CA
A. MELANOMA
B. PANCREATIC CANCER
C. CERVICAL CANCER
D. COLORECTAL CANCER
MELANOMA
3 STRIKES DRIVE CANCER
Breakthrough: KRAS
Expansion: CDK2NA
Invasion: SMAD4, TP53
A. MELANOMA
B. PANCREATIC CANCER
C. CERVICAL CANCER
D. COLORECTAL CANCER
PANCREATIC CANCER
3 STRIKES DRIVE CANCER
Breakthrough: TP53, RB
Expansion: PIK3CA
Invasion: MAPK1, STK11, FBXw7
A. MELANOMA
B. PANCREATIC CANCER
C. CERVICAL CANCER
D. COLORECTAL CANCER
CERVICAL CANCER
3 STRIKES DRIVE CANCER
Breakthrough: APC
Expansion: KRAS
Invasion: SMAD4, TP53, PIK3CA, FBXW7
A. MELANOMA
B. PANCREATIC CANCER
C. CERVICAL CANCER
D. COLORECTAL CANCER
COLORECTAL CANCER
CHROMOSOME IN CANCER CELLS
Abnormal in number
Abnormal in structure
joins parts of non - homologous chromosomes can hike expression of a gene turning it into an oncogene
TRANSLOCATION
can increase the number of copies of an oncogene
DUPLICATIONS
may remove a tumor- suppressor gene
DELETION
Coined in 2011, shatters several chromosomes and may kill the cell/trigger cancer
CHROMOTHRIPSIS
3 EXAMPLES OF GENES THAT CANACTIVATE PROTO-ONCOGENES
Virus infecting a cell may insert DNA nest to a proto- oncogene
Viruses cause cervical cancer, Kaposi sarcoma
A. VIRAL GENE
B. A GENE ENCODING A HORMONE
C. PARTS OF ANTIBODY GENES
VIRAL GENE
3 EXAMPLES OF GENES THAT CANACTIVATE PROTO-ONCOGENES
- Normally very actively transcribed
Example: inversion on chromosome 11 places a proto-oncogene next to a DNA sequence that controls transcription of the parathyroid hormone gene
A. VIRAL GENE
B. A GENE ENCODING A HORMONE
C. PARTS OF ANTIBODY GENES
A GENE ENCODING A HORMONE
3 EXAMPLES OF GENES THAT CANACTIVATE PROTO-ONCOGENES
Among the most highly transcribed
Examples:
a) Cervical and anal cancer following HPV infection may begin when proto- oncogenes are mistakenly activated with antibody genes b) Burkitt lymphoma(cancer common in Africa): large tumor develops from lymph glands near the jaw
Proto-oncogene on chromosome 8 moves to chromosome 14, next to a
highly expressed antibody gene lymph glands near the jaw
Proto-oncogene on chromosome 8 moves to chromosome 14, next to a
highly expressed antibody gene
A. VIRAL GENE
B. A GENE ENCODING A HORMONE
C. PARTS OF ANTIBODY GENES
PARTS OF ANTIBODY GENES
A PROTO-ONCOGENE MAY ALSO BE TRANSCRIBED & TRANSLATED WITH ANOTHER GENE AS IF THEY ARE ONE GENE
T OR F?
TRUE
Double gene product
Activates/lifts control of cell division
Example:
ACUTE PROMYELOCYTIC
LEUKEMIA
FUSION PROTEIN
Translocation between chromosomes 15 & 17 brings together a gene coding for the retinoic acid cell surface receptor & and an oncogene, myl.
ACUTE PROMYELOCYTIC LEUKEMIA
ANOTHER WAY THAT AN ONCOGENE CAN CAUSE CANCER
BY EXCESSIVE RESPONSE TO GROWTH FACTOR
Cell surface receptors for epidermal growth factor
Product of an oncogene
Affected cells of about 25%of women with breast cancer have 1 - 2 million copies of the protein
HER2 PROTEINS
HER2 PROTEINS function as a __________
TYROSINE KINASE
a monoclonal antibody, based drug
HERCEPTIN (trastuzumab)
Normal function: Inhibit expression of genes involved in all of the activities that turn a cell cancerous
Can result to cancer when they are lost/silenced/deleted/ if the promoter regions blinds too many methyl (CH3)
groups, which blocks transcription
Example:
WILMS’ TUMOR
TUMOR-SUPPRESSOR GENES
Loss of tumor suppression
Gene is deleted that normally halts mitosis in the rapidly developing kidney
WILM’S TUMOR
Rare childhood eye tumor, occurs in about 1 in 20,000 infants
Causes:
a. 1 germline mutant allele for RB1 gene in each of their cells & then cancer develops in a somatic cell where the second copy mutates (2 point mutations/deletions, 1 germline, & 1 somatic)
b. Sporadic cases: 2 somatic mutations in RB1 gene, 1 on each copy of chromosome 13 Cancer starts in a cone cell of the retina (provide color vision)
Mutations in RB1 gene cause other cancers (bone, bladder, breast,
RETINOBLASTOMA (RB)
Single gene that causes a variety of cancers when mutant (a cell with damaged DNA is permitted to divide resulting to cancer)
Occur only in somatic cells
Point mutation/deletion in the gene causes more than half of human cancers
Mediator: “the guardian of the genome”
Example: type of skin cancer caused by p53 mutation in skin cells damaged from repeated sunburns
P53 GENE
Normal function: cellular adhesion protein found in tissue linings
When deleted, cancer results
Example:
FAMILIAL DIFFUSE GASTRIC CANCER
E-CADHERIN GENE
“exon skipping” missense mutation in the E-cadherin gene that deleted an entire exon
Treatment: surgical removal of stomach (total gastrectomy)
FAMILIAL DIFFUSE GASTRIC CANCER
2 major breast cancer susceptibility genes
Account for 15-20% of the 5% cases that are familial
Mutations in these genes is inherited in an autosomal dominant manner with incomplete penetrance
BRCA1 & BRCA2 GENES
Risk of inheriting breast (mutations in the ends of the gene) & or ovarian cancer (mutations in the middle part of the gene)
Most common mutation: deletion of 2 adjacent DNA bases
BRCA1
Acts as a tumor-suppressor by helping maintain genomic integrity & preventing the formation of cancerous cells
Women: 45-70% risk of breast cancer & 10-20% risk of ovarian cancer
Men: at an increased risk of breast cancer, prostate cancer, & pancreatic cancer
Other cancers: colon, kidney, gallbladder, skin,
BRCA2
ENVIRONMENTAL CAUSES OF CANCER
CHEMICAL EXPOSURES
DIET
TOBACCO SMOKE
UV RADIATION
BOTH ENVIRONMENTAL AND GENETIC FACTOR
ENVIRONMENTAL CAUSES OF CANCER
Toxic pesticides, herbicides, fungicides, fumigants (non- Hodgkin’s lymphoma tumors)
A. CHEMICAL EXPOSURES
B. DIET
C. TOBACCO SMOKE
D. UV RADIATION
E. BOTH ENVIRONMENTAL AND GENETIC FACTOR
CHEMICAL EXPOSURES
ENVIRONMENTAL CAUSES OF CANCER
- Vegetable-poor, meaty diet: heterocyclic aromatic amines (carcinogenic) accumulate & elevate cancer risk (colon)
Cruciferous vegetables: (broccoli
& brussel sprouts): release chemical that activate enzymes detoxifying animes
A. CHEMICAL EXPOSURES
B. DIET
C. TOBACCO SMOKE
D. UV RADIATION
E. BOTH ENVIRONMENTAL AND GENETIC FACTOR
DIET
ENVIRONMENTAL CAUSES OF CANCER
- Major cause of cancer (lung, mouth, throat, etc.)
2nd hand smoke exposure is also linked to an increased risk of cancer
Carcinogens: benzene, formaldehyde, & polycyclic aromatic hydrocarbons (PAHs)
A. CHEMICAL EXPOSURES
B. DIET
C. TOBACCO SMOKE
D. UV RADIATION
E. BOTH ENVIRONMENTAL AND GENETIC FACTOR
TOBACCO SMOKE
ENVIRONMENTAL CAUSES OF CANCER
- Sun/artificial sources (skin cancer)
A. CHEMICAL EXPOSURES
B. DIET
C. TOBACCO SMOKE
D. UV RADIATION
E. BOTH ENVIRONMENTAL AND GENETIC FACTOR
UV RADIATION
ENVIRONMENTAL CAUSES OF CANCER
- Melanoma (type of skin cancer): sun exposure elevates risk, but certain gene variants (MC1R gene) known for imparting red hair, fair skin, freckles, double the risk even if the person avoids intense sunlight
A. CHEMICAL EXPOSURES
B. DIET
C. TOBACCO SMOKE
D. UV RADIATION
E. BOTH ENVIRONMENTAL AND GENETIC FACTOR
BOTH ENVIRONMENTAL AND GENETIC FACTOR
CANCER DIAGNOSIS & TREATMENTS
COMMON STEPS & METHODS IN THE DIAGNOSTIC PROCESS FOR CANCER:
- MEDICAL HISTORY & PHYSICAL EXAMINATION
- LABORATORY TESTS
- IMAGING TESTS
- BIOPSY
- PATHOLOGY AND HISTOPATHOLOGY
- STAGING
COMMON STEPS & METHODS IN THE DIAGNOSTIC PROCESS FOR CANCER:
- Symptoms, risk factors, family history, & previous medical records; visible signs or abnormalities
A. MEDICAL HISTORY & PHYSICAL EXAMINATION
B. LABORATORY TESTS
C. IMAGING TESTS
D. BIOPSY
E. PATHOLOGY AND HISTOPATHOLOGY
F. STAGING
MEDICAL HISTORY & PHYSICAL EXAMINATION
COMMON STEPS & METHODS IN THE DIAGNOSTIC PROCESS FOR CANCER:
- Evaluate various aspects of body’s functioning
CBC, liver function tests, kidney function test, tumor markers, & genetic testing
A. MEDICAL HISTORY & PHYSICAL EXAMINATION
B. LABORATORY TESTS
C. IMAGING TESTS
D. BIOPSY
E. PATHOLOGY AND HISTOPATHOLOGY
F. STAGING
LABORATORY TESTS
COMMON STEPS & METHODS IN THE DIAGNOSTIC PROCESS FOR CANCER:
- VISUALIZE internal structures of the
body & detect any abnormal growths/masses
X-rays, CT scans, MRI scans, ultrasound, PET scans
A. MEDICAL HISTORY & PHYSICAL EXAMINATION
B. LABORATORY TESTS
C. IMAGING TESTS
D. BIOPSY
E. PATHOLOGY AND HISTOPATHOLOGY
F. STAGING
IMAGING TESTS
COMMON STEPS & METHODS IN THE DIAGNOSTIC PROCESS FOR CANCER:
- Removal of a sample tissue/cells from a suspicious area for lab analysis
A. MEDICAL HISTORY & PHYSICAL EXAMINATION
B. LABORATORY TESTS
C. IMAGING TESTS
D. BIOPSY
E. PATHOLOGY AND HISTOPATHOLOGY
F. STAGING
BIOPSY
COMMON STEPS & METHODS IN THE DIAGNOSTIC PROCESS FOR CANCER:
- Examination of a tissue under a microscope
A. MEDICAL HISTORY & PHYSICAL EXAMINATION
B. LABORATORY TESTS
C. IMAGING TESTS
D. BIOPSY
E. PATHOLOGY AND HISTOPATHOLOGY
F. STAGING
PATHOLOGY & HISTOPATHOLOGY
COMMON STEPS & METHODS IN THE DIAGNOSTIC PROCESS FOR CANCER:
- Performed once a cancer diagnosis is confirmed
Evaluating the size of the tumor, involvement of nearby lymph nodes, & presence of metastasis
A. MEDICAL HISTORY & PHYSICAL EXAMINATION
B. LABORATORY TESTS
C. IMAGING TESTS
D. BIOPSY
E. PATHOLOGY AND HISTOPATHOLOGY
F. STAGING
STAGING
TRADITIONAL WAYS OF TREATING
CANCER
- Removal of primary tumor before it has invaded healthy tissue & spread through the bloodstream
A. CHEMOTHERAPY
B. SURGERY
C. RADIATION THERAPY
SURGERY
TRADITIONAL WAYS OF TREATING
CANCER
- Use of drugs to kill/inhibit the growth of cancer cells
A. CHEMOTHERAPY
B. SURGERY
C. RADIATION THERAPY
CHEMOTHERAPY
TRADITIONAL WAYS OF TREATING
CANCER
- Use of high-energy radiation to target & destroy cancer cells
A. SURGERY
B. RADIATION THERAPY
C. CHEMOTHERAPY
RADIATION THERAPY
NEW APPROACH TO DIAGNOSING &
TREATING CANCER
- Targeted therapy drugs designed to specifically inhibit the activity of tyrosine kinases
A. GENE EXPRESSION PROFILING
B. CHIMERIC ANTIGEN RECEPTORS(CAR) TECHNOLOGY
C. LIQUID BIOPSY
D. TYROSINE KINASE INHIBITOR
TYROSINE KINASE INHIBITOR
NEW APPROACH TO DIAGNOSING &
TREATING CANCER
- Specifically describe the type of cell that turns cancerous, which informs treatment choices
A. GENE EXPRESSION PROFILING
B. CHIMERIC ANTIGEN RECEPTORS(CAR) TECHNOLOGY
C. LIQUID BIOPSY
D. TYROSINE KINASE INHIBITOR
GENE EXPRESSION PROFILING
NEW APPROACH TO DIAGNOSING &
TREATING CANCER
- Creates DNA instructions for a hybrid surface protein (CAR) onTcells that the body does not normally synthesize
A. GENE EXPRESSION PROFILING
B. CHIMERIC ANTIGEN RECEPTORS(CAR) TECHNOLOGY
C. LIQUID BIOPSY
D. TYROSINE KINASE INHIBITOR
CHIMERIC ANTIGEN RECEPTORS(CAR) TECHNOLOGY
NEW APPROACH TO DIAGNOSING &
TREATING CANCER
- Checking DNA pieces in the blood plasma for oncogene/ tumor suppressor mutation
DNA detected is called cell-free/ circulating tumor DNA (ctDNA)
Detects cancer recurrence (may have new mutations)
Useful for monitoring response to treatment (if the drug is working, level of ctDNA will decrease)
A. GENE EXPRESSION PROFILING
B. CHIMERIC ANTIGEN RECEPTORS(CAR) TECHNOLOGY
C. LIQUID BIOPSY
D. TYROSINE KINASE INHIBITOR
LIQUID BIOPSY