Genetic Basis of Cancer: Study Notes

Genetic Basis of Cancer

Overview of Cancer

Cancer is a disease characterized by uncontrolled cell division, resulting from the accumulation of genetic and epigenetic changes. There are over 100 types of human cancers, classified by the cell type affected. Cancer progression typically involves multiple steps, beginning with a single cell (clonal origin), followed by benign growth, malignant transformation, and ultimately metastasis.

• Clonal Origin: Most cancers originate from a single cell that acquires mutations.

• Multistep Process: Cancer development involves a series of genetic changes, starting with a benign lesion and progressing to malignancy.

• Malignancy: Malignant cells are invasive (invade healthy tissues) and metastatic (spread to other parts of the body).

• Key Terms: Malignant (cancerous and invasive), Invasive (invading healthy tissue), Metastatic (spreading to distant sites).

Genetic Changes in Cancer

Cancer arises from mutations in two main categories of genes:

• Oncogenes: Mutant genes that are overexpressed and promote cancerous growth (gain-of-function mutations).

• Tumor-Suppressor Genes: Genes that normally prevent cancer; loss-of-function mutations in these genes allow cancer to develop.

Oncogenes

Proto-Oncogenes and Oncogenes

Proto-oncogenes are normal genes that regulate cell growth and division. When mutated, they become oncogenes, which promote abnormal cell proliferation.

• Gain-of-Function Mutations: Oncogenes may be overexpressed, produce overly active proteins, or be expressed in inappropriate cell types.

• Cell Signaling Pathways: Oncogenes often encode proteins involved in cell signaling, such as growth factor receptors, intracellular signaling proteins, and transcription factors.

Activation of Cell-Signaling Pathways

Growth factors like epidermal growth factor (EGF) bind to cell surface receptors, initiating a cascade that leads to cell division. Oncogenes can disrupt this regulation, causing continuous signaling for cell proliferation.

• Key proteins in the EGF pathway: EGF receptor, GRB2, Sos, Ras, Raf-1, MEK, MAPK, and transcription factors (Myc, Jun, Fos).

• Activation sequence: EGF → EGF receptor → GRB2/Sos → Ras (GTP-bound) → Raf-1 → MEK → MAPK → transcription factors → gene expression.

Examples of Proto-Oncogenes

Gene	Cellular Function of Coded Protein
sis	Platelet-derived growth factor
int-2	Fibroblast growth factor
erbB	EGF receptor
fms	NGF receptor
ras	GTP/GDP-binding protein
raf	Serine/threonine kinase
src	Tyrosine kinase
abl	Tyrosine kinase

Mechanisms Converting Proto-Oncogenes to Oncogenes

• Missense Mutations: Single amino acid changes can activate oncogenes (e.g., H-ras Gly12Val mutation).

• Gene Amplification: Increased copy number leads to overproduction of protein (e.g., c-myc, N-myc, erbB-2).

• Chromosomal Translocations: Rearrangement places proto-oncogenes under new regulatory elements or creates fusion proteins (e.g., BCR-ABL in chronic myelogenous leukemia).

• Viral Integration: Viruses can activate proto-oncogenes by inserting near them or providing strong promoters/enhancers (e.g., avian leukosis virus near c-myc, src gene in Rous sarcoma virus).

Functional Cycle of Ras Protein

Ras is a GTPase that cycles between active (GTP-bound) and inactive (GDP-bound) states. Mutations that reduce GTPase activity or increase GDP-GTP exchange keep Ras active, promoting continuous cell division signaling.

• Normal Cycle: Ras-GDP (inactive) ⇄ Ras-GTP (active)

• Cancer Mutation: Impaired GTP hydrolysis keeps Ras in the active state.

Tumor-Suppressor Genes

Role and Types

Tumor-suppressor genes prevent uncontrolled cell proliferation. Inactivation (loss-of-function) increases cancer risk. They are negative regulators of cell growth, and their mutated forms are typically recessive.

• Categories:

  • Proteins that negatively regulate cell division (e.g., Rb, p16, NF1, APC)

  • Proteins that maintain genome integrity (e.g., p53, BRCA-1, BRCA-2)

Retinoblastoma and the Two-Hit Hypothesis

Retinoblastoma is a childhood eye tumor explained by Knudson's two-hit hypothesis: both alleles of the rb gene must be inactivated for cancer to develop.

• Hereditary Form: One defective allele is inherited; only one additional somatic mutation is needed (early onset, bilateral, multiple tumors).

• Sporadic Form: Both mutations occur somatically in the same cell (late onset, unilateral, single tumor).

Molecular Function of Rb

The Rb protein binds and inhibits E2F, a transcription factor required for cell cycle progression. Phosphorylation of Rb releases E2F, allowing cell division. Loss of Rb function leads to constitutive E2F activity and uncontrolled proliferation.

p53: The Master Tumor-Suppressor Gene

The p53 gene encodes a transcription factor that responds to cellular stress, especially DNA damage. About 50% of human cancers involve p53 mutations.

• Functions:

  • Activates DNA repair genes

  • Induces cell cycle arrest (e.g., via p21, which inhibits cyclin/CDK complexes)

  • Promotes apoptosis (programmed cell death) via caspases

• Pathways: p53 regulates genes involved in apoptosis (e.g., PUMA, BAX), senescence, cell cycle arrest, DNA repair, and metabolism.

Selected Tumor-Suppressor Genes and Their Functions

Gene	Function
rb	Negative regulator of E2F; inhibits transcription of genes for DNA replication and cell division
p16	Inhibits cyclin-dependent kinases; controls G1 to S phase transition
NF1	Stimulates Ras GTPase activity; loss leads to overactive Ras
APC	Negative regulator of cell-signaling pathway for cell division
p53	Checkpoint protein; senses DNA damage, induces cell cycle arrest or apoptosis
BRCA-1/2	DNA repair; promote apoptosis if repair fails

Genome Integrity and Cell Cycle Checkpoints

Genome maintenance mechanisms prevent mutations and the survival of mutant cells. Checkpoint proteins monitor DNA integrity and chromosome segregation, halting the cell cycle if errors are detected.

• Key Checkpoints: G1, G2, and Metaphase (M) checkpoints.

• Cyclins/CDKs: Drive cell cycle progression; checkpoint proteins can inhibit their activity if damage is detected.

DNA Repair and Cancer

DNA repair enzymes are crucial for genome maintenance. Defects in these enzymes (e.g., in nucleotide excision repair, as in xeroderma pigmentosum) increase cancer risk by allowing mutations to accumulate.

Silencing of Tumor-Suppressor Genes

Tumor-suppressor genes can be inactivated by:

• Mutations (e.g., promoter inactivation, early stop codons)

• Aneuploidy (chromosome loss)

• Epigenetic changes (e.g., DNA methylation)

Multiple Genetic Changes and Cancer Progression

Colorectal Cancer as a Model

Colorectal cancer develops through a series of genetic changes:

1. Loss of APC tumor-suppressor gene (chromosome 5): small benign polyp

2. Activation of ras oncogene (chromosome 12): Class II adenoma

3. Loss of DCC tumor-suppressor gene (chromosome 18): Class III adenoma

4. Loss of p53 tumor-suppressor gene (chromosome 17): malignant carcinoma

5. Additional mutations: metastasis

Many cancers involve mutations in both coding and noncoding RNAs, as well as chromosomal abnormalities (deletions, duplications, translocations).

Chromosomal Abnormalities in Cancer

Cancer cells often display abnormal karyotypes, including extra or missing chromosomes and marker chromosomes formed by chromosomal rearrangements.

Inherited Forms of Cancer

Germ-Line Mutations and Loss of Heterozygosity (LOH)

About 5–10% of cancers are due to inherited mutations, usually in tumor-suppressor genes. Individuals heterozygous for a loss-of-function allele are predisposed to cancer; cancer develops when the normal allele is lost (LOH).

• Inheritance Pattern: Often appears dominant at the organismal level due to high risk, but both alleles must be inactivated at the cellular level.

• Examples: BRCA-1, BRCA-2, rb, p53, APC, NF1, VHL, RET (oncogene).

Familial Breast Cancer Example

• Individuals with one mutant BRCA-1 allele are at increased risk; cancer develops after somatic loss of the remaining functional allele.

• Pattern is autosomal dominant with incomplete penetrance.

Epigenetics and Cancer

Role of Epigenetic Changes

Epigenetic modifications can promote cancer by increasing proto-oncogene expression or silencing tumor-suppressor genes. Major mechanisms include:

• DNA Methylation: Hypermethylation at CpG islands can silence tumor-suppressor genes.

• Histone Modification: Acetylation, methylation, phosphorylation can alter gene expression.

• Chromatin Remodeling: Changes in nucleosome positioning can affect gene accessibility.

Chromatin-Modifying Protein Mutations in Cancer

Type of Modification	Protein	Function	Cancer Types
DNA methylation	DNA methyltransferase	Methylates DNA	Acute myeloid leukemia
Histone acetylation	Histone acetyltransferase	Adds acetyl groups to histones	Colorectal, breast, pancreatic
Histone methylation	Histone methyltransferase	Adds methyl groups to histones	Renal, breast
Histone demethylation	Histone demethylase	Removes methyl groups from histones	Multiple myeloma, esophageal
Histone phosphorylation	Histone kinase	Adds phosphate groups to histones	Medulloblastoma, glioma
Chromatin remodeling	SWI/SNF complex	Alters histone positions	Lung, breast, prostate, pancreatic

Epigenetics: Causation vs. Correlation

Not all epigenetic changes associated with cancer are causative. Associations may be direct (causing disease), secondary (resulting from disease), or indirect (due to a third factor).

Environmental Agents and Epigenetic Changes

Agent	Occurrence	Associated Cancers
Polycyclic aromatic hydrocarbons	Tobacco smoke, exhaust, charbroiled food	Lung, breast, stomach, skin
Benzene	Tobacco smoke, exhaust	Leukemia, lymphoma, myeloma
Endocrine disruptors	Pesticides, plastics	Breast, prostate, thyroid
Cadmium	Tobacco, batteries	Lung, breast
Nickel	Mining, welding, jewelry, batteries	Lung, nasal
Arsenic	Lead alloys, agriculture, insecticides	Skin, bladder, kidney, liver

These agents may alter chromatin-modifying proteins, contributing to cancer development.

Cancer Therapeutics

Overview of Treatment Strategies

• Physical methods (e.g., surgery, radiation)

• Killing actively dividing cells (chemotherapy)

• Targeted drug therapy

• Hormone therapy

• Immunotherapy

Chemotherapy: Killing Actively Dividing Cells

• DNA-Damaging Agents: Alkylating agents damage DNA to prevent cell division (e.g., used for lung, breast, ovary, leukemia, lymphoma, myeloma, sarcoma).

• DNA Replication Inhibitors: Drugs like irinotecan inhibit topoisomerase I, blocking DNA replication (effective in colon and lung cancer).

• Mitotic Inhibitors: Vinblastine and vincristine disrupt the mitotic spindle, halting cell division (used for breast, lung, myelomas, lymphomas, leukemias).

Targeted Drug Therapies

• Estrogen Receptor (ER) Blockade: Tamoxifen binds ER, preventing estrogen-driven gene expression and cell division in breast cancer.

• HER2 Inhibition: Dacomitinib binds the kinase domain of HER2, blocking autophosphorylation and cell division in HER2-overexpressing cancers.

• BCR-ABL Fusion Protein Inhibition: Imatinib blocks ATP binding to the BCR-ABL fusion protein, preventing phosphorylation of signaling proteins and halting cell division in chronic myeloid leukemia.

Immunotherapy

• Monoclonal Antibodies (mAbs): Laboratory-made antibodies that target cancer cells for immune destruction, deliver cytotoxic agents, or inhibit overexpressed proteins.

• Checkpoint Inhibitors: Drugs that block immune checkpoints, enhancing immune response against cancer.

• T-cell Transfer Therapy: Patient's T cells are expanded and reinfused to attack cancer.

• Immune System Modulators: Drugs/proteins that boost immune response.

• Cancer Vaccines: Stimulate immune response against cancer-specific antigens.

Epigenetic Therapies

• DNA Methyltransferase Inhibitors: Drugs like 5-azacytidine and decitabine reduce DNA methylation, potentially reactivating silenced tumor-suppressor genes (used in leukemia).

• miRNA-Based Therapies: Experimental approaches targeting noncoding RNAs and miRNA processing to modulate gene expression in cancer cells.

Summary Table: Key Differences Between Oncogenes and Tumor-Suppressor Genes

Feature	Oncogenes	Tumor-Suppressor Genes
Normal Function	Promote cell growth/division	Inhibit cell growth/division
Mutation Effect	Gain-of-function (dominant)	Loss-of-function (recessive)
Role in Cancer	Activated forms promote malignancy	Inactivated forms promote malignancy

Key Equations and Concepts

• Knudson's Two-Hit Hypothesis: Both alleles of a tumor-suppressor gene must be inactivated for cancer to develop.

• Cell Cycle Regulation: $G_1 \rightarrow S \rightarrow G_2 \rightarrow M$

• Ras Protein Cycle: $\text{Ras-GDP (inactive)} \xleftrightarrow{\text{GDP-GTP exchange}} \text{Ras-GTP (active)}$

Additional info: This guide integrates and expands upon the accessible reading version of Chapter 25, providing definitions, mechanisms, and examples for all major concepts relevant to the genetic basis of cancer, including tables and diagrams described in text form for clarity and completeness.