Oncogenes and Tumour Suppressor Genes – Comprehensive Study Notes

Learning Outcomes

Explain what a tumour suppressor gene (TSG) is.
Explain what an oncogene is and how oncogenes arise.
Describe how oncogenes and TSGs function and can drive cancer.
Identify key molecular pathways involving oncogenes and tumour-suppressor genes.

Key Terms

Proto-oncogene: Normal gene that can become an oncogene after mutation/over-expression.
Oncogene: Gene whose activation, over-expression, or mutation promotes oncogenesis.
Oncogenesis / Carcinogenesis: Process through which healthy cells transform into cancer cells.
Oncovirus: Virus capable of causing cancer.
Retrovirus: RNA virus able to make a complementary DNA copy that integrates into host genome (e.g., HIV, RSV).
Tumour-suppressor gene (TSG): Gene encoding a protein that restrains cell growth/division or promotes apoptosis; loss or inactivation fosters oncogenesis.

Tumour-Suppressor Genes (TSGs)

General Principles

Cancer-promoting mutations are loss-of-function (often deletions or inactivating substitutions).
Each somatic cell carries two alleles (maternal & paternal); one functional allele usually produces enough suppressor protein for normal control → behaves recessively at the cellular level.
Both alleles must be inactivated to abolish TSG function ("two-hit" model).
Germ-line (inherited) TSG mutations occur in several familial cancer syndromes, e.g.
- $APC$ mutation → Familial Adenomatous Polyposis → ↑ colon-cancer risk.
- Germ-line $TP53$ mutations → Li-Fraumeni syndrome.
Most TSG mutations in sporadic cancers are somatic (non-inherited); $\approx$ half of all human tumours have an acquired $TP53$ mutation.

Functional Classes

Gatekeeper TSGs
- Direct negative regulators of cell proliferation.
- Encode proteins that inhibit cell-cycle progression, induce apoptosis, suppress angiogenesis, or enhance cell adhesion.
- Prototype: pRB (product of $RB1$ ).
Caretaker TSGs
- Maintain genomic integrity by facilitating DNA-damage recognition/repair.
- Prevent the accumulation of oncogenic mutations.
- Prototype: p53 (product of $TP53$ ); DNA repair enzymes (e.g., BRCA1/2, MSH2, MLH1) often grouped here.

Retinoblastoma (RB) – Case Study of a Gatekeeper

Clinical Picture

Rare paediatric eye cancer (usually <5 yrs).
Arises from retinal progenitor cells; may be unilateral or bilateral.
$\approx 40\%$ of cases: germ-line $RB1$ mutation → bilateral disease.
$\approx 60\%$ : purely somatic mutations → unilateral disease.
Early detection → $\approx 95\%$ cure; extra-ocular spread is often fatal.

Molecular Mechanism of pRB

G1 checkpoint requires E2F transcription factors to initiate synthesis of S-phase genes.
Hypophosphorylated pRB binds & inhibits E2F → blocks S-phase entry.
Cyclin D / CDK4,6 phosphorylate pRB → pRB releases E2F → cell progresses to S phase.
Loss or mutation of pRB abolishes E2F control → constitutive S-phase entry.
One intact allele is sufficient for normal control; biallelic loss unleashes uncontrolled proliferation.

Knudson’s Two-Hit Hypothesis

First hit: inherited (germ-line) or early somatic mutation in one $RB1$ allele.
Second hit: independent somatic mutation deletes/inactivates the remaining allele.
Explains early, bilateral tumours in hereditary cases versus late, unilateral tumours in sporadic cases.

Dominant vs Recessive Viewpoints

Cellular level: $RB1$ behaves recessively (both alleles must be lost).
Organism level: germ-line carriers exhibit dominant cancer predisposition (only one additional somatic hit needed).

DNA-Repair TSGs & Indirect Effects

Mutations in caretaker genes (e.g., BRCA1/2, MSH2) elevate global mutation rates, thereby indirectly fostering activation of oncogenes and inactivation of additional TSGs.

The p53 Pathway – Universal Genome Guardian

Core Facts

p53: sequence-specific transcription factor; encoded by $TP53$ on chromosome 17.
$\sim 50\%$ of human cancers harbour p53 mutations.
Stressors that activate p53: nucleotide depletion, UV/ionising radiation, oncogene signalling, hypoxia, transcriptional blockade.

Anti-Tumour Mechanisms (p53 Effector Network)

Cell-cycle arrest
- Highest activity at G1/S checkpoint; induces $p21^{CIP1}$ which inhibits Cyclin-E/CDK2 & Cyclin-A/CDK1,2 → reversible or irreversible (senescence) arrest.
DNA repair promotion
- Up-regulates genes such as GADD45 and p53R2 for nucleotide excision & base-excision repair.
Blockage of angiogenesis
- Alters transcription of VEGF and thrombospondin genes, limiting tumour vascularisation when p53 is intact.
Apoptosis induction
- Transactivates BAX and other pro-apoptotic BCL-2 family members → mitochondrial permeabilisation & caspase activation.

Regulation of p53 Stability

Mdm2 (E3 ubiquitin ligase)
- Binds p53 transactivation domain, exports p53 from nucleus, ubiquitinates → proteasomal degradation.
Stress signals activate ATM/ATR kinases → phosphorylate p53 → prevent Mdm2 binding → p53 stabilisation.
ARF (product of $CDKN2A$ locus) sequesters Mdm2, acting as a "decoy" to preserve p53 during oncogenic stress.

Pathological Scenarios

Loss of p53 → unchecked proliferation, defective apoptosis, genomic instability.
Some missense mutants cannot bind Mdm2 → paradoxical p53 accumulation that fails to transactivate target genes.
Li-Fraumeni syndrome: germ-line $TP53$ mutation → $\approx 50\%$ cancer risk by age 30.

Cell-Cycle Checkpoints & CDK Inhibitors (CKIs)

p53 regulates both G1/S and G2/M checkpoints.
CKIs (p21, p27, p57, p16, p17, p18, p19) inhibit Cyclin–CDK complexes across multiple phases.
G1 early phase is mitogen-dependent; after the R-point cells commit to division even if growth factors wane.
Hypophosphorylated pRB + chromatin modifiers (HDACs, methyltransferases) silence S-phase genes pre-R point.

Viral Oncogenes – Historical Insight

Oncogene mutations are generally dominant (gain-of-function).
1911 Peyton Rous: cell-free filtrate from chicken sarcoma → induced sarcoma in healthy chickens → Rous Sarcoma Virus (RSV).
1958: RSV transforms fibroblasts in vitro → loss of contact inhibition, anchorage independence, morphological changes.
1976: v-src identified as the RSV oncogene → first proof that a cellular gene can cause cancer when hijacked.
Retroviral oncogenes have been pivotal for the genetic model of cancer.

Proto-Oncogene → Oncogene Conversion

General Concepts

Proto-oncogenes normally promote proliferation; activation leads to constitutive signalling.
Inherited proto-oncogene mutations exist but most oncogenic alterations are somatic.

Major Activation Mechanisms

Chromosomal rearrangements
- Translocation, inversion, deletion, duplication can:
  • Place proto-oncogene under a strong heterologous promoter/enhancer → ↑ expression.
  • Create fusion proteins with novel, constitutively active functions.
Gene duplication (amplification)
- Extra gene copies → over-abundant oncoprotein.
Point mutation
- Alters coding sequence → increases intrinsic activity or confers resistance to regulation.

Example 1 – Burkitt’s Lymphoma (c-MYC)

Translocation $t(8;14)(q24;q32)$ (or less often $t(8;2), t(8;22)$ ).
Puts c-MYC next to immunoglobulin heavy- or light-chain enhancers → continuous MYC expression.
Immunoglobulin loci (IgH, Igκ, Igλ) provide very strong, constitutive promoters designed for antibody production.
Overexpressed MYC drives transcription of genes for cell-cycle entry, metabolism, ribosome biogenesis.
Chromosomal translocations are especially frequent in leukaemias & lymphomas.

Example 2 – RAS Family (Most Common Human Oncogene)

Proteins: HRAS, KRAS (4A/4B), NRAS; act as GDP/GTP binary switches for downstream effectors (Raf, PI3K).
Normal cycle: GDP-bound (inactive) → GEFs exchange GDP→GTP (active) → GAPs stimulate GTP hydrolysis.
Oncogenic point mutations (G12, G13, Q61, etc.) abolish GTPase activity → RAS locked in GTP-bound state.
Gain-of-function is dominant: only one mutated allele suffices (“one-hit”).
RAS mutations found in $20{-}30\%$ of all tumours.

Three Canonical Gain-of-Function Categories (Review)

Point Mutation (activation or deregulation)
Gene Amplification (↑ copy number → ↑ protein)
Chromosomal Translocation (promoter swap or fusion protein)

Comparative Summary – TSGs vs Oncogenes

Feature	Tumour-Suppressor Gene	Oncogene
Mutation Type	Loss-of-function, recessive at cellular level (two-hits)	Gain-of-function, dominant (one-hit)
Normal Role	Inhibit proliferation, promote apoptosis, maintain genome	Promote proliferation, survival, growth
Cancer Mechanism	Deletion, nonsense, frameshift, epigenetic silencing	Point mutation, amplification, translocation, viral capture
Familial Examples	$RB1$ (Retinoblastoma), $APC$ (FAP), $TP53$ (Li-Fraumeni)	$RET$ (MEN2), $HRAS$ (Costello), $MET$ (HPRC)

Ethical / Clinical / Practical Implications

Germ-line TSG mutations necessitate genetic counselling & surveillance of at-risk relatives.
Targeted therapies exploit oncogene addiction (e.g., Imatinib for BCR-ABL, EGFR inhibitors for mutant EGFR).
Synthetic-lethal approaches (e.g., PARP inhibitors in BRCA1/2-deficient cancers) leverage caretaker-gene loss.
Viral vaccination (HPV) and anti-viral therapy reduce oncogenic virus burden.
Identification of p53 status influences treatment: p53-deficient tumours often resist DNA-damaging chemo but may be sensitive to mitotic spindle poisons.

Numerical / Statistical Nuggets

$\ge 50\%$ of cancers harbour a p53 mutation.
$40\%$ of retinoblastoma cases involve germ-line $RB1$ mutation; $60\%$ are purely somatic.
RAS mutations account for $20{-}30\%$ of all human tumours.
Li-Fraumeni: $\approx 50\%$ cancer incidence by age 30.
Early-treated retinoblastoma cure rate: $\approx 95\%$ .

Connections to Broader Principles

Cell-cycle checkpoints, DNA-damage signalling (ATM/ATR), and chromatin regulation (histone modifications) integrate with TSG and oncogene pathways.
Hallmarks of cancer (Hanahan & Weinberg): sustaining proliferative signalling (oncogenes), evading growth suppressors (TSGs), resisting cell death, inducing angiogenesis, enabling replicative immortality, genome instability.
Multistep carcinogenesis: sequential oncogene activation and TSG inactivation accumulate → malignant transformation.

Take-Home Messages

TSGs and oncogenes constitute two complementary genetic pillars of cancer biology.
pRB and p53 are prototypical gatekeeper and caretaker TSGs, respectively.
Oncogene activation usually involves gain of abnormal function; TSG involvement usually involves loss.
Knudson’s two-hit model explains recessive behaviour of TSGs and dominant familial predisposition.
Understanding these pathways lays the groundwork for molecularly targeted cancer therapies, risk prediction, and preventive strategies.