Cancer Cytogenetics: Chromosomal Changes and Implications

Aneuploidy

Gain or loss of entire chromosomes.

Trisomy 8

An example of aneuploidy involving an extra copy of chromosome 8.

Monosomy 7

An example of aneuploidy involving the loss of one copy of chromosome 7.

Translocations

Exchange of genetic material between non-homologous chromosomes, often leading to oncogene activation.

t(9;22)

A translocation associated with Chronic Myeloid Leukemia (CML) that forms the Philadelphia chromosome.

BCR-ABL fusion gene

A gene created by the t(9;22) translocation that promotes uncontrolled cell growth.

t(8;14)

A translocation affecting the c-MYC oncogene, driving tumor formation in Burkitt Lymphoma.

Deletions

Loss of a chromosomal segment, often removing tumor suppressor genes.

Deletion of 13q14

An example of a deletion in Retinoblastoma that leads to loss of tumor suppressor genes like TP53 or RB1.

Amplifications

Increased copies of oncogenes, resulting in excessive gene expression.

HER2/neu amplification

An example of amplification in Breast Cancer that leads to overexpression of HER2, promoting aggressive tumor growth.

Inversions

A segment of a chromosome is reversed within the same chromosome.

Inversion of Chromosome 16

An example affecting the core-binding factor gene in Acute Myeloid Leukemia (AML).

Cell Cycle Control

Disrupts normal regulation, leading to uncontrolled proliferation.

Loss of RB1 Function

Loss of function of RB1, a key regulator of the G1/S checkpoint, leads to unchecked cell cycle progression.

Cyclin D1 Amplification

Overexpression of Cyclin D1, an oncogene that promotes G1 → S phase progression, driving tumor growth.

Evasion of Apoptosis

Loss of tumor suppressors allows cells to evade programmed cell death.

p53 Mutation or Loss

Loss or mutation of TP53 prevents damaged cells from undergoing apoptosis, leading to cancer progression.

BCL-2 Overexpression

Overexpression of BCL-2, an anti-apoptotic protein, allows cancer cells to survive indefinitely.

Acute Promyelocytic Leukemia (APL)

A condition where t(15;17) translocation creates the PML-RARA fusion gene, blocking differentiation of myeloid precursor cells.

Chronic Myeloid Leukemia (CML)

A condition where the Philadelphia chromosome (t(9;22)) disrupts hematopoietic stem cell differentiation.

Genomic Instability

Chromosomal abnormalities cause genomic instability, leading to accumulation of mutations.

Mechanisms of Genomic Instability

Defective DNA repair mechanisms, loss of tumor suppressor genes, and errors in chromosome segregation.

Oncogenes

Mutated or overexpressed versions of normal cellular genes that drive cancer cell growth and survival.

Point mutations

Can activate oncogenes, leading to unregulated cell growth.

RAS (G12V mutation)

Causes constitutively active RAS protein, promoting continuous cell proliferation.

Oncogene amplification

Increases the number of gene copies, leading to overproduction of oncogene proteins.

HER2/neu amplification in breast cancer

Overexpression of the HER2 receptor leads to excessive growth signaling.

Chromosomal Translocations

Certain translocations result in the fusion of oncogenes, leading to cancer development.

RAS (HRAS, KRAS, NRAS)

Cell growth signaling associated with pancreatic, colon, lung cancers.

MYC

Regulates cell cycle, apoptosis, metabolism associated with Burkitt lymphoma, neuroblastoma.

ABL1

Tyrosine kinase signaling associated with chronic myeloid leukemia (CML).

Tumor suppressor genes

Regulate cell division, repair DNA damage, and induce apoptosis.

TP53 (guardian of the genome)

Mutated in over 50% of cancers, preventing apoptosis in damaged cells.

RB1 gene deletion

Leads to retinoblastoma, osteosarcoma.

BRCA1 methylation

Silences DNA repair function in breast and ovarian cancers.

Two-Hit Hypothesis (Knudson's Hypothesis)

Both alleles of a tumor suppressor gene must be inactivated for cancer to develop.

TP53

Regulates cell cycle, DNA repair, apoptosis found in over 50% of cancers.

RB1

Controls G1/S checkpoint associated with retinoblastoma, osteosarcoma.

BRCA1/BRCA2

DNA repair associated with breast, ovarian, prostate cancers.

PTEN

Inhibits PI3K/AKT pathway associated with various cancers.

Gene fusions

Arise from chromosomal rearrangements that combine two separate genes into a new fusion gene.

t(9;22) in CML

Creates the Philadelphia chromosome, forming the BCR-ABL1 fusion gene.

BCR-ABL1 fusion in CML

Activates tyrosine kinase, driving cell growth.

PML-RARA fusion in APL

Blocks maturation of white blood cells, causing accumulation of immature cancerous cells.

BCR-ABL1 detection

Crucial for diagnosing CML.

Imatinib (Gleevec)

Inhibits BCR-ABL1, leading to remission in CML patients.

BCR-ABL1

t(9;22) (Philadelphia chromosome) causes constitutive tyrosine kinase activity, leading to uncontrolled cell division.

PML-RARA

t(15;17) blocks myeloid differentiation, causing accumulation of immature cells.

EWS-FLI1

t(11;22) activates oncogenic gene expression, driving tumor growth.

Oncogenes

Act like the accelerator, driving cell growth and division.

Oncogenes

Act like the accelerator, driving cell growth and division; mutations or amplifications make them hyperactive, pushing cancer forward.

Tumor Suppressor Genes

Work as brakes, regulating cell division; when mutated, deleted, or silenced, the brakes fail, allowing uncontrolled proliferation.

Gene Fusions

Can either activate oncogenes or inactivate tumor suppressor genes, further accelerating cancer progression.

Fluorescence In Situ Hybridization (FISH)

Detects and localizes specific DNA sequences on chromosomes; identifies chromosomal translocations, gene amplifications, and deletions.

Comparative Genomic Hybridization (CGH)

Detects chromosomal imbalances (gains/losses) in tumor cells.

Conventional CGH

Detects large chromosomal changes.

Array CGH (aCGH)

Identifies subtle imbalances & copy number variations (CNVs).

Karyotyping

Standard method for detecting large chromosomal alterations (e.g., translocations, aneuploidy).

Next-Generation Sequencing (NGS)

Detects mutations at the molecular level, including SNVs, indels, and structural variants.

Polymerase Chain Reaction (PCR)

Identifies specific gene mutations or fusion genes.

Immunohistochemistry (IHC)

Detects protein overexpression in cancer; commonly used to identify gene amplifications.

Chromothripsis

A catastrophic genomic event where one or a few chromosomes undergo massive shattering and chaotic rearrangement in a single event.

Chromosomal Shattering

A chromosome or chromosomal region fragments into tens to hundreds of pieces.

Reassembly

The DNA repair machinery randomly stitches the broken fragments back together, causing deletions, duplications, inversions, and translocations.

Triggering Factors of Chromothripsis

Ionizing radiation or severe DNA damage, telomere crisis leading to end-to-end chromosome fusions, and mitotic errors.

Localized Genomic Chaos

Unlike gradual genomic instability, chromothripsis affects specific chromosomes or regions rather than the entire genome.

Signature Genomic Patterns

Discontinuous DNA copy number changes and clustered breakpoints localized to one or a few chromosomes.

Unique Rearrangements

Extensive rearrangements and loss of heterozygosity in affected regions.

Loss of Tumor Suppressor Genes

Chromosomal rearrangements delete key tumor suppressors, removing growth regulation.

Activation of Oncogenes

Fusion of oncogenes to active regulatory regions leads to overexpression, driving cancer progression.

Genomic Instability

Increases the mutational burden, enabling cancer cells to adapt and survive.

Bone Cancers (Osteosarcoma)

Found in ~25% of cases, driving genomic chaos.

Brain Cancers (Glioblastoma Multiforme)

Highly aggressive tumors frequently show chromothripsis.

Hematologic Malignancies (AML)

Observed in some acute myeloid leukemia cases.

Soft Tissue Sarcomas

Seen in Ewing sarcoma and other aggressive tumors.

Cytogenetic Techniques

Karyotyping identifies highly abnormal chromosomal structures.

Whole-Genome Sequencing (WGS)

Identifies clustered breakpoints and chaotic rearrangements with high resolution.

Prognostic Significance of Chromothripsis

Chromothripsis is associated with a poor prognosis due to high genomic instability.

Telomeres

Repetitive DNA sequences (TTAGGG in humans) at chromosome ends, capped with specialized proteins to protect chromosomal ends from being recognized as DNA damage.

Functions of Telomeres

Protect chromosome ends from degradation and fusion, maintain genomic stability by preventing chromosome shortening during replication, and act as a mitotic clock, limiting the number of cell divisions.

Telomere Dysfunction

Occurs when telomeres become critically short or lose their protective capping, leading to genomic instability.

Telomere Attrition

Normal somatic cells experience telomere shortening due to the end replication problem, with oxidative stress accelerating this process.

Dysfunctional Telomere Capping

Mutations in telomere-binding proteins (TRF1, TRF2, POT1) disrupt capping, exposing chromosome ends.

Consequences of Telomere Dysfunction

Chromosomal fusions, Breakage-Fusion-Bridge (BFB) cycles, and activation of the DNA Damage Response (DDR).

Breakage-Fusion-Bridge (BFB) Cycles

Short or uncapped telomeres are recognized as double-strand breaks, leading to chromosome ends fusing and creating dicentric chromosomes.

Genomic Instability

Leads to widespread chromosomal abnormalities, a hallmark of cancer.

Avoidance of Senescence & Apoptosis

Normally, telomere dysfunction activates DDR, leading to cellular senescence or apoptosis; mutations in TP53 or RB1 allow pre-cancerous cells to bypass these mechanisms.

Role of Telomerase

Telomerase is a ribonucleoprotein enzyme that adds telomeric repeats to chromosome ends, preventing shortening.

Telomerase Reactivation in Cancer

Occurs in ~85-90% of cancer cases, allowing cancer cells to maintain telomere length and achieve replicative immortality.

TERT Promoter Mutations

Increase TERT gene transcription and are found in melanoma, glioblastoma, and bladder cancer.

Epigenetic Changes

Hypomethylation of the TERT promoter or chromatin modifications can activate telomerase.

Alternative Lengthening of Telomeres (ALT)

A telomerase-independent mechanism of telomere elongation seen in 10-15% of cancers.

Mechanism of ALT

Relies on homologous recombination, copying sequences from other telomeres or extrachromosomal telomeric DNA.

Cancers Associated with ALT

Common in mesenchymal-origin cancers, such as osteosarcoma and soft tissue sarcomas.

Impact of Telomere Dysfunction in Early Stage Cancer

Telomere shortening in precancerous lesions leads to chromosomal instability and mutations.

Impact of Telomere Dysfunction in Late Stage Cancer

Telomerase or ALT activation stabilizes telomeres, enabling indefinite cancer cell proliferation.

Examples in Cancer

Lung Cancer: TERT promoter mutations and telomerase reactivation are common; Melanoma: Frequently associated with TERT promoter mutations.

Telomerase Reactivation in Breast Cancer

Telomerase is reactivated in the majority of breast cancer cases, contributing to tumor progression by preventing telomere shortening.

Diagnostic Biomarkers

TERT promoter mutations in cell-free DNA (cfDNA) from blood or tissue biopsies can serve as cancer biomarkers.