Chromosomal Changes

Slide 1 · Chromosomal Changes

Chromosomal alterations in cancer: mechanisms, examples, and clinical significance

Translocations · Deletions · Amplification · Chromothripsis

Dr Abu Suraih Sakhri

MBBS, MD (Pathology)

www.abusuraihsakhri.com

Slide 2 · Learning outcomes

Classify numerical and structural chromosomal changes in tumor cells.

Explain enhancer substitution, fusion oncogenes, deletion and amplification.

Relate recurrent abnormalities to selected neoplasms and targeted therapy.

Interpret chromothripsis and the limits of the source evidence.

Slide 3 · The central biological consequence

Chromosomal alteration

Structural rearrangement or altered chromosome number

Gene dysregulation

Gain of oncogenic function or loss of restraint

Neoplastic phenotype

Proliferation, survival or blocked differentiation

Different chromosome lesions converge on changed activity of cancer-associated genes.

Slide 4 · Chromosome number versus structure

Numerical change

Whole chromosomes gained or lost

Aneuploidy is common in tumor genomes

May appear during progression or early in some contexts

Structural change

DNA segments moved, deleted, inserted or amplified

Can create recurrent tumor-specific lesions

May directly alter proto-oncogenes or tumor suppressors

Slide 5 · Recurrent changes are not random trivia

Characteristic lesions have been identified in most leukemias and lymphomas.

Many sarcomas and an increasing number of carcinomas also have recurrent changes.

A recurrent breakpoint is a clue to a gene important in the tumor.

Chromosome-level changes provide biological and clinical information.

Slide 6 · When do chromosome alterations arise?

Often later

Changes accompany progression

Sometimes early

Telomere loss can precede transformation

Key interpretation

Timing depends on the underlying tumor pathway

Chromosome damage can sometimes be an initiating lesion, not merely a late event.

Slide 7 · Genomic instability enables additional lesions

Normal p53-dependent checkpoints limit persistence of grossly damaged genomes.

Loss of p53 function permits survival of cells with structural chromosome damage.

Error-prone end joining can preserve rearranged chromosomes.

Genomic instability can accelerate acquisition of cancer-promoting changes.

Slide 8 · Two complementary ways to study the cancer karyotype

Metaphase karyotyping

Morphologic identification of metaphase chromosomes

Historically the foundational approach

Provides chromosome-scale patterns

Genome-sequence reconstruction

Chromosomes reconstructed from deeply sequenced cancer DNA

Recognizes simple and complex rearrangements

Increasingly used in research; Future clinical replacement is uncertain

Slide 9 · From a breakpoint to a candidate cancer gene

Find recurrent breakpoints

Chromosome anomaly is reproducible

Map nearby genes

Look for oncogenes or tumor suppressors

Test functional consequence

Overexpression, fusion or gene loss

Recurrent breakpoints can identify cancer-associated genes such as MYC, BCL2, ABL, APC and RB.

Slide 10 · Why chromosomal changes matter clinically

Diagnosis

Some lesions help define a tumor type.

Prognosis

Selected abnormalities correlate with disease course.

Therapy and monitoring

Fusion proteins can be drug targets; Molecular products can track treatment response.

Slide 11 · Structural lesions: The core mechanisms

Alteration

Translocation

Regulatory element substitution or fusion gene

Typical consequence

Deletion

Tumor suppressor loss; Sometimes promoter juxtaposition or fusion

Slide 12 · How translocation can activate an oncogene

DNA double-strand breaks

At least two genomic sites

Rejoining of broken ends

Derivative chromosomes form

Oncogenic consequence

New regulatory context or fusion coding region

Breakage and rejoining alone do not guarantee malignancy; The affected genes determine biological significance.

Slide 13 · The two fundamental translocation outcomes

Enhancer/promoter substitution

Proto-oncogene coding region stays intact

New, highly active regulation raises protein abundance

Prototype: MYC–IGH in Burkitt lymphoma

Fusion gene

Parts of two coding regions become joined

Novel chimeric protein with altered function

Prototype: BCR::ABL in CML

Slide 14 · Schematic reciprocal translocation

Before rearrangement

After rearrangement

Chromosome A

Chromosome B

Derivative chromosome

Reciprocal derivative

Break + rejoin

1. Two original chromosomes

2. Breakpoints and rejoined segments

3. Two derivative chromosomes

Slide 15 · Regulatory substitution changes expression—not sequence

Intact MYC coding region

Gene retains identity

IGH regulatory environment

Highly active in B lineage cells

High MYC expression

A proliferation-associated oncoprotein is overproduced

The position of the breakpoint governs the precise mechanism.

Slide 16 · Fusion changes the protein itself

Coding segment from gene 1

One partner contributes sequence

Coding segment from gene 2

A second partner contributes sequence

Chimeric oncoprotein

Novel activity drives oncogenic signaling or blocks differentiation

The consequence depends on the functional domains assembled.

Slide 17 · Double-strand breaks are prerequisite events

Translocations require breakage at two or more genomic locations.

Broken ends are joined into derivative chromosomes.

The source identifies nonhomologous end joining in BCR::ABL formation.

The oncogenic product is the causal focus—not merely the abnormal karyotype.

Slide 18 · Why lymphoid cells are vulnerable to translocations

Antigen receptor gene recombination normally involves regulated DNA breaks.

Both B- and T-cell progenitors rearrange antigen receptor genes.

Class switching occurs in antigen-stimulated mature B cells.

Mistargeted breakage or joining can juxtapose powerful receptor-locus regulation with oncogenes.

Slide 19 · Antigen receptor locus predicts lineage

Immunoglobulin locus involved

The associated tumor is of B-cell origin.

Regulatory regions of active immunoglobulin genes may drive an oncogene.

Examples: MYC, CCND1 or BCL2 with IGH.

T-cell receptor locus involved

The associated tumor is of T-cell origin.

Antigen receptor rearrangement offers a route to oncogenic juxtaposition.

The oncogenic partner varies across lymphoid tumors.

Slide 20 · MYC in normal proliferating cells

MYC is a proto-oncogene whose expression is normally tightly controlled.

High MYC expression is physiologic chiefly in actively dividing cells.

The tumor-promoting lesion in Burkitt lymphoma primarily changes regulation.

The coding region can remain intact despite strong oncogenic consequences.

Slide 21 · Burkitt lymphoma: T(8;14)(q24;q32)

Before rearrangement

After rearrangement

Chromosome 8 · MYC

Chromosome 14 · IGH

MYC next to IGH regulation

Reciprocal derivative

Break + rejoin

1. MYC resides at 8q24

2. IGH locus lies at 14q32

3. MYC becomes controlled by an active B-cell regulatory environment

Slide 22 · Burkitt: Regulatory relocation to excessive MYC

MYC locus at 8q24

Normal control in proliferating cells

T(8;14) places MYC near IGH

IGH elements substitute for MYC regulation

Persistent MYC overexpression

Oncogenic proliferation program

The MYC–immunoglobulin rearrangement is central to Burkitt lymphoma pathogenesis.

Slide 23 · Burkitt: Read the notation accurately

T denotes a chromosomal translocation.

(8;14) identifies the chromosomes involved.

(q24;q32) identifies the chromosomal arm/band positions.

In this example, MYC is at 8q24 and IGH is at 14q32.

Slide 24 · MYC activation is not a MYC fusion protein

What changes in Burkitt lymphoma

Regulatory context of MYC

Abundance and timing of MYC expression

Relationship to an immunoglobulin locus

What does not need to change

MYC coding sequence may remain unaltered

No MYC–IGH hybrid protein is required

Chromosomal juxtaposition is the pathogenic mechanism

Slide 25 · Selected translocations in lymphoid tumors

Tumor

Rearrangement

Key genes

Burkitt lymphoma

T(8;14)(q24;q32)

MYC / IGH

Mantle cell lymphoma

T(11;14)(q13;q32)

CCND1 / IGH

Follicular lymphoma

T(14;18)(q32;q21)

IGH / BCL2

Slide 26 · BCR::ABL: The Philadelphia chromosome

CML is the prototypic malignancy associated with the Philadelphia chromosome.

The translocation joins sequences from ABL on chromosome 9 and BCR on chromosome 22.

BCR::ABL is formed on derivative chromosome 22.

The rearrangement also occurs in a subset of B-cell acute lymphoblastic leukemias.

Slide 27 · T(9;22) creates a fusion gene

Before rearrangement

After rearrangement

Chromosome 9 · ABL

Chromosome 22 · BCR

Derivative chromosome

Partner derivative

Break + rejoin

1. ABL breakpoint: Chromosome 9

2. BCR breakpoint: Chromosome 22

3. Derivative chromosome 22 carries BCR::ABL

Slide 28 · BCR–ABL: Constitutive kinase signaling

BCR::ABL fusion DNA

Chimeric coding sequence

BCR–ABL fusion protein

Tyrosine kinase activity is constitutive

Oncogenic signaling

Sustained cell-growth and survival signals

Gene/fusion transcript notation BCR::ABL; Protein written BCR–ABL.

Slide 29 · Why CML molecular tests are clinically useful

At initial evaluation

Detect the BCR::ABL fusion or its RNA product.

The source identifies fusion detection as essential for diagnosis of CML.

Links malignancy to a specific driver.

During kinase inhibitor therapy

Quantify the fusion gene product or transcript.

Molecular measurements follow treatment response.

Converts genomic mechanism into a longitudinal marker.

Slide 30 · Why BCR–ABL is a therapeutic target

The abnormal kinase has constitutive enzymatic activity.

An oncogenic enzyme can be inhibited pharmacologically.

BCR–ABL kinase inhibitors are an established example in the source.

A genomic abnormality can predict sensitivity to mechanism-directed treatment.

Slide 31 · Fusion oncogenes: Two principal output classes

Kinase fusion

Creates an overactive signaling enzyme.

Primary effect: Persistent downstream oncogenic signals.

Example: BCR–ABL.

Nuclear regulatory fusion

Alters transcription or chromatin regulation.

Primary effect can be failure of differentiation.

Example: PML–RARA.

Slide 32 · Acute promyelocytic leukemia: Central genetic event

APML is virtually always associated with t(15;17) in the supplied chapter.

The reciprocal rearrangement generates PML::RARA.

The fusion protein incorporates portions of PML and retinoic acid receptor α (RARα).

Unlike a constitutive kinase, the central abnormality is transcriptional regulation.

Slide 33 · PML::RARA derives from t(15;17)

Before rearrangement

After rearrangement

Chromosome 15 · PML

Chromosome 17 · RARA

Derivative chromosome

Partner derivative

Break + rejoin

1. PML is a nuclear regulatory partner

2. RARA encodes retinoic acid receptor α

3. PML::RARA joins coding sequences from both genes

Slide 34 · Normal RARα supports myeloid differentiation

Retinoid available

Binds physiologic RARα complex

DNA-bound transcription complex

Activates retinoid-responsive genes

Myeloid maturation

Progenitors differentiate toward neutrophils

Normal RARα is part of a DNA-binding transcription factor complex.

Slide 35 · Unliganded PML–RARA blocks maturation

PML–RARA has reduced retinoid affinity

Physiologic retinoid is insufficient

Repressor complexes remain recruited

Differentiation genes stay inhibited

Promyelocytes accumulate

Normal hematopoietic elements are displaced

Failure of maturation causes abnormal accumulation of myeloid progenitors.

Slide 36 · Normal RARα versus PML–RARA

Normal retinoid response

Retinoids bind the receptor complex.

Activating transcriptional cofactors support gene expression.

Neutrophil differentiation proceeds.

Pathologic fusion response

Reduced affinity at physiologic retinoid levels.

Repressor recruitment inhibits the target genes.

Differentiation is arrested.

Slide 37 · ATRA reverses the transcriptional block

Pharmacologic ATRA

Ligand can bind PML–RARA

Repressor displacement

Activation-associated complexes are recruited

Differentiation gene expression

Neoplastic precursors mature

ATRA changes the fusion-protein complex from a repressive to a differentiation-permitting state.

Slide 38 · ATRA also promotes fusion-protein clearance

ATRA binds PML–RARA

Changes complex configuration

Ubiquitination and proteolysis

Fusion protein becomes less stable

Reduced transcriptional repression

Supports maturation and disease-cell clearance

Proteasomal removal reduces persistence of the differentiation-blocking complex.

Slide 39 · Differentiation therapy: A mechanistic success

APML illustrates treatment of a malignant phenotype by inducing maturation.

Differentiated neutrophils have a limited lifespan rather than indefinite self-renewal.

The source describes marrow clearance over several days and recovery of hematopoiesis.

The paradigm motivated efforts against other nuclear fusion oncoproteins.

Slide 40 · Three prototypes of oncogenic chromosome rearrangement

Tumor

Molecular lesion

Functional result

Burkitt lymphoma

MYC near IGH regulatory region

MYC overexpression

CML

BCR::ABL fusion

Constitutive tyrosine kinase

APML

PML::RARA fusion

Transcriptional repression; Maturation arrest

Slide 41 · Selected myeloid leukemia translocations

Tumor in source

Translocation

Affected genes

CML

T(9;22)(q34;q11)

ABL / BCR

AML

T(8;21)(q22;q22)

RUNX1T1 / RUNX1

APML

T(15;17)(q22;q21)

PML / RARA

Slide 42 · Examples beyond lymphoid and myeloid neoplasia

Setting

Translocation

Affected genes

Ewing sarcoma

T(11;22)(q24;q12)

FLI1 / EWSR1

Prostatic adenocarcinoma

T(7;21)(p22;q22)

ETV1 / TMPRSS2

Prostatic adenocarcinoma

T(17;21)(p21;q22)

ETV4 / TMPRSS2

Slide 43 · Deletion is not synonymous with oncogene loss

Deletions are frequent chromosomal structural abnormalities in cancer.

Most familiar consequence: Loss of a tumor suppressor gene.

But some deletions activate oncogenes through regulatory juxtaposition.

Others create a fusion gene by bringing two coding segments together.

Slide 44 · Tumor suppressor deletion: Loss of restraint

Chromosomal segment deleted

Tumor suppressor locus is affected

Reduced suppressor function

Control of growth or survival weakens

Neoplastic selection

A clone with a growth advantage may expand

The consequence depends on which growth-restraining gene is removed.

Slide 45 · Examples of tumor suppressor loss

RB locus in retinoblastoma

Chromosome 13q14 deletion can involve RB.

RB is a tumor suppressor linked to cell-cycle restraint.

An example of chromosomal loss in cancer.

VHL locus in renal carcinoma

Chromosome 3p deletion can involve VHL.

Loss of VHL function is common in renal cell carcinoma.

Different locus, same general deletion principle.

Slide 46 · Small deletion can activate an intact oncogene

Remove an intervening segment

Deletion changes DNA neighborhood

Bring TAL1 close to active promoter

Regulatory juxtaposition occurs

Increase TAL1 expression

Transcription factor is overproduced

Deletion can activate a nearby proto-oncogene without altering its coding sequence.

Slide 47 · TAL1 deletion: A T-ALL example

The source reports small chromosome 1 deletions in about 25% of T-cell ALL.

These deletions juxtapose TAL1 with a nearby active promoter.

The result is increased TAL1 transcription-factor expression.

This is a regulatory mechanism rather than tumor suppressor deletion.

Slide 48 · An intrachromosomal rearrangement can produce a fusion

Two genes on the same chromosome

EML4 and ALK sequences are brought together

Intrachromosomal rejoining

DNA sequences are rejoined

EML4::ALK fusion

Constitutively active chimeric kinase

Fusion of partner sequences creates a new kinase-driving oncogene.

Slide 49 · EML4::ALK in lung adenocarcinoma

The supplied chapter reports the fusion in about 5% of lung adenocarcinomas.

The intrachromosomal rearrangement joins EML4 and ALK sequences.

The encoded EML4–ALK protein has constitutive tyrosine kinase activity.

The kinase is an important therapeutic target.

Slide 50 · Deletions have distinct functional outcomes

Deletion pattern

RB / VHL deleted

Loss of tumor suppressor function

Biological consequence

Regulatory intervening DNA removed near TAL1

Active promoter drives TAL1 overexpression

Slide 51 · Insertions and microsatellite expansion

DNA insertions can also alter the function of cancer-associated genes.

The text emphasizes expansions of DNA microsatellite sequences.

Such insertions are a feature of cancers with defective mismatch repair.

This distinguishes small sequence changes from large karyotypic rearrangements.

Slide 52 · Gene amplification increases oncogene dosage

Reduplication of oncogene DNA

Copy number rises

Many gene copies in one cell

Can reach several hundred copies

Oncogene overexpression

Protein activity may rise accordingly

Some amplifications create recognizable structural cytogenetic patterns.

Slide 53 · Two cytogenetic manifestations of amplification

Double minutes

Many small extrachromosomal DNA structures.

Often circular DNA, capable of high copy number.

Appear as separate elements in karyotypes.

Homogeneous staining region

Amplified sequences inserted into a chromosome.

Region lacks normal light/dark band pattern.

Appears uniformly stained on the chromosome.

Slide 54 · Double minutes: Extrachromosomal DNA

Main chromosomal DNA

Amplified extrachromosomal units

1. Multiple small DNA elements

2. Amplified oncogene sequence

3. Extrachromosomal, often circular DNA

Schematic—not a stained metaphase spread

Slide 55 · Homogeneous staining regions

Banding pattern retained

Broad uniform amplified region

1. Amplified segment inserted in a chromosome

2. Banding pattern becomes homogeneous

3. The oncogene may be relocated from its usual locus

Schematic—not a stained metaphase spread

Slide 56 · MYCN amplification in neuroblastoma

Mechanism

Amplification raises copies of the MYCN oncogene (termed NMYC in source).

The chapter reports amplification in 25–30% of neuroblastomas.

This is gene-dosage dysregulation.

Clinical implication

MYCN amplification is associated with poor prognosis.

The abnormality is a prognostic marker in this example.

Do not interpret this association as a drug-response test.

Slide 57 · ERBB2 amplification in breast carcinoma

Mechanism

ERBB2 gene amplification increases HER2 receptor abundance.

The supplied chapter reports amplification in about 20% of breast cancers.

This is a molecularly defined subset.

Clinical implication

Therapy directed against HER2 is effective in this subset.

Here the marker has predictive treatment relevance.

The slide does not specify current testing criteria.

Slide 58 · Different roles of chromosome biomarkers

Biomarker

Example

Clinical role in source

Diagnostic

BCR::ABL in CML

Establishes a defining fusion

Monitoring

Quantified BCR::ABL product

Tracks response to kinase inhibition

Prognostic

MYCN amplification in neuroblastoma

Associated with poor prognosis

Predictive

ERBB2 amplification in breast cancer

Identifies HER2-directed treatment context

Slide 59 · Genome sequencing exposes hidden complexity

Whole-genome reconstruction detects many simple rearrangements.

Small deletions, duplications and inversions can evade classic cytogenetics.

Some tumor genomes also contain clustered, highly complex rearrangements.

Chromothripsis is the source’s example of catastrophic structural change.

Slide 60 · Chromothripsis: Break and reassemble

One catastrophic episode

Dozens to hundreds of chromosome breaks

Fragmented DNA repaired

Pieces rejoined without original order

Derivative chromosomes

Numerous deletions, rearrangements and amplifications

The initiating cause of catastrophic chromosomal breakage remains uncertain.

Slide 61 · Chromothripsis: Shattered chromosome schematic

Intact chromosomal segments

Complex reassembled chromosome

Before damage

After misrepair

Fragmentation + rejoining

1. One or several chromosomes may fragment

2. DNA repair rejoins numerous pieces

3. Reassembled material carries complex structural changes

Slide 62 · Chromothripsis: Observed versus hypothesized

Reported

Observed in roughly 1–2% of cancers overall.

Described as particularly common in osteosarcoma and glioma.

Can create multiple rearrangements simultaneously.

Proposed explanation

Origin of the breaks is uncertain.

A single catastrophe might change several cancer genes at once.

Accelerated carcinogenesis remains presented as a hypothesis.

Slide 63 · Not every rearrangement has the same evidentiary status

A recurrent lesion may be closely associated with a tumor type.

A fusion can be a validated tumor driver or actionable enzyme.

A complex genome may contain passenger alterations as well as drivers.

Chromothripsis as an accelerator of cancer is a proposed mechanism in this source.

Slide 64 · Mechanism-to-consequence synthesis

Lesion

Molecular effect

Representative example

Regulatory translocation

Increased oncogene expression

MYC / IGH

Fusion translocation

Chimeric kinase

BCR::ABL

Transcriptional fusion

Blocked maturation

PML::RARA

Deletion

Suppressor loss or oncogene activation

RB; TAL1; EML4::ALK

Amplification

Increased oncogene dosage

MYCN; ERBB2

Slide 65 · Application: Recognize regulatory translocation

QUESTION

A lymphoma has t(8;14)(q24;q32) and high MYC expression. Is a MYC–IGH chimeric protein required?

ANSWER

No. The usual mechanism is relocation of largely intact MYC into an active immunoglobulin regulatory environment.

Gene-expression dysregulation need not require fusion of coding regions.

The hallmark molecular output is MYC overexpression.

Slide 66 · Application: Interpret a kinase fusion

QUESTION

A leukemia harbors BCR::ABL on derivative chromosome 22. What functional abnormality follows?

ANSWER

The fusion encodes a constitutively active BCR–ABL tyrosine kinase.

Fusion proteins can be pharmacologic targets.

Fusion transcript quantification can monitor response in CML.

Slide 67 · Application: Explain a differentiation therapy

QUESTION

Why can pharmacologic ATRA counter the maturation arrest of PML::RARA-positive APML?

ANSWER

It binds the fusion complex, relieves transcriptional repression and promotes fusion-protein degradation.

This enables transcription of maturation-associated genes.

The treatment mechanism differs from kinase inhibition.

Slide 68 · Application: Infer an effect of small deletion

QUESTION

A short deletion juxtaposes TAL1 with an active promoter. Which category of molecular lesion is most relevant?

ANSWER

Oncogene activation by regulatory juxtaposition, not obligatory loss of a tumor suppressor.

Deletion can increase transcription of an intact gene.

The chromosomal size alone does not determine biological effect.

Slide 69 · Application: Distinguish prognostic from predictive

QUESTION

Compare MYCN amplification in neuroblastoma with ERBB2 amplification in breast cancer. What differs clinically?

ANSWER

The source emphasizes adverse prognosis for MYCN and effective HER2-directed therapy for ERBB2.

Do not equate a prognostic association with prediction of drug response.

Molecular consequence and clinical use should be specified separately.

Slide 70 · Five principles to retain

Structural changes can alter expression or create novel oncogenic proteins.

A tumor-defining translocation may be a regulatory swap or a coding fusion.

Deletions may remove suppressors or unexpectedly activate oncogenes.

Amplification changes gene dosage; Double minutes and HSRs are distinct patterns.

Chromothripsis represents exceptional rearrangement complexity with unresolved causation.

Slide 71 · A practical interpretation checklist

Classify the alteration: chromosome number, DNA rearrangement, segment loss, or copy-number gain.

Determine the gene-level effect: dysregulated expression, fusion protein, or tumor suppressor loss.

Specify its clinical use: diagnosis, prognosis, treatment selection, or response monitoring.

Distinguish demonstrated molecular drivers from proposed effects of catastrophic rearrangement.