Epigenetic Changes

Slide 1 · Epigenetic Changes

Chromatin regulation, gene expression and malignant behavior

DNA methylation

Histone regulation

Cancer phenotype

Dr Abu Suraih Sakhri

MBBS, MD (Pathology)

www.abusuraihsakhri.com

Slide 2 · Teaching outcomes: Interpreting the cancer epigenome

Distinguish DNA-sequence lesions from abnormal control of gene expression.

Explain promoter methylation, histone marks, chromatin remodeling and enhancer contacts.

Connect epigenetic lesions to nuclear appearance, tumor lineage, therapy and reversible resistance.

Molecular mechanism

Clinicopathologic meaning

Critical interpretation

Slide 3 · Epigenetics regulates phenotype without changing the DNA code

Epigenetic mechanisms change how genomic information is read, not the underlying base sequence.

Their effects on transcription alter cell behavior, differentiation and disease phenotype.

Cancer may have both sequence mutations and dysregulated epigenetic states.

DNA sequence

Base order

Epigenetic control

Access and transcription

Distinct mechanisms • possible convergence

Slide 4 · Identical genomes can support distinct cell identities

Differentiated cell types express distinct gene programs despite nearly identical genomic DNA.

Chromatin accessibility helps select which genes are active in each lineage.

Cancer emerges within a pre-existing lineage-specific regulatory environment.

Shared genome

Cell lineage A

Gene program

Cell lineage B

Gene program

Slide 5 · Four interacting controls shape transcription

DNA methylation changes the chemical state of regulatory DNA.

Histone modification changes chromatin packing and recruitment of regulatory proteins.

Nucleosome positioning and long-range enhancer contacts control promoter access.

DNA methylation

Histone modifications

Nucleosome positioning

Enhancer–promoter looping

Slide 6 · Chromatin packages DNA but also governs its use

Nucleosomes are DNA wrapped around histone protein cores.

Packing is not uniform: Chromatin can be compact or relatively accessible.

Its organization controls whether transcriptional machinery reaches regulatory DNA.

Original nucleosome schematic

Histone core

Linker DNA

Slide 7 · The nucleosome is the fundamental regulatory unit

The core octamer contains two copies each of histones H2A, H2B, H3 and H4.

Approximately 147 DNA base pairs wrap around the histone core.

Linker DNA connects nucleosomes; Histone H1 associates with linker regions.

Original nucleosome schematic

Histone core

Linker DNA

H2A / H2B / H3 / H4 × 2

Slide 8 · Euchromatin and heterochromatin represent different access states

Euchromatin is relatively dispersed and is associated with active transcription.

Heterochromatin is cytochemically dense and generally transcriptionally inactive.

These are functional chromatin states, not changes in DNA sequence.

Accessible

Compact

Euchromatin

Accessible

Heterochromatin

Compact

Regulatory access determines transcription

Slide 9 · Gene activity depends on access to promoter DNA

Chromatin opening makes DNA more accessible to transcription factors and RNA polymerase.

Chromatin compaction restricts access and generally reduces transcription.

Local architecture—not merely the presence of a gene—determines whether it is expressed.

Accessible

Compact

Open chromatin

Accessible promoter

Compact chromatin

Restricted promoter

Regulatory access determines transcription

Slide 10 · Writers, readers and erasers interpret histone marks

Writers deposit chemical modifications on histone proteins.

Readers recognize specific marked histones and recruit regulatory activities.

Erasers remove marks; Remodelers reposition nucleosomes on DNA.

Writer

Deposits a mark

Reader

Binds a mark

Eraser

Removes a mark

Remodeler

Repositions nucleosomes

Slide 11 · DNA marks and histone marks act at different substrates

DNA methyltransferases chemically modify cytosine residues in DNA.

Histone-modifying enzymes act on protein residues in nucleosomes.

The two systems cooperate to create context-specific transcriptional states.

DNA

Cytosine methylation

Histones

Protein modifications

Distinct mechanisms • possible convergence

Slide 12 · DNA methylation can silence regulatory regions

Methylation of DNA is generated by DNA methyltransferases.

High methylation at gene regulatory elements generally associates with transcriptional silencing.

The meaning of methylation must be interpreted in its genomic location.

Gene regulatory region

Promoter

Methyl marks

Reduced regulatory-region transcription

Slide 13 · Promoter methylation can switch off a tumor suppressor

Selective hypermethylation at a tumor-suppressor promoter can diminish its transcription.

Protein output is reduced even when that allele retains an intact coding sequence.

This is an epigenetic route to loss of tumor suppressor activity.

Gene regulatory region

Promoter

Methyl marks

Reduced tumor suppressor transcription

Slide 14 · CpG dinucleotides provide DNA methylation sites

The chemical modification targets cytosine bases, commonly at CpG dinucleotides.

A promoter region can acquire abnormal local hypermethylation in cancer.

The regulatory consequence is gene-dependent; Methylation is not a universal on–off label.

Gene regulatory region

Promoter

Methyl marks

Reduced regulatory-region transcription

Slide 15 · DNA methyltransferases write a reversible epigenetic mark

DNA methyltransferase enzymes establish DNA methylation states.

The cell also possesses processes and proteins that reverse or interpret methylation.

Cancer-associated mutations can affect proteins controlling the methylation landscape.

DNA methyltransferase

Methylated regulatory DNA

Enzymatically mediated change

Slide 16 · Tumor suppressor silencing may involve both alleles

Promoter hypermethylation affecting one tumor-suppressor allele.

The partner allele may be lost through deletion or disabled by mutation.

Combined loss can eliminate tumor-suppressive function without identical lesions in both copies.

Two copies of a tumor suppressor

Allele 1

Promoter hypermethylation

Allele 2

Mutation or deletion

Functional loss

Slide 17 · Promoter hypermethylation is distinct from coding mutation

Coding mutation alters the DNA base sequence of the gene.

Promoter hypermethylation changes transcriptional regulation at an otherwise potentially intact allele.

Both can converge on reduced functional tumor-suppressor protein.

Coding mutation

Altered gene product

Promoter methylation

Reduced transcription

Distinct mechanisms • possible convergence

Slide 18 · CDKN2A illustrates epigenetic tumor suppressor loss

The CDKN2A locus can be hypermethylated in several malignancies.

This complex locus encodes the p14/ARF and p16/INK4a tumor suppressors.

These proteins feed into the p53 and RB tumor-suppressive pathways, respectively.

CDKN2A

P14/ARF → p53 pathway

P16/INK4a → RB pathway

Slide 19 · P14/ARF supports the p53 defense program

One CDKN2A-derived tumor suppressor is p14/ARF.

Its activity to enhancement of the p53 tumor-suppressor pathway.

Epigenetic silencing of the locus can therefore affect a major anticancer defense.

CDKN2A expression

P14/ARF

P53 pathway

Slide 20 · P16/INK4a contributes to RB-mediated growth control

A second CDKN2A-derived protein is p16/INK4a.

Its tumor-suppressive effect enhances RB pathway activity.

Loss of CDKN2A expression can therefore compromise RB-associated growth restraint.

CDKN2A expression

P16/INK4a

RB pathway

Slide 21 · Global methylation disturbance affects multiple genes

Many cancers have abnormal DNA methylation extending beyond a single promoter.

Some regions may gain methylation while others lose it.

Consequences include inappropriate increases or decreases in expression across many loci.

Schematic methylation map (not quantitative)

Abnormal gain or loss across multiple regions

Slide 22 · Local and genome-wide methylation changes are not synonyms

Local promoter hypermethylation offers a mechanism for suppressing a specific gene.

Global dysregulation describes an altered genome-wide pattern of methylation.

Both may coexist in an individual cancer cell.

Feature

Local change

Genome-wide change

Scale

A promoter / locus

Many genomic regions

Effect

Silencing of a target gene

Diverse expression changes

Cancer link

Tumor-suppressor inactivation

Regulatory network disruption

Slide 23 · The expression effect of altered methylation is context-specific

Genome-wide changes do not uniformly increase or decrease all transcripts.

A gene may be overexpressed or underexpressed according to local regulatory changes.

Methylation findings require locus-level interpretation rather than a single global direction.

Abnormal methylation landscape

Some genes

Underexpressed

Other genes

Overexpressed

Slide 24 · Acute myeloid leukemia provides a methylation-regulator example

DNMT3A among DNA-methylation regulators mutated in acute myeloid leukemia.

A mutation in an epigenetic enzyme can disturb expression of numerous downstream genes.

This links a genetic driver lesion to an abnormal epigenomic state.

DNMT3A mutation

Aberrant DNA methylation

Altered gene expression

Slide 25 · Genetic lesions can reprogram epigenetic state

Mutations in genes encoding epigenetic regulators are recurrent in cancers.

The resulting defective proteins can alter methylation, histone marks or nucleosome positioning.

Genomic alteration and epigenomic dysregulation are therefore mechanistically connected.

Regulator gene mutation

Epigenomic disruption

Malignant gene program

Slide 26 · Histone modifications change transcriptional competence

Histone proteins undergo acetylation, methylation and phosphorylation.

The effect depends on the modification and the specific residue affected.

Histone marks can recruit factors that open or compact nearby chromatin.

Acetyl

Methyl

Phosphate

Effect depends on mark and position

Slide 27 · Histone acetylation generally favors accessible chromatin

Histone acetyltransferases add acetyl groups to lysine residues.

The modification generally promotes more open chromatin and gene transcription.

This is a tendency, not a rule that every acetylation event independently activates every gene.

HAT adds acetyl groups

Histone lysine acetylation

More accessible chromatin

Slide 28 · Histone acetyltransferases act as chromatin writers

Histone acetyltransferases (HATs) catalyze addition of acetyl marks.

Open chromatin makes regulatory DNA more accessible to transcriptional machinery.

Alteration of acetylation regulators in cancer can reshape the transcriptional program.

Histone acetyltransferase

Acetylated histone lysines

Enzymatically mediated change

Slide 29 · Histone deacetylases remove the acetyl mark

Histone deacetylases (HDACs) erase acetyl groups from histones.

Their activity generally favors chromatin condensation and reduced transcription.

Because the mark is enzymatically removable, this system can be pharmacologically targeted.

Histone deacetylase

Deacetylated histone lysines

Enzymatically mediated change

Slide 30 · Histone acetylation is a dynamic balance

Acetyltransferases and deacetylases have opposing enzymatic activities.

The transcriptional state can shift as marks are written or erased.

Net expression changes depend on the broader chromatin regulatory context.

HATs

Add acetyl groups

HDACs

Remove acetyl groups

Slide 31 · Histone methylation is not uniformly repressive

Specific enzymes methylate lysine and arginine residues on histones.

Methylation of distinct histone lysines can associate with activation or repression.

The position of the mark is crucial to its functional meaning.

Acetyl

Methyl

Phosphate

Effect depends on mark and position

Slide 32 · Residue identity determines the meaning of a histone mark

Two methylated histones need not have equivalent transcriptional effects.

Readers recognize particular modification patterns and recruit appropriate regulators.

Interpreting a mark requires its biochemical and chromosomal context.

Methyl mark A

Activation-associated

Methyl mark B

Repression-associated

Distinct mechanisms • possible convergence

Slide 33 · Histone phosphorylation can alter access in either direction

Histone serine residues can acquire phosphate groups.

Depending on the affected position, associated chromatin may open or compact.

The mark cannot be interpreted correctly without its specific molecular context.

Acetyl

Methyl

Phosphate

Effect depends on mark and position

Slide 34 · Readers translate marks into cellular consequences

Chromatin reader proteins bind modified histones bearing recognized marks.

They help recruit or organize downstream regulatory activities.

A mark influences expression through the proteins and complexes that respond to it.

Writer

Deposits a mark

Reader

Binds a mark

Eraser

Removes a mark

Remodeler

Repositions nucleosomes

Slide 35 · Chromatin remodelers move nucleosomes on DNA

Remodeling complexes reposition nucleosomes relative to regulatory DNA.

This can expose or conceal promoters and other regulatory sites.

Cancer-associated lesions in remodeling components can alter access to entire gene programs.

Nucleosomes obscure promoter

Promoter

Remodeling exposes a regulatory region

Slide 36 · Nucleosome positioning is independent of gene sequence

The same promoter sequence can be accessible in one chromatin configuration.

A differently placed nucleosome can obscure that regulatory sequence.

Distinct gene activity does not require alteration of the underlying promoter DNA.

Accessible

Compact

Euchromatin

Accessible

Heterochromatin

Compact

Regulatory access determines transcription

Slide 37 · Enhancer–promoter looping adds a three-dimensional layer

Chromatin organizing factors modulate long-distance contacts along DNA.

An enhancer may be brought near a promoter by higher-order looping.

Altered genome organization can influence the strength of transcriptional programs.

Along linear DNA: Widely separated loci

Enhancer

Promoter

Chromatin folding

Enhancer

Promoter

Spatial proximity enables regulatory contact

Slide 38 · The malignant epigenome reflects several interacting layers

Promoter methylation, histone marks and nucleosome placement jointly influence access.

Enhancer contacts add spatial control over transcription.

A mutation in one regulatory component can propagate to many target genes.

Abnormal epigenetic state

Gene expression

Differentiation

Drug response

Schematic: Interacting downstream outcomes

Slide 39 · Abnormal nuclear appearance reflects chromatin disturbance

Cancer nuclei may show hyperchromasia, chromatin clumping or clearing.

These histomorphologic alterations to disordered chromatin organization.

Nuclear morphology therefore provides a visible correlate, not a complete readout, of epigenomic regulation.

Schematic nuclear chromatin appearances

Hyperchromatic

Clumped

Vesicular

Concept diagram; Not a histology specimen

Slide 40 · Hyperchromasia is a morphologic observation—not a methylation assay

Hyperchromatic tumor nuclei stain more darkly at light microscopy.

Chromatin organization contributes to this appearance.

The finding does not identify which epigenetic enzyme or promoter is abnormal.

Schematic nuclear chromatin appearances

Hyperchromatic

Clumped

Vesicular

Concept diagram; Not a histology specimen

Slide 41 · Chromatin clumping and clearing are alternative patterns

Clumped chromatin yields coarse, uneven nuclear density.

Vesicular chromatin describes a paler, more open-appearing nuclear pattern.

Both may be encountered in malignancy; Neither specifies a unique molecular lesion.

Schematic nuclear chromatin appearances

Hyperchromatic

Clumped

Vesicular

Concept diagram; Not a histology specimen

Slide 42 · Microscopic appearance cannot specify the epigenetic genotype

Chromatin texture may be abnormal in a cancer biopsy.

Determining whether a writer, eraser or remodeler is mutated requires molecular testing.

The slide-level distinction prevents overinterpretation of histology.

Morphology

Chromatin appearance

Molecular analysis

Specific gene lesion

Distinct mechanisms • possible convergence

Slide 43 · Cancer genomes repeatedly disrupt epigenetic regulators

Sequencing has revealed recurrent mutations in genes for DNA and histone regulation.

Genes encoding nucleosome-positioning machinery are also affected.

Some driver mutations directly involve genes encoding histone proteins.

DNA methylation genes

Histone-modifier genes

Chromatin-remodeler genes

Histone protein genes

Slide 44 · Regulatory gene lesions cluster by biochemical function

Methylation regulators change DNA or histone methyl marks.

Acetylation enzymes influence histone acetyl marks.

Remodelers affect nucleosome placement; Histone-gene mutations alter nucleosome components.

DNA methylation

DNMT3A

Histone methylation

KMT2A; KMT2D

Histone acetylation

CREBBP; EP300

Chromatin remodeling

ARID1A; SNF5; PBRM1

Histone components

H3F3A; HIST1H3B

Slide 45 · DNMT3A mutations connect DNA methylation to leukemia

DNMT3A is listed as a DNA methylation regulator Table 7.9.

Acute myeloid leukemia is an example of a cancer harboring DNMT3A mutations.

The target is the regulatory machinery, not merely a downstream gene promoter.

DNMT3A

DNA methylation regulator

Acute myeloid leukemia

Slide 46 · KMT2A highlights histone methylation in infant leukemia

KMT2A is listed among genes with a histone-methylation function.

Acute leukemia in infants as an associated tumor category.

The example illustrates the link between chromatin regulation and malignant hematopoiesis.

KMT2A

Histone methylation

Acute leukemia in infants

Slide 47 · KMT2D links histone methylation to follicular lymphoma

KMT2D encodes a regulator of histone methylation.

It is listed as mutated in follicular lymphoma.

The disease association is an example rather than a universal marker of all lymphomas.

KMT2D

Histone methylation

Follicular lymphoma

Slide 48 · CREBBP and EP300 connect acetylation machinery to lymphoma

CREBBP and EP300 appear among histone-acetylation regulators mutated in cancer.

Diffuse large B-cell lymphoma as an associated tumor.

Enzyme dysfunction may modify lineage-appropriate gene expression programs.

CREBBP / EP300

Histone acetylation

Diffuse large B-cell lymphoma

Slide 49 · ARID1A illustrates disrupted nucleosome positioning

ARID1A is involved in chromatin remodeling and nucleosome positioning.

Its mutation with ovarian clear cell and endometrial carcinomas.

The consequence involves chromatin accessibility rather than a direct DNA base change in target genes.

ARID1A

Chromatin remodeling

Ovarian clear cell / endometrial carcinoma

Slide 50 · SNF5 links chromatin remodeling to malignant rhabdoid tumor

SNF5 is included among nucleosome-positioning and remodeling regulators.

Robbins Table 7.9 identifies malignant rhabdoid tumor as a characteristic association.

This illustrates how a chromatin-regulator lesion may be central to a specific cancer.

SNF5

Nucleosome positioning

Malignant rhabdoid tumor

Slide 51 · PBRM1 is a remodeling gene associated with renal cancer

PBRM1 is included in the nucleosome positioning/chromatin remodeling group.

Renal carcinoma is its example association in the Robbins table.

This adds a second cancer lineage in which remodeling machinery is genetically altered.

PBRM1

Chromatin remodeling

Renal carcinoma

Slide 52 · Cancer driver lesions can involve histones themselves

The histone H3 variant genes H3F3A and HIST1H3B.

These genes are associated with pediatric gliomas in Table 7.9.

The affected component is a nucleosomal histone, not just a modifying enzyme.

H3F3A / HIST1H3B

Histone H3 variants

Pediatric gliomas

Slide 53 · An epigenetic lesion may drive a network-wide phenotype

A mutated chromatin regulator can alter the expression of many targets.

Consequences may contribute to growth, differentiation and self-renewal abnormalities.

A regulatory mutation should not be equated with a single, invariant downstream effect.

Regulator mutation

Multiple gene changes

Malignant behavior

Slide 54 · Cell lineage restricts the oncogenic effect of some genes

Normal lineage identity depends on a cell-specific epigenetic expression program.

An oncogenic lesion acts within that existing regulatory context.

The same gene can therefore have distinct cancer effects in different tissues.

Same signaling gene

Lineage A

Regulated targets

Lineage B

Regulated targets

Slide 55 · Some cancer genes are broad; Others are lineage-restricted

RAS, MYC and TP53 are altered or dysregulated across many cancer types.

These with lineage-restricted associations such as RB, VHL and APC.

Epigenetic context helps explain why particular genes matter in particular cell identities.

Pattern

Examples

Interpretation

Broadly involved

RAS, MYC, TP53

Many tumor lineages

Lineage-restricted

RB, VHL, APC

Specific cellular context

Mechanistic principle

Epigenetic state

Controls target availability

Slide 56 · NOTCH1 demonstrates context-dependent cancer behavior

NOTCH1 to show that the same signaling family has divergent oncogenic roles.

Its tumor-suppressive or oncogenic effect depends on tumor lineage and mutation type.

The principle follows from the different target programs available in different cells.

NOTCH1

Skin squamous cancer

Loss of function

T-cell acute leukemia

Gain of function

Impaired differentiation

Growth program / MYC

Slide 57 · NOTCH1 loss promotes cutaneous squamous carcinogenesis

In cutaneous squamous cell carcinoma, NOTCH1 can be a tumor suppressor.

Loss-of-function mutations impair differentiation.

This does not imply that all NOTCH signaling is growth-suppressive in every tissue.

NOTCH1 loss of function

Impaired differentiation

Squamous carcinogenesis

Slide 58 · NOTCH1 activation promotes T-cell acute lymphoblastic leukemia

In T-cell acute lymphoblastic leukemia, NOTCH1 is a recurrent oncogene.

Gain-of-function mutations drive pro-growth transcription, including MYC.

This effect contrasts sharply with NOTCH1 loss in skin squamous carcinoma.

NOTCH1 gain of function

Pro-growth program / MYC

T-cell acute leukemia

Slide 59 · The NOTCH1 example separates gene identity from gene effect

The gene name alone does not determine whether a lesion is oncogenic or suppressive.

Cell lineage and the type of mutation determine biological consequences.

The underlying epigenomic environment helps define responsive transcriptional targets.

NOTCH1

Skin squamous cancer

Loss of function

T-cell acute leukemia

Gain of function

Impaired differentiation

Growth program / MYC

Slide 60 · Cancer epigenetics also influences differentiation and self-renewal

Epigenetic programs help maintain normal lineage identity and maturation.

Cancer-associated changes may disturb differentiation and patterns of self-renewal.

These properties contribute to the malignant phenotype beyond proliferation alone.

Altered epigenetic program

Changed cell identity

Malignant phenotype

Slide 61 · Reversible enzymatic marks create therapeutic opportunities

Many epigenetic states are maintained by enzymes that can be inhibited.

Unlike fixed base-sequence mutations, some epigenetic marks are reversible.

Drug development targets modifiers of histones, DNA methylation and other chromatin processes.

Reversible epigenetic modification

Enzyme can be pharmacologically targeted

Potential restoration of gene regulation

Slide 62 · HDAC inhibitors exploit reversible histone acetylation

HDACs remove acetyl groups from histones.

Inhibitors of HDACs are approved for certain lymphoid tumors,.

The rationale is interference with an enzyme that helps sustain aberrant chromatin states.

HDAC inhibition

Altered acetylation state

Therapeutic effect in some tumors

Slide 63 · DNA methylation inhibitors are used in myeloid tumors

DNA methylation inhibitors as therapies for myeloid tumors.

Part of the rationale is possible reactivation of epigenetically silenced tumor suppressors.

The proposed molecular rationale should not be equated with a proven mechanism in every patient.

Methylation inhibitor

Changed DNA methylation

Potential gene reactivation

Slide 64 · Epigenetic drug action is not always gene-specific

Methylation and histone regulators may influence many genomic loci.

Effects can therefore extend beyond any one silenced tumor-suppressor gene.

This complexity limits simplistic predictions based on a single epigenetic mark.

Chromatin-modifying therapy

Gene expression

Differentiation

Drug response

Schematic: Interacting downstream outcomes

Slide 65 · Intratumoral epigenetic heterogeneity adds another variable

Cancer cells in a single tumor can differ in their epigenetic states.

This diversity may arise alongside underlying genetic heterogeneity.

Distinct regulatory programs can produce different responses to a common drug exposure.

Different regulatory states within one tumor

Slide 66 · Epigenetic heterogeneity can produce drug tolerance

Not all treatment-resistant cells necessarily carry a new fixed DNA mutation.

An altered, potentially reversible state may reduce drug sensitivity.

This state-based route to resistance complicates treatment strategies.

Genetic resistance

Stable sequence lesion

Epigenetic tolerance

Potentially reversible state

Distinct mechanisms • possible convergence

Slide 67 · EGFR-inhibited lung cancer provides a reversible example

Lung cancer cells that become resistant to EGF receptor inhibition.

Epigenetic changes can contribute to the resistant phenotype.

When inhibitor exposure stops, the cells may recover their previous inhibitor-sensitive state.

Before treatment

Sensitive

On EGFR inhibition

Resistant state

After withdrawal

Sensitivity returns

Slide 68 · Drug withdrawal can reveal phenotypic reversibility

A resistant state present during treatment does not always persist after drug removal.

Reappearance of drug sensitivity supports a reversible component in the response.

It is not evidence that all resistance mechanisms in lung cancer are epigenetic.

Before treatment

Sensitive

On EGFR inhibition

Resistant state

After withdrawal

Sensitivity returns

Slide 69 · Resistance mechanisms must be interpreted mechanistically

Genetic selection and epigenetic state change can both influence tumor evolution.

Only some drug-resistant phenotypes are reversible.

Phenotypic reversal is useful mechanistic evidence but does not identify a unique histone or DNA mark.

Question

Genetic route

Epigenetic route

Primary alteration

Sequence change

Regulatory state change

Potential reversal

Often fixed in clone

May reverse when context changes

Evidence needed

Genomic studies

State and functional studies

Slide 70 · Clinicopathologic interpretation uses multiple evidence levels

Morphology can reveal chromatin disturbance but not its specific molecular cause.

Molecular data identify lesions in chromatin-regulatory genes or histone variants.

Functional findings establish whether a regulatory state changes phenotype or drug response.

Morphologic observation

Molecular characterization

Functional interpretation

Slide 71 · Case application: Loss of CDKN2A expression

A tumor has reduced CDKN2A transcription with promoter hypermethylation.

Question: Which two downstream tumor-suppressive signaling axes may be affected?

Answer: P14/ARF–p53 and p16/INK4a–RB; Verify other-allele status separately.

CDKN2A

P14/ARF → p53

P16/INK4a → RB

Slide 72 · Case application: Opposite NOTCH1 roles

One lesion shows NOTCH1 loss in cutaneous squamous carcinoma.

Another shows NOTCH1 activation in T-cell acute lymphoblastic leukemia.

Interpretation: Lineage-specific target programs allow suppressive versus oncogenic effects.

NOTCH1

Skin squamous cancer

Loss of function

T-cell acute leukemia

Gain of function

Impaired differentiation

Growth program / MYC

Slide 73 · Case application: Transient drug resistance

An EGFR-inhibited lung cancer population becomes drug-tolerant.

Sensitivity returns after the inhibitor is withdrawn.

This behavior is consistent with a reversible epigenetic contribution; It does not exclude genetic heterogeneity.

Before treatment

Sensitive

On EGFR inhibition

Resistant state

After withdrawal

Sensitivity returns

Slide 74 · Integrated model: Genotype, epigenome and tumor behavior

Mutations in epigenetic regulators can modify chromatin state and transcription.

Cell lineage determines which target programs are biologically accessible.

Epigenetic heterogeneity may modify drug sensitivity within a tumor.

Abnormal epigenetic state

Gene expression

Differentiation

Drug response

Schematic: Interacting downstream outcomes

Slide 75 · Core distinctions to retain

Promoter hypermethylation can inactivate a tumor suppressor; Genome-wide methylation changes are more heterogeneous.

Histone marks, nucleosome movement and enhancer loops regulate gene access.

Cancer-associated mutations target chromatin regulators and sometimes histone proteins themselves.

Mechanism

Cancer phenotype

Clinical interpretation

Slide 76 · Clinical implications of the epigenetic model

Chromatin abnormalities have morphologic, transcriptional and therapeutic relevance.

Epigenetic reversibility provides drug targets yet may enable transient resistance.

Interpret each gene lesion in the lineage and molecular context in which it occurs.

Mechanism

Cancer phenotype

Clinical interpretation