1. Meaning of Epigenetics

• Epigenetics = regulation of gene expression without altering DNA sequence
• Heritable through cell division
• Reversible in principle
• Analogy: dimmer switch vs. rewiring
• dimmer switch = epigenetics
• cutting/reconnecting wires = mutation

2. Major Epigenetic Mechanisms

Two dominant layers of epigenetic regulation:

1. Histone modifications

– post-translational modification of histone tails

– influences how tightly DNA is wound

1. relaxed = transcription ON
2. condensed = transcription OFF
2. DNA methylation
• methyl groups attached to CpG cytosines
• generally associated with gene silencing

3. Epigenetic Patterns: Normal vs Cancer Cells

Normal Cells

• most of the genome is intentionally silenced
• DNA methylation + histone changes keep unnecessary genes OFF
• ensures:
• gene expression matches tissue identity
• stable cell function

Cancer Cells

Characteristic pattern shift:

• Global hypomethylation 🔓

– genome becomes unstable and permissive

– supports chromosomal instability, rearrangements, activation of repeats

• Promoter hypermethylation 🔒

– especially in tumor suppressor gene promoters

– transcription blocked

– genes remain intact but permanently silenced

Key point: cancer can inactivate tumor suppressors without mutation, by silencing them epigenetically.

4. How Hypo- and Hypermethylation Drive Cancer

Promoter hypermethylation

• tumor suppressor promoters (e.g., CDKN2A, MLH1) become methylated
• ↓ tumor suppressor transcription
• ↓ checkpoints + DNA repair
• → uncontrolled proliferation and genomic instability

Global hypomethylation

• demethylation of repetitive sequences
• promotes:
• chromosomal instability
• transposition
• rearrangements
• → genomic chaos that favors cancer evolution

Analogy:

🚗 cancer = brakes stuck OFF + accelerator switches failing randomly.

5. Mutations in Epigenetic Regulators

Some cancers mutate genes that write, read, or erase epigenetic marks:

• DNMTs = writers
• TET enzymes = demethylation
• HDACs/HATs = histone modification enzymes

Although epigenetic marks are reversible,

mutations in epigenetic machinery lock in a cancer-favorable epigenome.

Example: TET2 mutation in AML → cannot demethylate DNA → tumor suppressor promoters stay methylated → remain OFF.

6. Epigenetic Context & Gene Behavior

• gene function depends on epigenetic environment
• same DNA sequence behaves differently depending on which genes are ON/OFF

Example: NOTCH1

• oncogene in T-cell leukemia
• tumor suppressor in squamous cell carcinoma

Analogy: 🎭 same actor, different role, depending on the stage.

7. Summary Comparison: Normal vs Cancer Cells

8. Clinical significance and therapy

• epigenetic dysregulation explains cancer heterogeneity
• therapies target epigenetic enzymes:
• DNMT inhibitors
• HDAC inhibitors
• aim = reactivate silenced tumor suppressors
• response varies due to epigenetic context

Key memory trick:

Cancer epigenetics =

🔓 genome unlocked (hypomethylation) +

🔒 tumor suppressors locked (hypermethylation)

→ instability + growth.

MCQs – Epigenetic Modifications in Cancer

MCQ 1

A lung carcinoma shows global hypomethylation + CDKN2A promoter hypermethylation. Mechanism?

A. Loss of methylation increases tumor suppressor activity

B. Global hypomethylation destabilizes genome; promoter hypermethylation silences TS genes

C. Both activate oncogenes

D. Hypomethylation silences housekeeping genes, hypermethylation increases TS expression

Correct answer: B

MCQ 2

Which finding illustrates epigenetic context?

A. BRCA1 mutations always cause cancer

B. NOTCH1 oncogene in T-cell leukemia but tumor suppressor in squamous cancer

C. TP53 not influenced by epigenetics

D. KRAS independent of epigenetic marks

Correct answer: B

MCQ 3

A DNMT inhibitor is given to colorectal cancer with hypermethylated MLH1 promoter. Outcome?

A. ↑ MLH1 expression: restores mismatch repair

B. ↑ MLH1 worsens instability

C. ↓ MLH1: impaired repair

D. No change: methylation irreversible

Correct answer: A

MCQ 4

What distinguishes epigenetic changes from mutations?

A. Epigenetics alters DNA sequence

B. Epigenetics reversible/heritable; mutations permanent sequence changes

C. Both irreversible

D. Epigenetics only affects oncogenes

Correct answer: B

MCQ 5

AML patient has TET2 loss-of-function mutation. Expected result?

A. Global hypomethylation → ↑ TS activity

B. Failure to demethylate → promoter hypermethylation → TS silencing

C. ↑ histone acetylation globally

D. Loss of methylation → TS activation

Correct answer: B

Final Take-Home Messages

• Epigenetics regulates expression without altering sequence.
• Cancer distorts these mechanisms through:
• global hypomethylation → instability
• promoter hypermethylation → tumor suppressor silencing
• mutations in epigenetic regulators → lock-in effects
• Epigenetic context determines how genes behave in different tumors.
• Therapies aim to reverse these marks but responses vary.

Epigenetics in Cancer — සිංහලෙන් by point note

1. Epigenetics කියන්නේ මොකක්ද?

• Epigenetics කියන්නේ DNA sequence එක වෙනස් නොකර gene expression regulate කරන එක.
• ඒ කියන්නේ gene එකේ letters/change වෙන එකක් නෙවෙයි, gene eka ON ද OFF ද කියලා control කරන එක.
• මේ changes cell division වලින් පස්සෙත් තවත් cells වලට යන්න පුළුවන්.
• මේවා theoretically reversible — අරගෙ DNA mutation වගේ permanent rewiring එකක් නෙවෙයි.

Simple idea

• Mutation = wire කපලා අලුත් කරපු වගේ
• Epigenetics = light dimmer switch එක adjust කරන වගේ

මතක තියාගන්න:

DNA code එක same, හැබැයි ඒක use කරන විදිහ වෙනස් වෙනවා.

2. ප්‍රධාන epigenetic mechanisms දෙක

Epigenetic regulation වල major layers දෙකක් තියෙනවා:

A. Histone modifications

• DNA එක histone proteins වටේ wound වෙලා තියෙනවා.
• Histone tails වල වෙන post-translational modifications නිසා DNA tight ද loose ද කියලා වෙනස් වෙනවා.

Effect

• DNA relaxed / open නම් → transcription ON
• DNA condensed / tightly packed නම් → transcription OFF

B. DNA methylation

• Methyl groups attach වෙන්නේ සාමාන්‍යයෙන් CpG cytosines වලට.
• මේක බොහෝ වෙලාවට gene silencing එක්ක සම්බන්ධයි.

Core idea:

Histone modification + DNA methylation එකතු වෙලා gene expression control කරනවා.

3. Normal cells වල epigenetic pattern

Normal cells වල:

• genome එකේ ලොකු කොටසක් intentional ලෙස silenced කරලා තියෙනවා
• හැම gene එකක්ම හැම cell එකකම ON වෙලා නෑ
• cell type එකට ඕන genes විතරයි active වෙන්නේ

මෙකට හේතුව

• DNA methylation
• Histone changes

මේකෙන් වෙන්නේ

• tissue identity maintain වෙනවා
• liver cell එක liver වගේ හැසිරෙනවා
• muscle cell එක muscle වගේ හැසිරෙනවා
• cell function stable වෙනවා
• unnecessary genes OFF වෙලා ඉන්නවා

Simple memory line:

Normal cell එක disciplined — ඕන genes විතරක් ON.

4. Cancer cells වල epigenetic pattern

Cancer cells වල normal pattern එක disturb වෙනවා.

Main changes දෙක

1. Global hypomethylation
2. Promoter hypermethylation

5. Global hypomethylation කියන්නේ මොකක්ද?

• Genome එකේ overall methylation level එක අඩු වෙන එක
• ඒ කියන්නේ සාමාන්‍යයෙන් silent වෙලා ඉන්න parts unlock වෙනවා

Result

• genome unstable වෙනවා
• chromosomal instability වැඩි වෙනවා
• rearrangements වෙන්න පුළුවන්
• repetitive sequences activate වෙන්න පුළුවන්
• transposition වැඩි වෙන්න පුළුවන්

Cancer වල significance

මේක cancer evolution එකට help කරන chaotic environment එකක් හදනවා.

Simple idea:

Genome එකේ safety locks ගොඩක් අයින් වෙනවා.

6. Promoter hypermethylation කියන්නේ මොකක්ද?

• gene promoter region එකේ methylation වැඩි වෙන එක
• විශේෂයෙන් tumor suppressor genes වල promoters මේ විදිහට methylate වෙන්න පුළුවන්

Result

• transcription block වෙනවා
• gene physically intact වුනත් express වෙන්නේ නෑ
• ඒ කියන්නේ gene එක මැරෙලා නැහැ, silent කරලා

Important

Cancer එකට tumor suppressor gene එක inactivate කරන්න mutation එකක්ම ඕන නෑ

epigenetic silencing එකෙන්ත් පුළුවන්.

7. Hypomethylation + Hypermethylation එකතුවෙන් cancer drive වෙන්නේ කොහොමද?

A. Promoter hypermethylation

උදාහරණ:

• CDKN2A
• MLH1

මේ tumor suppressor promoters methylate වුනොත්:

• tumor suppressor transcription අඩු වෙනවා
• checkpoints අඩු වෙනවා
• DNA repair අඩු වෙනවා
• uncontrolled proliferation වැඩි වෙනවා
• genomic instability තවත් වැඩි වෙනවා

B. Global hypomethylation

• repetitive sequences demethylate වෙනවා
• chromosome instability වැඩි වෙනවා
• rearrangements / transposition වැඩි වෙනවා

Overall effect

• genome unstable
• tumor suppressors silent
• cancer grow වෙන්න highly favorable state එකක් හැදෙනවා

Best memory image

Cancer epigenetics =

• genome unlocked 🔓
• tumor suppressors locked 🔒

8. Analogy එකෙන් තේරුම් ගන්න

Cancer cell එක car එකක් වගේ හිතන්න:

• Tumor suppressors = brakes
• Oncogenic drive / instability = accelerator problems

Epigenetic cancer pattern

• brakes OFF
• accelerator control also abnormal
• car එක control නැතුව යනවා

ඒකයි cancer cell proliferation uncontrolled වෙන්නේ.

9. Epigenetic regulator genes mutate වෙන එක

සමහර cancers වල problem එක marks වල විතරක් නෙවෙයි,

epigenetic machinery එකේ genes වලත් mutations තියෙනවා.

Important groups

• DNMTs = writers
• methylation marks දානවා
• TET enzymes = demethylation side එක
• HDACs / HATs = histone modification enzymes

Why important?

Epigenetic marks reversible වුනත්,

මේ machinery mutate වුනොත් cancer-favorable epigenome එක lock වෙන්න පුළුවන්.

10. TET2 mutation example

Example

• TET2 mutation in AML

Normal TET2 function

• DNA demethylation help කරනවා

TET2 mutation වුනොත්

• DNA properly demethylate කරන්න බැරි වෙනවා
• tumor suppressor promoters methylated තත්වයේ ඉන්නවා
• ඒ genes OFF ම තියාගන්නවා

Result

• tumor suppressor silencing continue වෙනවා
• cancer progression ට support වෙනවා

Exam line:

TET2 loss → failure of demethylation → persistent promoter methylation → tumor suppressor OFF.

11. Epigenetic context කියන්නේ මොකක්ද?

• gene behavior එක DNA sequence එකෙන් විතරක් decide වෙන්නේ නෑ
• gene එක ඉන්න epigenetic environment එකත් වැදගත්

Meaning

එකම gene එක,

• එක tumor එකක oncogene වගේ වැඩ කරයි
• වෙන tumor එකක tumor suppressor වගේ වැඩ කරයි

12. NOTCH1 example

• NOTCH1
• T-cell leukemia වල oncogene
• squamous cell carcinoma වල tumor suppressor

Why?

Gene එක same වුනත්, surrounding epigenetic context + cellular setting වෙනස්.

Simple analogy

එකම actor කෙනා,

• එක drama එකක villain
• තව drama එකක hero

එහෙම තමයි same gene different tumors වල different roles play කරන්නේ.

13. Normal cells vs Cancer cells — comparison

Normal cells

• DNA methylation regulated
• genes proper control යටතේ
• unnecessary genes OFF
• tumor suppressors normal ලෙස work කරනවා
• cell behavior predictable
• function stable

Cancer cells

• DNA methylation dysregulated
• global hypomethylation
• promoter hypermethylation
• tumor suppressor genes epigenetically silenced
• epigenetic regulator mutations common
• cell behavior unstable and heterogeneous

14. මේක clinically වැදගත් වෙන්නේ ඇයි?

• cancer එකේ heterogeneity explain කරන්න epigenetics help කරනවා
• එකම tissue cancer එකක් වුනත් patients අතර behavior වෙනස් වෙන්න පුළුවන්
• response to treatment වෙනස් වෙන්නත් පුළුවන්
• gene intact වුනත් expression blocked නම් disease behavior වෙනස් වෙනවා

15. Therapy වල relevance

Epigenetic changes target කරන්න therapy තියෙනවා:

Examples

• DNMT inhibitors
• HDAC inhibitors

Aim

• silenced වෙලා තියෙන tumor suppressor genes නැවත reactivate කරන එක

But

• response හැමෝටම එක වගේ නෑ
• මොකද tumor එකේ epigenetic context වෙනස්

16. High-yield final concept

Cancer epigenetics වල biggest idea එක:

දෙකම එකට වෙයි

• Global hypomethylation → genome unstable වෙනවා
• Promoter hypermethylation → tumor suppressors silent වෙනවා

End result

• instability + growth advantage + cancer progression

Easy exam summary

Epigenetics කියන්නේ

• DNA sequence වෙනස් නොකර gene expression control කරන mechanism

Main mechanisms

• Histone modifications
• DNA methylation

Cancer වල main pattern

• Global hypomethylation
• Promoter hypermethylation

Global hypomethylation result

• genome instability
• chromosomal rearrangements
• activation of repetitive elements

Promoter hypermethylation result

• tumor suppressor silencing
• checkpoints and DNA repair loss

Regulator mutations

• DNMT, TET, HDAC, HAT mutations cancer support කරන epigenome එක lock කරන්න පුළුවන්

Clinical relevance

• explains heterogeneity
• targeted by epigenetic therapyMCQs with simple explanations