Cancer Genetics

Cancer

• a group of diseases characterized by ______ (controllable/uncontrollable) growth and spread of ______ (normal/abnormal) cells

• ______ multiplication/_______ leads to the formation of a lump of tissue or tumor

• tumor cells invade the __________ tissues and may travel to a distant site to form new tumors

• the process by which tumor cells spread to distant sites is called ______

• uncontrollable, abnormal

• uncontrolled, proliferation

• surrounding

• metastasis

Cancer Risk Factors

Carcinogens —> substances capable of causing cancer

• Lifestyle Factors —> ______, ______, ______ light, ______ fat diet

• Environmental Factors —> ______ radiation + ______ radiation

• Chemical Agents —> ______ drugs, certain ______ agents, ______ ______

• Infectious Agents —> (4)

• smoking, alcohol, UV, high

• UV, ionizing

• immunosuppressive, antineoplastic, coal tar

• hepatitis B/C, HIV, HPV, H. pylori

Etiology of Cancer

• not fully ______

• carcinogenesis is a ______ process regulated by ______ —> ______ steps

1. initiation: exposure to ______ that causes DNA damage —> ______ mutation

2. promotion: growth of ______ cells —> pre-neoplastic lesion —> ______ (reversible/irreversible)

3. conversion: mutated cell becomes ______ occurs __________ years after prior stages —> ______ (reversible/irreversible)

4. progession: further ______ changes, tumor ______ into local tissues, distant ______ —> ______ (reversible/irreversible)

• understood

• multistep, genes, four

• carcinogen, irreversible 

• mutated, reversible

• cancerous, 5-20, irreversible

• genetic, invasion, metastases, irreversible

Tumor Origin and Classification

• tumors arise from any _____ type and may be named based on tissue type:

  • epithelial —> ______

  • connective (muscle, bone, cartilage) —> ______

  • lymphoid/blood/bone marrow —> ______, ______, ______

• tumors may also be classified as:

  • ______ site —> lung, colon, etc.

  • degree of ______ (poorly differentiated vs. well differentiated)

  • ______ (insulinoma)

  • ______ or ______

• tumors that end in “-oma” —> ______

• tumors that end in “-carcinoma” —> ______

• a tumor is treated according to the site of ______

• tissure

• cacinoma

• sarcoma

• lymphoma, leukemia, myeloma

• anatomic

• differentiation

• function

• benign, malignant

• benign

• malignant

• origination

Benign vs. Malignant Tumors

• Benign

  • grow ______

  • ______ capsule

  • ______ (non-invasive/invasive)

  • ______ (well/poorly) differentiated

  • ______ (high/low) mitotic index

  • ______ (does/does not) metastasize

• Malignant

  • grow ______

  • ______ encapsulated

  • ______ (non-invasive/invasive)

  • ______ (well/poorly) differentiated

  • ______ (high/low) mitotic index

  • ______ (does/does not) metastasize

• slowly

• well-defined

• non-invasive

• well

• low

• does not

• rapidly

• non

• invasive

• poorly

• high

• does

Benign Tumor Complications

Benign tumors can still cause complications such as:

• __________

• Brain tumors → __________ effects

• Secretion of __________ (e.g., thyroid adenoma → thyroid hormone; pituitary adenoma → growth hormone)

• Leiomyoma → __________ and __________ symptoms

• pain

• CNS

• hormones

• heavy menstrual bleeding, urinary

Cancer Diagnosis

• requires a ______ (tissue sample) for pathological diagnosis

• Types include:

  • ______/______ biopsy

  • ______ biopsy

  • ______ cytology

• biopsy

• incisional/excisional

• needle

• exfoliative

Cancer Staging (TNM System)

• staging is based on tumor ______, ______ ______ involvement, and ______

• T (tumor):

  • Tx = tumor cannot be __________

  • Tis = carcinoma __________

  • T0 = no __________ of tumor

  • T1–T4 = size or extent of __________ tumor

• N (node):

  • Nx = node cannot be __________

  • N0–N3 = degree of __________ to regional lymph nodes

• M (metastasis):

  • M0 = ______ distant metastasis

  • M1 = __________ of distant metastasis

• Stage I: ______ prognosis

• Stage IV: ______ prognosis

• size, lymph node, metastasis

• evaluated

• in situ

• signs

• primary

• evaulated

• spread

• no

• presence

• best

• worst

Cell Division and Cell Cycle

Interphase consists of three phases:

1. G₁ phase – gap between __________ and __________ phase

2. S phase – where __________ occurs

3. G₂ phase – gap between __________ and __________ phase

• G₁ and G₂ allow __________.

• M (mitotic), S (synthesis)

• DNA replication

• S, M

• cell growth

How does cancer develop?

• cancer is a ______ disease and ______ process that takes time to develop —> often years

• it arises through a series of ______ alterations in DNA

• a ______ mutation does not necessarily lead to cancer —> _____ mutations must also occur

• usually, about ______ mutations are required for development of most cancers

• at each step, mutated cells gain a __________ advantage, leading to __________ of those cells

• the most important genetic alterations occur in __________ and __________

• genetic, multi-step

• somatic

• germline, somatic

• three

• growth, expansion

• tumor suppressor genes, proto-oncogenes

Germline vs. Somatic

• Germline:

  • ______ (inherited/acquired)

  • found in ______ and ______ cells and EVERY cell in the body

• Somatic:

  • ______ during a person’s lifetime

  • ______ to specific cells/tissues

• inherited

• egg, sperm

• acquired

• limited

Tumor Suppressor Genes in Cancer Development

• normally suppresses ______ ______, repair ______ mistakes or induce ______

• inactivation of tumor suppressor genes can lead to ______ development

  • Mechanisms of Inactivation:

    • ______ mutations

    • ______/______

    • gene ______ —> epigenetic change

• cell division, DNA, apoptosis

Tumor Suppressor Genes —> Examples

• ______

• BRCA 1/2 → drug class: __________ inhibitors → example: __________

• Retinoblastoma (Rb) → drug class: __________ inhibitors → example: __________

• p53

• PARP, olaparib

• CDK4/6, palbociclib

Porto-Oncogene in Cancer Development

• promote ______ ______ or reduce occurrence of ______

• when proto-oncogene mutates, they become ______ due to the over-activation of the gene

• over-activation = ______ development

• mechanisms of oncogene activation:

  • ______ mutation —> RAS

  • DNA ______ —> HER2

  • chromosomal ______ —> BCR-ABL 

• cell division, apoptosis

• oncogene

• cancer

• point

• amplification

• rearrangement

Oncogene Examples

• RAS → inhibitor: __________

• EGFR → inhibitor: __________

• HER2 → inhibitor: __________

• VEGF → inhibitor: __________

• BCR-ABL → inhibitor: __________

• sotorasib

• osimertinib

• trastuzumab

• bevacizumab

• imatinib

Retinoblastoma (Rb): Tumor Suppressor Genes

• >70% of human tumors have a mutation that leads to the ______ or ______ of Rb

• normally, Rb inhibits the ______ ______ by inhibiting transcription factors such as ______

• CDK 2, 4, and 6 inactivate Rb via ______, releasing transcription factors that allow progression from ______ to ______ phase

• relevant drug class —> ______ inhibitors —> ______ (Ibrance)

• these drugs inhibit Rb ______/______, restoring Rb’s ability to suppress the cell cycle

• used in the treatment of ______ cancer

• loss, inactivation

• cell cycle, E2F1-3

• phosphorylation, G1, S

• CDK 4/6, palbociclib

• phosphorylation/inactivation

• breast

BCRA1/BCRA2: Tumor Suppressor Genes 

• involved in the ______ ______ (HRR) repair pathway, which repairs ______ DNA (dsDNA) breaks

• cells with BRCA1/2 mutations are deficient in their ability to repair dsDNA breaks and must rely on ______ repair mechanisms such as ______ ______ repair (BER)

• BER is mediated by ______

• relevant drug class: ______ inhibitors —> ______ (Lynparza)

• PARP inhibitors block the alternative repair pathway used by ______ cells, leading to cell death through ______ ______

• used in the treatment of ______, ______, ______ cancers

• homologous recombination, double-stranded

• alternative, base excision

• PARP1

• PARP, olaparib

• BRCA-deficient, synthetic lethality

• prostate, breast, ovarian

BCR-ABL: Oncogene

• present in cells with translocation of chromosomes ______ and ______

• the gene product (BCR-ABL fusion protein) has constitutive ______ ______ activity, which activates signaling pathways via ______ of substrates

• relevant disease state: ______ ______ ______ (CML)

• relevant drug class: ______ inhibitors —> ______ (Gleevec)

• BCR-ABL inhibitors bind to the ______ domain and block the ______ of the substrate

• , 22

• tyrosine kinase, phosphorylation

• chronic myelogenous leukemia

• BCR-ABL, Imatinib

• kinase, phosphorylation

what is the first drug to inhibit a gene product that is only found in cancers?

Imatinib (Gleevec)

Growth Factors: Oncogenes

Several mechanisms in oncogenesis:

• ______ of growth factors

• ______ ______ of growth factor receptors

• ______ of growth factor receptors

• Example: ______ ______ growth factor (VEGF)

• relevant drug class: ______ inhibitors —> ______ (Avastin and biosimilars)

• MOAs:

  • bind the growth factor (VEGF A/B) —> ______

  • bind the VEGF receptor to block binding of VEGF —> ______

  • inhibit VEGF receptor’s intracellular kinase —>

• VEGF targeting agents inhibit ______

• overproduction

• activating mutations

• overexpression

• vascular endothelial

• VEGF, bevacizumab

• bevacizumab

• ramucirumab

• sunitinib

• angiogenesis

Relevant Mechanisms of Drug Resistance

• Changes in target

  • Acquisition of ______ mutation in gene

  • Upregulation of ______

• Change in the affected pathway

  • Use of ______/______ or enhanced DNA repair pathways

  • Develop new ______/______ to bypass effects of the drug

• Epigenetic changes

  • Turn genes __________ that affect treatment response

  • Development/enhancement of ______ ______ mechanism

• new

• expression

• alternative/enhanced

• pathways/signals

• on/off

• drug efflux

Cancer is a heterogeneous disease

• Tumors have unique genomic and phenotypic features that vary at multiple levels.

• Genetic heterogeneity:

  • Cells within a single tumor are not genetically identical.

  • Mutations accumulate over time during tumor growth.

  • Many mutations are passenger mutations (not clinically significant).

  • Driver mutations promote tumor growth/progression and are often actionable/druggable.

Levels of Cancer Heterogeneity

Cancer heterogeneity occurs across three major levels:

1. Intratumor heterogeneity

   • Differences among cells within one tumor mass.

   • Multiple subclones exist inside a single tumor.

2. Intertumor heterogeneity

   • Differences between a patient’s primary tumor and their metastatic tumors.

3. Interpatient heterogeneity

   • Differences between tumors found in different patients.

Why is tumor heterogeneity important?

1. Interpatient heterogeneity

• Different tumor types require different treatments (e.g., breast cancer vs prostate cancer).

• Even tumors of the same type may need different treatments due to differences in each patient’s tumor genetics.

• This concept forms the basis of precision medicine, where treatments are tailored to the specific molecular features of each patient’s cancer.

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2. Intratumor and Intertumor heterogeneity

• These types of heterogeneity can strongly influence drug response and resistance.

• If all tumor cells shared the same genetic makeup, they would likely respond uniformly to therapy.

• However, because tumors contain multiple genetically distinct subclones:

  • Some cells may respond to treatment.

  • Others may survive and lead to treatment failure or resistance.

• This genetic diversity makes it less likely that a single therapy will eliminate all tumor cells.

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Intratumor / Intertumor heterogeneity

• The effectiveness of targeted therapy depends on whether the target mutation is present in all tumor cells.

  • Example: If a tumor has an EGFR mutation, an EGFR inhibitor can produce a complete response only if every tumor cell carries the mutation.

  • If some cells lack the mutation → they survive, leading to resistance and tumor regrowth.

• Combining drugs with different mechanisms of action may help eliminate diverse tumor cell populations and reduce resistance.

Models of Tumor Heterogeneity

1. Clonal Evolution (CE) Model

• All malignant cells start as biologically similar.

• Over time, they accumulate genomic or epigenetic alterations in a stepwise manner.

• Selective pressures cause certain clones to expand while others die out.

• This creates genetically diverse subpopulations within the tumor.

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2. Cancer Stem Cell (CSC) Model

• Tumor contains a small subset of cancer stem cells (CSCs).

• CSCs:

  • Have the ability to self-renew.

  • Generate the heterogeneous populations of cancer cells in the tumor.

• Only CSCs drive tumor growth, progression, and recurrence.

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3. Plasticity Model (unites both CE and CSC models)

• Cancer cells can interconvert:

  • Differentiated cancer cells ↔ cancer stem–like cells.

• This means tumors can shift between CE-like evolution and CSC-driven behavior.

Clinical Application of Tumor Heterogeneity Models

Clonal Evolution (CE) Model

• If this model is correct:

  • Most cells in the tumor can proliferate, metastasize, and contribute to disease progression.

• Therapeutic implication:

  • Treatments must aim to eliminate most or all tumor cells, since many cells have malignant potential.

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Cancer Stem Cell (CSC) Model

• If this model is correct:

  • Only a small subset of cancer stem cells (CSCs) drive tumor initiation, growth, and progression.

• Therapeutic implication:

  • Therapies should specifically target CSCs, because eliminating them could prevent tumor recurrence and progression.

Therapeutic Options Are Driven by Tumor Heterogeneity

Treatment depends on both:

• Tumor type

• Presence of actionable genetic alterations

Examples:

Cancer Type	Common Treatment (no mutation identified)	Targeted Treatment (if mutation identified)
Non–small cell lung cancer (NSCLC)	Platinum + Taxane	- PD-L1 > 50%: PD-1 inhibitor - EGFR mutation: EGFR inhibitor - ALK rearrangement: ALK inhibitor
Breast cancer	Anthracycline + Alkylating agent	- HER2+: trastuzumab, pertuzumab, docetaxel - Hormone receptor+: antiestrogen + CDK4/6 inhibitor

Take-home points

• Treatments differ based on tumor type and tumor genetics.

• When cancer recurs, new mutations may appear, so re-testing is often needed to guide therapy.

Precision / Personalized Medicine

What is it?

• A major clinical application of tumor heterogeneity.

• Precision medicine = tailoring prevention and treatment strategies to the specific characteristics of the patient and their tumor.

  • Factors include genes, environment, and lifestyle.

• In cancer therapeutics, this means:

  • Choosing treatment based on the tumor’s specific molecular alterations.

• Key concept: Treatment is not one-size-fits-all.

How Precision Medicine Works in Cancer

Guided by genetic and biomarker testing

• Tumors are tested for mutations or biomarkers that may determine which therapies will be effective.

• Alterations can pinpoint whether targeted therapies (e.g., EGFR inhibitors, HER2 therapies, PD-1 inhibitors) should be used.

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Somatic vs. Germline mutation testing

Somatic mutations

• Occur in tumor cells only (not inherited).

• Testing is usually done on a tumor biopsy sample.

• Some assays use blood to detect circulating tumor DNA.

Germline mutations

• Inherited mutations present in all cells.

• Testing is done using:

  • Cheek swab

  • Saliva

  • Blood sample

Precision / Personalized Medicine: How it Works

Step-by-step process

1. Patient is diagnosed with cancer.

2. A tumor sample is sent for mutation/biomarker analysis.

3. The analysis identifies actionable or druggable targets

   • Examples: mutations, fusion proteins, other biomarkers.

4. Therapy is selected based on the actionable targets found.

   • This ensures treatment is tailored to the tumor’s specific molecular profile.

Mutation / Biomarker Analysis in Precision Medicine

Companion Diagnostics (CDx)

• Defined as:
  A medical device, often an in vitro diagnostic test, that provides information essential for the safe and effective use of a corresponding drug or biologic.

• CDx tests determine which patients can benefit from certain targeted therapies.

• They identify mutations or alterations that are required for treatment with specific drugs (e.g., EGFR inhibitors, HER2 therapies, PARP inhibitors).

Examples of CDx tests

• FoundationOne (comprehensive genomic profiling)

• BRACAnalysis (BRCA1/2 mutation testing)

Precision/Personalized Medicine: Mutation/Biomarker Analysis

Key Points

• Some drugs are approved only for patients who have specific genetic alterations or mutations.

  • These drugs often must be paired with an FDA-cleared Companion Diagnostic (CDx).

• Companion Diagnostics (CDx) identify whether a patient’s tumor contains the required mutation/alteration.

  • This determines whether the patient is eligible for the targeted therapy.

• The FDA maintains a searchable list of all cleared or approved CDx devices (in vitro and imaging tools).

Case

A 67-year-old patient has relapsed acute myeloid leukemia (AML).
The oncology fellow asks whether the patient is a candidate for enasidenib (Idhifa), a targeted therapy.

Key Question:

What information do we need to make a recommendation?

Answer

We need to know whether the patient’s AML cells have an IDH2 mutation.

Why?

• Enasidenib is FDA-approved ONLY for AML patients with an IDH2 mutation, confirmed by an FDA-approved diagnostic test.

• Without the mutation, the drug would not be effective and should not be used.

Precision / Personalized Medicine: Tumor/Tissue/Site-Agnostic Indications

Key Concept

• Precision medicine has led to tumor-agnostic (or tissue-agnostic) drug approvals.

• Tumor-agnostic indication =
  The FDA approval does not specify a tumor type or location.
  Instead, the drug is approved only based on the presence of a specific molecular alteration, regardless of where the cancer originated.

Important Features

• Any tumor type can be treated if the required mutation or molecular feature is present.

• Example: A drug may be used for colon cancer, lung cancer, or thyroid cancer as long as the tumor has the same actionable mutation.

Examples of Precision Medicine Approvals

Typical FDA-approved indications (tumor-specific)

These are approved for specific cancer types:

• Tisotumab vedotin (Tivdak)

  • For cervical cancer that has progressed after ≥1 prior therapy.

• Osimertinib (Tagrisso)

  • For non–small cell lung cancer (NSCLC) with

    • EGFR exon 19 deletion or

    • EGFR exon 21 L858R mutation (mutation-positive).

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Tumor/Tissue/Site-Agnostic FDA-approved indications

These drugs are approved based solely on a molecular alteration, not tumor type:

• Larotrectinib (Vitrakvi)

  • For solid tumors with an NTRK gene fusion.

• Dabrafenib (Tafinlar)

  • For solid tumors with a BRAF V600E mutation.

DNA Packaging: Chromatin and Chromosomes

DNA → Chromatin → Chromosome

• DNA alone is a double-stranded molecule.

• Chromatin = DNA + structural proteins (mainly histones).

  • This is the default form of DNA in the nucleus.

• Chromosome = the fully condensed, organized structure of chromatin formed during cell division(mitosis/meiosis).

Chromatin vs. Chromosomes

Chromatin

• Definition: DNA + histone proteins that package DNA in the nucleus.

• Physical State: Loosely packed (variable).

• When Present: Throughout the cell cycle, especially interphase.

• Function:

  • Allows gene expression

  • Allows DNA replication and repair

• Types:

  • Euchromatin: loosely packed, transcriptionally active

  • Heterochromatin: tightly packed, transcriptionally silent

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Chromosome

• Definition: Condensed, tightly organized form of chromatin seen during cell division.

• Physical State: Tightly packed and coiled.

• When Present: Visible during mitosis and meiosis (especially metaphase).

• Function: Ensures accurate segregation of DNA to daughter cells.

• Form: Discrete structures, each containing one DNA molecule plus associated proteins.

Organization of Eukaryotic Chromosomes

Nucleosomes

• Fundamental repeating units of chromatin.

• Made of:

  • Double-stranded DNA wrapped around

  • Histone proteins (forming “beads on a string”).

Chromatin Structure Hierarchy

1. DNA wraps around histones → nucleosomes

2. Nucleosomes coil → chromatin fiber

3. Chromatin fibers loop and condense further

4. Highly condensed chromatin folds → chromosome

This hierarchical packaging allows:

• Large amounts of DNA to fit inside the nucleus

• Controlled access for transcription, replication, and repair

Nucleosome Structure

Histones

• There are 5 types of histone proteins:

  • H2A, H2B, H3, H4 (core histones)

  • H1 (linker histone)

• Histones contain a high percentage of positively charged amino acids (e.g., lysine, arginine).

• These “+” charges attract the “–” charges on DNA’s phosphate backbone, resulting in strong DNA–histone interaction.

• DNA and histones are tightly associated, enabling efficient packaging.

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Nucleosome Components

Histone Core (Octamer)

• Formed by:

  • 2 copies each of H2A, H2B, H3, and H4

• This octamer is the “spool” that DNA wraps around.

DNA Wrapping

• ~147 base pairs of DNA wrap around the histone octamer.

• Histone tails extend out from the core and help maintain DNA binding.

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Role of Histone H1

• H1 binds DNA at the entry and exit points where DNA joins and leaves the nucleosome.

• Acts like a clamp:

  • Locks DNA in place.

  • Helps stabilize higher-order chromatin structure.

Epigenetics

What is epigenetics?

• The study of how cells control gene expression without changing the DNA sequence.

• Epigenetic changes allow cells to regulate gene activity in a reversible, non-permanent way.

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Key Features

• Epigenetic modifications:

  • Can be maintained through cell divisions.

  • Can sometimes be inherited across generations.

• They do not alter the underlying DNA sequence—only gene expression patterns.

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Relevance to Cancer

Epigenetic changes can contribute to cancer development by:

1. Reducing transcription of tumor suppressor genes
   → leads to decreased protection against uncontrolled cell growth.

2. Increasing transcription of oncogenes
   → promotes abnormal cell proliferation.

Because of this, epigenetic mechanisms are targets for anticancer therapies.

Modes of Epigenetic Modifications

• Epigenetic changes regulate gene expression without altering the DNA nucleotide sequence.

• These modifications are also targetable by drugs, making them important in cancer therapy.

Three major modes of epigenetic regulation:1) DNA Modification

• Typically refers to DNA methylation (addition of methyl groups to cytosine bases).

• Usually silences gene expression.

2) Histone Modification

• Includes acetylation, methylation, phosphorylation, ubiquitination, etc.

• Alters how tightly DNA is wound around histones.

  • Acetylation → loosens chromatin → increases transcription

  • Deacetylation → tightens chromatin → decreases transcription

3) Noncoding RNA

• miRNAs, lncRNAs, and others regulate gene expression by:

  • Binding mRNA

  • Affecting translation

  • Influencing chromatin structure

DNA Modification

What is DNA methylation?

• The most common type of epigenetic modification.

• Involves the addition of a methyl group (CH₃) to DNA.

• Methylation occurs without altering the DNA sequence itself.

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Effects on Gene Expression

• Hypermethylation (increased methylation):

  • Reduces transcription → gene is “turned off.”

  • Often occurs at gene promoters.

• Hypomethylation can lead to inappropriate gene activation.

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Relevance to Cancer

• Abnormal methylation patterns can silence tumor suppressor genes.

• These changes can contribute to cancer development and progression.

DNA Methyltransferases (DNMTs)

What do DNMTs do?

• DNMTs add methyl groups to DNA.

Three major types:

• DNMT1

• DNMT3A

• DNMT3B

Mechanism

• All three DNMTs transfer a methyl group to the C5 position of cytosine, forming:

  • 5-methylcytosine

This modification is key for:

• Gene regulation

• Chromatin structure

• Stable inheritance of epigenetic marks during cell division

DNA Methylation in Tumorigenesis

How abnormal methylation contributes to cancer

Cancer is associated with two major methylation abnormalities:

1. Genome-wide hypomethylation

• Leads to:

  • Activation of proto-oncogenes

  • Genomic instability

• This promotes tumor initiation and progression.

2. Promoter hypermethylation

• Leads to:

  • Silencing of tumor suppressor genes

• Example: Overactivity of DNMT1 causes excessive methylation → tumor suppressor genes are turned off → cancer progression.

Example

• DNMT1 is overexpressed in pancreatic cancer, contributing to hypermethylation and gene silencing.

Targeting DNA Methylation to Treat Cancer

Decitabine (5-aza-2’-deoxycytidine)

Drug class

• Hypomethylating agent (HMA)

• DNA methyltransferase (DNMT) inhibitor

Clinical use

• Treats:

  • Leukemia

  • Myelodysplastic syndromes (MDS)

• These conditions often involve hypermethylation and gene silencing.

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Mechanism of Action

• Decitabine is a cytosine analog.

• During DNA replication:

  • It becomes incorporated into DNA.

  • DNMT1 binds to decitabine and becomes covalently trapped and inactivated.

  • This causes depletion of active DNMT1.

Result

• Reduced DNA methylation

• Increased transcription of silenced genes, promoting:

  • Cell differentiation

  • Reduced proliferation

  • Apoptosis

This reverses the hypermethylated, gene-silencing environment that drives cancer.

Histone Modification

Histone modifications change how tightly DNA interacts with histone proteins.

• These changes regulate chromatin structure, which in turn regulates gene expression.

• Modifications occur mainly on histone tails.

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Types of Histone Modifications

1. Acetylation*

2. Methylation*

3. Phosphorylation

4. Ubiquitination

These modifications can either:

• Disrupt histone–DNA interactions → loosen chromatin → ↑ gene expression, or

• Strengthen histone–DNA interactions → tighten chromatin → ↓ gene expression

Histone Acetylation

Acetylation

• Adds a negative charge to lysine residues on histone tails.

• Negative histone tails repel negatively charged DNA.

• Leads to:

  • Chromatin relaxation (euchromatin)

  • Increased gene expression

Deacetylation

• Removes the negative charge from lysines.

• DNA binds more tightly to histones.

• Leads to:

  • Condensed chromatin (heterochromatin)

  • Reduced gene expression

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Regulation of Acetylation/Deacetylation

HATs — Histone Acetyltransferases

• Add acetyl groups.

• Promote open chromatin and gene activation.

HDACs — Histone Deacetylases

• Remove acetyl groups.

• Promote closed chromatin and gene repression.

Cancer Connection

• Imbalance in acetylation can promote cancer progression.

• HDAC is overexpressed in many cancers, contributing to tumor suppressor gene silencing.

Targeting HDAC to Treat Cancer

Vorinostat (Zolinza)

Drug Class

• HDAC inhibitor

Indication

• Cutaneous T-cell lymphoma

Mechanism

• Inhibits HDAC → prevents removal of acetyl groups

• Increases histone acetylation, restoring normal gene expression

• Reactivates tumor suppressor genes

• Promotes:

  • Cell cycle arrest

  • Differentiation

  • Anti-tumor effects

Histone Methylation

Key Concepts

• Histone methylation can increase OR decrease gene expression depending on:

  • Which amino acid on the histone is methylated

  • How many methyl groups are added (mono-, di-, tri-methylation)

Enzymes involved

1. Histone methyltransferases (HMTs)

   • Add methyl groups → increase methylation

2. Histone demethylases (HDMs)

   • Remove methyl groups → decrease methylation

Cancer Connection

• Imbalances in methylation enzymes can disrupt normal gene regulation.

• This may lead to:

  • Abnormal gene silencing

  • Oncogene activation

  • Cancer development

Targeting Histone Methylation to Treat Cancer

Tazemetostat (Tazverik)

Drug Class

• Histone methyltransferase (HMT) inhibitor

Target

• Specifically inhibits EZH2 (a key HMT)

Indication

• Relapsed/refractory follicular lymphoma

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Normal Function of EZH2

• EZH2 adds methyl groups to histones (especially H3K27)

• This increases methylation → gene silencing

• Overactivity of EZH2 blocks differentiation and promotes cancer cell survival.

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Mechanism of Tazemetostat

• Inhibits EZH2 → decreases histone methylation

• Allows previously silenced genes to be transcribed again, including:

  • Genes controlling the cell cycle

  • Genes promoting apoptosis

Effects in Cancer Cells

• Restores normal gene expression

• Leads to:

  • Cell cycle arrest

  • Differentiation

  • Apoptosis

Targeting Histone Methylation to Treat Cancer

Follicular Lymphoma (Untreated)

• EZH2, part of the PRC2 complex, adds methyl groups to histone H3 at lysine 27 (H3K27me3).

• This methylation leads to:

  • Gene repression → tumor suppressor genes (e.g., IRF4, PRMD1, CDKN1A, CDKN2A) are turned off.

• As a result:

  • Cancer cells do not differentiate

  • Cancer cells continue proliferating

Bottom line:
Overactive EZH2 = too much histone methylation = silencing tumor suppressor genes → lymphoma growth.

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Follicular Lymphoma Treated with Tazemetostat

• Tazemetostat inhibits EZH2, preventing H3K27 methylation.

• This reduces gene silencing and allows key genes to be activated, including:

  • IRF4

  • PRMD1

  • CDKN1A

  • CDKN2A

Consequences in cancer cells:

• Gene activation restored

• Cell cycle arrest

• Apoptosis (programmed cell death)

Bottom line:
Inhibiting EZH2 reverses abnormal methylation → restores tumor suppressor gene expression → slows or kills cancer cells.