Diseases Caused by Trinucleotide Repeat Expansions

Slide 1 · Diseases Caused by

Trinucleotide-Repeat Expansions

Genetic instability • molecular pathology • clinicopathologic correlations

Dr Abu Suraih Sakhri

MBBS, MD (Pathology)

www.abusuraihsakhri.com

Slide 2 · Learning objectives

Define repeat expansion as a dynamic mutation and explain anticipation.

Predict pathogenic mechanisms from repeat location: UTR, intron, or coding exon.

Contrast FMR1 full-mutation disease with FMR1 premutation-associated disorders.

Connect the molecular defects in Huntington disease, Friedreich ataxia, and myotonic dystrophy to their clinical phenotypes.

Slide 3 · Expanded repeats alter gene function by multiple routes

Unstable tandem DNA repeat

Intergenerational expansion

Altered gene product

Tissue-selective disease

The mutation mechanism is shared; The molecular consequences are not identical.

Slide 4 · A tandem repeat becomes pathogenic when it expands

Unexpanded locus

Expanded locus

CGG

CGG

CGG

CGG

CGG

CGG

CGG

CGG

CGG

CGG

CGG

CGG

CGG

Illustrative unit count; Not a diagnostic threshold

Stable range

Repeat tract remains below the disease-associated expansion threshold.

Pathogenic expansion

The enlarged repeat alters gene expression, RNA processing, or protein function.

Slide 5 · Trinucleotide repeats are a form of dynamic mutation

The repeat tract may change length during transmission between generations.

Allele size and stability can influence phenotype and age at manifestation.

This instability helps explain patterns not captured by simple Mendelian segregation.

Expansion beyond a locus-specific threshold can impair gene expression or protein function.

Slide 6 · Anticipation links repeat growth to earlier or more severe disease

Repeat-bearing parent

Germline repeat instability

Larger transmitted allele

Shift in phenotype

Anticipation describes more severe or earlier manifestations in successive generations.

Its presence and parental transmission pattern are disease-specific.

Slide 7 · Repeat location is a major pathogenic determinant

An expansion in a regulatory region can suppress transcription.

A noncoding transcript can acquire toxic RNA-binding properties.

A coding CAG expansion produces an elongated polyglutamine tract.

Untranslated region (UTR)

Intron

Protein-coding exon

Slide 8 · Coding and noncoding repeat sites are distinct

5′

3′

Promoter

5′ UTR

Intron

Coding exon

3′ UTR

CGG / FMR1

GAA / FXN

CAG / HTT

Illustrative gene layout • sites represent different genes, not one continuous locus

Slide 9 · Three core mechanisms of repeat-expansion disease

Mutated region

Primary molecular change

Representative disease

5′ untranslated region

FMR1 methylation / silencing

Fragile X syndrome

Intron

Reduced FXN expression

Friedreich ataxia

Protein-coding exon

Expanded polyglutamine protein

Huntington disease

Noncoding transcript

RNA-mediated gain of function

Myotonic dystrophy type 1

Slide 10 · Gain and loss of function are not interchangeable

Loss of function: The cell lacks sufficient functional gene product.

Protein gain of function: Mutant protein acquires harmful properties.

RNA gain of function: Expanded-repeat RNA perturbs RNA-binding proteins.

The same locus can produce different disorders at different repeat lengths.

Slide 11 · Transcriptional silencing: A route to loss of function

Expanded noncoding DNA

Altered chromatin / methylation

Reduced transcription

Protein deficiency

Gene silencing decreases formation of the normal protein.

FMR1 full mutation and intronic FXN expansion illustrate distinct silencing contexts.

Slide 12 · Toxic RNA: Transcription without harmless function

Expanded noncoding repeat

Expanded-repeat RNA

RNA-binding protein sequestration

Altered cell physiology

Repeat-containing RNA can bind and sequester regulatory proteins.

Disordered RNA processing may occur despite continued transcription.

Slide 13 · Polyglutamine toxicity: A coding expansion

CAG expansion in exon

Long polyglutamine tract

Toxic protein effects

Selected neuron injury

CAG encodes glutamine; Expansion lengthens a protein’s glutamine tract.

Mutant protein misfolding and altered cellular interactions contribute to injury.

Slide 14 · Disease–repeat–gene map

Disorder

Gene

Repeat / location

Fragile X syndrome

FMR1

CGG; 5′ UTR

Huntington disease

HTT

CAG; Coding exon

Friedreich ataxia

FXN

GAA; Intron

Myotonic dystrophy type 1

DMPK

CTG; Noncoding transcript

Kennedy disease

AR

CAG; Coding region

Slide 15 · Fragile X syndrome: The FMR1 locus

Fragile X syndrome is an X-linked disorder associated with CGG expansion.

The repeat lies in the 5′ untranslated region of FMR1 on Xq27.3.

The major full-mutation mechanism is epigenetic silencing and loss of FMRP.

A premutation may instead remain transcribed and produce distinct disease.

Slide 16 · FMR1 alleles form a molecular spectrum

Typical-range allele

Limited CGG tract

Premutation

Expanded, transcribed FMR1

Full mutation

Very large CGG tract; Silencing

The gene dosage and toxic-RNA consequences differ markedly across classes

Slide 17 · FMR1 repeat lengths: Interpret the source cautiously

Typical alleles with relatively short CGG tracts (average about 29).

Premutations are described as approximately 55–200 CGG repeats.

Full mutations are very large expansions, generally exceeding about 200 repeats.

The source uses slightly differing full-mutation bounds across text and table; Do not substitute those approximations for laboratory interpretation.

Slide 18 · Full FMR1 expansion promotes transcriptional shutdown

Large CGG expansion

Promoter-region methylation

FMR1 gene silencing

FMRP deficiency

Dense methylation reaches the 5′ region and promoter of FMR1.

Transcriptional suppression markedly reduces FMRP production.

Slide 19 · FMRP regulates neuronal messenger RNA

FMRP is expressed widely, with high abundance in brain and testis.

It binds selected mRNAs and associates with neuronal transport complexes.

FMRP helps regulate where and when proteins are synthesized at synapses.

Loss of these controls disrupts the cellular basis of neuronal adaptation.

Slide 20 · FMRP connects mRNA transport to synaptic translation

Nucleus

FMRP–mRNA transport complex

Dendritic synapse

With FMRP

Localized translation is regulated in response to neuronal signals.

With FMRP deficiency

Dysregulated translation contributes to impaired synaptic plasticity.

Slide 21 · Loss of FMRP disrupts synaptic plasticity

Reduced FMRP

Disinhibited local translation

Synaptic protein imbalance

Impaired plasticity

FMRP deficiency with increased translation of bound synaptic mRNAs.

Imbalanced synaptic protein production compromises plasticity relevant to learning and memory.

Slide 22 · Fragile X syndrome: Neurodevelopmental consequences

Intellectual disability is a major phenotype, particularly in affected males.

Autism spectrum manifestations, hyperactivity and anxiety are recognized.

Epilepsy and behavioral dysregulation can accompany developmental impairment.

Expression varies among affected individuals and between sexes.

Slide 23 · Fragile X syndrome: Characteristic physical findings

Long face, prominent mandible and large/everted ears may be present.

Macroorchidism is a distinctive finding in postpubertal affected males.

Hyperextensible joints, high-arched palate and mitral valve prolapse may occur.

Absence of a stereotypic appearance does not exclude the diagnosis.

Slide 24 · Why the phenotype is not purely a “facial syndrome”

The molecular defect chiefly affects RNA regulation within cells.

Synaptic protein homeostasis explains the strong neurodevelopmental emphasis.

Physical signs are variable and may be subtle.

Molecular testing is decisive when clinical suspicion is appropriate.

FMR1 expansion

FMRP reduction

Neuronal dysfunction

Slide 25 · Sex-specific effects reflect X-linked biology

Males have a single X chromosome and are often more severely affected.

Females with a full mutation may have variable manifestations.

Patterns of X-chromosome inactivation contribute to clinical heterogeneity.

Inheritance depends on both the expanded allele and the transmitting parent.

Slide 26 · Maternal transmission can expand an FMR1 premutation

Illustrative transmission of an FMR1 premutation

Premutation-carrying grandfather

Premutation-carrying daughter

Child inheriting expanded full mutation

Paternal transmission usually involves modest repeat change

Substantial expansion may occur during maternal transmission

This is a risk illustration, not a deterministic offspring prediction

Slide 27 · The historical “normal transmitting male” pattern

Some premutation-carrying males may not show the classical fragile X phenotype.

These males transmit their X chromosome to all daughters, not to sons.

Daughters carrying premutations may pass expanded alleles to their children.

This pedigree pattern historically helped reveal repeat instability.

Slide 28 · Anticipation in fragile X is linked to oogenesis

Inherited FMR1 premutation

Maternal germline instability

Possible full-mutation expansion

Affected offspring

Greater full-mutation expansion during maternal transmission.

Clinical penetrance in descendants is not predicted from Mendelian allele inheritance alone.

Slide 29 · A full FMR1 mutation is not equivalent to a premutation

Full mutation: Promoter methylation and FMRP deficiency dominate.

Premutation: FMR1 RNA production continues and toxic-RNA effects may occur.

The classic syndrome and adult-onset premutation disorders have distinct mechanisms.

Allele size alone does not replace molecular and clinical characterization.

Slide 30 · Molecular testing can assess repeat tract length

Flanking PCR primers

Repeat-containing amplicon

Fragment length assessment

Important limitation

Very large expansions may not amplify efficiently by conventional PCR; The source describes Southern blotting as an alternative.

Slide 31 · The diagnostic assay has an amplification limitation

Flanking PCR amplifies the sequence containing the repeat tract.

Product length can distinguish shorter alleles and many premutations.

Very large expanded alleles may be difficult to amplify conventionally.

Southern blot analysis when a large expansion cannot be characterized by conventional PCR.

Slide 32 · Diagnosing fragile X requires mechanism-aware interpretation

A detected expansion must be interpreted in its allele-size category.

Clinical signs do not reliably distinguish all premutation carriers from noncarriers.

Assay limitations matter when apparent absence of an amplicon may reflect an enlarged repeat.

Genetic counseling must consider the transmitting parent and reproductive context.

Slide 33 · FMR1 premutations are biologically active

Premutations are not simply clinically silent intermediates.

The expanded locus remains transcribed rather than undergoing full-mutation silencing.

Expanded FMR1 RNA can acquire toxic properties.

The associated phenotypes differ from classic fragile X syndrome.

Slide 34 · Premutation-associated disease is an RNA-mediated process

Transcribed premutation

Expanded FMR1 mRNA

Sequestration of RNA-binding proteins

Cell dysfunction

Expanded CGG-containing RNA recruits proteins away from their normal functions.

RNA/protein aggregates and nuclear inclusions are described in affected tissues.

Slide 35 · Fragile X–associated tremor/ataxia syndrome

An adult-onset progressive neurologic syndrome in some FMR1 premutation carriers.

Characteristic findings include intention tremor and cerebellar ataxia.

Progression to parkinsonian features can occur.

Nuclear inclusions involving expanded FMR1 RNA and bound proteins.

Slide 36 · Fragile X–associated primary ovarian insufficiency

Premutation-carrying females can develop ovarian dysfunction before age 40.

Features include menstrual irregularity and diminished fertility.

Elevated FSH and reduced anti-Müllerian hormone.

Intracellular expanded-RNA aggregates may contribute to follicular damage; The exact mechanism is less established.

Slide 37 · Premutation and full mutation produce different outcomes

Property

FMR1 premutation

FMR1 full mutation

Gene expression

Transcription persists

Epigenetic silencing predominant

Molecular mechanism

Toxic CGG-containing RNA

Reduced / absent FMRP

Representative phenotype

Tremor/ataxia; Ovarian insufficiency

Neurodevelopmental fragile X syndrome

Typical timing

Often adult onset

Early developmental manifestations

Slide 38 · Clinical application: Developmental phenotype

CLINICAL PATTERN

A boy has intellectual disability, prominent ears and macroorchidism after puberty.

PATHOLOGIC INTERPRETATION

A large FMR1 CGG expansion with epigenetic silencing explains the syndrome through reduced FMRP.

Slide 39 · Clinical application: Adult premutation phenotype

CLINICAL PATTERN

An older man develops intention tremor and progressive gait ataxia; Family history suggests an FMR1 expansion.

PATHOLOGIC INTERPRETATION

Consider fragile X–associated tremor/ataxia syndrome: A transcribed premutation with RNA-mediated toxicity.

Slide 40 · Huntington disease exemplifies a coding repeat expansion

Autosomal dominant neurodegeneration with movement and cognitive manifestations.

An expanded CAG tract occurs in the first exon of HTT.

CAG encodes glutamine, making huntingtin an expanded polyglutamine protein.

The primary pathogenic concept is toxic gain of protein function.

Slide 41 · HTT CAG expansion changes a protein, not simply transcript abundance

CAG expansion in HTT exon

Expanded glutamine tract

Altered huntingtin behavior

Striatal neurodegeneration

DNA → protein composition → selective neuronal injury

Slide 42 · Repeat length influences age at Huntington onset

An inverse association between repeat number and age at onset.

Longer expanded tracts are associated with earlier manifestations.

Paternal transmission is especially relevant to further repeat expansion.

The disease-specific pattern contrasts with maternal expansion in fragile X.

Slide 43 · Huntington molecular injury is multifactorial

Mutant huntingtin can dysregulate transcriptional regulators.

Impaired mitochondrial-related responses may increase vulnerability to oxidative stress.

Reduced brain-derived neurotrophic factor and altered proteostasis may contribute.

No single inclusion-based mechanism explains all cellular injury.

Slide 44 · Neuronal inclusions are not necessarily the toxic species

Mutant huntingtin aggregates occur in striatal and cortical neurons.

Inclusions are a pathologic hallmark, not proof of the immediate injury mechanism.

Experimental observations compatible with sequestration of toxic species.

A visible aggregate can therefore be associated with a protective response.

Slide 45 · Huntington morphology: Striatum atrophy

Normal schematic

Caudate / putamen preserved

Ventricular caliber relatively small

Huntington disease

Marked striatal neuronal loss

Secondary ventricular enlargement

Schematic relationships only; Not gross or histologic evidence

Slide 46 · The striatum links structure to chorea

Loss of caudate and putaminal neurons is the dominant gross pathologic feature.

Striatal circuits normally participate in damping motor output.

Disrupted inhibitory circuitry contributes to involuntary hyperkinetic movements.

Caudate atrophy may coexist with ventricular enlargement.

Slide 47 · Huntington disease: The clinical trajectory

Chorea and other involuntary movements are characteristic.

Cognitive and affective dysfunction may evolve to severe dementia.

Later bradykinesia or rigidity may follow initial hyperkinetic manifestations.

A progressive, ultimately fatal disease course.

Slide 48 · Huntington anticipation is often paternal

Expanded paternal HTT allele

Germline CAG instability

Longer CAG tract in offspring

Potential earlier onset

In the text, repeat expansion is associated with spermatogenesis.

An expanded allele inherited from an affected father may produce earlier onset.

Slide 49 · Clinical application: Autosomal dominant chorea

CLINICAL PATTERN

An adult with a family history of progressive chorea develops involuntary movements and cognitive change.

PATHOLOGIC INTERPRETATION

HTT coding CAG expansion produces mutant huntingtin; Caudate/putaminal neuron loss links the genotype to the motor phenotype.

Slide 50 · Friedreich ataxia is a noncoding repeat disease

Autosomal recessive disorder with progressive ataxia and systemic involvement.

The GAA expansion lies in the first intron of FXN.

An altered chromatin environment decreases frataxin expression.

Loss of frataxin affects mitochondrial metabolism rather than polyglutamine production.

Slide 51 · FXN expansion disrupts mitochondrial function

Intronic GAA expansion in FXN

Reduced frataxin expression

Mitochondrial dysfunction

Neural + cardiac injury

Chromatin changes accompany suppression of FXN transcription.

Reduced iron–sulfur cluster function and excess mitochondrial iron can increase oxidative stress.

Slide 52 · Frataxin deficiency affects iron–sulfur cluster function

Frataxin contributes to mitochondrial iron–sulfur cluster enzyme assembly.

Reduced frataxin decreases oxidative phosphorylation capacity.

Increased free mitochondrial iron may add oxidative stress.

High-energy-demand neural and cardiac tissues are clinically prominent.

Slide 53 · Friedreich ataxia: Characteristic neurologic findings

Gait ataxia typically precedes hand clumsiness and dysarthria.

Weakness, sensory neuropathy and impaired joint-position sense are common.

Deep tendon reflexes may be depressed or absent.

An extensor plantar response can coexist with absent peripheral reflexes.

Slide 54 · Friedreich ataxia: The cardiac connection

Cardiomyopathy is a major extra-neurologic manifestation.

Arrhythmias and heart failure contribute substantially to morbidity.

Diabetes can accompany the disorder.

The multisystem phenotype reflects widespread effects of mitochondrial dysfunction.

Slide 55 · Huntington versus Friedreich ataxia

Feature

Huntington disease

Friedreich ataxia

Inheritance

Autosomal dominant

Autosomal recessive

Repeat / gene

CAG / HTT

GAA / FXN

Molecular lesion

Polyglutamine gain of function

Reduced frataxin expression

Characteristic phenotype

Chorea and cognitive decline

Ataxia, neuropathy, cardiomyopathy

Slide 56 · Clinical application: Recessive ataxia

CLINICAL PATTERN

A child develops progressive gait ataxia, impaired position sense, absent reflexes and cardiomyopathy.

PATHOLOGIC INTERPRETATION

Intronic GAA expansion in FXN can reduce frataxin expression, causing a neurocardiac mitochondrial phenotype.

Slide 57 · Myotonic dystrophy type 1 expands a noncoding CTG tract

Myotonic dystrophy is an autosomal dominant, multisystem disease.

Myotonic dystrophy type 1 (DM1) involves CTG expansion in DMPK.

Expanded-repeat RNA mediates a toxic gain of function.

Manifestations include myotonia, weakness, cataracts, endocrine and cardiac abnormalities.

Slide 58 · Myotonic dystrophy: RNA toxicity disrupts splicing

Expanded DMPK CTG tract

Expanded-repeat RNA

Splicing regulator sequestration

Altered CLCN1 splicing

Muscle phenotype

Decreased functional chloride-channel expression contributes to persistent muscle excitability (myotonia).

Slide 59 · CLCN1 mis-splicing helps explain myotonia

Expanded-repeat RNA sequesters muscle splicing regulators.

Alternative splicing of CLCN1 reduces normal muscle chloride-channel function.

Decreased chloride conductance alters membrane excitability.

The result is delayed relaxation after voluntary muscle contraction.

Slide 60 · RNA splicing defects extend beyond chloride channels

Altered insulin-receptor isoform splicing may contribute to insulin resistance.

Myotonic dystrophy affects multiple organs, not just skeletal muscle.

Disease severity is not explained solely by repeat length.

Severe congenital disease is associated in the text with larger expansions.

Slide 61 · Trinucleotide and tetranucleotide expansions are distinct

DM1 involves a CTG trinucleotide repeat in DMPK.

DM2 involves a CCTG tetranucleotide repeat in CNBP.

Both illustrate pathogenic expanded-repeat RNA effects.

Do not incorrectly classify all repeat-expansion syndromes as trinucleotide diseases.

Slide 62 · Spinocerebellar ataxias include polyglutamine forms

Several autosomal dominant spinocerebellar ataxias involve coding CAG expansions.

Examples include SCA1, SCA2, SCA3, SCA6 and SCA7.

Dentatorubral-pallidoluysian atrophy is another polyglutamine example.

Some other ataxia syndromes instead involve noncoding repeat expansions.

Slide 63 · Repeat-expansion mechanisms: Integrated comparison

Disease / gene

Primary defect

Principal clinical theme

Fragile X / FMR1 full

FMRP loss of function

Neurodevelopmental impairment

FMR1 premutation

Expanded RNA toxicity

Tremor/ataxia; Ovarian dysfunction

Huntington / HTT

Mutant polyglutamine protein

Chorea and cognitive decline

Friedreich / FXN

Frataxin deficiency

Ataxia with cardiomyopathy

Myotonic dystrophy / DMPK

Aberrant RNA splicing

Myotonia and multisystem disease

Slide 64 · Recognize the mechanism from clinical context

Childhood intellectual disability with suggestive X-linked family history → assess FMR1 full mutation.

Late-life intention tremor and ataxia with FMR1 family history → consider premutation-associated syndrome.

Progressive chorea plus autosomal dominant inheritance → consider HTT CAG expansion.

Childhood ataxia with cardiomyopathy → consider FXN GAA expansion.

Slide 65 · Predict molecular pathology from expansion location

FMR1 5′ UTR expansion → promoter methylation and reduced FMRP when full mutation.

FXN intronic GAA expansion → altered chromatin and reduced frataxin.

HTT exonic CAG expansion → polyglutamine protein gain of function.

DMPK repeat-containing RNA → sequestration of splicing regulators.

Slide 66 · Integrated case: Muscle symptoms and cataracts

CLINICAL PATTERN

An adult has delayed hand-grip relaxation, muscle weakness and early cataracts.

PATHOLOGIC INTERPRETATION

A DMPK CTG expansion can produce toxic RNA and splicing defects; Impaired CLCN1 expression is linked to myotonia.

Slide 67 · Common interpretation pitfalls

Do not confuse the presence of repeat expansion with one universal cellular mechanism.

Do not assume all expanded alleles have the same penetrance or intergenerational behavior.

Do not equate FMR1 premutation disorders with FMR1 full-mutation syndrome.

Do not interpret a negative conventional PCR result without considering very large expansions.

Slide 68 · Key clinicopathologic synthesis

Repeat tract location determines whether DNA, RNA or protein becomes the dominant pathological substrate.

Germline instability explains anticipation and parent-of-origin effects.

FMR1 full mutations impair protein availability; Premutations can cause RNA toxicity.

HTT, FXN and DMPK show how distinct molecular lesions yield different target-organ phenotypes.

Slide 69 · Primary source and extended textbook sections

Robbins, Cotran & Kumar: Pathologic Basis of Disease. 11th edition (2026).

Chapter 5 — Genes and Human Diseases: repeat expansions, fragile X and molecular analysis.

Chapter 28 — The Central Nervous System: Huntington disease, spinocerebellar ataxias and Friedreich ataxia.

Chapter 27 — Peripheral Nerves and Skeletal Muscles: myotonic dystrophy.