Genetics, Trinucleotide

Mechanism

Microsatellites are parts of the genome consisting of short repeat units, including trinucleotide repeats.[5]  Some trinucleotide repeats are present in untranslated regions (UTRs) of the genome, but some are also present in exonic sequences.[5] Their exact function and mechanism in normal replication and transcription are not yet well understood, but their ability to contribute to disease is well documented.[5] In the general population, the number of trinucleotide repeats can vary widely from person to person and often does not contribute to disease or pathology, or correlate with the number of copies, unless it exceeds the threshold for a particular disease. Each disease state appears to require a certain number of trinucleotide repeats, known as the threshold value, above which the disease state manifests phenotypically. 

Anticipation is a genetic phenomenon commonly seen in trinucleotide repeat disorders such as Huntington disease and myotonic dystrophy, in which symptoms manifest at earlier ages with each subsequent generation. Therefore, as the number of trinucleotide repeats increases in an affected patient's progeny, symptoms may manifest earlier and be more severe.

Testing

Diagnosis of trinucleotide repeat disorders is often possible via a detailed personal history and physical exam. Family history can often be beneficial, obviating the need for expensive genetic testing. However, for primary disease diagnosis and at the patient's request, genetic testing for the number of trinucleotide repeats provides a definitive diagnosis. 

Pathophysiology

If trinucleotide repeats occur in exonic sequences, increasing copy numbers can affect transcription and protein translation, contributing to pathology. However, many also occur in UTRs, and although they may not affect pathology, they can still contribute to disease.[5] Trinucleotide repeats have been noted to be particularly unstable[2], causing increased copy numbers and pathology in those who are genetically predisposed. Most trinucleotide repeat disorders have a strong genetic basis and an extensive family history across multiple generations. Increasing trinucleotide repeat copy numbers can be seen across successive generations, resulting in earlier disease onset than in the previous generation, a phenomenon known as anticipation. 

The mechanism by which trinucleotide repeats cause disease is still under extensive study, but some theories have emerged about what contributes to trinucleotide repeat instability. One study points to mismatch repair (MMR) proteins and their role in promoting instability through overexpression.[1] MMR proteins are one of many essential DNA repair pathways that protect cells from mutations and subsequent severe pathology. However, overexpression can make them mutagenic, contributing to trinucleotide repeat expansion.[1][6] Base excision repair (BER) has also been shown to contribute to trinucleotide repeat instability, especially after successive repairs from base oxidation.[6] BER is the mechanism by which damaged bases are removed and replaced in the DNA to prevent mutations and DNA strand breaks. However, the mechanism is not always effective and can contribute to trinucleotide repeat expansions with multiple repair cycles.[6] 

Clinical Significance

DNA repeat expansions underlie about 20 to 30 neurodegenerative and neuromuscular disorders in humans.[6][7] Here, we focus on the five most prominent and well-known TNR disorders. Those are spinocerebellar ataxia (SCA), Huntington disease, Fragile X syndrome, myotonic dystrophy, and Friedreich ataxia.

SCA has many types, but we will focus on Type 1 as an example. Spinocerebellar ataxia Type 1 is an autosomal dominant disorder that involves a CAG repeat in the ataxin (ATXN1) gene on chromosome 6.[8] Normally, there are 6 to 39 repeats, but people with SCA1 have over 40 repeats, which contributes to the disease pathology.[8] These patients develop progressive cerebellar ataxia due to destruction of Purkinje cells in the cerebellum. They will have permanent and progressive loss of balance, coordination, dysarthria, dysmetria, ophthalmoplegia, and eventual numbness and weakness of the muscles of the extremities.[8] Life expectancy ranges between 10 and 30 years after symptoms first present.[8]

Huntington disease is an autosomal dominant disorder that involves a CAG repeat in the huntingtin (HTT) gene on chromosome 4.[9] The condition usually occurs with more than 39 trinucleotide repeats, leading to destruction of GABAergic neurons in the caudate nucleus.[9] These patients develop a progressive movement disorder, known as chorea, characterized by rapid, involuntary, jerky movements affecting the trunk, face, and proximal limbs. Also, patients will have neuropsychiatric disturbances and a fairly rapid neurocognitive decline.[9] Life expectancy ranges from 10 to 20 years after symptom onset.[9]

Fragile X syndrome is an X-linked dominant disorder that involves a CGG repeat in the fragile X mental retardation 1 (FMR1) gene on the X chromosome.[10] Patients usually have over 200 repeats.[10] The large number of repeats causes hypermethylation of the gene's promoter.[10] Fragile X syndrome is the most common cause of an inherited intellectual disability, and these patients will have autism, seizures, a long face, a large jaw, and macroorchidism.

There are a few different types of myotonic dystrophy, but we will again focus just on type 1 as an example. Myotonic dystrophy type 1 is an autosomal dominant disorder that involves a CTG repeat in the dystrophia myotonica protein kinase (DMPK) gene on chromosome 19.[11] Normal copy numbers range from 5 to 37, but affected individuals can have up to several thousand trinucleotide repeats.[11] These repeats cause abnormal splicing and subsequent RNA processing.[11]  Patients will have cataracts, gonadal atrophy, frontal balding, and muscle weakness starting in the face, neck, and distal extremities, eventually involving the heart muscle and other internal organs in later stages of the disease.[12] 

Friedreich ataxia is an autosomal recessive disorder involving a GAA repeat in the frataxin (FXN) gene on chromosome 9.[13] Normal repeat numbers are around 40.[13] Researchers have cited a disease threshold of 70, but repeat numbers in affected individuals are usually as high as 600 to 900.[13] Frataxin is an iron-binding protein, and the excessive amount of repeats impairs normal mitochondrial functions.[13] Patients develop degeneration of the spinal cord tracts, specifically the corticospinal tract (leading to upper motor neuron signs), the dorsal columns (leading to impaired fine touch, proprioception, and vibration sense), and the spinocerebellar tract (leading to ataxia). Other features include vertebral deformities, diabetes mellitus, and hypertrophic cardiomyopathy. It is the involvement of the cardiac tissue that is the eventual cause of death at a relatively early age.