Genetics, Trinucleotide


Article Author:
Katie Nordick


Article Editor:
Yasir Al Khalili


Editors In Chief:
Linda Lindsay


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James Hughes
Beata Beatty
Beenish Sohail
Nazia Sadiq
Hajira Basit
Phillip Hynes


Updated:
7/22/2019 10:04:50 AM

Introduction

Trinucleotide repeats are sets of three nucleotides present in succession in various copy numbers throughout the human genome.[1] These areas of the genome are unstable and polymorphic.[2] Trinucleotide repeat disorders are a series of conditions caused by triplets in a mutated gene that are present in greater number than found in normal genetic sequencing.[3] These abnormal sequences are known as "expansions" and present across many stages of human development and numerous cell types.[3] Repetitive sequences of genetic code are quite common. However, when these sequences grow beyond the scope of what would be considered normal, they cause disease. While the human genome has mechanisms to protect against these expansions, patients present with what can be severe neuromuscular and neurodegenerative disorders.[4] There have been many diseases discovered by TNR expansions, but the most prominent are spinocerebellar ataxia, Huntington disease, Fragile X syndrome, myotonic dystrophy, and Friedrich ataxia. These disorders, as well as the genetic and molecular development of these disorders, will be discussed below. 

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 terms of normal replication and transcription are not yet precisely known, but their ability to contribute to disease is well-documented.[5] In the general population, the numbers of trinucleotide repeats can vary widely from person to person, and often do not contribute to any disease or pathology or have any correlation with the number of copies unless they are above the threshold number of copies specific 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. 

Testing

Diagnosis of trinucleotide repeats 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, in primary disease diagnosis and upon patient request, genetic testing for the number of trinucleotide repeats provides a definitive diagnosis. 

Pathophysiology

If trinucleotide repeats exist in exonic sequences, an increasing number of copies can have an effect on transcription and translation of proteins contributing to pathology. However, many also occur in UTRs, and, while it would appear not to affect pathology, they actually 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 of the disease in multiple generations. Increasing copy numbers of the trinucleotide repeats can be seen in successive generations, resulting in an earlier disease onset than 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 in the cell to protect from mutations and the subsequent development of severe pathology. However, they have been shown to be mutagenic at high numbers as a result of overexpression, contributing to trinucleotide repeat expansion.[1][6] Base excision repair (BER) has also been shown to play a role in contributing 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 are the underlying pathology in about 20 to 30 neurodegenerative and neuromuscular disorders in humans.[6][7] Here, we will focus on the five most prominent and well-known of the TNR disorders. Those are spinocerebellar ataxia (SCA), Huntington disease, Fragile X syndrome, myotonic dystrophy, and Friedrich ataxia.

There are many different types of SCA, 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 those with SCA1 will have over 40 repeats contributing to the disease pathology seen.[8] These patients will have progressive cerebellar ataxia due to the destruction of the 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 is usually seen with more than 39 trinucleotide repeats, leading to the destruction of GABAergic neurons in the caudate nucleus.[9] These patients will have a progressive onset of a 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 the onset of symptoms.[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 promoter site of the gene.[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 those affected with the disease 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 at the face, neck, and distal extremities, eventually involving the heart muscle and other internal organs in later stages of the disease.[12] 

Friedrich 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 the threshold for the disease at 70, but trinucleotide repeat numbers in those affected 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 will have degeneration of the spinal cord tracts, specifically degeneration of 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. 


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Genetics, Trinucleotide - Questions

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A 35-year-old female presents with involuntary movements of her arms and face for the past 6 months. She says that the episodes are unpredictable and have been occurring more frequently over the past month. She further states that her father had similar episodes starting at age 45 and passed away from an unknown "brain disease" at age 50. What is the mechanism of her suspected underlying disease?



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A 15-year-old male presents to the clinic with the onset of progressive muscle weakness, increased thirst, increased urination, and slurred speech. Examination shows prominent scoliosis, a staggering gait, and crackles upon auscultation of the lungs. He is a new patient to the clinic. He denies any other significant past medical history, allergies, or medications. His mother mentions that he is the third of five boys in the family and that his oldest brother has similar symptoms. What is the most likely genetic mechanism underlying this patient's presentation?



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A 25-year-old male presents for an annual physical. Over the past year, he notes that he has had more difficulty seeing at night, worsening frontal balding, and worsening muscle weakness. Physical examination shows opacification of the lenses in the eyes bilaterally, extensive balding, and 3/5 muscle weakness of all four extremities. What is the most likely underlying genetic mechanism of this patient's disease presentation?



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A 15-year-old boy with a past medical history of autism spectrum disorder and seizures presents for an annual clinic visit with his father. He is new to the clinic. On exam, he has large ears and a long face. He is noted to have a mid-systolic click on cardiac auscultation. He has no allergies. He is on levetiracetam for his seizure disorder. His father notes that a maternal uncle has similar medical problems. What is the underlying genetic mechanism contributing to this patient's presentation?



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A 35-year-old female presents with progressive difficulty walking and slurred speech for the past year and a half. On exam, moderate dysarthria, dysdiadochokinesia, dysmetria, and a wide-based gait are observed. She is a new patient to the clinic and notes that she has no other significant past medical history. She has no allergies, takes no medications, and has never used any tobacco or illicit drugs. She rarely drinks alcohol and never has more than two drinks at a time. She does note that her paternal grandmother passed away at age 65 and her father passed away at age 57. Both had similar symptoms that began in their 40s and progressed to severe dementia. She also has an older brother who is now 40 years old and has the same symptoms, which also began around age 33. What is the underlying genetic defect of this patient's disease presentation?



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Genetics, Trinucleotide - References

References

A brief history of triplet repeat diseases., Budworth H,McMurray CT,, Methods in molecular biology (Clifton, N.J.), 2013     [PubMed]
Richard GF,Kerrest A,Dujon B, Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiology and molecular biology reviews : MMBR. 2008 Dec;     [PubMed]
Guo J,Chen L,Li GM, DNA mismatch repair in trinucleotide repeat instability. Science China. Life sciences. 2017 Oct;     [PubMed]
Den Dunnen WFA, Trinucleotide repeat disorders. Handbook of clinical neurology. 2017;     [PubMed]
McMurray CT, Mechanisms of trinucleotide repeat instability during human development. Nature reviews. Genetics. 2010 Nov;     [PubMed]
Mirkin SM, Expandable DNA repeats and human disease. Nature. 2007 Jun 21;     [PubMed]
Kovtun IV,McMurray CT, Features of trinucleotide repeat instability in vivo. Cell research. 2008 Jan;     [PubMed]
Opal P,Ashizawa T, Spinocerebellar Ataxia Type 1 1993;     [PubMed]
McColgan P,Tabrizi SJ, Huntington's disease: a clinical review. European journal of neurology. 2018 Jan;     [PubMed]
Zafarullah M,Tassone F, Molecular Biomarkers in Fragile X Syndrome. Brain sciences. 2019 Apr 27;     [PubMed]
André LM,van Cruchten RTP,Willemse M,Wansink DG, (CTG)n repeat-mediated dysregulation of MBNL1 and MBNL2 expression during myogenesis in DM1 occurs already at the myoblast stage. PloS one. 2019;     [PubMed]
Cook A,Giunti P, Friedreich's ataxia: clinical features, pathogenesis and management. British medical bulletin. 2017 Dec 1;     [PubMed]
Banach M,Rakowicz M,Antczak J,Rola R,Witkowski G,Waliniowska E, [Cardiac, respiratory and sleep disorders in patients with myotonic dystrophy]. Przeglad lekarski. 2009;     [PubMed]

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