The molecular pathogenesis of repeat expansion diseases

Biochemical Society Transactions ◽

10.1042/bst20200143 ◽

2021 ◽

Author(s):

Yuzo Fujino ◽

Yoshitaka Nagai

Keyword(s):

Tandem Repeats ◽

Research Direction ◽

Repeat Expansion ◽

Repeat Sequence ◽

Loss Of Function ◽

Cgg Repeat ◽

Function Mechanism ◽

Coding Regions ◽

Monogenic Diseases ◽

Common Pathogenesis

Expanded short tandem repeats in the genome cause various monogenic diseases, particularly neurological disorders. Since the discovery of a CGG repeat expansion in the FMR1 gene in 1991, more than 40 repeat expansion diseases have been identified to date. In the coding repeat expansion diseases, in which the expanded repeat sequence is located in the coding regions of genes, the toxicity of repeat polypeptides, particularly misfolding and aggregation of proteins containing an expanded polyglutamine tract, have been the focus of investigation. On the other hand, in the non-coding repeat expansion diseases, in which the expanded repeat sequence is located in introns or untranslated regions, the toxicity of repeat RNAs has been the focus of investigation. Recently, these repeat RNAs were demonstrated to be translated into repeat polypeptides by the novel mechanism of repeat-associated non-AUG translation, which has extended the research direction of the pathological mechanisms of this disease entity to include polypeptide toxicity. Thus, a common pathogenesis has been suggested for both coding and non-coding repeat expansion diseases. In this review, we briefly outline the major pathogenic mechanisms of repeat expansion diseases, including a loss-of-function mechanism caused by repeat expansion, repeat RNA toxicity caused by RNA foci formation and protein sequestration, and toxicity by repeat polypeptides. We also discuss perturbation of the physiological liquid-liquid phase separation state caused by these repeat RNAs and repeat polypeptides, as well as potential therapeutic approaches against repeat expansion diseases.

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Evidence for an FMR1 mRNA Gain-Of-Function Toxicity Mechanism in the Pathogenesis of Fragile-X Associated Premature Ovarian Insufficiency

10.21203/rs.3.rs-904337/v1 ◽

2021 ◽

Author(s):

Roseanne Rosario ◽

Hazel Stewart ◽

Nila Roy Choudhury ◽

Gracjan Michlewski ◽

Nicolas Charlet-Berguerand ◽

...

Keyword(s):

Granulosa Cell ◽

Cell Model ◽

Fragile X ◽

Repeat Sequence ◽

Premature Ovarian Insufficiency ◽

Gain Of Function ◽

Ovarian Insufficiency ◽

Cgg Repeat ◽

Function Mechanism

Abstract Fragile X-associated premature ovarian insufficiency (FXPOI) is caused by expansion of a CGG repeat sequence located in the 5’ untranslated region of the FMR1 gene. Women with FXPOI have a depleted ovarian reserve, resulting in amenorrhea, hypoestrogenism, and loss of fertility before the age of 40. FXPOI is caused by CGG sequence expansions to lengths between 55 and 200 repeats, known as a FMRI premutation, however the mechanism by which the premutation drives disease pathogenesis remains unclear. Two main hypotheses exist, which describe an mRNA toxic gain-of-function mechanism or that repeat-associated non-AUG (RAN) translation results in the production of an abnormal protein, called FMRpolyG. We have developed an in vitro granulosa cell model of the FMR1 premutation by ectopically expressing CGG-repeat RNA and FMRpolyG protein. We show that expanded CGG-repeat RNA accumulated in intranuclear RNA structures, and these aggregates were able to cause significant granulosa cell death independent of FMRpolyG expression. Furthermore, using an innovative RNA pulldown, mass spectrometry-based approach we have identified proteins that bind CGG-repeat RNA in granulosa cells in vitro, and thus may be deregulated as consequence of this interaction. Collectively, these data provide evidence for the contribution of an mRNA gain-of-function mechanism to FXPOI disease biology.

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Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS

Scientific Reports ◽

10.1038/s41598-021-87097-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yogeeshwar Ajjugal ◽

Narendar Kolimi ◽

Thenmalarchelvi Rathinavelan

Keyword(s):

Rna Binding ◽

Trinucleotide Repeat ◽

Rna Binding Proteins ◽

Fragile X ◽

Repeat Expansion ◽

Mobility Shift ◽

Cgg Repeat ◽

Dna And Rna ◽

Structural Choice ◽

Sense Strand

AbstractCGG tandem repeat expansion in the 5′-untranslated region of the fragile X mental retardation-1 (FMR1) gene leads to unusual nucleic acid conformations, hence causing genetic instabilities. We show that the number of G…G (in CGG repeat) or C…C (in CCG repeat) mismatches (other than A…T, T…A, C…G and G…C canonical base pairs) dictates the secondary structural choice of the sense and antisense strands of the FMR1 gene and their corresponding transcripts in fragile X-associated tremor/ataxia syndrome (FXTAS). The circular dichroism (CD) spectra and electrophoretic mobility shift assay (EMSA) reveal that CGG DNA (sense strand of the FMR1 gene) and its transcript favor a quadruplex structure. CD, EMSA and molecular dynamics (MD) simulations also show that more than four C…C mismatches cannot be accommodated in the RNA duplex consisting of the CCG repeat (antisense transcript); instead, it favors an i-motif conformational intermediate. Such a preference for unusual secondary structures provides a convincing justification for the RNA foci formation due to the sequestration of RNA-binding proteins to the bidirectional transcripts and the repeat-associated non-AUG translation that are observed in FXTAS. The results presented here also suggest that small molecule modulators that can destabilize FMR1 CGG DNA and RNA quadruplex structures could be promising candidates for treating FXTAS.

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Spatially coordinated heterochromatinization of distal short tandem repeats in fragile X syndrome

10.1101/2021.04.23.441217 ◽

2021 ◽

Author(s):

Linda Zhou ◽

Chunmin Ge ◽

Thomas Malachowski ◽

Ji Hun Kim ◽

Keerthivasan Raanin Chandradoss ◽

...

Keyword(s):

Fragile X Syndrome ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Fragile X ◽

Repeat Expansion ◽

Genome Wide ◽

A Genome ◽

In Trans ◽

Surveillance Mechanism ◽

Short Tandem

AbstractShort tandem repeat (STR) instability is causally linked to pathologic transcriptional silencing in a subset of repeat expansion disorders. In fragile X syndrome (FXS), instability of a single CGG STR tract is thought to repress FMR1 via local DNA methylation. Here, we report the acquisition of more than ten Megabase-sized H3K9me3 domains in FXS, including a 5-8 Megabase block around FMR1. Distal H3K9me3 domains encompass synaptic genes with STR instability, and spatially co-localize in trans concurrently with FMR1 CGG expansion and the dissolution of TADs. CRISPR engineering of mutation-length FMR1 CGG to normal-length preserves heterochromatin, whereas cut-out to pre-mutation-length attenuates a subset of H3K9me3 domains. Overexpression of a pre-mutation-length CGG de-represses both FMR1 and distal heterochromatinized genes, indicating that long-range H3K9me3-mediated silencing is exquisitely sensitive to STR length. Together, our data uncover a genome-wide surveillance mechanism by which STR tracts spatially communicate over vast distances to heterochromatinize the pathologically unstable genome in FXS.One-Sentence SummaryHeterochromatinization of distal synaptic genes with repeat instability in fragile X is reversible by overexpression of a pre-mutation length CGG tract.

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Short Tandem Repeats Used in Preimplantation Genetic Testing of Β-Thalassemia: Genetic Polymorphisms For 15 Linked Loci in the Vietnamese Population

Open Access Macedonian Journal of Medical Sciences ◽

10.3889/oamjms.2019.840 ◽

2019 ◽

Vol 7 (24) ◽

pp. 4383-4388

Author(s):

Dang Tien Truong ◽

Ngo Van Nhat Minh ◽

Dinh Phuong Nhung ◽

Hoang Van Luong ◽

Do Quyet ◽

...

Keyword(s):

At Risk ◽

Genetic Testing ◽

Tandem Repeats ◽

Drop Out ◽

Preimplantation Genetic Testing ◽

Thalassemia Patient ◽

Gene Assay ◽

Monogenic Diseases ◽

Vietnamese Population ◽

Short Tandem

BACKGROUND: β-thalassemia is one of the most common monogenic diseases worldwide. Preimplantation genetic testing (PGT) of β-thalassemia is performed to avoid affected pregnancies has become increasingly popular worldwide. In which, the indirect analysis using short tandem repeat (STRs) linking with HBB gene to detect different β-globin (HBB) gene mutation is a simple, accurate, economical and also provides additional control of contamination and allele-drop-out ADO. AIM: This study established microsatellite markers for PGT of Vietnamese β-thalassemia patient. METHODS: Fifteen (15) STRs gathered from 5 populations were identified by in silico tools within 1 Mb flanking the HBB gene. The multiplex PCR reaction was optimized and performed on 106 DNA samples from at-risk families. RESULTS: After estimating, PIC values were ≥ 0.7 for all markers, with expected heterozygosity and observed heterozygosity values ranged from 0.81 to 0.92 and 0.53 to 0.86, respectively. One hundred percent of individuals had at least seven heterozygous markers and were found to be heterozygous for at least two markers on either side of the HBB gene. The STRs panel was successfully performed on one at-risk family. CONCLUSION: In general, a pentadecaplex marker (all < 1 Mb from the HBB gene) assay was constituted for β-thalassemia PGT on Vietnamese population.

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FMRP Levels in Human Peripheral Blood Leukocytes Correlates with Intellectual Disability

Diagnostics ◽

10.3390/diagnostics11101780 ◽

2021 ◽

Vol 11 (10) ◽

pp. 1780

Author(s):

Mark Roth ◽

Lucienne Ronco ◽

Diego Cadavid ◽

Blythe Durbin-Johnson ◽

Randi J. Hagerman ◽

...

Keyword(s):

Mental Retardation ◽

Intellectual Disability ◽

Peripheral Blood ◽

Fragile X ◽

Repeat Expansion ◽

Repeat Number ◽

Cgg Repeat ◽

Fragile X Mental Retardation ◽

Cgg Repeats ◽

Fmr1 Mrna

Fragile X syndrome (FXS) is the most common form of inherited intellectual disability. FXS is an X-linked, neurodevelopmental disorder caused by a CGG trinucleotide repeat expansion in the 5′ untranslated region (UTR) of the Fragile X Mental Retardation gene, FMR1. Greater than 200 CGG repeats results in epigenetic silencing of the gene leading to the deficiency or absence of Fragile X mental retardation protein (FMRP). The loss of FMRP is considered the root cause of FXS. The relationship between neurological function and FMRP expression in peripheral blood mononuclear cells (PBMCs) has not been well established. Assays to detect and measure FMR1 and FMRP have been described; however, none are sufficiently sensitive, precise, or quantitative to properly characterize the relationships between cognitive ability and CGG repeat number, FMR1 mRNA expression, or FMRP expression measured in PBMCs. To address these limitations, two novel immunoassays were developed and optimized, an electro-chemiluminescence immunoassay and a multiparameter flow cytometry assay. Both assays were performed on PMBCs isolated from 27 study participants with FMR1 CGG repeats ranging from normal to full mutation. After correcting for methylation, a significant positive correlation between CGG repeat number and FMR1 mRNA expression levels and a significant negative correlation between FMRP levels and CGG repeat expansion was observed. Importantly, a high positive correlation was observed between intellectual quotient (IQ) and FMRP expression measured in PBMCs.

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The Landscape of Human STR Variation

10.1101/004671 ◽

2014 ◽

Cited By ~ 1

Author(s):

Thomas F. Willems ◽

Melissa Gymrek ◽

Gareth Highnam ◽

The Genomes Project ◽

David Mittelman ◽

...

Keyword(s):

Tandem Repeats ◽

Phase 1 ◽

Genetic Diseases ◽

Point Mutations ◽

Graphical Interface ◽

Loss Of Function ◽

Human Reference Genome ◽

Str Loci ◽

Classical Point ◽

Short Tandem

Short Tandem Repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across over 1,000 individuals in phase 1 of the 1000 Genomes Project. This process nearly saturated common STR variations. After employing a series of quality controls, we utilize this call set to analyze determinants of STR variation, assess the human reference genome?s representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations. The resource is publicly available at http://strcat.teamerlich.org/ both in raw format and via a graphical interface.

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5′ UTR CGG repeat expansion in GIPC1 is associated with oculopharyngodistal myopathy

Brain ◽

10.1093/brain/awaa426 ◽

2020 ◽

Author(s):

Jianying Xi ◽

Xilu Wang ◽

Dongyue Yue ◽

Tonghai Dou ◽

Qunfeng Wu ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Trinucleotide Repeat ◽

Late Onset ◽

Age At Onset ◽

Large Family ◽

Repeat Expansion ◽

Chain Reaction ◽

Cgg Repeat ◽

Sporadic Cases ◽

Polymerase Chain

Abstract Oculopharyngodistal myopathy is a late-onset degenerative muscle disorder characterized by ptosis and weakness of the facial, pharyngeal, and distal limb muscles. A recent report suggested a non-coding trinucleotide repeat expansion in LRP12 to be associated with the disease. Here we report a genetic study in a Chinese cohort of 41 patients with the clinical diagnosis of oculopharyngodistal myopathy (21 cases from seven families and 20 sporadic cases). In a large family with 12 affected individuals, combined haplotype and linkage analysis revealed a maximum two-point logarithm of the odds (LOD) score of 3.3 in chromosomal region chr19p13.11-p13.2 and narrowed the candidate region to an interval of 4.5 Mb. Using a comprehensive strategy combining whole-exome sequencing, long-read sequencing, repeat-primed polymerase chain reaction and GC-rich polymerase chain reaction, we identified an abnormal CGG repeat expansion in the 5′ UTR of the GIPC1 gene that co-segregated with disease. Overall, the repeat expansion in GIPC1 was identified in 51.9% independent pedigrees (4/7 families and 10/20 sporadic cases), while the repeat expansion in LRP12 was only identified in one sporadic case (3.7%) in our cohort. The number of CGG repeats was <30 in controls but >60 in affected individuals. There was a slight correlation between repeat size and the age at onset. Both repeat expansion and retraction were observed during transmission but somatic instability was not evident. These results further support that non-coding CGG repeat expansion plays an essential role in the pathogenesis of oculopharyngodistal myopathy.

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