1
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Bhattacharyya N, Chai N, Hafford-Tear NJ, Sadan AN, Szabo A, Zarouchlioti C, Jedlickova J, Leung SK, Liao T, Dudakova L, Skalicka P, Parekh M, Moghul I, Jeffries AR, Cheetham ME, Muthusamy K, Hardcastle AJ, Pontikos N, Liskova P, Tuft SJ, Davidson AE. Deciphering novel TCF4-driven mechanisms underlying a common triplet repeat expansion-mediated disease. PLoS Genet 2024; 20:e1011230. [PMID: 38713708 PMCID: PMC11101122 DOI: 10.1371/journal.pgen.1011230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/17/2024] [Accepted: 03/19/2024] [Indexed: 05/09/2024] Open
Abstract
Fuchs endothelial corneal dystrophy (FECD) is an age-related cause of vision loss, and the most common repeat expansion-mediated disease in humans characterised to date. Up to 80% of European FECD cases have been attributed to expansion of a non-coding CTG repeat element (termed CTG18.1) located within the ubiquitously expressed transcription factor encoding gene, TCF4. The non-coding nature of the repeat and the transcriptomic complexity of TCF4 have made it extremely challenging to experimentally decipher the molecular mechanisms underlying this disease. Here we comprehensively describe CTG18.1 expansion-driven molecular components of disease within primary patient-derived corneal endothelial cells (CECs), generated from a large cohort of individuals with CTG18.1-expanded (Exp+) and CTG 18.1-independent (Exp-) FECD. We employ long-read, short-read, and spatial transcriptomic techniques to interrogate expansion-specific transcriptomic biomarkers. Interrogation of long-read sequencing and alternative splicing analysis of short-read transcriptomic data together reveals the global extent of altered splicing occurring within Exp+ FECD, and unique transcripts associated with CTG18.1-expansions. Similarly, differential gene expression analysis highlights the total transcriptomic consequences of Exp+ FECD within CECs. Furthermore, differential exon usage, pathway enrichment and spatial transcriptomics reveal TCF4 isoform ratio skewing solely in Exp+ FECD with potential downstream functional consequences. Lastly, exome data from 134 Exp- FECD cases identified rare (minor allele frequency <0.005) and potentially deleterious (CADD>15) TCF4 variants in 7/134 FECD Exp- cases, suggesting that TCF4 variants independent of CTG18.1 may increase FECD risk. In summary, our study supports the hypothesis that at least two distinct pathogenic mechanisms, RNA toxicity and TCF4 isoform-specific dysregulation, both underpin the pathophysiology of FECD. We anticipate these data will inform and guide the development of translational interventions for this common triplet-repeat mediated disease.
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Affiliation(s)
- Nihar Bhattacharyya
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Niuzheng Chai
- University College London Institute of Ophthalmology, London, United Kingdom
| | | | - Amanda N. Sadan
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Anita Szabo
- University College London Institute of Ophthalmology, London, United Kingdom
| | | | - Jana Jedlickova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Szi Kay Leung
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Tianyi Liao
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Pavlina Skalicka
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Mohit Parekh
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Ismail Moghul
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Aaron R. Jeffries
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Michael E. Cheetham
- University College London Institute of Ophthalmology, London, United Kingdom
| | | | - Alison J. Hardcastle
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Nikolas Pontikos
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Stephen J. Tuft
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Alice E. Davidson
- University College London Institute of Ophthalmology, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
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2
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Cabrera GT, Meijboom KE, Abdallah A, Tran H, Foster Z, Weiss A, Wightman N, Stock R, Gendron T, Gruntman A, Giampetruzzi A, Petrucelli L, Brown RH, Mueller C. Artificial microRNA suppresses C9ORF72 variants and decreases toxic dipeptide repeat proteins in vivo. Gene Ther 2024; 31:105-118. [PMID: 37752346 DOI: 10.1038/s41434-023-00418-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 05/28/2023] [Accepted: 08/11/2023] [Indexed: 09/28/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that affects motor neurons, causing progressive muscle weakness and respiratory failure. The presence of an expanded hexanucleotide repeat in chromosome 9 open reading frame 72 (C9ORF72) is the most frequent mutation causing familial ALS and frontotemporal dementia (FTD). To determine if suppressing expression of C9ORF72 gene products can reduce toxicity, we designed a set of artificial microRNAs (amiRNA) targeting the human C9ORF72 gene. Here we report that an AAV9-mediated amiRNA significantly suppresses expression of the C9ORF72 mRNA, protein, and toxic dipeptide repeat proteins generated by the expanded repeat in the brain and spinal cord of C9ORF72 transgenic mice.
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Affiliation(s)
- Gabriela Toro Cabrera
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Katharina E Meijboom
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Abbas Abdallah
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Helene Tran
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Zachariah Foster
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Nicholas Wightman
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Rachel Stock
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Tania Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, FL, 32224, USA
| | - Alisha Gruntman
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Anthony Giampetruzzi
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd., Jacksonville, FL, 32224, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
| | - Christian Mueller
- Department of Pediatrics and Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
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3
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Anderson R, Das MR, Chang Y, Farenhem K, Schmitz CO, Jain A. CAG repeat expansions create splicing acceptor sites and produce aberrant repeat-containing RNAs. Mol Cell 2024; 84:702-714.e10. [PMID: 38295802 PMCID: PMC10923110 DOI: 10.1016/j.molcel.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/07/2023] [Accepted: 01/08/2024] [Indexed: 02/04/2024]
Abstract
Expansions of CAG trinucleotide repeats cause several rare neurodegenerative diseases. The disease-causing repeats are translated in multiple reading frames and without an identifiable initiation codon. The molecular mechanism of this repeat-associated non-AUG (RAN) translation is not known. We find that expanded CAG repeats create new splice acceptor sites. Splicing of proximal donors to the repeats produces unexpected repeat-containing transcripts. Upon splicing, depending on the sequences surrounding the donor, CAG repeats may become embedded in AUG-initiated open reading frames. Canonical AUG-initiated translation of these aberrant RNAs may account for proteins that have been attributed to RAN translation. Disruption of the relevant splice donors or the in-frame AUG initiation codons is sufficient to abrogate RAN translation. Our findings provide a molecular explanation for the abnormal translation products observed in CAG trinucleotide repeat expansion disorders and add to the repertoire of mechanisms by which repeat expansion mutations disrupt cellular functions.
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Affiliation(s)
- Rachel Anderson
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Michael R Das
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Yeonji Chang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Kelsey Farenhem
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Cameron O Schmitz
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Ankur Jain
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA.
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4
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Papp D, Hernandez LA, Mai TA, Haanen TJ, O’Donnell MA, Duran AT, Hernandez SM, Narvanto JE, Arguello B, Onwukwe MO, Mirkin SM, Kim JC. Massive contractions of myotonic dystrophy type 2-associated CCTG tetranucleotide repeats occur via double-strand break repair with distinct requirements for DNA helicases. G3 (BETHESDA, MD.) 2024; 14:jkad257. [PMID: 37950892 PMCID: PMC10849350 DOI: 10.1093/g3journal/jkad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/06/2023] [Accepted: 10/19/2023] [Indexed: 11/13/2023]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetic disease caused by expanded CCTG DNA repeats in the first intron of CNBP. The number of CCTG repeats in DM2 patients ranges from 75 to 11,000, yet little is known about the molecular mechanisms responsible for repeat expansions or contractions. We developed an experimental system in Saccharomyces cerevisiae that enables the selection of large-scale contractions of (CCTG)100 within the intron of a reporter gene and subsequent genetic analysis. Contractions exceeded 80 repeat units, causing the final repetitive tract to be well below the threshold for disease. We found that Rad51 and Rad52 are involved in these massive contractions, indicating a mechanism that uses homologous recombination. Srs2 helicase was shown previously to stabilize CTG, CAG, and CGG repeats. Loss of Srs2 did not significantly affect CCTG contraction rates in unperturbed conditions. In contrast, loss of the RecQ helicase Sgs1 resulted in a 6-fold decrease in contraction rate with specific evidence that helicase activity is required for large-scale contractions. Using a genetic assay to evaluate chromosome arm loss, we determined that CCTG and reverse complementary CAGG repeats elevate the rate of chromosomal fragility compared to a short-track control. Overall, our results demonstrate that the genetic control of CCTG repeat contractions is notably distinct among disease-causing microsatellite repeat sequences.
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Affiliation(s)
- David Papp
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Luis A Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Theresa A Mai
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Terrance J Haanen
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Meghan A O’Donnell
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Ariel T Duran
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sophia M Hernandez
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Jenni E Narvanto
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Berenice Arguello
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Marvin O Onwukwe
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Jane C Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA 92078, USA
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5
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Chung TH, Zhuravskaya A, Makeyev EV. Regulation potential of transcribed simple repeated sequences in developing neurons. Hum Genet 2023:10.1007/s00439-023-02626-1. [PMID: 38153590 DOI: 10.1007/s00439-023-02626-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Simple repeated sequences (SRSs), defined as tandem iterations of microsatellite- to satellite-sized DNA units, occupy a substantial part of the human genome. Some of these elements are known to be transcribed in the context of repeat expansion disorders. Mounting evidence suggests that the transcription of SRSs may also contribute to normal cellular functions. Here, we used genome-wide bioinformatics approaches to systematically examine SRS transcriptional activity in cells undergoing neuronal differentiation. We identified thousands of long noncoding RNAs containing >200-nucleotide-long SRSs (SRS-lncRNAs), with hundreds of these transcripts significantly upregulated in the neural lineage. We show that SRS-lncRNAs often originate from telomere-proximal regions and that they have a strong potential to form multivalent contacts with a wide range of RNA-binding proteins. Our analyses also uncovered a cluster of neurally upregulated SRS-lncRNAs encoded in a centromere-proximal part of chromosome 9, which underwent an evolutionarily recent segmental duplication. Using a newly established in vitro system for rapid neuronal differentiation of induced pluripotent stem cells, we demonstrate that at least some of the bioinformatically predicted SRS-lncRNAs, including those encoded in the segmentally duplicated part of chromosome 9, indeed increase their expression in developing neurons to readily detectable levels. These and other lines of evidence suggest that many SRSs may be expressed in a cell type and developmental stage-specific manner, providing a valuable resource for further studies focused on the functional consequences of SRS-lncRNAs in the normal development of the human brain, as well as in the context of neurodevelopmental disorders.
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Affiliation(s)
- Tek Hong Chung
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK.
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6
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Maltby CJ, Krans A, Grudzien SJ, Palacios Y, Muiños J, Suárez A, Asher M, Khurana V, Barmada SJ, Dijkstra AA, Todd PK. AAGGG repeat expansions trigger RFC1-independent synaptic dysregulation in human CANVAS Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571345. [PMID: 38168171 PMCID: PMC10760133 DOI: 10.1101/2023.12.13.571345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a late onset, recessively inherited neurodegenerative disorder caused by biallelic, non-reference pentameric AAGGG(CCCTT) repeat expansions within the second intron of replication factor complex subunit 1 (RFC1). To investigate how these repeats cause disease, we generated CANVAS patient induced pluripotent stem cell (iPSC) derived neurons (iNeurons) and utilized calcium imaging and transcriptomic analysis to define repeat-elicited gain-of-function and loss-of-function contributions to neuronal toxicity. AAGGG repeat expansions do not alter neuronal RFC1 splicing, expression, or DNA repair pathway functions. In reporter assays, AAGGG repeats are translated into pentapeptide repeat proteins that selectively accumulate in CANVAS patient brains. However, neither these proteins nor repeat RNA foci were detected in iNeurons, and overexpression of these repeats in isolation did not induce neuronal toxicity. CANVAS iNeurons exhibit defects in neuronal development and diminished synaptic connectivity that is rescued by CRISPR deletion of a single expanded allele. These phenotypic deficits were not replicated by knockdown of RFC1 in control neurons and were not rescued by ectopic expression of RFC1. These findings support a repeat-dependent but RFC1-independent cause of neuronal dysfunction in CANVAS, with important implications for therapeutic development in this currently untreatable condition.
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Affiliation(s)
- Connor J. Maltby
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
| | - Samantha J. Grudzien
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yomira Palacios
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Muiños
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- UM SMART Undergraduate Summer Program, University of Michigan, Ann Arbor, MI, USA
| | - Andrea Suárez
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Postbaccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, USA
| | - Melissa Asher
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Vikram Khurana
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sami J. Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Anke A. Dijkstra
- Department of Pathology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter K. Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, USA
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7
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Khalifah BA, Alghamdi SA, Alhasan AH. Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts. Front Bioeng Biotechnol 2023; 11:1244377. [PMID: 38047291 PMCID: PMC10690607 DOI: 10.3389/fbioe.2023.1244377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
Human transcriptome can undergo RNA mis-splicing due to spliceopathies contributing to the increasing number of genetic diseases including muscular dystrophy (MD), Alzheimer disease (AD), Huntington disease (HD), myelodysplastic syndromes (MDS). Intron retention (IR) is a major inducer of spliceopathies where two or more introns remain in the final mature mRNA and account for many intronic expansion diseases. Potential removal of such introns for therapeutic purposes can be feasible when utilizing bioinformatics, catalytic RNAs, and nano-drug delivery systems. Overcoming delivery challenges of catalytic RNAs was discussed in this review as a future perspective highlighting the significance of utilizing synthetic biology in addition to high throughput deep sequencing and computational approaches for the treatment of mis-spliced transcripts.
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Affiliation(s)
- Bashayer A. Khalifah
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ali H. Alhasan
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
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8
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Yang S, Wijegunawardana D, Sheth U, Veire AM, Salgado JMS, Agrawal M, Zhou J, Pereira JD, Gendron TF, Guo JU. Aberrant splicing exonizes C9ORF72 repeat expansion in ALS/FTD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566896. [PMID: 38014069 PMCID: PMC10680656 DOI: 10.1101/2023.11.13.566896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
A nucleotide repeat expansion (NRE) in the first annotated intron of the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). While C9 NRE-containing RNAs can be translated into several toxic dipeptide repeat proteins, how an intronic NRE can assess the translation machinery in the cytoplasm remains unclear. By capturing and sequencing NRE-containing RNAs from patient-derived cells, we found that C9 NRE was exonized by the usage of downstream 5' splice sites and exported from the nucleus in a variety of spliced mRNA isoforms. C9ORF72 aberrant splicing was substantially elevated in both C9 NRE + motor neurons and human brain tissues. Furthermore, NREs above the pathological threshold were sufficient to activate cryptic splice sites in reporter mRNAs. In summary, our results revealed a crucial and potentially widespread role of repeat-induced aberrant splicing in the biogenesis, localization, and translation of NRE-containing RNAs.
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9
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Anderson R, Das M, Chang Y, Farenhem K, Jain A. CAG repeat expansions create splicing acceptor sites and produce aberrant repeat-containing RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562581. [PMID: 37904984 PMCID: PMC10614865 DOI: 10.1101/2023.10.16.562581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Expansions of CAG trinucleotide repeats cause several rare neurodegenerative diseases. The disease-causing repeats are translated in multiple reading frames, without an identifiable initiation codon. The molecular mechanism of this repeat-associated non-AUG (RAN) translation is not known. We find that expanded CAG repeats create new splice acceptor sites. Splicing of proximal donors to the repeats produces unexpected repeat-containing transcripts. Upon splicing, depending on the sequences surrounding the donor, CAG repeats may become embedded in AUG-initiated open reading frames. Canonical AUG-initiated translation of these aberrant RNAs accounts for proteins that are attributed to RAN translation. Disruption of the relevant splice donors or the in-frame AUG initiation codons is sufficient to abrogate RAN translation. Our findings provide a molecular explanation for the abnormal translation products observed in CAG trinucleotide repeat expansion disorders and add to the repertoire of mechanisms by which repeat expansion mutations disrupt cellular functions.
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Affiliation(s)
- Rachel Anderson
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Michael Das
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Yeonji Chang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Kelsey Farenhem
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Ankur Jain
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
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10
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Abdi MH, Zamiri B, Pazuki G, Sardari S, Pearson CE. Pathogenic CANVAS-causing but not nonpathogenic RFC1 DNA/RNA repeat motifs form quadruplex or triplex structures. J Biol Chem 2023; 299:105202. [PMID: 37660923 PMCID: PMC10563062 DOI: 10.1016/j.jbc.2023.105202] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023] Open
Abstract
Biallelic expansions of various tandem repeat sequence motifs are possible in RFC1 (replication factor C subunit 1), encoding the DNA replication/repair protein RFC1, yet only certain repeat motifs cause cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS). CANVAS presents enigmatic puzzles: The pathogenic path for CANVAS neither is known nor is it understood why some, but not all expanded, motifs are pathogenic. The most common pathogenic repeat is (AAGGG)n•(CCCTT)n, whereas (AAAAG)n•(CTTTT)n is the most common nonpathogenic motif. While both intronic motifs can be expanded and transcribed, only r(AAGGG)n is retained in the mutant RFC1 transcript. We show that only the pathogenic forms unusual nucleic acid structures. Specifically, DNA and RNA of the pathogenic d(AAGGG)4 and r(AAGGG)4 form G-quadruplexes in potassium solution. Nonpathogenic repeats did not form G-quadruplexes. Triple-stranded structures are formed by the pathogenic motifs but not by the nonpathogenic motifs. G- and C-richness of the pathogenic strands favor formation of G•G•G•G-tetrads and protonated C+-G Hoogsteen base pairings, involved in quadruplex and triplex structures, respectively, stabilized by increased hydrogen bonds and pi-stacking interactions relative to A-T Hoogsteen pairs that could form by the nonpathogenic motif. The ligand, TMPyP4, binds the pathogenic quadruplexes. Formation of quadruplexes and triplexes by pathogenic repeats supports toxic-DNA and toxic-RNA modes of pathogenesis at the RFC1 gene and the RFC1 transcript. Our findings with short repeats provide insights into the disease specificity of pathogenic repeat motif sequences and reveal nucleic acid structural features that may be pathogenically involved and targeted therapeutically.
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Affiliation(s)
- Mohammad Hossein Abdi
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Bita Zamiri
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran.
| | - Gholamreza Pazuki
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Soroush Sardari
- Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Christopher E Pearson
- Program of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.
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11
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Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science 2023; 381:eadd1250. [PMID: 37733848 DOI: 10.1126/science.add1250] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter gene expression, yet how they regulate transcription remains unknown. We found that STRs modulate transcription factor (TF)-DNA affinities and apparent on-rates by about 70-fold by directly binding TF DNA-binding domains, with energetic impacts exceeding many consensus motif mutations. STRs maximize the number of weakly preferred microstates near target sites, thereby increasing TF density, with impacts well predicted by statistical mechanics. Confirming that STRs also affect TF binding in cells, neural networks trained only on in vivo occupancies predicted effects identical to those observed in vitro. Approximately 90% of TFs preferentially bound STRs that need not resemble known motifs, providing a cis-regulatory mechanism to target TFs to genomic sites.
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Affiliation(s)
- Connor A Horton
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amr M Alexandari
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Michael G B Hayes
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emil Marklund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia M Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Arjun K Aditham
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Nilay Shah
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Peter H Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Ariel Afek
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
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12
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Marzullo M, Coni S, De Simone A, Canettieri G, Ciapponi L. Modeling Myotonic Dystrophy Type 2 Using Drosophila melanogaster. Int J Mol Sci 2023; 24:14182. [PMID: 37762484 PMCID: PMC10532015 DOI: 10.3390/ijms241814182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/04/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Myotonic dystrophy 2 (DM2) is a genetic multi-systemic disease primarily affecting skeletal muscle. It is caused by CCTGn expansion in intron 1 of the CNBP gene, which encodes a zinc finger protein. DM2 disease has been successfully modeled in Drosophila melanogaster, allowing the identification and validation of new pathogenic mechanisms and potential therapeutic strategies. Here, we describe the principal tools used in Drosophila to study and dissect molecular pathways related to muscular dystrophies and summarize the main findings in DM2 pathogenesis based on DM2 Drosophila models. We also illustrate how Drosophila may be successfully used to generate a tractable animal model to identify novel genes able to affect and/or modify the pathogenic pathway and to discover new potential drugs.
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Affiliation(s)
- Marta Marzullo
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (M.M.)
| | - Sonia Coni
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Assia De Simone
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (M.M.)
| | - Gianluca Canettieri
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy
- Istituto Pasteur Italia, Fondazione Cenci Bolognetti, 00161 Rome, Italy
| | - Laura Ciapponi
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (M.M.)
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13
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Wang S, Sun S. Translation dysregulation in neurodegenerative diseases: a focus on ALS. Mol Neurodegener 2023; 18:58. [PMID: 37626421 PMCID: PMC10464328 DOI: 10.1186/s13024-023-00642-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
RNA translation is tightly controlled in eukaryotic cells to regulate gene expression and maintain proteome homeostasis. RNA binding proteins, translation factors, and cell signaling pathways all modulate the translation process. Defective translation is involved in multiple neurological diseases including amyotrophic lateral sclerosis (ALS). ALS is a progressive neurodegenerative disorder and poses a major public health challenge worldwide. Over the past few years, tremendous advances have been made in the understanding of the genetics and pathogenesis of ALS. Dysfunction of RNA metabolisms, including RNA translation, has been closely associated with ALS. Here, we first introduce the general mechanisms of translational regulation under physiological and stress conditions and review well-known examples of translation defects in neurodegenerative diseases. We then focus on ALS-linked genes and discuss the recent progress on how translation is affected by various mutant genes and the repeat expansion-mediated non-canonical translation in ALS.
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Affiliation(s)
- Shaopeng Wang
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shuying Sun
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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14
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Su T, Hollas MAR, Fellers RT, Kelleher NL. Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics. Annu Rev Biomed Data Sci 2023; 6:357-376. [PMID: 37561601 PMCID: PMC10840079 DOI: 10.1146/annurev-biodatasci-020722-044021] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Alternative splicing is pivotal to the regulation of gene expression and protein diversity in eukaryotic cells. The detection of alternative splicing events requires specific omics technologies. Although short-read RNA sequencing has successfully supported a plethora of investigations on alternative splicing, the emerging technologies of long-read RNA sequencing and top-down mass spectrometry open new opportunities to identify alternative splicing and protein isoforms with less ambiguity. Here, we summarize improvements in short-read RNA sequencing for alternative splicing analysis, including percent splicing index estimation and differential analysis. We also review the computational methods used in top-down proteomics analysis regarding proteoform identification, including the construction of databases of protein isoforms and statistical analyses of search results. While many improvements in sequencing and computational methods will result from emerging technologies, there should be future endeavors to increase the effectiveness, integration, and proteome coverage of alternative splicing events.
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Affiliation(s)
- Taojunfeng Su
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA;
| | - Michael A R Hollas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Neil L Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA;
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
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15
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Shankar VG, Klann E. Size matters: Fighting repeat expansion size in fragile X syndrome using antisense oligonucleotides. Proc Natl Acad Sci U S A 2023; 120:e2309678120. [PMID: 37440569 PMCID: PMC10372623 DOI: 10.1073/pnas.2309678120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023] Open
Affiliation(s)
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY10003
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York, NY10016
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16
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Van't Spijker HM, Almeida S. How villains are made: The translation of dipeptide repeat proteins in C9ORF72-ALS/FTD. Gene 2023; 858:147167. [PMID: 36621656 PMCID: PMC9928902 DOI: 10.1016/j.gene.2023.147167] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
A hexanucleotide repeat expansion in the C9ORF72 gene is the most common genetic alteration associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). These neurodegenerative diseases share genetic, clinical and pathological features. The mutation in C9ORF72 appears to drive pathogenesis through a combination of loss of C9ORF72 normal function and gain of toxic effects due to the repeat expansion, which result in aggregation prone expanded RNAs and dipeptide repeat (DPR) proteins. Studies in cellular and animal models indicate that the DPR proteins are the more toxic species. Thus, a large body of research has focused on identifying the cellular pathways most directly impacted by these toxic proteins, with the goal of characterizing disease pathogenesis and nominating potential targets for therapeutic development. The preventative block of the production of the toxic proteins before they can cause harm is a second strategy of intense focus. Despite the considerable amount of effort dedicated to this prophylactic approach, it is still unclear how the DPR proteins are synthesized from RNAs harboring repeat expansions. In this review, we summarize our current knowledge of the specific protein translation mechanisms shown to account for the synthesis of DPR proteins. We will then discuss how enhanced understanding of the composition of these toxic effectors could help in refining disease mechanisms, and paving the way to identify and design effective prophylactic therapies for C9ORF72 ALS-FTD.
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Affiliation(s)
- Heleen M Van't Spijker
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Sandra Almeida
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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17
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Hamanaka K, Yamauchi D, Koshimizu E, Watase K, Mogushi K, Ishikawa K, Mizusawa H, Tsuchida N, Uchiyama Y, Fujita A, Misawa K, Mizuguchi T, Miyatake S, Matsumoto N. Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans. Genome Res 2023; 33:435-447. [PMID: 37307504 PMCID: PMC10078293 DOI: 10.1101/gr.277335.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/22/2023] [Indexed: 03/29/2023]
Abstract
Tandem repeats (TRs) are one of the largest sources of polymorphism, and their length is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in cis (spl-TRs), no large-scale study has been conducted. In this study, we established a genome-wide catalog of 9537 spl-TRs with a total of 58,290 significant TR-splicing associations across 49 tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci for repeat expansion diseases, spinocerebellar ataxia 6 (SCA6) and 12 (SCA12). Splicing alterations by these spl-TRs were compatible with those observed in SCA6 and SCA12. Thus, our comprehensive spl-TR catalog may help elucidate the pathomechanism of genetic diseases.
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Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | | | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kei Watase
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kaoru Mogushi
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kinya Ishikawa
- The Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hidehiro Mizusawa
- Department of Neurology, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
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18
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Abstract
PURPOSE OF REVIEW Myotonic dystrophy type 1 (DM1) and myotonic dystrophy type 2 (DM2) are genetic disorders affecting skeletal and smooth muscle, heart, brain, eyes, and other organs. The multisystem involvement and disease variability of myotonic dystrophy have presented challenges for clinical care and research. This article focuses on the diagnosis and management of the disease. In addition, recent advances in characterizing the diverse clinical manifestations and variability of the disease are discussed. RECENT FINDINGS Studies of the multisystem involvement of myotonic dystrophy, including the most lethal cardiac and respiratory manifestations and their molecular underpinnings, expand our understanding of the myotonic dystrophy phenotype. Advances have been made in understanding the molecular mechanisms of both types of myotonic dystrophy, providing opportunities for developing targeted therapeutics, some of which have entered clinical trials in DM1. SUMMARY Continued efforts focus on advancing our molecular and clinical understanding of DM1 and DM2. Accurately measuring and monitoring the diverse and variable clinical manifestations of myotonic dystrophy in clinic and in research is important to provide adequate care, prevent complications, and find treatments that improve symptoms and life quality.
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19
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Bush JA, Meyer SM, Fuerst R, Tong Y, Li Y, Benhamou RI, Aikawa H, Zanon PRA, Gibaut QMR, Angelbello AJ, Gendron TF, Zhang YJ, Petrucelli L, Heick Jensen T, Childs-Disney JL, Disney MD. A blood-brain penetrant RNA-targeted small molecule triggers elimination of r(G 4C 2) exp in c9ALS/FTD via the nuclear RNA exosome. Proc Natl Acad Sci U S A 2022; 119:e2210532119. [PMID: 36409902 PMCID: PMC9860304 DOI: 10.1073/pnas.2210532119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
A hexanucleotide repeat expansion in intron 1 of the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia, or c9ALS/FTD. The RNA transcribed from the expansion, r(G4C2)exp, causes various pathologies, including intron retention, aberrant translation that produces toxic dipeptide repeat proteins (DPRs), and sequestration of RNA-binding proteins (RBPs) in RNA foci. Here, we describe a small molecule that potently and selectively interacts with r(G4C2)exp and mitigates disease pathologies in spinal neurons differentiated from c9ALS patient-derived induced pluripotent stem cells (iPSCs) and in two c9ALS/FTD mouse models. These studies reveal a mode of action whereby a small molecule diminishes intron retention caused by the r(G4C2)exp and allows the liberated intron to be eliminated by the nuclear RNA exosome, a multi-subunit degradation complex. Our findings highlight the complexity of mechanisms available to RNA-binding small molecules to alleviate disease pathologies and establishes a pipeline for the design of brain penetrant small molecules targeting RNA with novel modes of action in vivo.
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Affiliation(s)
- Jessica A. Bush
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Samantha M. Meyer
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Rita Fuerst
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Yuquan Tong
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Yue Li
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Raphael I. Benhamou
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Haruo Aikawa
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Patrick R. A. Zanon
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Quentin M. R. Gibaut
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Alicia J. Angelbello
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | | | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL32224
| | | | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus CDK-8000, Denmark
| | - Jessica L. Childs-Disney
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
- Department of Neuroscience, The Scripps Research Institute and UF Scripps Biomedical Research, University of Florida, Jupiter, FL33458
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20
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Isiktas AU, Eshov A, Yang S, Guo JU. Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation. CELL REPORTS METHODS 2022; 2:100334. [PMID: 36452875 PMCID: PMC9701603 DOI: 10.1016/j.crmeth.2022.100334] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
A common pathological feature of RNAs containing expanded repeat sequences is their propensity to aggregate in cells. While some repeat RNA aggregates have been shown to cause toxicity by sequestering RNA-binding proteins, the molecular mechanism of aggregation remains unclear. Here, we devised an efficient method to generate long tandem repeat DNAs de novo and applied it to systematically determine the sequence features underlying RNA aggregation. Live-cell imaging of repeat RNAs indicated that aggregation was promoted by multivalent RNA-RNA interactions via either canonical or noncanonical base pairs. While multiple runs of two consecutive base pairs were sufficient, longer runs of base pairs such as those formed by GGGGCC hexanucleotide repeats further enhanced aggregation. In summary, our study provides a unifying model for the molecular basis of repeat RNA aggregation and a generalizable approach for identifying the sequence and structural determinants underlying the distinct properties of repeat DNAs and RNAs.
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Affiliation(s)
- Atagun U. Isiktas
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Aziz Eshov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Suzhou Yang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Junjie U. Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
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21
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Benkirane M, Da Cunha D, Marelli C, Larrieu L, Renaud M, Varilh J, Pointaux M, Baux D, Ardouin O, Vangoethem C, Taulan M, Daumas Duport B, Bergougnoux A, Corbillé AG, Cossée M, Juntas Morales R, Tuffery-Giraud S, Koenig M, Isidor B, Vincent MC. RFC1 nonsense and frameshift variants cause CANVAS: clues for an unsolved pathophysiology. Brain 2022; 145:3770-3775. [PMID: 35883251 DOI: 10.1093/brain/awac280] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/13/2022] [Accepted: 07/03/2022] [Indexed: 01/27/2023] Open
Abstract
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) is an inherited late-onset neurological disease caused by bi-allelic AAGGG pentanucleotide expansions within intron 2 of RFC1. Despite extensive studies, the pathophysiological mechanism of these intronic expansions remains elusive. We screened by clinical exome sequencing two unrelated patients presenting with late-onset ataxia. A repeat-primer polymerase chain reaction was used for RFC1 AAGGG intronic expansion identification. RFC1 mRNA expression was assessed by quantitative reverse transcription-polymerase chain reaction. We identified the first two CANVAS affected patients who are compound heterozygous for RFC1 truncating variants (p.Arg388* and c.575delA, respectively) and a pathological AAGGG expansion. RFC1 expression studies in whole blood showed a significant reduction of RFC1 mRNA for both patients compared to three patients with bi-allelic RFC1 expansions. In conclusion, this observation provides clues that suggest bi-allelic RFC1 conditional loss-of-function as the cause of the disease.
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Affiliation(s)
- Mehdi Benkirane
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France.,Genetics and Pathophysiology of NeuroMuscular Disorders, PhyMedExp Research Unit, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Dylan Da Cunha
- Genetics and Pathophysiology of NeuroMuscular Disorders, PhyMedExp Research Unit, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Cecilia Marelli
- Department of Neurology, Montpellier Hospital, Montpellier, France.,Molecular Mechanisms of Neurodegenerative Dementia (MMDN), EPHE University of Montpellier, INSERM, Montpellier, France
| | - Lise Larrieu
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France
| | - Mathilde Renaud
- Department of Medical Genetics, Nancy Hospital, Nancy, France
| | - Jessica Varilh
- Genetics and Pathophysiology of NeuroMuscular Disorders, PhyMedExp Research Unit, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Morgane Pointaux
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France
| | - David Baux
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France
| | - Olivier Ardouin
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France
| | - Charles Vangoethem
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France
| | - Magali Taulan
- Genetics and Pathophysiology of NeuroMuscular Disorders, PhyMedExp Research Unit, CNRS, INSERM, University of Montpellier, Montpellier, France
| | | | - Anne Bergougnoux
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France.,Genetics and Pathophysiology of NeuroMuscular Disorders, PhyMedExp Research Unit, CNRS, INSERM, University of Montpellier, Montpellier, France
| | | | - Mireille Cossée
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France.,Genetics and Pathophysiology of NeuroMuscular Disorders, PhyMedExp Research Unit, CNRS, INSERM, University of Montpellier, Montpellier, France
| | | | - Sylvie Tuffery-Giraud
- Genetics and Pathophysiology of NeuroMuscular Disorders, PhyMedExp Research Unit, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Michel Koenig
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France.,Genetics and Pathophysiology of NeuroMuscular Disorders, PhyMedExp Research Unit, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Bertrand Isidor
- Department of Medical Genetics, Nantes Hospital, Nantes, France
| | - Marie-Claire Vincent
- Department of Molecular Genetics, Institut Universitaire de Recherche Clinique (IURC), Montpellier Hospital, Montpellier, France.,Genetics and Pathophysiology of NeuroMuscular Disorders, PhyMedExp Research Unit, CNRS, INSERM, University of Montpellier, Montpellier, France
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22
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Ly S, Didiot MC, Ferguson CM, Coles AH, Miller R, Chase K, Echeverria D, Wang F, Sadri-Vakili G, Aronin N, Khvorova A. Mutant huntingtin messenger RNA forms neuronal nuclear clusters in rodent and human brains. Brain Commun 2022; 4:fcac248. [PMID: 36458209 PMCID: PMC9707646 DOI: 10.1093/braincomms/fcac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/14/2022] [Accepted: 10/12/2022] [Indexed: 01/25/2023] Open
Abstract
Mutant messenger RNA (mRNA) and protein contribute to the clinical manifestation of many repeat-associated neurological disorders, with the presence of nuclear RNA clusters being a common pathological feature. Yet, investigations into Huntington's disease-caused by a CAG repeat expansion in exon 1 of the huntingtin (HTT) gene-have primarily focused on toxic protein gain-of-function as the primary disease-causing feature. To date, mutant HTT mRNA has not been identified as an in vivo hallmark of Huntington's disease. Here, we report that, in two Huntington's disease mouse models (YAC128 and BACHD-97Q-ΔN17), mutant HTT mRNA is retained in the nucleus. Widespread formation of large mRNA clusters (∼0.6-5 µm3) occurred in 50-75% of striatal and cortical neurons. Cluster formation was independent of age and driven by expanded repeats. Clusters associate with chromosomal transcriptional sites and quantitatively co-localize with the aberrantly processed N-terminal exon 1-intron 1 mRNA isoform, HTT1a. HTT1a mRNA clusters are observed in a subset of neurons from human Huntington's disease post-mortem brain and are likely caused by somatic expansion of repeats. In YAC128 mice, clusters, but not individual HTT mRNA, are resistant to antisense oligonucleotide treatment. Our findings identify mutant HTT/HTT1a mRNA clustering as an early, robust molecular signature of Huntington's disease, providing in vivo evidence that Huntington's disease is a repeat expansion disease with mRNA involvement.
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Affiliation(s)
| | | | | | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kathryn Chase
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Feng Wang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Ghazaleh Sadri-Vakili
- Mass General Institute for Neurodegenerative Disease, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Neil Aronin
- Correspondence may also be addressed to: Neil Aronin 368 Plantation Street, Albert Sherman Center Worcester, MA 01655, USA. E-mail:
| | - Anastasia Khvorova
- Correspondence to: Anastasia Khvorova 368 Plantation Street, Albert Sherman Center Worcester, MA 01655, USA E-mail:
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23
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Li Y, Li J, Wang J, Zhang S, Giles K, Prakash TP, Rigo F, Napierala JS, Napierala M. Premature transcription termination at the expanded GAA repeats and aberrant alternative polyadenylation contributes to the Frataxin transcriptional deficit in Friedreich's ataxia. Hum Mol Genet 2022; 31:3539-3557. [PMID: 35708503 PMCID: PMC9558844 DOI: 10.1093/hmg/ddac134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/12/2022] [Accepted: 06/05/2022] [Indexed: 11/18/2022] Open
Abstract
Frataxin deficiency in Friedreich's ataxia results from transcriptional downregulation of the FXN gene caused by expansion of the intronic trinucleotide guanine-adenine-adenine (GAA) repeats. We used multiple transcriptomic approaches to determine the molecular mechanism of transcription inhibition caused by long GAAs. We uncovered that transcription of FXN in patient cells is prematurely terminated upstream of the expanded repeats leading to the formation of a novel, truncated and stable RNA. This FXN early terminated transcript (FXN-ett) undergoes alternative, non-productive splicing and does not contribute to the synthesis of functional frataxin. The level the FXN-ett RNA directly correlates with the length of the longer of the two expanded GAA tracts. Targeting GAAs with antisense oligonucleotides or excision of the repeats eliminates the transcription impediment, diminishes expression of the aberrant FXN-ett, while increasing levels of FXN mRNA and frataxin. Non-productive transcription may represent a common phenomenon and attractive therapeutic target in diseases caused by repeat-mediated transcription aberrations.
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Affiliation(s)
- Yanjie Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Jixue Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Jun Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Siyuan Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Keith Giles
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Frank Rigo
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Jill S Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
- Department of Neurology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd., Birmingham, AL 35294, USA
- Department of Neurology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
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24
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Davies K, Szmulewicz DJ, Corben LA, Delatycki M, Lockhart PJ. RFC1-Related Disease. Neurol Genet 2022; 8:e200016. [PMID: 36046423 PMCID: PMC9425222 DOI: 10.1212/nxg.0000000000200016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/22/2022] [Indexed: 01/03/2023]
Abstract
In 2019, a biallelic pentanucleotide repeat expansion in the gene encoding replication factor C subunit 1 (RFC1) was reported as a cause of cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS). In addition, biallelic expansions were shown to account for up to 22% of cases with late-onset ataxia. Since this discovery, the phenotypic spectrum reported to be associated with RFC1 expansions has extended beyond the initial conditions to include pure cerebellar ataxia, isolated somatosensory impairment, combinations of the 2, and parkinsonism, leading to a potentially broad differential diagnosis. Genetic studies suggest RFC1 expansions may be the most common genetic cause of ataxia and are likely underdiagnosed. This review summarizes the current molecular and clinical knowledge of RFC1-related disease, with a focus on the evaluation of recent phenotype associations and highlighting the current challenges in clinical pathways to diagnosis and molecular testing.
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25
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Development of Therapeutic Approaches for Myotonic Dystrophies Type 1 and Type 2. Int J Mol Sci 2022; 23:ijms231810491. [PMID: 36142405 PMCID: PMC9499601 DOI: 10.3390/ijms231810491] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Myotonic Dystrophies type 1 (DM1) and type 2 (DM2) are complex multisystem diseases without disease-based therapies. These disorders are caused by the expansions of unstable CTG (DM1) and CCTG (DM2) repeats outside of the coding regions of the disease genes: DMPK in DM1 and CNBP in DM2. Multiple clinical and molecular studies provided a consensus for DM1 pathogenesis, showing that the molecular pathophysiology of DM1 is associated with the toxicity of RNA CUG repeats, which cause multiple disturbances in RNA metabolism in patients' cells. As a result, splicing, translation, RNA stability and transcription of multiple genes are misregulated in DM1 cells. While mutant CCUG repeats are the main cause of DM2, additional factors might play a role in DM2 pathogenesis. This review describes current progress in the translation of mechanistic knowledge in DM1 and DM2 to clinical trials, with a focus on the development of disease-specific therapies for patients with adult forms of DM1 and congenital DM1 (CDM1).
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26
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Marshall JNG, Fröhlich A, Li L, Pfaff AL, Middlehurst B, Spargo TP, Iacoangeli A, Lang B, Al-Chalabi A, Koks S, Bubb VJ, Quinn JP. A polymorphic transcriptional regulatory domain in the amyotrophic lateral sclerosis risk gene CFAP410 correlates with differential isoform expression. Front Mol Neurosci 2022; 15:954928. [PMID: 36131690 PMCID: PMC9484465 DOI: 10.3389/fnmol.2022.954928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/22/2022] [Indexed: 11/15/2022] Open
Abstract
We describe the characterisation of a variable number tandem repeat (VNTR) domain within intron 1 of the amyotrophic lateral sclerosis (ALS) risk gene CFAP410 (Cilia and flagella associated protein 410) (previously known as C21orf2), providing insight into how this domain could support differential gene expression and thus be a modulator of ALS progression or risk. We demonstrated the VNTR was functional in a reporter gene assay in the HEK293 cell line, exhibiting both the properties of an activator domain and a transcriptional start site, and that the differential expression was directed by distinct repeat number in the VNTR. These properties embedded in the VNTR demonstrated the potential for this VNTR to modulate CFAP410 expression. We extrapolated these findings in silico by utilisation of tagging SNPs for the two most common VNTR alleles to establish a correlation with endogenous gene expression. Consistent with in vitro data, CFAP410 isoform expression was found to be variable in the brain. Furthermore, although the number of matched controls was low, there was evidence for one specific isoform being correlated with lower expression in those with ALS. To address if the genotype of the VNTR was associated with ALS risk, we characterised the variation of the CFAP410 VNTR in ALS cases and matched controls by PCR analysis of the VNTR length, defining eight alleles of the VNTR. No significant difference was observed between cases and controls, we noted, however, the cohort was unlikely to contain sufficient power to enable any firm conclusion to be drawn from this analysis. This data demonstrated that the VNTR domain has the potential to modulate CFAP410 expression as a regulatory element that could play a role in its tissue-specific and stimulus-inducible regulation that could impact the mechanism by which CFAP410 is involved in ALS.
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Affiliation(s)
- Jack N. G. Marshall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Li Li
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Department of Psychiatry, National Clinical Research Centre for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Abigail L. Pfaff
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Thomas P. Spargo
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- NIHR Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, King's College London, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- NIHR Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, King's College London, London, United Kingdom
| | - Bing Lang
- Department of Psychiatry, National Clinical Research Centre for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Neurology, King's College Hospital, London, United Kingdom
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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27
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Baud A, Derbis M, Tutak K, Sobczak K. Partners in crime: Proteins implicated in
RNA
repeat expansion diseases. WIRES RNA 2022; 13:e1709. [PMID: 35229468 PMCID: PMC9539487 DOI: 10.1002/wrna.1709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Baud
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Magdalena Derbis
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Katarzyna Tutak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Krzysztof Sobczak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
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28
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Vořechovský I. Selection of Olduvai Domains during Evolution: A Role for Primate-Specific Splicing Super-Enhancer and RNA Guanine Quadruplex in Bipartite NBPF Exons. Brain Sci 2022; 12:brainsci12070874. [PMID: 35884681 PMCID: PMC9313022 DOI: 10.3390/brainsci12070874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Abstract
Olduvai protein domains (also known as DUF1220 or NBPF) have undergone the greatest human-specific increase in the copy number of any coding region in the genome. Their repeat number was strongly associated with the evolutionary expansion of brain volumes, neuron counts and cognitive abilities, as well as with disorders of the autistic spectrum. Nevertheless, the domain function and cellular mechanisms underlying the positive selection of Olduvai DNA sequences in higher primates remain obscure. Here, I show that the inclusion of Olduvai exon doublets in mature transcripts is facilitated by a potent splicing enhancer that was created through duplication within the first exon. The enhancer is the strongest among the NBPF transcripts and further promotes the already high splicing activity of the unexpanded first exons of the two-exon domains, safeguarding the expanded Olduvai exon doublets in the mature transcriptome. The duplication also creates a predicted RNA guanine quadruplex that may regulate the access to spliceosomal components of the super-enhancer and influence the splicing of adjacent exons. Thus, positive Olduvai selection during primate evolution is likely to result from a combination of multiple targets in gene expression pathways, including RNA splicing.
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Affiliation(s)
- Igor Vořechovský
- Faculty of Medicine, University of Southampton, HDH, MP808, Southampton SO16 6YD, UK
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29
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Jenquin JR, O’Brien AP, Poukalov K, Lu Y, Frias JA, Shorrock HK, Richardson JI, Mazdiyasni H, Yang H, Huigens RW, Boykin D, Ranum LP, Cleary JD, Wang ET, Berglund JA. Molecular characterization of myotonic dystrophy fibroblast cell lines for use in small molecule screening. iScience 2022; 25:104198. [PMID: 35479399 PMCID: PMC9035709 DOI: 10.1016/j.isci.2022.104198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/30/2021] [Accepted: 04/01/2022] [Indexed: 01/05/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are common forms of adult onset muscular dystrophy. Pathogenesis in both diseases is largely driven by production of toxic-expanded repeat RNAs that sequester MBNL RNA-binding proteins, causing mis-splicing. Given this shared pathogenesis, we hypothesized that diamidines, small molecules that rescue mis-splicing in DM1 models, could also rescue mis-splicing in DM2 models. While several DM1 cell models exist, few are available for DM2 limiting research and therapeutic development. Here, we characterize DM1 and DM2 patient-derived fibroblasts for use in small molecule screens and therapeutic studies. We identify mis-splicing events unique to DM2 fibroblasts and common events shared with DM1 fibroblasts. We show that diamidines can partially rescue molecular phenotypes in both DM1 and DM2 fibroblasts. This study demonstrates the potential of fibroblasts as models for DM1 and DM2, which will help meet an important need for well-characterized DM2 cell models.
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Affiliation(s)
- Jana R. Jenquin
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Alana P. O’Brien
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Kiril Poukalov
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Yidan Lu
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jesus A. Frias
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Hannah K. Shorrock
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Jared I. Richardson
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Hormoz Mazdiyasni
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Hongfen Yang
- Department of Medicinal Chemistry, Center for Natural Products Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Robert W. Huigens
- Department of Medicinal Chemistry, Center for Natural Products Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - David Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Laura P.W. Ranum
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - John Douglas Cleary
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Eric T. Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - J. Andrew Berglund
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
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30
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Mechanistic and Therapeutic Insights into Ataxic Disorders with Pentanucleotide Expansions. Cells 2022; 11:cells11091567. [PMID: 35563872 PMCID: PMC9099484 DOI: 10.3390/cells11091567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023] Open
Abstract
Pentanucleotide expansion diseases constitute a special class of neurodegeneration. The repeat expansions occur in non-coding regions, have likely arisen from Alu elements, and often result in autosomal dominant or recessive phenotypes with underlying cerebellar neuropathology. When transcribed (potentially bidirectionally), the expanded RNA forms complex secondary and tertiary structures that can give rise to RNA-mediated toxicity, including protein sequestration, pentapeptide synthesis, and mRNA dysregulation. Since several of these diseases have recently been discovered, our understanding of their pathological mechanisms is limited, and their therapeutic interventions underexplored. This review aims to highlight new in vitro and in vivo insights into these incurable diseases.
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31
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Yadav Y, Sharma SN, Shakya DK. Detection of Tandem Repeats in DNA Sequences Using Short-Time Ramanujan Fourier Transform. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1583-1591. [PMID: 33493119 DOI: 10.1109/tcbb.2021.3053656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Tandem repeats in genomic sequences are characterized by two or more contiguous copies of a pattern of nucleotides. The role of these repeats as molecular markers is well established in various genetic disorders, human evolution studies, DNA forensics and intron retention. In this work a computational method has been developed for the extraction of both exact and approximate tandem repeats. The proposed algorithm uses Ramanujan Fourier Transform (RFT) to identify periodicities in the DNA sequences. Since RFT estimates the period directly, rather than inferring it from the signal's spectrum, it provides a more sensitive and rapid detection of tandem repeats as compared to other available popular computational methods.
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32
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van 't Spijker HM, Stackpole EE, Almeida S, Katsara O, Liu B, Shen K, Schneider RJ, Gao FB, Richter JD. Ribosome profiling reveals novel regulation of C9ORF72 GGGGCC repeat-containing RNA translation. RNA (NEW YORK, N.Y.) 2022; 28:123-138. [PMID: 34848561 PMCID: PMC8906550 DOI: 10.1261/rna.078963.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
GGGGCC (G4C2) repeat expansion in the first intron of C9ORF72 causes amyotrophic lateral sclerosis and frontotemporal dementia. Repeat-containing RNA is translated into dipeptide repeat (DPR) proteins, some of which are neurotoxic. Using dynamic ribosome profiling, we identified three translation initiation sites in the intron upstream of (G4C2) repeats; these sites are detected irrespective of the presence or absence of the repeats. During translocation, ribosomes appear to be stalled on the repeats. An AUG in the preceding C9ORF72 exon initiates a uORF that inhibits downstream translation. Polysome isolation indicates that unspliced (G4C2) repeat-containing RNA is a substrate for DPR protein synthesis. (G4C2) repeat-containing RNA translation is 5' cap-independent but inhibited by the initiation factor DAP5, suggesting an interplay with uORF function. These results define novel translational mechanisms of expanded (G4C2) repeat-containing RNA in disease.
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Affiliation(s)
- Heleen M van 't Spijker
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Emily E Stackpole
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Sandra Almeida
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Olga Katsara
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Botao Liu
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Kuang Shen
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Robert J Schneider
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
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33
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Shah JS, Milevskiy MJG, Petrova V, Au AYM, Wong JJL, Visvader JE, Schmitz U, Rasko JEJ. Towards resolution of the intron retention paradox in breast cancer. Breast Cancer Res 2022; 24:100. [PMID: 36581993 PMCID: PMC9798573 DOI: 10.1186/s13058-022-01593-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND After many years of neglect in the field of alternative splicing, the importance of intron retention (IR) in cancer has come into focus following landmark discoveries of aberrant IR patterns in cancer. Many solid and liquid tumours are associated with drastic increases in IR, and such patterns have been pursued as both biomarkers and therapeutic targets. Paradoxically, breast cancer (BrCa) is the only tumour type in which IR is reduced compared to adjacent normal breast tissue. METHODS In this study, we have conducted a pan-cancer analysis of IR with emphasis on BrCa and its subtypes. We explored mechanisms that could cause aberrant and pathological IR and clarified why normal breast tissue has unusually high IR. RESULTS Strikingly, we found that aberrantly decreasing IR in BrCa can be largely attributed to normal breast tissue having the highest occurrence of IR events compared to other healthy tissues. Our analyses suggest that low numbers of IR events in breast tumours are associated with poor prognosis, particularly in the luminal B subtype. Interestingly, we found that IR frequencies negatively correlate with cell proliferation in BrCa cells, i.e. rapidly dividing tumour cells have the lowest number of IR events. Aberrant RNA-binding protein expression and changes in tissue composition are among the causes of aberrantly decreasing IR in BrCa. CONCLUSIONS Our results suggest that IR should be considered for therapeutic manipulation in BrCa patients with aberrantly low IR levels and that further work is needed to understand the cause and impact of high IR in other tumour types.
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Affiliation(s)
- Jaynish S. Shah
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia ,grid.1002.30000 0004 1936 7857Australian Centre for Blood Diseases, Central Clinical School, Monash University and Alfred Health, Melbourne, VIC Australia
| | - Michael J. G. Milevskiy
- grid.1042.70000 0004 0432 4889ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Veronika Petrova
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia
| | - Amy Y. M. Au
- grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia
| | - Justin J. L. Wong
- grid.1013.30000 0004 1936 834XEpigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050 Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Jane E. Visvader
- grid.1042.70000 0004 0432 4889ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Ulf Schmitz
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1011.10000 0004 0474 1797Department of Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 James Cook Drive, Townsville, QLD 4811 Australia ,grid.1011.10000 0004 0474 1797Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, 4878 Australia
| | - John E. J. Rasko
- grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Camperdown, Australia ,grid.413249.90000 0004 0385 0051Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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Gall-Duncan T, Sato N, Yuen RKC, Pearson CE. Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. Genome Res 2022; 32:1-27. [PMID: 34965938 PMCID: PMC8744678 DOI: 10.1101/gr.269530.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/29/2021] [Indexed: 11/25/2022]
Abstract
Expansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans. TRs are a common form of genetic variation with biological consequences, observed, so far, in humans, dogs, plants, oysters, and yeast. Repeat diseases show atypical clinical features, genetic anticipation, and multiple and partially penetrant phenotypes among family members. Discovery of disease-causing repeat expansion loci accelerated through technological advances in DNA sequencing and computational analyses. Between 2019 and 2021, 17 new disease-causing TR expansions were reported, totaling 63 TR loci (>69 diseases), with a likelihood of more discoveries, and in more organisms. Recent and historical lessons reveal that properly assessed clinical presentations, coupled with genetic and biological awareness, can guide discovery of disease-causing unstable TRs. We highlight critical but underrecognized aspects of TR mutations. Repeat motifs may not be present in current reference genomes but will be in forthcoming gapless long-read references. Repeat motif size can be a single nucleotide to kilobases/unit. At a given locus, repeat motif sequence purity can vary with consequence. Pathogenic repeats can be "insertions" within nonpathogenic TRs. Expansions, contractions, and somatic length variations of TRs can have clinical/biological consequences. TR instabilities occur in humans and other organisms. TRs can be epigenetically modified and/or chromosomal fragile sites. We discuss the expanding field of disease-associated TR instabilities, highlighting prospects, clinical and genetic clues, tools, and challenges for further discoveries of disease-causing TR instabilities and understanding their biological and pathological impacts-a vista that is about to expand.
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Affiliation(s)
- Terence Gall-Duncan
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nozomu Sato
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| | - Ryan K C Yuen
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christopher E Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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35
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Kumari A, Sedehizadeh S, Brook JD, Kozlowski P, Wojciechowska M. Differential fates of introns in gene expression due to global alternative splicing. Hum Genet 2021; 141:31-47. [PMID: 34907472 PMCID: PMC8758631 DOI: 10.1007/s00439-021-02409-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023]
Abstract
The discovery of introns over four decades ago revealed a new vision of genes and their interrupted arrangement. Throughout the years, it has appeared that introns play essential roles in the regulation of gene expression. Unique processing of excised introns through the formation of lariats suggests a widespread role for these molecules in the structure and function of cells. In addition to rapid destruction, these lariats may linger on in the nucleus or may even be exported to the cytoplasm, where they remain stable circular RNAs (circRNAs). Alternative splicing (AS) is a source of diversity in mature transcripts harboring retained introns (RI-mRNAs). Such RNAs may contain one or more entire retained intron(s) (RIs), but they may also have intron fragments resulting from sequential excision of smaller subfragments via recursive splicing (RS), which is characteristic of long introns. There are many potential fates of RI-mRNAs, including their downregulation via nuclear and cytoplasmic surveillance systems and the generation of new protein isoforms with potentially different functions. Various reports have linked the presence of such unprocessed transcripts in mammals to important roles in normal development and in disease-related conditions. In certain human neurological-neuromuscular disorders, including myotonic dystrophy type 2 (DM2), frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS) and Duchenne muscular dystrophy (DMD), peculiar processing of long introns has been identified and is associated with their pathogenic effects. In this review, we discuss different mechanisms involved in the processing of introns during AS and the functions of these large sections of the genome in our biology.
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Affiliation(s)
- Anjani Kumari
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Saam Sedehizadeh
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - John David Brook
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. .,Department of Rare Human Diseases, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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36
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Conboy JG. A Deep Exon Cryptic Splice Site Promotes Aberrant Intron Retention in a Von Willebrand Disease Patient. Int J Mol Sci 2021; 22:13248. [PMID: 34948044 PMCID: PMC8706089 DOI: 10.3390/ijms222413248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
A translationally silent single nucleotide mutation in exon 44 (E44) of the von Willebrand factor (VWF) gene is associated with inefficient removal of intron 44 in a von Willebrand disease (VWD) patient. This intron retention (IR) event was previously attributed to reordered E44 secondary structure that sequesters the normal splice donor site. We propose an alternative mechanism: the mutation introduces a cryptic splice donor site that interferes with the function of the annotated site to favor IR. We evaluated both models using minigene splicing reporters engineered to vary in secondary structure and/or cryptic splice site content. Analysis of splicing efficiency in transfected K562 cells suggested that the mutation-generated cryptic splice site in E44 was sufficient to induce substantial IR. Mutations predicted to vary secondary structure at the annotated site also had modest effects on IR and shifted the balance of residual splicing between the cryptic site and annotated site, supporting competition among the sites. Further studies demonstrated that introduction of cryptic splice donor motifs at other positions in E44 did not promote IR, indicating that interference with the annotated site is context dependent. We conclude that mutant deep exon splice sites can interfere with proper splicing by inducing IR.
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Affiliation(s)
- John G Conboy
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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37
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Bush JA, Aikawa H, Fuerst R, Li Y, Ursu A, Meyer SM, Benhamou RI, Chen JL, Khan T, Wagner-Griffin S, Van Meter MJ, Tong Y, Olafson H, McKee KK, Childs-Disney JL, Gendron TF, Zhang Y, Coyne AN, Wang ET, Yildirim I, Wang KW, Petrucelli L, Rothstein JD, Disney MD. Ribonuclease recruitment using a small molecule reduced c9ALS/FTD r(G 4C 2) repeat expansion in vitro and in vivo ALS models. Sci Transl Med 2021; 13:eabd5991. [PMID: 34705518 DOI: 10.1126/scitranslmed.abd5991] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Jessica A Bush
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Haruo Aikawa
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Rita Fuerst
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Yue Li
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Andrei Ursu
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Samantha M Meyer
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Raphael I Benhamou
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jonathan L Chen
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Tanya Khan
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Sarah Wagner-Griffin
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Montina J Van Meter
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Yuquan Tong
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Hailey Olafson
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Kendra K McKee
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Yongjie Zhang
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Alyssa N Coyne
- Robert Packard Center for ALS Research, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Eric T Wang
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Kye Won Wang
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Jeffrey D Rothstein
- Robert Packard Center for ALS Research, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Matthew D Disney
- Department of Chemistry, Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
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38
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Verzat C, Harley J, Patani R, Luisier R. Image-based deep learning reveals the responses of human motor neurons to stress and VCP-related ALS. Neuropathol Appl Neurobiol 2021; 48:e12770. [PMID: 34595747 PMCID: PMC9298273 DOI: 10.1111/nan.12770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 11/28/2022]
Abstract
AIMS Although morphological attributes of cells and their substructures are recognised readouts of physiological or pathophysiological states, these have been relatively understudied in amyotrophic lateral sclerosis (ALS) research. METHODS In this study, we integrate multichannel fluorescence high-content microscopy data with deep learning imaging methods to reveal-directly from unsegmented images-novel neurite-associated morphological perturbations associated with (ALS-causing) VCP-mutant human motor neurons (MNs). RESULTS Surprisingly, we reveal that previously unrecognised disease-relevant information is withheld in broadly used and often considered 'generic' biological markers of nuclei (DAPI) and neurons ( β III-tubulin). Additionally, we identify changes within the information content of ALS-related RNA binding protein (RBP) immunofluorescence imaging that is captured in VCP-mutant MN cultures. Furthermore, by analysing MN cultures exposed to different extrinsic stressors, we show that heat stress recapitulates key aspects of ALS. CONCLUSIONS Our study therefore reveals disease-relevant information contained in a range of both generic and more specific fluorescent markers and establishes the use of image-based deep learning methods for rapid, automated and unbiased identification of biological hypotheses.
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Affiliation(s)
- Colombine Verzat
- Genomics and Health Informatics Group, Idiap Research Institute, Martigny, Switzerland
| | - Jasmine Harley
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Rickie Patani
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Raphaëlle Luisier
- Genomics and Health Informatics Group, Idiap Research Institute, Martigny, Switzerland
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39
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Lampasona A, Almeida S, Gao FB. Translation of the poly(GR) frame in C9ORF72-ALS/FTD is regulated by cis-elements involved in alternative splicing. Neurobiol Aging 2021; 105:327-332. [PMID: 34157654 PMCID: PMC8338774 DOI: 10.1016/j.neurobiolaging.2021.04.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 12/31/2022]
Abstract
GGGGCC (G4C2) repeat expansion in the first intron of C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia, two devastating age-dependent neurodegenerative disorders. Both sense and antisense repeat RNAs can be translated into 5 different dipeptide repeat proteins, such as poly(GR), which is toxic in various cellular and animal models. However, it remains unknown how poly(GR) is synthesized in patient neurons. Using a reporter construct containing 70 G4C2 repeats flanked by human intronic and exonic sequences, we show that translation of the poly(GR) frame does not depend on repeats or the CUG start codon in the poly(GA) frame, suggesting poly(GR) is not produced after ribosomal frameshifting in the poly(GA) frame. However, deletion analysis suggests that translation of the poly(GR) frame depends on the length of the intronic sequence 5' adjacent to G4C2 repeats. Moreover, several 5´ cis elements that are predicted to be involved in alternative splicing regulates poly(GR) synthesis. These results suggest that translation of repeat RNAs in the poly(GR) frame is regulated by multiple cis elements, likely through RNA secondary structures and/or associated RNA binding proteins.
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Affiliation(s)
- Alexa Lampasona
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sandra Almeida
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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40
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Malik I, Kelley CP, Wang ET, Todd PK. Molecular mechanisms underlying nucleotide repeat expansion disorders. Nat Rev Mol Cell Biol 2021; 22:589-607. [PMID: 34140671 PMCID: PMC9612635 DOI: 10.1038/s41580-021-00382-6] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 02/05/2023]
Abstract
The human genome contains over one million short tandem repeats. Expansion of a subset of these repeat tracts underlies over fifty human disorders, including common genetic causes of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (C9orf72), polyglutamine-associated ataxias and Huntington disease, myotonic dystrophy, and intellectual disability disorders such as Fragile X syndrome. In this Review, we discuss the four major mechanisms by which expansion of short tandem repeats causes disease: loss of function through transcription repression, RNA-mediated gain of function through gelation and sequestration of RNA-binding proteins, gain of function of canonically translated repeat-harbouring proteins, and repeat-associated non-AUG translation of toxic repeat peptides. Somatic repeat instability amplifies these mechanisms and influences both disease age of onset and tissue specificity of pathogenic features. We focus on the crosstalk between these disease mechanisms, and argue that they often synergize to drive pathogenesis. We also discuss the emerging native functions of repeat elements and how their dynamics might contribute to disease at a larger scale than currently appreciated. Lastly, we propose that lynchpins tying these disease mechanisms and native functions together offer promising therapeutic targets with potential shared applications across this class of human disorders.
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Affiliation(s)
- Indranil Malik
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Chase P Kelley
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
- Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
- VA Ann Arbor Healthcare System, Ann Arbor, MI, USA.
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41
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Nuclear export and translation of circular repeat-containing intronic RNA in C9ORF72-ALS/FTD. Nat Commun 2021; 12:4908. [PMID: 34389711 PMCID: PMC8363653 DOI: 10.1038/s41467-021-25082-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 07/16/2021] [Indexed: 12/14/2022] Open
Abstract
C9ORF72 hexanucleotide GGGGCC repeat expansion is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat-containing RNA mediates toxicity through nuclear granules and dipeptide repeat (DPR) proteins produced by repeat-associated non-AUG translation. However, it remains unclear how the intron-localized repeats are exported and translated in the cytoplasm. We use single molecule imaging approach to examine the molecular identity and spatiotemporal dynamics of the repeat RNA. We demonstrate that the spliced intron with G-rich repeats is stabilized in a circular form due to defective lariat debranching. The spliced circular intron, instead of pre-mRNA, serves as the translation template. The NXF1-NXT1 pathway plays an important role in the nuclear export of the circular intron and modulates toxic DPR production. This study reveals an uncharacterized disease-causing RNA species mediated by repeat expansion and demonstrates the importance of RNA spatial localization to understand disease etiology. Hexanucleotide repeat expansion in the intron 1 of the C9ORF72 gene can cause amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). Here the authors use single molecule imaging to show nuclear export and translation of circular repeat-containing C9ORF72 intronic RNA.
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42
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Bae JH, Zhang DY. Predicting stability of DNA bulge at mononucleotide microsatellite. Nucleic Acids Res 2021; 49:7901-7908. [PMID: 34308470 PMCID: PMC8373066 DOI: 10.1093/nar/gkab616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/14/2022] Open
Abstract
Mononucleotide microsatellites are clinically and forensically crucial DNA sequences due to their high mutability and abundance in the human genome. As a mutagenic intermediate of an indel in a microsatellite and a consequence of probe hybridization after such mutagenesis, a bulge with structural degeneracy sliding within a microsatellite is formed. Stability of such dynamic bulges, however, is still poorly understood despite their critical role in cancer genomics and neurological disease studies. In this paper, we have built a model that predicts the thermodynamics of a sliding bulge at a microsatellite. We first identified 40 common bulge states that can be assembled into any sliding bulges, and then characterized them with toehold exchange energy measurement and the partition function. Our model, which is the first to predict the free energy of sliding bulges with more than three repeats, can infer the stability penalty of a sliding bulge of any sequence and length with a median prediction error of 0.22 kcal/mol. Patterns from the prediction clearly explain landscapes of microsatellites observed in the literature, such as higher mutation rates of longer microsatellites and C/G microsatellites.
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Affiliation(s)
- Jin H Bae
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.,Systems, Synthetic, and Physical Biology, Rice University, Houston, TX 77005, USA
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43
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Wagner-Griffin S, Abe M, Benhamou RI, Angelbello AJ, Vishnu K, Chen JL, Childs-Disney JL, Disney MD. A Druglike Small Molecule that Targets r(CCUG) Repeats in Myotonic Dystrophy Type 2 Facilitates Degradation by RNA Quality Control Pathways. J Med Chem 2021; 64:8474-8485. [PMID: 34101465 DOI: 10.1021/acs.jmedchem.1c00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myotonic dystrophy type 2 (DM2) is one of >40 microsatellite disorders caused by RNA repeat expansions. The DM2 repeat expansion, r(CCUG)exp (where "exp" denotes expanded repeating nucleotides), is harbored in intron 1 of the CCHC-type zinc finger nucleic acid binding protein (CNBP). The expanded RNA repeat causes disease by a gain-of-function mechanism, sequestering various RNA-binding proteins including the pre-mRNA splicing regulator MBNL1. Sequestration of MBNL1 results in its loss-of-function and concomitant deregulation of the alternative splicing of its native substrates. Notably, this r(CCUG)exp causes retention of intron 1 in the mature CNBP mRNA. Herein, we report druglike small molecules that bind the structure adopted by r(CCUG)exp and improve DM2-associated defects. These small molecules were optimized from screening hits from an RNA-focused small-molecule library to afford a compound that binds r(CCUG)exp specifically and with nanomolar affinity, facilitates endogenous degradation of the aberrantly retained intron in which it is harbored, and rescues alternative splicing defects.
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Affiliation(s)
- Sarah Wagner-Griffin
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Masahito Abe
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Raphael I Benhamou
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Kamalakannan Vishnu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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44
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Cerebellar ataxia, neuropathy, vestibular areflexia syndrome: genetic and clinical insights. Curr Opin Neurol 2021; 34:556-564. [PMID: 34227574 DOI: 10.1097/wco.0000000000000961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW This review aims to summarise the present cerebellar ataxia, neuropathy, vestibular ataxia syndrome (CANVAS) literature, providing both clinical and genetic insights that might facilitate the timely clinical and genetic diagnosis of this disease. RECENT FINDINGS Recent advancements in the range of the clinical features of CANVAS have aided the development of a broader, more well-defined clinical diagnostic criteria. Additionally, the identification of a biallelic repeat expansion in RFC1 as the cause of CANVAS and a common cause of late-onset ataxia has opened the door to the potential discovery of a pathogenic mechanism, which in turn, may lead to therapeutic advancements and improved patient care. SUMMARY The developments in the clinical and genetic understanding of CANVAS will aid the correct and timely diagnosis of CANVAS, which continues to prove challenging within the clinic. The insights detailed within this review will raise the awareness of the phenotypic spectrum and currently known genetics. We also speculate on the future directions of research into CANVAS.
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45
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Ziff OJ, Taha DM, Crerar H, Clarke BE, Chakrabarti AM, Kelly G, Neeves J, Tyzack GE, Luscombe NM, Patani R. Reactive astrocytes in ALS display diminished intron retention. Nucleic Acids Res 2021; 49:3168-3184. [PMID: 33684213 PMCID: PMC8034657 DOI: 10.1093/nar/gkab115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
Reactive astrocytes are implicated in amyotrophic lateral sclerosis (ALS), although the mechanisms controlling reactive transformation are unknown. We show that decreased intron retention (IR) is common to human-induced pluripotent stem cell (hiPSC)-derived astrocytes carrying ALS-causing mutations in VCP, SOD1 and C9orf72. Notably, transcripts with decreased IR and increased expression are overrepresented in reactivity processes including cell adhesion, stress response and immune activation. This was recapitulated in public-datasets for (i) hiPSC-derived astrocytes stimulated with cytokines to undergo reactive transformation and (ii) in vivo astrocytes following selective deletion of TDP-43. We also re-examined public translatome sequencing (TRAP-seq) of astrocytes from a SOD1 mouse model, which revealed that transcripts upregulated in translation significantly overlap with transcripts exhibiting decreased IR. Using nucleocytoplasmic fractionation of VCP mutant astrocytes coupled with mRNA sequencing and proteomics, we identify that decreased IR in nuclear transcripts is associated with enhanced nonsense mediated decay and increased cytoplasmic expression of transcripts and proteins regulating reactive transformation. These findings are consistent with a molecular model for reactive transformation in astrocytes whereby poised nuclear reactivity-related IR transcripts are spliced, undergo nuclear-to-cytoplasmic translocation and translation. Our study therefore provides new insights into the molecular regulation of reactive transformation in astrocytes.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK
| | - Doaa M Taha
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21511, Egypt
| | - Hamish Crerar
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Benjamin E Clarke
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Anob M Chakrabarti
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Giulia E Tyzack
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.,Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK
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46
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Characterization of C9orf72 haplotypes to evaluate the effects of normal and pathological variations on its expression and splicing. PLoS Genet 2021; 17:e1009445. [PMID: 33780440 PMCID: PMC8031855 DOI: 10.1371/journal.pgen.1009445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 04/08/2021] [Accepted: 02/25/2021] [Indexed: 11/19/2022] Open
Abstract
Expansion of the hexanucleotide repeat (HR) in the first intron of the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in Caucasians. All C9orf72-ALS/FTD patients share a common risk (R) haplotype. To study C9orf72 expression and splicing from the mutant R allele compared to the complementary normal allele in ALS/FTD patients, we initially created a detailed molecular map of the single nucleotide polymorphism (SNP) signature and the HR length of the various C9orf72 haplotypes in Caucasians. We leveraged this map to determine the allelic origin of transcripts per patient, and decipher the effects of pathological and normal HR lengths on C9orf72 expression and splicing. In C9orf72 ALS patients’ cells, the HR expanded allele, compared to non-R allele, was associated with decreased levels of a downstream initiated transcript variant and increased levels of transcripts initiated upstream of the HR. HR expanded R alleles correlated with high levels of unspliced intron 1 and activation of cryptic donor splice sites along intron 1. Retention of intron 1 was associated with sequential intron 2 retention. The SNP signature of C9orf72 haplotypes described here enables allele-specific analysis of transcriptional products and may pave the way to allele-specific therapeutic strategies. Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are progressive neurodegenerative diseases, whose most frequent genetic cause is hexanucleotide repeat (HR) expansion from normal 2 to 20 repeats to pathological hundreds of repeats within a non-coding region of the C9orf72 gene. Haplotype is a specific combination of multiple polymorphic sites along a chromosome that are inherited together in block. We characterized the single nucleotide polymorphism (SNP) signature and HR length of the major C9orf72 haplotypes in Caucasians to identify the allelic origin of C9orf72 transcripts per patient and determine the effects of expanded HR on C9orf72 gene expression and splicing. In C9orf72 ALS patients’ cells, the HR expanded allele, compared to non-R allele, was associated with decreased levels of downstream initiated transcript variant, increased levels of upstream initiated transcripts, accumulation of introns 1 and 2, and abnormal splicing at cryptic splice sites along intron 1. The C9orf72 haplotypes DNA signatures described here are valuable for studying C9-ALS/FTD pathogenesis and for developing allele-specific therapeutic strategies.
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Song X, Yang T, Zhang X, Yuan Y, Yan X, Wei Y, Zhang J, Zhou C. Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level. Front Genet 2021; 12:622724. [PMID: 33719337 PMCID: PMC7953163 DOI: 10.3389/fgene.2021.622724] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/05/2021] [Indexed: 02/05/2023] Open
Abstract
Microsatellite or simple sequence repeat (SSR) instability within genes can induce genetic variation. The SSR signatures remain largely unknown in different clades within Euarchontoglires, one of the most successful mammalian radiations. Here, we conducted a genome-wide characterization of microsatellite distribution patterns at different taxonomic levels in 153 Euarchontoglires genomes. Our results showed that the abundance and density of the SSRs were significantly positively correlated with primate genome size, but no significant relationship with the genome size of rodents was found. Furthermore, a higher level of complexity for perfect SSR (P-SSR) attributes was observed in rodents than in primates. The most frequent type of P-SSR was the mononucleotide P-SSR in the genomes of primates, tree shrews, and colugos, while mononucleotide or dinucleotide motif types were dominant in the genomes of rodents and lagomorphs. Furthermore, (A)n was the most abundant motif in primate genomes, but (A)n, (AC)n, or (AG)n was the most abundant motif in rodent genomes which even varied within the same genus. The GC content and the repeat copy numbers of P-SSRs varied in different species when compared at different taxonomic levels, reflecting underlying differences in SSR mutation processes. Notably, the CDSs containing P-SSRs were categorized by functions and pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations, highlighting their roles in transcription regulation. Generally, this work will aid future studies of the functional roles of the taxonomic features of microsatellites during the evolution of mammals in Euarchontoglires.
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Affiliation(s)
- Xuhao Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
| | - Tingbang Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
| | - Xinyi Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Ying Yuan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Xianghui Yan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Yi Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
| | - Jun Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.,Institute of Ecology, China West Normal University, Nanchong, China
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48
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Otero BA, Poukalov K, Hildebrandt RP, Thornton CA, Jinnai K, Fujimura H, Kimura T, Hagerman KA, Sampson JB, Day JW, Wang ET. Transcriptome alterations in myotonic dystrophy frontal cortex. Cell Rep 2021; 34:108634. [PMID: 33472074 PMCID: PMC9272850 DOI: 10.1016/j.celrep.2020.108634] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
Myotonic dystrophy (DM) is caused by expanded CTG/CCTG repeats, causing symptoms in skeletal muscle, heart, and central nervous system (CNS). CNS issues are debilitating and include hypersomnolence, executive dysfunction, white matter atrophy, and neurofibrillary tangles. Here, we generate RNA-seq transcriptomes from DM and unaffected frontal cortex and identify 130 high-confidence splicing changes, most occurring only in cortex, not skeletal muscle or heart. Mis-spliced exons occur in neurotransmitter receptors, ion channels, and synaptic scaffolds, and GRIP1 mis-splicing modulates kinesin association. Optical mapping of expanded CTG repeats reveals extreme mosaicism, with some alleles showing >1,000 CTGs. Mis-splicing severity correlates with CTG repeat length across individuals. Upregulated genes tend to be microglial and endothelial, suggesting neuroinflammation, and downregulated genes tend to be neuronal. Many gene expression changes strongly correlate with mis-splicing, suggesting candidate biomarkers of disease. These findings provide a framework for mechanistic and therapeutic studies of the DM CNS. Otero et al. characterize DM1 frontal cortex transcriptomes and observe extreme CTG repeat lengths even in individuals showing modest mis-splicing. Mis-splicing is enriched in ion channels, neurotransmitter receptors, and synaptic scaffolds, in some cases potentially altering synaptic trafficking. Inferred expression signatures from microglia and endothelial cells suggest neuroinflammation.
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Affiliation(s)
- Brittney A Otero
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Kiril Poukalov
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Ryan P Hildebrandt
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Kenji Jinnai
- Department of Neurology, National Hospital Organization Hyogo-Chuo Hospital, Sanda, Japan
| | - Harutoshi Fujimura
- Department of Neurology, National Hospital Organization Toneyama Hospital, Osaka, Japan
| | - Takashi Kimura
- Department of Neurology, Hyogo College of Medicine, Nichinomiya, Japan
| | | | | | - John W Day
- Department of Neurology, Stanford University, Palo Alto, CA, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL, USA.
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49
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Angelbello AJ, Benhamou RI, Rzuczek SG, Choudhary S, Tang Z, Chen JL, Roy M, Wang KW, Yildirim I, Jun AS, Thornton CA, Disney MD. A Small Molecule that Binds an RNA Repeat Expansion Stimulates Its Decay via the Exosome Complex. Cell Chem Biol 2020; 28:34-45.e6. [PMID: 33157036 DOI: 10.1016/j.chembiol.2020.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/08/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022]
Abstract
Many diseases are caused by toxic RNA repeats. Herein, we designed a lead small molecule that binds the structure of the r(CUG) repeat expansion [r(CUG)exp] that causes myotonic dystrophy type 1 (DM1) and Fuchs endothelial corneal dystrophy (FECD) and rescues disease biology in patient-derived cells and in vivo. Interestingly, the compound's downstream effects are different in the two diseases, owing to the location of the repeat expansion. In DM1, r(CUG)exp is harbored in the 3' untranslated region, and the compound has no effect on the mRNA's abundance. In FECD, however, r(CUG)exp is located in an intron, and the small molecule facilitates excision of the intron, which is then degraded by the RNA exosome complex. Thus, structure-specific, RNA-targeting small molecules can act disease specifically to affect biology, either by disabling the gain-of-function mechanism (DM1) or by stimulating quality control pathways to rid a disease-affected cell of a toxic RNA (FECD).
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Affiliation(s)
- Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Raphael I Benhamou
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Suzanne G Rzuczek
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Shruti Choudhary
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Zhenzhi Tang
- Department of Neurology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Jonathan L Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Madhuparna Roy
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Kye Won Wang
- Department of Chemistry, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Ilyas Yildirim
- Department of Chemistry, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Albert S Jun
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Charles A Thornton
- Department of Neurology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
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50
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Monteuuis G, Schmitz U, Petrova V, Kearney PS, Rasko JEJ. Holding on to Junk Bonds: Intron Retention in Cancer and Therapy. Cancer Res 2020; 81:779-789. [PMID: 33046441 DOI: 10.1158/0008-5472.can-20-1943] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]
Abstract
Intron retention (IR) in cancer was for a long time overlooked by the scientific community, as it was previously considered to be an artifact of a dysfunctional spliceosome. Technological advancements made in the last decade offer unique opportunities to explore the role of IR as a widespread phenomenon that contributes to the transcriptional diversity of many cancers. Numerous studies in cancer have shed light on dysregulation of cellular mechanisms that lead to aberrant and pathologic IR. IR is not merely a mechanism of gene regulation, but rather it can mediate cancer pathogenesis and therapeutic resistance in various human diseases. The burden of IR in cancer is governed by perturbations to mechanisms known to regulate this phenomenon and include epigenetic variation, mutations within the gene body, and splicing factor dysregulation. This review summarizes possible causes for aberrant IR and discusses the role of IR in therapy or as a consequence of disease treatment. As neoepitopes originating from retained introns can be presented on the cancer cell surface, the development of personalized cancer vaccines based on IR-derived neoepitopes should be considered. Ultimately, a deeper comprehension about the origins and consequences of aberrant IR may aid in the development of such personalized cancer vaccines.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Veronika Petrova
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia
| | - Padraic S Kearney
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia. .,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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