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Baralle M, Romano M. Age-Related Alternative Splicing: Driver or Passenger in the Aging Process? Cells 2023; 12:2819. [PMID: 38132139 PMCID: PMC10742131 DOI: 10.3390/cells12242819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying gene isoform levels and functions. These changes may contribute to aging alterations rather than just reflect declining RNA quality control. Three main splicing types-intron retention, cassette exons, and cryptic exons-play key roles in age-related complexity. These events modify protein domains and increase nonsense-mediated decay, shifting protein isoform levels and functions. This may potentially drive aging or serve as a biomarker. Fluctuations in splicing factor expression also occur with aging. Somatic mutations in splicing genes can also promote aging and age-related disease. The interplay between splicing and aging has major implications for aging biology, though differentiating correlation and causation remains challenging. Declaring a splicing factor or event as a driver requires comprehensive evaluation of the associated molecular and physiological changes. A greater understanding of how RNA splicing machinery and downstream targets are impacted by aging is essential to conclusively establish the role of splicing in driving aging, representing a promising area with key implications for understanding aging, developing novel therapeutical options, and ultimately leading to an increase in the healthy human lifespan.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy;
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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Liu D, Liu Y, Zhang X, Wang Y, Zhang C, Zheng S. An Exploration of Mutagenesis in a Family with Cleidocranial Dysplasia without RUNX2 Mutation. Front Genet 2021; 12:748111. [PMID: 34737766 PMCID: PMC8560734 DOI: 10.3389/fgene.2021.748111] [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: 07/27/2021] [Accepted: 09/29/2021] [Indexed: 11/22/2022] Open
Abstract
Cleidocranial dysplasia (CCD) is an autosomal dominant inheritable skeletal disorder characterized by cranial dysplasia, clavicle hypoplasia, and dental abnormalities. Mutations involving Runt-related transcription factor 2 (RUNX2) are currently the only known molecular etiology for CCD but are not identified in all CCD patients. No RUNX2 abnormality can be detected in about 20–30% of patients, and the molecular cause remains unknown. The present study includes a family case with typical features of CCD. RUNX2 mutation was first screened by sequencing analysis, and no mutation was detected. Copy number alterations of the RUNX2 gene were then measured by quantitative PCR and multiplex ligation-dependent probe amplification (MLPA). No copy number variation in RUNX2 could be detected. We performed whole-exome sequencing (WES) to identify the underlying genetic mutations. Unexpectedly, no abnormalities could be detected in genes related to the RUNX2 signaling pathway. Therefore, it was supposed that other new unknown gene variations might contribute to the CCD phenotype. We focused on Immunoglobulin superfamily member 10 (IGSF10), a gene related to bone development. An IGSF10 frameshift mutation (c.6001_6002delCT, p.Leu2001Valfs*24) was detected by WES. Sanger sequencing verified that this mutation was only detected in the patient and her affected mother but not in her unaffected father. Bioinformatics studies demonstrated that this mutation could change the 3D structure of the IGSF10 protein and severely damage its function. In addition, alkaline phosphatase (ALP) activity and the ability to form mineralized nodules were inhibited by IGSF10 knockdown compared with normal controls. The expression of bone sialoprotein (BSP) was significantly reduced by IGSF10 knockdown, but not that of other osteogenic markers. Our results provide new genetic evidence that IGSF10 mutation might contribute to CCD.
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Affiliation(s)
- Dandan Liu
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yang Liu
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - XianLi Zhang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China.,Department of Stomatology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Yixiang Wang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Central Laboratory, Department of Oral and Maxillofacial Surgery, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - Chenying Zhang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
| | - Shuguo Zheng
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Department of Preventive Dentistry, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, China
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Keegan NP, Fletcher S. A spotter's guide to SNPtic exons: The common splice variants underlying some SNP-phenotype correlations. Mol Genet Genomic Med 2021; 10:e1840. [PMID: 34708937 PMCID: PMC8801146 DOI: 10.1002/mgg3.1840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/12/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Cryptic exons are typically characterised as deleterious splicing aberrations caused by deep intronic mutations. However, low-level splicing of cryptic exons is sometimes observed in the absence of any pathogenic mutation. Five recent reports have described how low-level splicing of cryptic exons can be modulated by common single-nucleotide polymorphisms (SNPs), resulting in phenotypic differences amongst different genotypes. METHODS We sought to investigate whether additional 'SNPtic' exons may exist, and whether these could provide an explanatory mechanism for some of the genotype-phenotype correlations revealed by genome-wide association studies. We thoroughly searched the literature for reported cryptic exons, cross-referenced their genomic coordinates against the dbSNP database of common SNPs, then screened out SNPs with no reported phenotype associations. RESULTS This method discovered five probable SNPtic exons in the genes APC, FGB, GHRL, MYPBC3 and OTC. For four of these five exons, we observed that the phenotype associated with the SNP was compatible with the predicted splicing effect of the nucleotide change, whilst the fifth (in GHRL) likely had a more complex splice-switching effect. CONCLUSION Application of our search methods could augment the knowledge value of future cryptic exon reports and aid in generating better hypotheses for genome-wide association studies.
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Affiliation(s)
- Niall Patrick Keegan
- Murdoch University, Murdoch, Western Australia, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Perth, Western Australia, Australia.,Perron Institute, Perth, Western Australia, Australia
| | - Sue Fletcher
- Murdoch University, Murdoch, Western Australia, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Perth, Western Australia, Australia.,University of Western Australia, Perth, Western Australia, Australia
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Matsuo M. Antisense Oligonucleotide-Mediated Exon-skipping Therapies: Precision Medicine Spreading from Duchenne Muscular Dystrophy. JMA J 2021; 4:232-240. [PMID: 34414317 PMCID: PMC8355726 DOI: 10.31662/jmaj.2021-0019] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/13/2021] [Indexed: 11/12/2022] Open
Abstract
In 1995, we were the first to propose antisense oligonucleotide (ASO)-mediated exon-skipping therapy for the treatment of Duchenne muscular dystrophy (DMD), a noncurable, progressive muscle-wasting disease. DMD is caused by deletion mutations in one or more exons of the DMD gene that shift the translational reading frame and create a premature stop codon, thus prohibiting dystrophin production. The therapy aims to correct out-of-frame mRNAs to produce in-frame transcripts by removing an exon during splicing, with the resumption of dystrophin production. As this treatment is recognized as the most promising, many extensive studies have been performed to develop ASOs that induce the skipping of DMD exons. In 2016, an ASO designed to skip exon 51 was first approved by the Food and Drug Administration, which accelerated studies on the use of ASOs to treat other monogenic diseases. The ease of mRNA editing by ASO-mediated exon skipping has resulted in the further application of exon-skipping therapy to nonmonogenic diseases, such as diabetes mellites. Recently, this precision medicine strategy was drastically transformed for the emergent treatment of only one patient with one ASO, which represents a future aspect of ASO-mediated exon-skipping therapy for extremely rare diseases. Herein, the invention of ASO-mediated exon-skipping therapy for DMD and the current applications of ASO-mediated exon-skipping therapies are reviewed, and future perspectives on this therapeutic strategy are discussed. This overview will encourage studies on ASO-mediated exon-skipping therapy and will especially contribute to the development of treatments for noncurable diseases.
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Affiliation(s)
- Masafumi Matsuo
- KNC Department of Nucleic Acid Drug Discovery, Department of Physical Rehabilitation and Research Center for Locomotion Biology, Kobe Gakuin University, Kobe, Japan
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6
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Moles-Fernández A, Domènech-Vivó J, Tenés A, Balmaña J, Diez O, Gutiérrez-Enríquez S. Role of Splicing Regulatory Elements and In Silico Tools Usage in the Identification of Deep Intronic Splicing Variants in Hereditary Breast/Ovarian Cancer Genes. Cancers (Basel) 2021; 13:cancers13133341. [PMID: 34283047 PMCID: PMC8268271 DOI: 10.3390/cancers13133341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary There is a significant percentage of hereditary breast and ovarian cancer (HBOC) cases that remain undiagnosed, because no pathogenic variant is detected through massively parallel sequencing of coding exons and exon-intron boundaries of high-moderate susceptibility risk genes. Deep intronic regions may contain variants affecting RNA splicing, leading ultimately to disease, and hence they may explain several cases where the genetic cause of HBOC is unknown. This study aims to characterize intronic regions to identify a landscape of “exonizable” zones and test the efficiency of two in silico tools to detect deep intronic variants affecting the mRNA splicing process. Abstract The contribution of deep intronic splice-altering variants to hereditary breast and ovarian cancer (HBOC) is unknown. Current computational in silico tools to predict spliceogenic variants leading to pseudoexons have limited efficiency. We assessed the performance of the SpliceAI tool combined with ESRseq scores to identify spliceogenic deep intronic variants by affecting cryptic sites or splicing regulatory elements (SREs) using literature and experimental datasets. Our results with 233 published deep intronic variants showed that SpliceAI, with a 0.05 threshold, predicts spliceogenic deep intronic variants affecting cryptic splice sites, but is less effective in detecting those affecting SREs. Next, we characterized the SRE profiles using ESRseq, showing that pseudoexons are significantly enriched in SRE-enhancers compared to adjacent intronic regions. Although the combination of SpliceAI with ESRseq scores (considering ∆ESRseq and SRE landscape) showed higher sensitivity, the global performance did not improve because of the higher number of false positives. The combination of both tools was tested in a tumor RNA dataset with 207 intronic variants disrupting splicing, showing a sensitivity of 86%. Following the pipeline, five spliceogenic deep intronic variants were experimentally identified from 33 variants in HBOC genes. Overall, our results provide a framework to detect deep intronic variants disrupting splicing.
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Affiliation(s)
- Alejandro Moles-Fernández
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
| | - Joanna Domènech-Vivó
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
| | - Anna Tenés
- Area of Clinical and Molecular Genetics, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
- Medical Oncology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Orland Diez
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
- Area of Clinical and Molecular Genetics, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
- Correspondence: (O.D.); (S.G.-E.)
| | - Sara Gutiérrez-Enríquez
- Hereditary Cancer Genetics Group, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.M.-F.); (J.D.-V.); (J.B.)
- Correspondence: (O.D.); (S.G.-E.)
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Riepe TV, Khan M, Roosing S, Cremers FPM, 't Hoen PAC. Benchmarking deep learning splice prediction tools using functional splice assays. Hum Mutat 2021; 42:799-810. [PMID: 33942434 PMCID: PMC8360004 DOI: 10.1002/humu.24212] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/16/2021] [Accepted: 04/17/2021] [Indexed: 12/21/2022]
Abstract
Hereditary disorders are frequently caused by genetic variants that affect pre-messenger RNA splicing. Though genetic variants in the canonical splice motifs are almost always disrupting splicing, the pathogenicity of variants in the noncanonical splice sites (NCSS) and deep intronic (DI) regions are difficult to predict. Multiple splice prediction tools have been developed for this purpose, with the latest tools employing deep learning algorithms. We benchmarked established and deep learning splice prediction tools on published gold standard sets of 71 NCSS and 81 DI variants in the ABCA4 gene and 61 NCSS variants in the MYBPC3 gene with functional assessment in midigene and minigene splice assays. The selection of splice prediction tools included CADD, DSSP, GeneSplicer, MaxEntScan, MMSplice, NNSPLICE, SPIDEX, SpliceAI, SpliceRover, and SpliceSiteFinder-like. The best-performing splice prediction tool for the different variants was SpliceRover for ABCA4 NCSS variants, SpliceAI for ABCA4 DI variants, and the Alamut 3/4 consensus approach (GeneSplicer, MaxEntScacn, NNSPLICE and SpliceSiteFinder-like) for NCSS variants in MYBPC3 based on the area under the receiver operator curve. Overall, the performance in a real-time clinical setting is much more modest than reported by the developers of the tools.
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Affiliation(s)
- Tabea V. Riepe
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Human Genetics and Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Mubeen Khan
- Department of Human Genetics and Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Susanne Roosing
- Department of Human Genetics and Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Peter A. C. 't Hoen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
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Qian Y, Hu G, Chen M, Liu B, Yan K, Zhou C, Yu Y, Dong M. Novel deep intronic and frameshift mutations causing a TRIP11-related disorder. Am J Med Genet A 2021; 185:2482-2487. [PMID: 34014608 DOI: 10.1002/ajmg.a.62260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/19/2021] [Accepted: 04/24/2021] [Indexed: 11/06/2022]
Abstract
Mutations of the thyroid hormone receptor interactor 11 gene (TRIP11, OMIM: 604505) at 14q32.12 have been associated with the autosomal recessive achondrogenesis type IA (ACG1A, OMIM: 200600) or osteochondrodysplasia (ODCD, OMIM: 184260). In this clinical report of a Chinese family, the mother had two consecutive pregnancies with similar aberrant phenotypes in the fetuses showing severe limb shortening. Whole exome sequencing (WES) of DNA from the second fetus identified a heterozygous frameshift mutation (NM_004239: c.3852delT) of TRIP11. Although this was consistent with the fetal clinical phenotypes, initial review of the WES results implied another novel mutation. To test this, we used high-precision clinical exome sequencing (HPCES) and found a mutation in Intron 18 of TRIP11 (c.5457+77T>G). Moreover, the sequencing depth of this mutation was only 3× that of WES compared with 161× that by HPCES. To ascertain the pathogenesis of the mutation (c.5457+77T>G), RT-PCR conducted using the parents' blood samples showed a 77-bp intronic sequence in the transcripts, which might have encoded for a shortened protein because of early termination due to code shifting. Our study furthers current understanding of deep intron function and provides a novel diagnostic method of deep intragenic mutations in families having two or more consecutive pregnancies with similar aberrant fetal phenotypes.
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Affiliation(s)
- Yeqing Qian
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Gang Hu
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Min Chen
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Bei Liu
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Kai Yan
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
| | - Caiyun Zhou
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China
| | - Yanqin Yu
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China
| | - Minyue Dong
- Women's Hospital, School of Medicine, Zhejiang University, Zhejiang, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1, Xueshi Road, Zhejiang, China
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Xiao H, Zhou WH. [Application of RNA sequencing in clinical diagnosis of Mendelian disease]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:1138-1142. [PMID: 33059815 PMCID: PMC7568994 DOI: 10.7499/j.issn.1008-8830.2005004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Gene panel and whole exome sequencing are now commonly used to detect Mendelian disease, but the current molecular diagnostic rate of DNA sequencing is only 35%-50%. In recent years, RNA sequencing emerges as a promising diagnostic method. It can detect new pathogenic mutations, and analyze allele-specific expression. This will be helpful to understand the relationship between disease genotype and phenotype, and can complement genome sequencing in order to expand the traditional genomic diagnostic methods of Mendelian disease. RNA sequencing is expected to become a routine tool for diagnosing Mendelian diseases. This article reviews the application of RNA sequencing in the clinical diagnosis of Mendelian disease.
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Affiliation(s)
- Hui Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai 201102, China.
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Montalban G, Bonache S, Moles-Fernández A, Gisbert-Beamud A, Tenés A, Bach V, Carrasco E, López-Fernández A, Stjepanovic N, Balmaña J, Diez O, Gutiérrez-Enríquez S. Screening of BRCA1/2 deep intronic regions by targeted gene sequencing identifies the first germline BRCA1 variant causing pseudoexon activation in a patient with breast/ovarian cancer. J Med Genet 2019; 56:63-74. [PMID: 30472649 DOI: 10.1136/jmedgenet-2018-105606] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/16/2018] [Accepted: 10/28/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Genetic analysis of BRCA1 and BRCA2 for the diagnosis of hereditary breast and ovarian cancer (HBOC) is commonly restricted to coding regions and exon-intron boundaries. Although germline pathogenic variants in these regions explain about ~20% of HBOC cases, there is still an important fraction that remains undiagnosed. We have screened BRCA1/2 deep intronic regions to identify potential spliceogenic variants that could explain part of the missing HBOC susceptibility. METHODS We analysed BRCA1/2 deep intronic regions by targeted gene sequencing in 192 high-risk HBOC families testing negative for BRCA1/2 during conventional analysis. Rare variants (MAF <0.005) predicted to create/activate splice sites were selected for further characterisation in patient RNA. The splicing outcome was analysed by RT-PCR and Sanger sequencing, and allelic imbalance was also determined when heterozygous exonic loci were present. RESULTS A novel transcript was detected in BRCA1 c.4185+4105C>T variant carrier. This variant promotes the inclusion of a pseudoexon in mature mRNA, generating an aberrant transcript predicted to encode for a non-functional protein. Quantitative and allele-specific assays determined haploinsufficiency in the variant carrier, supporting a pathogenic effect for this variant. Genotyping of 1030 HBOC cases and 327 controls did not identify additional carriers in Spanish population. CONCLUSION Screening of BRCA1/2 intronic regions has identified the first BRCA1 deep intronic variant associated with HBOC by pseudoexon activation. Although the frequency of deleterious variants in these regions appears to be low, our study highlights the importance of studying non-coding regions and performing comprehensive RNA assays to complement genetic diagnosis.
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Affiliation(s)
- Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | | | | | - Anna Tenés
- Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Vanessa Bach
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Estela Carrasco
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Adrià López-Fernández
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Neda Stjepanovic
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
- Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
- Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
- Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
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11
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Bergougnoux A, Délétang K, Pommier A, Varilh J, Houriez F, Altieri JP, Koenig M, Férec C, Claustres M, Lalau G, Bienvenu T, Audrézet MP, Pagin A, Girodon E, Raynal C, Taulan-Cadars M. Functional characterization and phenotypic spectrum of three recurrent disease-causing deep intronic variants of the CFTR gene. J Cyst Fibros 2018; 18:468-475. [PMID: 30389601 DOI: 10.1016/j.jcf.2018.10.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND The CFTR genotype remains incomplete in 1% of Cystic Fibrosis (CF) cases, because only one or no disease-causing variants is detected after extended analysis. This fraction is probably higher in CFTR-Related Disorders (CFTR-RD). Deep-intronic CFTR variants are putative candidates to fill this gap. However, the recurrence, phenotypic spectrum and full molecular characterization of newly reported variants are unknown. METHODS Minigenes and analysis of CFTR transcripts in nasal epithelial cells were used to determine the impact on CFTR splicing of intronic variants that we previously identified by next generation sequencing of the whole CFTR locus. Phenotypic data were collected in 19 patients with CF and CFTR-RD, in whom one of the deep intronic variants has been detected. RESULTS Three deep-intronic variants promoted the inclusion of pseudo-exons (PE) in the CFTR transcript, hindering the synthesis of a functional protein. The c.2989-313A > T variant, detected in four patients with CF or CFTR-RD from three different families, led to the inclusion of a 118 bp PE. The c.3469-1304C > G variant promoted the inclusion of a 214 bp-PE and was identified in five patients with CF from four families. Haplotype analysis confirmed that this variant was associated with one CF chromosome of African origin. The most represented variant in our cohort was the c.3874-4522A > G, detected in 10 patients with various phenotypes, from male infertility to CF with pancreatic insufficiency. CONCLUSION These three deep intronic CFTR variants are associated with a large phenotypic spectrum, including typical CF. They should be included in CF diagnostic testing and carrier screening strategies.
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Affiliation(s)
- A Bergougnoux
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France; Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France.
| | - K Délétang
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - A Pommier
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - J Varilh
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - F Houriez
- AP-HP, HUPC, Hôpital Cochin, Laboratoire de Génétique et Biologie Moléculaires, Paris, France
| | - J P Altieri
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | - M Koenig
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France; Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - C Férec
- Inserm, UMR1078 Génétique, Génomique Fonctionnelle et Biotechnologies, France; Univ Brest, EFS, IBSAM, Brest, France; CHU de Brest, Laboratoire de Génétique Moléculaire, Brest, France
| | - M Claustres
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
| | - G Lalau
- Service de Toxicologie et Génopathies, Institut de Biochimie et Biologie Moléculaire, Centre Hospitalier Régional Universitaire, Lille, France
| | - T Bienvenu
- AP-HP, HUPC, Hôpital Cochin, Laboratoire de Génétique et Biologie Moléculaires, Paris, France
| | - M P Audrézet
- CHU de Brest, Laboratoire de Génétique Moléculaire, Brest, France
| | - A Pagin
- Service de Toxicologie et Génopathies, Institut de Biochimie et Biologie Moléculaire, Centre Hospitalier Régional Universitaire, Lille, France
| | - E Girodon
- AP-HP, HUPC, Hôpital Cochin, Laboratoire de Génétique et Biologie Moléculaires, Paris, France
| | - C Raynal
- CHU de Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
| | - M Taulan-Cadars
- Université de Montpellier, Laboratoire de Génétique de Maladies Rares, EA7402 Montpellier, France
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Pseudoexons provide a mechanism for allele-specific expression of APC in familial adenomatous polyposis. Oncotarget 2018; 7:70685-70698. [PMID: 27683109 PMCID: PMC5342583 DOI: 10.18632/oncotarget.12206] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022] Open
Abstract
Allele-specific expression (ASE) of the Adenomatous Polyposis Coli (APC) gene occurs in up to one-third of families with adenomatous polyposis (FAP) that have screened mutation-negative by conventional techniques. To advance our understanding of the genomic basis of this phenomenon, 54 APC mutation-negative families (21 with classical FAP and 33 with attenuated FAP, AFAP) were investigated. We focused on four families with validated ASE and scrutinized these families by sequencing of the blood transcriptomes (RNA-seq) and genomes (WGS). Three families, two with classical FAP and one with AFAP, revealed deep intronic mutations associated with pseudoexons. In all three families, intronic mutations (c.646-1806T>G in intron 6, c.1408+729A>G in intron 11, and c.1408+731C>T in intron 11) created new splice donor sites resulting in the insertion of intronic sequences (of 127 bp, 83 bp, and 83 bp, respectively) in the APC transcript. The respective intronic mutations were absent in the remaining polyposis families and the general population. Premature stop of translation as the predicted consequence as well as co-segregation with polyposis supported the pathogenicity of the pseudoexons. We conclude that next generation sequencing on RNA and genomic DNA is an effective strategy to reveal and validate pseudoexons that are regularly missed by traditional screening methods and is worth considering in apparent mutation-negative polyposis families.
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Mendes de Almeida R, Tavares J, Martins S, Carvalho T, Enguita FJ, Brito D, Carmo-Fonseca M, Lopes LR. Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PLoS One 2017; 12:e0182946. [PMID: 28797094 PMCID: PMC5552324 DOI: 10.1371/journal.pone.0182946] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/27/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High throughput sequencing technologies have revolutionized the identification of mutations responsible for genetic diseases such as hypertrophic cardiomyopathy (HCM). However, approximately 50% of individuals with a clinical diagnosis of HCM have no causal mutation identified. This may be due to the presence of pathogenic mutations located deep within the introns, which are not detected by conventional sequencing analysis restricted to exons and exon-intron boundaries. OBJECTIVE The aim of this study was to develop a whole-gene sequencing strategy to prioritize deep intronic variants that may play a role in HCM pathogenesis. METHODS AND RESULTS The full genomic DNA sequence of 26 genes previously associated with HCM was analysed in 16 unrelated patients. We identified likely pathogenic deep intronic variants in VCL, PRKAG2 and TTN genes. These variants, which are predicted to act through disruption of either splicing or transcription factor binding sites, are 3-fold more frequent in our cohort of probands than in normal European populations. Moreover, we found a patient that is compound heterozygous for a splice site mutation in MYBPC3 and the deep intronic VCL variant. Analysis of family members revealed that carriers of the MYBPC3 mutation alone do not manifest the disease, while family members that are compound heterozygous are clinically affected. CONCLUSION This study provides a framework for scrutinizing variation along the complete intronic sequence of HCM-associated genes and prioritizing candidates for mechanistic and functional analysis. Our data suggest that deep intronic variation contributes to HCM phenotype.
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Affiliation(s)
- Rita Mendes de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Tavares
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J. Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Dulce Brito
- Departamento de Cardiologia, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Luís Rocha Lopes
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
- Institute of Cardiovascular Science, University College London, London, United Kingdom
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Ramanouskaya TV, Grinev VV. The determinants of alternative RNA splicing in human cells. Mol Genet Genomics 2017; 292:1175-1195. [PMID: 28707092 DOI: 10.1007/s00438-017-1350-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022]
Abstract
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.
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15
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Normal and altered pre-mRNA processing in the DMD gene. Hum Genet 2017; 136:1155-1172. [DOI: 10.1007/s00439-017-1820-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
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16
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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Abstract
Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies.
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18
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Deltex1 Polymorphisms Are Associated with Hepatitis B Vaccination Non-Response in Southwest China. PLoS One 2016; 11:e0149199. [PMID: 26894927 PMCID: PMC4760674 DOI: 10.1371/journal.pone.0149199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/28/2016] [Indexed: 12/15/2022] Open
Abstract
Background Hepatitis B vaccination is the most important tool available for preventing hepatitis B virus (HBV) infection and reducing the prevalence of infection. However, epidemiological studies have demonstrated that morethan 5% of patients exhibit a non- or hypo-response to the HBV vaccine. Genetic variations associated with T cell immunity contribute to the immune response to HBV vaccination. The deltex 1 (DTX1) gene is involved in T cell anergy, which may also be associated with the immune response to the HBV vaccination. Methods We detected 10 single nucleotide polymorphisms (SNPs) in or around the DTX1 gene in 601 infants out of a population from Southwest China, including 299 high responders(HRs; HBsAb > 100 mIU/mL) and 302 non-responders (NRs; HBsAb < 10 mIU/mL). An additional validation study was performed, comprising 230 adult patients(135 HRs and 95 NRs) from Southwest China. Results This study found that the minor allele ‘G’ of rs2384077 (adjusted p = 2.63E-04,) and the minor allele ‘C’ of rs10744794 (adjusted p = 3.69E-04) in the first intron of the DTX1 gene were remarkably associated with the immune response to HBV vaccination in both infant and adult populations. Moreover, a subsequent analysis indicated that haplotypes (A-T, G-C) of the two SNPs were significantly associated with the immune response to HBV vaccination. Conclusions Two SNPs (rs2384077 and rs10744794) in an intron of DTX1 and the linkage disequilibrium (LD) block are significantly associated with the immune response to HBV vaccination. The functional element annotation of the LD block between the two SNPs contains four transcriptional regulatory elements. The results suggest that these two SNPs may be involved in the immune response to HBV vaccination.
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Singh HN, Rajeswari MR. Identification of genes containing expanded purine repeats in the human genome and their apparent protective role against cancer. J Biomol Struct Dyn 2015; 34:689-704. [PMID: 25990537 DOI: 10.1080/07391102.2015.1049553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Purine repeat sequences present in a gene are unique as they have high propensity to form unusual DNA-triple helix structures. Friedreich's ataxia is the only human disease that is well known to be associated with DNA-triplexes formed by purine repeats. The purpose of this study was to recognize the expanded purine repeats (EPRs) in human genome and find their correlation with cancer pathogenesis. We developed "PuRepeatFinder.pl" algorithm to identify non-overlapping EPRs without pyrimidine interruptions in the human genome and customized for searching repeat lengths, n ≥ 200. A total of 1158 EPRs were identified in the genome which followed Wakeby distribution. Two hundred and ninety-six EPRs were found in geneic regions of 282 genes (EPR-genes). Gene clustering of EPR-genes was done based on their cellular function and a large number of EPR-genes were found to be enzymes/enzyme modulators. Meta-analysis of 282 EPR-genes identified only 63 EPR-genes in association with cancer, mostly in breast, lung, and blood cancers. Protein-protein interaction network analysis of all 282 EPR-genes identified proteins including those in cadherins and VEGF. The two observations, that EPRs can induce mutations under malignant conditions and that identification of some EPR-gene products in vital cell signaling-mediated pathways, together suggest the crucial role of EPRs in carcinogenesis. The new link between EPR-genes and their functionally interacting proteins throws a new dimension in the present understanding of cancer pathogenesis and can help in planning therapeutic strategies. Validation of present results using techniques like NGS is required to establish the role of the EPR genes in cancer pathology.
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Affiliation(s)
- Himanshu Narayan Singh
- a Department of Biochemistry , All India Institute of Medical Sciences , Room No: 3005A, New Delhi 110029 , India
| | - Moganty R Rajeswari
- a Department of Biochemistry , All India Institute of Medical Sciences , Room No: 3005A, New Delhi 110029 , India
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Adamia S, Kriangkum J, Belch AR, Pilarski LM. Aberrant posttranscriptional processing of hyaluronan synthase 1 in malignant transformation and tumor progression. Adv Cancer Res 2015; 123:67-94. [PMID: 25081526 DOI: 10.1016/b978-0-12-800092-2.00003-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
It is becoming increasingly apparent that splicing defects play a key role in cancer, and that alterations in genomic splicing elements promote aberrant splicing. Alternative splicing increases the diversity of the human transcriptome and increases the numbers of functional gene products. However, dysregulation that leads to aberrant pre-mRNA splicing can contribute to cancer. Hyaluronan (HA), known to be an important component of cancer progression, is synthesized by hyaluronan synthases (HASs). In cancer cells, hyaluronan synthase 1 (HAS1) pre-mRNA is abnormally spliced to generate a family of aberrant splice variants (HAS1Vs) that synthesize extracellular and intracellular HA. HAS1Vs are clinically relevant, being found almost exclusively in malignant cells. Expression of aberrant HAS1Vs predicts poor survival in multiple myeloma. In this review, we summarize the unusual properties of HAS1Vs and their relationship to cancer. HAS1Vs form heterogeneous multimers with normally spliced HAS1 as well as with each other and with HAS3. Aberrant variants of HAS1 synthesize HA. Extracellular HA synthesized by HAS1Vs is likely to promote malignant spread. We speculate that synthesis of intracellular HA plays a fundamental and early role in oncogenesis by promoting genetic instability and the emergence of viable cancer variants that lead to aggressive disease.
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Affiliation(s)
- Sophia Adamia
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.
| | - Jitra Kriangkum
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Andrew R Belch
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Linda M Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
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