1
|
Szelest M, Giannopoulos K. Biological relevance of alternative splicing in hematologic malignancies. Mol Med 2024; 30:62. [PMID: 38760666 DOI: 10.1186/s10020-024-00839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024] Open
Abstract
Alternative splicing (AS) is a strictly regulated process that generates multiple mRNA variants from a single gene, thus contributing to proteome diversity. Transcriptome-wide sequencing studies revealed networks of functionally coordinated splicing events, which produce isoforms with distinct or even opposing functions. To date, several mechanisms of AS are deregulated in leukemic cells, mainly due to mutations in splicing and/or epigenetic regulators and altered expression of splicing factors (SFs). In this review, we discuss aberrant splicing events induced by mutations affecting SFs (SF3B1, U2AF1, SRSR2, and ZRSR2), spliceosome components (PRPF8, LUC7L2, DDX41, and HNRNPH1), and epigenetic modulators (IDH1 and IDH2). Finally, we provide an extensive overview of the biological relevance of aberrant isoforms of genes involved in the regulation of apoptosis (e. g. BCL-X, MCL-1, FAS, and c-FLIP), activation of key cellular signaling pathways (CASP8, MAP3K7, and NOTCH2), and cell metabolism (PKM).
Collapse
Affiliation(s)
- Monika Szelest
- Department of Experimental Hematooncology, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland.
| | - Krzysztof Giannopoulos
- Department of Experimental Hematooncology, Medical University of Lublin, Chodzki 1, 20-093, Lublin, Poland
| |
Collapse
|
2
|
Wang J, Yan L, Wang X, Jia R, Guo J. Surface PD-1 expression in T cells is suppressed by HNRNPK through an exonic splicing silencer on exon 3. Inflamm Res 2024:10.1007/s00011-024-01887-4. [PMID: 38698180 DOI: 10.1007/s00011-024-01887-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVE Immunotherapy targeting programmed cell death 1 (PDCD1 or PD-1) and its ligands has shown remarkable promise and the regulation mechanism of PD-1 expression has received arising attention in recent years. PDCD1 exon 3 encodes the transmembrane domain and the deletion of exon 3 produces a soluble protein isoform of PD-1 (sPD-1), which can enhance immune response by competing with full-length PD-1 protein (flPD-1 or surface PD-1) on T cell surface. However, the mechanism of PDCD1 exon 3 skipping is unclear. METHODS The online SpliceAid program and minigene expression system were used to analyze potential splicing factors involved in the splicing event of PDCD1 exon 3. The potential binding motifs of heterogeneous nuclear ribonucleoprotein K (HNRNPK) on exon 3 predicted by SpliceAid were mutated by site-directed mutagenesis technology, which were further verified by pulldown assay. Antisense oligonucleotides (ASOs) targeting the exonic splicing silencer (ESS) on PDCD1 exon 3 were synthesized and screened to suppress the skipping of exon 3. The alternative splicing of PDCD1 exon 3 was analyzed by semiquantitative reverse transcription PCR. Western blot and flow cytometry were performed to detect the surface PD-1 expression in T cells. RESULTS HNRNPK was screened as a key splicing factor that promoted PDCD1 exon 3 skipping, causing a decrease in flPD-1 expression on T cell membrane and an increase in sPD-1 expression. Mechanically, a key ESS has been identified on exon 3 and can be bound by HNRNPK protein to promote exon 3 skipping. Blocking the interaction between ESS and HNRNPK with an ASO significantly reduced exon 3 skipping. Importantly, HNRNPK can promote exon 3 skipping of mouse Pdcd1 gene as well. CONCLUSIONS Our study revealed a novel evolutionarily conserved regulatory mechanism of PD-1 expression. The splicing factor HNRNPK markedly promoted PDCD1 exon 3 skipping by binding to the ESS on PDCD1 exon 3, resulting in decreased expression of flPD-1 and increased expression of sPD-1 in T cells.
Collapse
Affiliation(s)
- Jiayun Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Lingyan Yan
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Xu Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
| | - Rong Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- RNA Institute, Wuhan University, Wuhan, 430072, China
| | - Jihua Guo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China.
- Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China.
| |
Collapse
|
3
|
Bauer M, Schöbel CM, Wickenhauser C, Seliger B, Jasinski-Bergner S. Deciphering the role of alternative splicing in neoplastic diseases for immune-oncological therapies. Front Immunol 2024; 15:1386993. [PMID: 38736877 PMCID: PMC11082354 DOI: 10.3389/fimmu.2024.1386993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Alternative splicing (AS) is an important molecular biological mechanism regulated by complex mechanisms involving a plethora of cis and trans-acting elements. Furthermore, AS is tissue specific and altered in various pathologies, including infectious, inflammatory, and neoplastic diseases. Recently developed immuno-oncological therapies include monoclonal antibodies (mAbs) and chimeric antigen receptor (CAR) T cells targeting, among others, immune checkpoint (ICP) molecules. Despite therapeutic successes have been demonstrated, only a limited number of patients showed long-term benefit from these therapies with tumor entity-related differential response rates were observed. Interestingly, splice variants of common immunotherapeutic targets generated by AS are able to completely escape and/or reduce the efficacy of mAb- and/or CAR-based tumor immunotherapies. Therefore, the analyses of splicing patterns of targeted molecules in tumor specimens prior to therapy might help correct stratification, thereby increasing therapy success by antibody panel selection and antibody dosages. In addition, the expression of certain splicing factors has been linked with the patients' outcome, thereby highlighting their putative prognostic potential. Outstanding questions are addressed to translate the findings into clinical application. This review article provides an overview of the role of AS in (tumor) diseases, its molecular mechanisms, clinical relevance, and therapy response.
Collapse
Affiliation(s)
- Marcus Bauer
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Chiara-Maria Schöbel
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Barbara Seliger
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
- Department of Good Manufacturing Practice (GMP) Development & Advanced Therapy Medicinal Products (ATMP) Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
- Institute for Medical Immunology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Simon Jasinski-Bergner
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
| |
Collapse
|
4
|
Norppa AJ, Chowdhury I, van Rooijen LE, Ravantti JJ, Snel B, Varjosalo M, Frilander MJ. Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome. Nucleic Acids Res 2024; 52:4037-4052. [PMID: 38499487 DOI: 10.1093/nar/gkae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
Here, we identify RBM41 as a novel unique protein component of the minor spliceosome. RBM41 has no previously recognized cellular function but has been identified as a paralog of U11/U12-65K, a known unique component of the U11/U12 di-snRNP. Both proteins use their highly similar C-terminal RRMs to bind to 3'-terminal stem-loops in U12 and U6atac snRNAs with comparable affinity. Our BioID data indicate that the unique N-terminal domain of RBM41 is necessary for its association with complexes containing DHX8, an RNA helicase, which in the major spliceosome drives the release of mature mRNA from the spliceosome. Consistently, we show that RBM41 associates with excised U12-type intron lariats, is present in the U12 mono-snRNP, and is enriched in Cajal bodies, together suggesting that RBM41 functions in the post-splicing steps of the minor spliceosome assembly/disassembly cycle. This contrasts with U11/U12-65K, which uses its N-terminal region to interact with U11 snRNP during intron recognition. Finally, while RBM41 knockout cells are viable, they show alterations in U12-type 3' splice site usage. Together, our results highlight the role of the 3'-terminal stem-loop of U12 snRNA as a dynamic binding platform for the U11/U12-65K and RBM41 proteins, which function at distinct stages of the assembly/disassembly cycle.
Collapse
Affiliation(s)
- Antto J Norppa
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Iftekhar Chowdhury
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura E van Rooijen
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Janne J Ravantti
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Markku Varjosalo
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| |
Collapse
|
5
|
Sparber P, Sharova M, Davydenko K, Pyankov D, Filatova A, Skoblov M. Deciphering the impact of coding and non-coding SCN1A gene variants on RNA splicing. Brain 2024; 147:1278-1293. [PMID: 37956038 DOI: 10.1093/brain/awad383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/26/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Variants that disrupt normal pre-mRNA splicing are increasingly being recognized as a major cause of monogenic disorders. The SCN1A gene, a key epilepsy gene that is linked to various epilepsy phenotypes, is no exception. Approximately 10% of all reported variants in the SCN1A gene are designated as splicing variants, with many located outside of the canonical donor and acceptor splice sites, and most have not been functionally investigated. However, given its restricted expression pattern, functional analysis of splicing variants in the SCN1A gene could not be routinely performed. In this study, we conducted a comprehensive analysis of all reported SCN1A variants and their potential to impact SCN1A splicing and conclude that splicing variants are substantially misannotated and under-represented. We created a splicing reporter system consisting of 18 splicing vectors covering all 26 protein-coding exons with different genomic contexts and several promoters of varying strengths in order to reproduce the wild-type splicing pattern of the SCN1A gene, revealing cis-regulatory elements essential for proper recognition of SCN1A exons. Functional analysis of 95 SCN1A variants was carried out, including all 68 intronic variants reported in the literature, located outside of the splice sites canonical dinucleotides; 21 exonic variants of different classes (synonymous, missense, nonsense and in-frame deletion) and six variants observed in patients with epilepsy. Interestingly, almost 20% of tested intronic variants had no influence on SCN1A splicing, despite being reported as causative in the literature. Moreover, we confirmed that the majority of predicted exonic variants affect splicing unravelling their true molecular mechanism. We used functional data to perform genotype-phenotype correlation, revealing distinct distribution patterns for missense and splice-affecting 'missense' variants and observed no difference in the phenotype severity of variants leading to in-frame and out-of-frame isoforms, indicating that the Nav1.1 protein is highly intolerant to structural variations. Our work demonstrates the importance of functional analysis in proper variant annotation and provides a tool for high-throughput delineation of splice-affecting variants in SCN1A in a whole-gene manner.
Collapse
Affiliation(s)
- Peter Sparber
- Research Centre for Medical Genetics, Laboratory of Functional Genomics, Moscow 115478, Russia
| | - Margarita Sharova
- Research Centre for Medical Genetics, Laboratory of Functional Genomics, Moscow 115478, Russia
| | - Ksenia Davydenko
- Research Centre for Medical Genetics, Laboratory of Functional Genomics, Moscow 115478, Russia
| | - Denis Pyankov
- Genomed Ltd., Research Department, Moscow 107014, Russia
| | - Alexandra Filatova
- Research Centre for Medical Genetics, Laboratory of Functional Genomics, Moscow 115478, Russia
| | - Mikhail Skoblov
- Research Centre for Medical Genetics, Laboratory of Functional Genomics, Moscow 115478, Russia
| |
Collapse
|
6
|
Nishimura K, Saika W, Inoue D. Minor introns impact on hematopoietic malignancies. Exp Hematol 2024; 132:104173. [PMID: 38309573 DOI: 10.1016/j.exphem.2024.104173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/25/2023] [Accepted: 01/03/2024] [Indexed: 02/05/2024]
Abstract
In the intricate orchestration of the central dogma, pre-mRNA splicing plays a crucial role in the post-transcriptional process that transforms DNA into mature mRNA. Widely acknowledged as a pivotal RNA processing step, it significantly influences gene expression and alters the functionality of gene product proteins. Although U2-dependent spliceosomes efficiently manage the removal of over 99% of introns, a distinct subset of essential genes undergo splicing with a different intron type, denoted as minor introns, using U12-dependent spliceosomes. Mutations in spliceosome component genes are now recognized as prevalent genetic abnormalities in cancer patients, especially those with hematologic malignancies. Despite the relative rarity of minor introns, genes containing them are evolutionarily conserved and play crucial roles in functions such as the RAS-MAPK pathway. Disruptions in U12-type minor intron splicing caused by mutations in snRNA or its regulatory components significantly contribute to cancer progression. Notably, recurrent mutations associated with myelodysplastic syndrome (MDS) in the minor spliceosome component ZRSR2 underscore its significance. Examination of ZRSR2-mutated MDS cells has revealed that only a subset of minor spliceosome-dependent genes, such as LZTR1, consistently exhibit missplicing. Recent technological advancements have uncovered insights into minor introns, raising inquiries beyond current understanding. This review comprehensively explores the importance of minor intron regulation, the molecular implications of minor (U12-type) spliceosomal mutations and cis-regulatory regions, and the evolutionary progress of studies on minor, aiming to provide a sophisticated understanding of their intricate role in cancer biology.
Collapse
Affiliation(s)
- Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan.
| | - Wataru Saika
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan; Department of Hematology, Shiga University of Medical Science, Ōtsu, Shiga, Japan
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan.
| |
Collapse
|
7
|
Perales S, Sigamani V, Rajasingh S, Gurusamy N, Bittel D, Czirok A, Radic M, Rajasingh J. scaRNA20 promotes pseudouridylatory modification of small nuclear snRNA U12 and improves cardiomyogenesis. Exp Cell Res 2024; 436:113961. [PMID: 38341080 PMCID: PMC10964393 DOI: 10.1016/j.yexcr.2024.113961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Non-coding RNAs, particularly small Cajal-body associated RNAs (scaRNAs), play a significant role in spliceosomal RNA modifications. While their involvement in ischemic myocardium regeneration is known, their role in cardiac development is unexplored. We investigated scaRNA20's role in iPSC differentiation into cardiomyocytes (iCMCs) via overexpression and knockdown assays. We measured scaRNA20-OE-iCMCs and scaRNA20-KD-iCMCs contractility using Particle Image Velocimetry (PIV), comparing them to control iCMCs. We explored scaRNA20's impact on alternative splicing via pseudouridylation (Ψ) of snRNA U12, analyzing its functional consequences in cardiac differentiation. scaRNA20-OE-iPSC differentiation increased beating colonies, upregulated cardiac-specific genes, activated TP53 and STAT3, and preserved contractility under hypoxia. Conversely, scaRNA20-KD-iCMCs exhibited poor differentiation and contractility. STAT3 inhibition in scaRNA20-OE-iPSCs hindered cardiac differentiation. RNA immunoprecipitation revealed increased Ψ at the 28th uridine of U12 RNA in scaRNA20-OE iCMCs. U12-KD iCMCs had reduced cardiac differentiation, which improved upon U12 RNA introduction. In summary, scaRNA20-OE in iPSCs enhances cardiomyogenesis, preserves iCMC function under hypoxia, and may have implications for ischemic myocardium regeneration.
Collapse
Affiliation(s)
- Selene Perales
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Vinoth Sigamani
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sheeja Rajasingh
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Narasimman Gurusamy
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Douglas Bittel
- Department of Biosciences, Kansas City University of Medicine and Biosciences, Kansas City, MO, USA
| | - Andras Czirok
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Marko Radic
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Johnson Rajasingh
- Department of Bioscience Research, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Medicine-Cardiology, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA.
| |
Collapse
|
8
|
Blázquez-Encinas R, García-Vioque V, Caro-Cuenca T, Moreno-Montilla MT, Mangili F, Alors-Pérez E, Ventura S, Herrera-Martínez AD, Moreno-Casado P, Calzado MA, Salvatierra Á, Gálvez-Moreno MA, Fernandez-Cuesta L, Foll M, Luque RM, Alcala N, Pedraza-Arevalo S, Ibáñez-Costa A, Castaño JP. Altered splicing machinery in lung carcinoids unveils NOVA1, PRPF8 and SRSF10 as novel candidates to understand tumor biology and expand biomarker discovery. J Transl Med 2023; 21:879. [PMID: 38049848 PMCID: PMC10696873 DOI: 10.1186/s12967-023-04754-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Lung neuroendocrine neoplasms (LungNENs) comprise a heterogeneous group of tumors ranging from indolent lesions with good prognosis to highly aggressive cancers. Carcinoids are the rarest LungNENs, display low to intermediate malignancy and may be surgically managed, but show resistance to radiotherapy/chemotherapy in case of metastasis. Molecular profiling is providing new information to understand lung carcinoids, but its clinical value is still limited. Altered alternative splicing is emerging as a novel cancer hallmark unveiling a highly informative layer. METHODS We primarily examined the status of the splicing machinery in lung carcinoids, by assessing the expression profile of the core spliceosome components and selected splicing factors in a cohort of 25 carcinoids using a microfluidic array. Results were validated in an external set of 51 samples. Dysregulation of splicing variants was further explored in silico in a separate set of 18 atypical carcinoids. Selected altered factors were tested by immunohistochemistry, their associations with clinical features were assessed and their putative functional roles were evaluated in vitro in two lung carcinoid-derived cell lines. RESULTS The expression profile of the splicing machinery was profoundly dysregulated. Clustering and classification analyses highlighted five splicing factors: NOVA1, SRSF1, SRSF10, SRSF9 and PRPF8. Anatomopathological analysis showed protein differences in the presence of NOVA1, PRPF8 and SRSF10 in tumor versus non-tumor tissue. Expression levels of each of these factors were differentially related to distinct number and profiles of splicing events, and were associated to both common and disparate functional pathways. Accordingly, modulating the expression of NOVA1, PRPF8 and SRSF10 in vitro predictably influenced cell proliferation and colony formation, supporting their functional relevance and potential as actionable targets. CONCLUSIONS These results provide primary evidence for dysregulation of the splicing machinery in lung carcinoids and suggest a plausible functional role and therapeutic targetability of NOVA1, PRPF8 and SRSF10.
Collapse
Affiliation(s)
- Ricardo Blázquez-Encinas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Víctor García-Vioque
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Teresa Caro-Cuenca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Pathology Service, Reina Sofía University Hospital, Córdoba, Spain
| | - María Trinidad Moreno-Montilla
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Federica Mangili
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Emilia Alors-Pérez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Sebastian Ventura
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Computer Sciences, University of Córdoba, Córdoba, Spain
| | - Aura D Herrera-Martínez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Paula Moreno-Casado
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Thoracic Surgery and Lung Transplantation Unit, Reina Sofa University Hospital, Córdoba, Spain
| | - Marco A Calzado
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Ángel Salvatierra
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Thoracic Surgery and Lung Transplantation Unit, Reina Sofa University Hospital, Córdoba, Spain
| | - María A Gálvez-Moreno
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Lynnette Fernandez-Cuesta
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Matthieu Foll
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Raúl M Luque
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Nicolas Alcala
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Sergio Pedraza-Arevalo
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
| | - Justo P Castaño
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
- CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), Córdoba, Spain.
| |
Collapse
|
9
|
Gao J, Han S, Deng B, Deng Y, Gao X. Research progress of additional pathogenic mutations in chronic neutrophilic leukemia. Ann Hematol 2023:10.1007/s00277-023-05550-6. [PMID: 37993585 DOI: 10.1007/s00277-023-05550-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023]
Abstract
Chronic neutrophilic leukemia (CNL) is a rare type of myeloproliferative neoplasm (MPN). Due to its nonspecific clinical symptoms and lack of specific molecular markers, it was previously difficult to distinguish it from other diseases with increased neutrophils. However, the discovery of the CSF3R mutation in CNL 10 years ago and the update of the diagnostic criteria by the World Health Organization (WHO) in 2016 brought CNL into a new era of molecular diagnosis. Next-generation sequencing (NGS) technology has led to the identification of numerous mutant genes in CNL. While CSF3R is commonly recognized as the driver mutation of CNL, other mutations have also been detected in CNL using NGS, including mutations in other signaling pathway genes (CBL, JAK2, NARS, PTPN11) and chromatin modification genes (ASXL1, SETBP1, EZH2), DNA methylation genes (DNMT3A, TET2), myeloid-related transcription factor genes (RUNX1, GATA2), and splicing and RNA metabolism genes (SRSF2, U2AF1). The coexistence of these mutated genes and CSF3R mutations, as well as the different evolutionary sequences of clones, deepens the complexity of CNL molecular biology. The purpose of this review is to summarize the genetic research findings of CNL in the last decade, focusing on the common mutated genes in CNL and their clinical significance, as well as the clonal evolution pattern and sequence of mutation acquisition in CNL, to provide a basis for the appropriate management of CNL patients.
Collapse
Affiliation(s)
- Jiapei Gao
- Department of Hematology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Shuai Han
- Yangzhou University Medical College, Yangzhou, Jiangsu Province, China
| | - Bin Deng
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yifan Deng
- Yangzhou University Medical College, Yangzhou, Jiangsu Province, China
| | - Xiaohui Gao
- Department of Hematology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu Province, China.
| |
Collapse
|
10
|
Larue GE, Roy SW. Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution. Nucleic Acids Res 2023; 51:10884-10908. [PMID: 37819006 PMCID: PMC10639083 DOI: 10.1093/nar/gkad797] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Spliceosomal introns are gene segments removed from RNA transcripts by ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second 'minor' spliceosome is responsible for processing a tiny minority of introns. Despite its seemingly modest role, minor splicing has persisted for roughly 1.5 billion years of eukaryotic evolution. Identifying minor introns in over 3000 eukaryotic genomes, we report diverse evolutionary histories including surprisingly high numbers in some fungi and green algae, repeated loss, as well as general biases in their positional and genic distributions. We estimate that ancestral minor intron densities were comparable to those of vertebrates, suggesting a trend of long-term stasis. Finally, three findings suggest a major role for neutral processes in minor intron evolution. First, highly similar patterns of minor and major intron evolution contrast with both functionalist and deleterious model predictions. Second, observed functional biases among minor intron-containing genes are largely explained by these genes' greater ages. Third, no association of intron splicing with cell proliferation in a minor intron-rich fungus suggests that regulatory roles are lineage-specific and thus cannot offer a general explanation for minor splicing's persistence. These data constitute the most comprehensive view of minor introns and their evolutionary history to date, and provide a foundation for future studies of these remarkable genetic elements.
Collapse
Affiliation(s)
- Graham E Larue
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA 95343, USA
| | - Scott W Roy
- Department of Molecular and Cell Biology, University of California Merced, Merced, CA 95343, USA
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| |
Collapse
|
11
|
Alors-Pérez E, Pedraza-Arevalo S, Blázquez-Encinas R, Moreno-Montilla MT, García-Vioque V, Berbel I, Luque RM, Sainz B, Ibáñez-Costa A, Castaño JP. Splicing alterations in pancreatic ductal adenocarcinoma: a new molecular landscape with translational potential. J Exp Clin Cancer Res 2023; 42:282. [PMID: 37880792 PMCID: PMC10601233 DOI: 10.1186/s13046-023-02858-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal cancers worldwide, mainly due to its late diagnosis and lack of effective therapies, translating into a low 5-year 12% survival rate, despite extensive clinical efforts to improve outcomes. International cooperative studies have provided informative multiomic landscapes of PDAC, but translation of these discoveries into clinical advances are lagging. Likewise, early diagnosis biomarkers and new therapeutic tools are sorely needed to tackle this cancer. The study of poorly explored molecular processes, such as splicing, can provide new tools in this regard. Alternative splicing of pre-RNA allows the generation of multiple RNA variants from a single gene and thereby contributes to fundamental biological processes by finely tuning gene expression. However, alterations in alternative splicing are linked to many diseases, and particularly to cancer, where it can contribute to tumor initiation, progression, metastasis and drug resistance. Splicing defects are increasingly being associated with PDAC, including both mutations or dysregulation of components of the splicing machinery and associated factors, and altered expression of specific relevant gene variants. Such disruptions can be a key element enhancing pancreatic tumor progression or metastasis, while they can also provide suitable tools to identify potential candidate biomarkers and discover new actionable targets. In this review, we aimed to summarize the current information about dysregulation of splicing-related elements and aberrant splicing isoforms in PDAC, and to describe their relationship with the development, progression and/or aggressiveness of this dismal cancer, as well as their potential as therapeutic tools and targets.
Collapse
Affiliation(s)
- Emilia Alors-Pérez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Sergio Pedraza-Arevalo
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Ricardo Blázquez-Encinas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - María Trinidad Moreno-Montilla
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Víctor García-Vioque
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Inmaculada Berbel
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain
- Reina Sofía University Hospital (HURS), Cordoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERObn), Córdoba, Spain
| | - Bruno Sainz
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas Alberto Sols CSIC-UAM, Madrid, Spain
- Cancer Stem Cells and Fibroinflammatory Microenvironment Group, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Area 3, Cancer, Madrid, Spain
- Gastrointestinal Tumours Research Programme, Biomedical Research Network in Cancer (CIBERONC), Madrid, Spain
| | - Alejandro Ibáñez-Costa
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.
- Reina Sofía University Hospital (HURS), Cordoba, Spain.
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Cordoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Cordoba, Spain.
- Reina Sofía University Hospital (HURS), Cordoba, Spain.
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERObn), Córdoba, Spain.
| |
Collapse
|
12
|
Alharazy S, Naseer MI. Use of whole exome sequencing for identification of genetic variants related to Growth Hormone Deficiency and Short Stature: A Family-Based Study. Pak J Med Sci 2023; 39:1337-1344. [PMID: 37680843 PMCID: PMC10480707 DOI: 10.12669/pjms.39.5.7601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/18/2023] [Accepted: 05/15/2023] [Indexed: 09/09/2023] Open
Abstract
Objective Genetic polymorphisms in genes involved in growth process and Vitamin-D metabolism form a significant etiology behind growth hormone deficiency and short stature. The aim of this study was to explore for known and unknown genes and variants related to growth hormone and short stature in a family based study using whole exome sequencing (WES). Method This family-based study included a family with members diagnosed with growth hormone deficiency, short stature and Vitamin-D deficiency (four boys affected and four boys non-affected). The participants were recruited from King Abdulaziz University Hospital (Jeddah, Saudi Arabia) and referred to King Fahad Centre for Medical Research (Jeddah, Saudi Arabia from April 2022 to June 2022. The consanguineous parents and one of the affected boys (aged 16 years old) underwent WES. Results Several variants in RNPC3, ACAN, GC, VDR and LRP2 were identified in index cases but not in controls. Novel frameshift and splice region variants in RNPC3 (c.358dupA, p.Arg120fs) were detected. Other missense variants were also observed including variants in ACAN (c.2591C>T, c.2789G>T, c.2815T>A, c.4207A>G, c.4523A>C and c.7119C>G), GC (rs4588 and rs7041) and LRP2 (rs2075252 and rs1991517). A start loss variant in VDR (rs2228570) with high impact was also observed. Conclusions Our findings suggest a potential association of these variants with growth hormone deficiency and short stature. In this study, novel pathogenic variants in RNPC3 were revealed as well as other variants in ACAN and in genes related to Vitamin-D metabolism (GC, VDR and LRP2) that some or all might be associated with growth hormone deficiency. Further large-scale studies are required to address the association of these variants with growth hormone deficiency and its subsequent short stature.
Collapse
Affiliation(s)
- Shatha Alharazy
- Shatha Alharazy Department of Physiology, Faculty of Medicine, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Muhammad Imran Naseer
- Muhammad Imran Naseer Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| |
Collapse
|
13
|
Zhou S, Van Bortle K. The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer. Wiley Interdiscip Rev RNA 2023; 14:e1782. [PMID: 36754845 PMCID: PMC10498592 DOI: 10.1002/wrna.1782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
14
|
Sullivan PJ, Gayevskiy V, Davis RL, Wong M, Mayoh C, Mallawaarachchi A, Hort Y, McCabe MJ, Beecroft S, Jackson MR, Arts P, Dubowsky A, Laing N, Dinger ME, Scott HS, Oates E, Pinese M, Cowley MJ. Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications. Genome Biol 2023; 24:118. [PMID: 37198692 PMCID: PMC10190034 DOI: 10.1186/s13059-023-02936-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are complementary but knowing which to use for each splicing context remains difficult. Here, we describe Introme, which uses machine learning to integrate predictions from several splice detection tools, additional splicing rules, and gene architecture features to comprehensively evaluate the likelihood of a variant impacting splicing. Through extensive benchmarking across 21,000 splice-altering variants, Introme outperformed all tools (auPRC: 0.98) for the detection of clinically significant splice variants. Introme is available at https://github.com/CCICB/introme .
Collapse
Affiliation(s)
- Patricia J Sullivan
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Ryan L Davis
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- Department of Neurogenetics, Kolling Institute, St. Leonards, NSW, Australia
- Sydney Medical School-Northern, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marie Wong
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Amali Mallawaarachchi
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia
- Clinical Genetics Unit, Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Sydney, Australia
| | - Yvonne Hort
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia
| | - Mark J McCabe
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Sarah Beecroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Matilda R Jackson
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- Australian Genomics, Parkville, VIC, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Andrew Dubowsky
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Nigel Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- Australian Genomics, Parkville, VIC, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Emily Oates
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Mark Pinese
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia.
| |
Collapse
|
15
|
Singh A, Pandey KK, Agrawal SK, Srivastava RK, Bhattacharyya S, Verma B. The SARS-CoV-2 UTR’s Intrudes Host RBP’s and Modulates Cellular Splicing. Adv Virol 2023; 2023:2995443. [PMID: 37065904 PMCID: PMC10098413 DOI: 10.1155/2023/2995443] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus that causes a potentially fatal respiratory disease known as coronavirus disease (COVID-19) and is responsible for the ongoing pandemic with increasing mortality. Understanding the host-virus interaction involved in SARS-CoV-2 pathophysiology will enhance our understanding of the mechanistic basis of COVID-19 infection. The characterization of post-transcriptional gene regulatory networks, particularly pre-mRNA splicing, and the identification and characterization of host proteins interacting with the 5′ and 3′UTRs of SARS-CoV-2 will improve our understanding of post-transcriptional gene regulation during SARS-CoV-2 pathogenesis. Here, we demonstrate that either SARS-CoV-2 infection or exogenous overexpression of the 5′ and 3’UTRs of the viral genomic RNAs, results in reduced mRNA levels possibly due to modulation of host cell pre-mRNA splicing. Further, we have investigated the potential RNA-binding proteins interacting with the 5′ and 3′UTRs, using in-silico approaches. Our results suggest that 5′ and 3′UTRs indeed interact with many RNA-binding proteins. Our results provide a primer for further investigations into the UTR-mediated regulation of splicing and related molecular mechanisms in host cells.
Collapse
Affiliation(s)
- Anjali Singh
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Kush Kumar Pandey
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
- Nebraska Center for Virology and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln 68583, NE, USA
| | - Shubham Kumar Agrawal
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Rupesh K. Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| |
Collapse
|
16
|
Lyu M, Lai H, Wang Y, Zhou Y, Chen Y, Wu D, Chen J, Ying B. Roles of alternative splicing in infectious diseases: from hosts, pathogens to their interactions. Chin Med J (Engl) 2023; 136:767-779. [PMID: 36893312 PMCID: PMC10150853 DOI: 10.1097/cm9.0000000000002621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT Alternative splicing (AS) is an evolutionarily conserved mechanism that removes introns and ligates exons to generate mature messenger RNAs (mRNAs), extremely improving the richness of transcriptome and proteome. Both mammal hosts and pathogens require AS to maintain their life activities, and inherent physiological heterogeneity between mammals and pathogens makes them adopt different ways to perform AS. Mammals and fungi conduct a two-step transesterification reaction by spliceosomes to splice each individual mRNA (named cis -splicing). Parasites also use spliceosomes to splice, but this splicing can occur among different mRNAs (named trans -splicing). Bacteria and viruses directly hijack the host's splicing machinery to accomplish this process. Infection-related changes are reflected in the spliceosome behaviors and the characteristics of various splicing regulators (abundance, modification, distribution, movement speed, and conformation), which further radiate to alterations in the global splicing profiles. Genes with splicing changes are enriched in immune-, growth-, or metabolism-related pathways, highlighting approaches through which hosts crosstalk with pathogens. Based on these infection-specific regulators or AS events, several targeted agents have been developed to fight against pathogens. Here, we summarized recent findings in the field of infection-related splicing, including splicing mechanisms of pathogens and hosts, splicing regulation and aberrant AS events, as well as emerging targeted drugs. We aimed to systemically decode host-pathogen interactions from a perspective of splicing. We further discussed the current strategies of drug development, detection methods, analysis algorithms, and database construction, facilitating the annotation of infection-related splicing and the integration of AS with disease phenotype.
Collapse
Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongli Lai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yili Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yi Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dongsheng Wu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jie Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| |
Collapse
|
17
|
Rogalska ME, Vivori C, Valcárcel J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 2023; 24:251-269. [PMID: 36526860 DOI: 10.1038/s41576-022-00556-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
Abstract
The removal of introns from mRNA precursors and its regulation by alternative splicing are key for eukaryotic gene expression and cellular function, as evidenced by the numerous pathologies induced or modified by splicing alterations. Major recent advances have been made in understanding the structures and functions of the splicing machinery, in the description and classification of physiological and pathological isoforms and in the development of the first therapies for genetic diseases based on modulation of splicing. Here, we review this progress and discuss important remaining challenges, including predicting splice sites from genomic sequences, understanding the variety of molecular mechanisms and logic of splicing regulation, and harnessing this knowledge for probing gene function and disease aetiology and for the design of novel therapeutic approaches.
Collapse
Affiliation(s)
- Malgorzata Ewa Rogalska
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Vivori
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- The Francis Crick Institute, London, UK
| | - Juan Valcárcel
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| |
Collapse
|
18
|
Tabib A, Richmond CM, McGaughran J. Delineating the phenotype of RNU4ATAC-related spliceosomopathy. Am J Med Genet A 2023; 191:1094-1100. [PMID: 36622817 DOI: 10.1002/ajmg.a.63110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 01/10/2023]
Abstract
Biallelic pathogenic variants in RNU4ATAC cause microcephalic osteodysplastic primordial dwarfism type I (MOPD1), Roifman syndrome (RS) and Lowry-Wood syndrome (LWS). These conditions demonstrate significant phenotypic heterogeneity yet have overlapping features. Although historically described as discrete conditions they appear to represent a phenotypic spectrum with clinical features not always aligning with diagnostic categories. Clinical variability and ambiguity in diagnostic criteria exist among each disorder. Here we report an individual with a novel genotype and phenotype spanning all three disorders, expanding the phenotypic spectrum of RNU4ATAC-related spliceosomeopathies.
Collapse
Affiliation(s)
- Amanda Tabib
- Paediatrics, John Hunter Children's Hospital, Newcastle, New South Wales, Australia
| | - Christopher M Richmond
- Genetic Health QLD, Royal Brisbane & Women's Hospital, Herston, Queensland, Australia.,School of Medicine, Griffith University, Southport, Queensland, Australia
| | - Julie McGaughran
- Genetic Health QLD, Royal Brisbane & Women's Hospital, Herston, Queensland, Australia.,Faculty of Medicine, University of Queensland, St. Lucia, Queensland, Australia
| |
Collapse
|
19
|
García-Ruiz S, Zhang D, Gustavsson EK, Rocamora-Perez G, Grant-Peters M, Fairbrother-Browne A, Reynolds RH, Brenton JW, Gil-Martínez AL, Chen Z, Rio DC, Botia JA, Guelfi S, Collado-Torres L, Ryten M. Splicing accuracy varies across human introns, tissues and age. bioRxiv 2023:2023.03.29.534370. [PMID: 37034741 PMCID: PMC10081249 DOI: 10.1101/2023.03.29.534370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigated mis-splicing using RNA-sequencing data from ~14K control samples and 42 human body sites, focusing on split reads partially mapping to known transcripts in annotation. We show that mis-splicing occurs at different rates across introns and tissues and that these splicing inaccuracies are primarily affected by the abundance of core components of the spliceosome assembly and its regulators. Using publicly available data on short-hairpin RNA-knockdowns of numerous spliceosomal components and related regulators, we found support for the importance of RNA-binding proteins in mis-splicing. We also demonstrated that age is positively correlated with mis-splicing, and it affects genes implicated in neurodegenerative diseases. This in-depth characterisation of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
Collapse
Affiliation(s)
- S García-Ruiz
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - D Zhang
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - E K Gustavsson
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - G Rocamora-Perez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - M Grant-Peters
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A Fairbrother-Browne
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - R H Reynolds
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - J W Brenton
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A L Gil-Martínez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - Z Chen
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - D C Rio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - J A Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - S Guelfi
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Verge Genomics, South San Francisco, CA, 94080, USA
| | - L Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA , 21205
| | - M Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| |
Collapse
|
20
|
Fritzler MJ, Bentow C, Beretta L, Palterer B, Perurena-Prieto J, Sanz-Martínez MT, Guillen-Del-Castillo A, Marín A, Fonollosa-Pla V, Callejas-Moraga E, Simeón-Aznar CP, Mahler M. Anti-U11/U12 Antibodies as a Rare but Important Biomarker in Patients with Systemic Sclerosis: A Narrative Review. Diagnostics (Basel) 2023; 13:diagnostics13071257. [PMID: 37046475 PMCID: PMC10093660 DOI: 10.3390/diagnostics13071257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Anti-nuclear (ANA) are present in approximately 90% of systemic sclerosis (SSc) patients and are key biomarkers in supporting the diagnosis and determining the prognosis of this disease. In addition to the classification criteria autoantibodies for SSc [i.e., anti-centromere, anti-topoisomerase I (Scl-70), anti-RNA polymerase III], other autoantibodies have been associated with important SSc phenotypes. Among them, anti-U11/U12 ribonucleoprotein (RNP) antibodies, also known as anti-RNPC-3, were first reported in a patient with SSc, but very little is known about their association and clinical utility. The U11/U12 RNP macromolecular complex consists of several proteins involved in alternative mRNA splicing. More recent studies demonstrated associations of anti-anti-U11/U12 antibodies with SSc and severe pulmonary fibrosis as well as with moderate to severe gastrointestinal dysmotility. Lastly, anti-U11/U12 autoantibodies have been strongly associated with malignancy in SSc patients. Here, we aimed to summarize the knowledge of anti-U11/U12/RNPC-3 antibodies in SSc, including their seroclinical associations in a narrative literature review.
Collapse
Affiliation(s)
- Marvin J. Fritzler
- Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Chelsea Bentow
- Research and Development, Werfen, Autoimmunity Headquarters and Technology Center, San Diego, CA 92131-1638, USA
| | - Lorenzo Beretta
- Scleroderma Unit and (Referral) Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milan, 20122 Milano, Italy
| | - Boaz Palterer
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Firenze, Italy
| | - Janire Perurena-Prieto
- Department of Immunology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Maria Teresa Sanz-Martínez
- Department of Immunology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Alfredo Guillen-Del-Castillo
- Unit of Systemic Autoimmune Diseases, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Ana Marín
- Department of Immunology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Vicent Fonollosa-Pla
- Unit of Systemic Autoimmune Diseases, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | | | - Carmen Pilar Simeón-Aznar
- Unit of Systemic Autoimmune Diseases, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Michael Mahler
- Research and Development, Werfen, Autoimmunity Headquarters and Technology Center, San Diego, CA 92131-1638, USA
- Correspondence: or
| |
Collapse
|
21
|
Khatri D, Putoux A, Cologne A, Kaltenbach S, Besson A, Bertiaux E, Guguin J, Fendler A, Dupont MA, Benoit-Pilven C, Qebibo L, Ahmed-Elie S, Audebert-Bellanger S, Blanc P, Rambaud T, Castelle M, Cornen G, Grotto S, Guët A, Guibaud L, Michot C, Odent S, Ruaud L, Sacaze E, Hamel V, Bordonné R, Leutenegger AL, Edery P, Burglen L, Attié-Bitach T, Mazoyer S, Delous M. Deficiency of the minor spliceosome component U4atac snRNA secondarily results in ciliary defects in human and zebrafish. Proc Natl Acad Sci U S A 2023; 120:e2102569120. [PMID: 36802443 PMCID: PMC9992838 DOI: 10.1073/pnas.2102569120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 12/12/2022] [Indexed: 02/23/2023] Open
Abstract
In the human genome, about 750 genes contain one intron excised by the minor spliceosome. This spliceosome comprises its own set of snRNAs, among which U4atac. Its noncoding gene, RNU4ATAC, has been found mutated in Taybi-Linder (TALS/microcephalic osteodysplastic primordial dwarfism type 1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes. These rare developmental disorders, whose physiopathological mechanisms remain unsolved, associate ante- and post-natal growth retardation, microcephaly, skeletal dysplasia, intellectual disability, retinal dystrophy, and immunodeficiency. Here, we report bi-allelic RNU4ATAC mutations in five patients presenting with traits suggestive of the Joubert syndrome (JBTS), a well-characterized ciliopathy. These patients also present with traits typical of TALS/RFMN/LWS, thus widening the clinical spectrum of RNU4ATAC-associated disorders and indicating ciliary dysfunction as a mechanism downstream of minor splicing defects. Intriguingly, all five patients carry the n.16G>A mutation, in the Stem II domain, either at the homozygous or compound heterozygous state. A gene ontology term enrichment analysis on minor intron-containing genes reveals that the cilium assembly process is over-represented, with no less than 86 cilium-related genes containing at least one minor intron, among which there are 23 ciliopathy-related genes. The link between RNU4ATAC mutations and ciliopathy traits is supported by alterations of primary cilium function in TALS and JBTS-like patient fibroblasts, as well as by u4atac zebrafish model, which exhibits ciliopathy-related phenotypes and ciliary defects. These phenotypes could be rescued by WT but not by pathogenic variants-carrying human U4atac. Altogether, our data indicate that alteration of cilium biogenesis is part of the physiopathological mechanisms of TALS/RFMN/LWS, secondarily to defects of minor intron splicing.
Collapse
Affiliation(s)
- Deepak Khatri
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Audrey Putoux
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Department of Genetics, Clinical Genetics Unit, Centre de Référence Maladies Rares des Anomalies du Développement, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Audric Cologne
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Institut national de recherche en sciences et technologies du numérique Erable, Laboratoire de Biométrie et Biologie Evolutive, UMR5558 CNRS, Université Claude Bernard Lyon 1, 69622Villeurbanne, France
| | - Sophie Kaltenbach
- Department of Histology Embryology and Cytogenetics, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, University of Paris, 75015Paris, France
| | - Alicia Besson
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Eloïse Bertiaux
- Department of Cell Biology, Sciences III, University of Geneva, 1211-Geneva, Switzerland
| | - Justine Guguin
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Adèle Fendler
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Marie A. Dupont
- Laboratory of hereditary kidney diseases, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Clara Benoit-Pilven
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Institut national de recherche en sciences et technologies du numérique Erable, Laboratoire de Biométrie et Biologie Evolutive, UMR5558 CNRS, Université Claude Bernard Lyon 1, 69622Villeurbanne, France
| | - Leila Qebibo
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
| | - Samira Ahmed-Elie
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
| | - Séverine Audebert-Bellanger
- Department of Genetics, Clinical Genetics Unit, Centre de Compétence Anomalies du Développement et Syndromes Polymalformatifs, Centre Hospitalier Universitaire Morvan, 29200Brest, France
| | | | | | - Martin Castelle
- Hematology-Immunology Unit, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, 75015Paris, France
| | - Gaëlle Cornen
- Pediatric service, Centre Hospitalier Morlaix, 29600Morlaix, France
| | - Sarah Grotto
- Clinical Genetics Unit, Maternité Port-Royal, Assistance Publique - Hôpitaux de Paris, Cochin Broca Hôtel-Dieu Hospitals75014Paris, France
| | - Agnès Guët
- Neonatal and Pediatric Units, Louis-Mourier Hospital, 92700Colombes, France
| | - Laurent Guibaud
- Pediatric and Fetal Imaging, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Caroline Michot
- Clinical Genetics Department, Centre de Référence Maladies Rares–Maladies Osseuses Constitutionnelles, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, 75015Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Hospitalier Universitaire Rennes, Centre de référence Anomalies du développement et syndromes malformatifs, Univ Rennes, CNRS, INSERM, Institut de Génétique et Développement de Rennes UMR 6290/ Equipe de Recherche Labellisée 1305, 35000Rennes, France
| | - Lyse Ruaud
- NeuroDiderot, UMR1141, University of Paris, 75019Paris, France
- Departement of Genetics, Assistance Publique - Hôpitaux de Paris, Robert Debré Hospital, 75019Paris, France
| | - Elise Sacaze
- Pediatric Service, Centre Hospitalier Régional Universitaire Brest, 29200Brest, France
| | - Virginie Hamel
- Department of Cell Biology, Sciences III, University of Geneva, 1211-Geneva, Switzerland
| | - Rémy Bordonné
- Institute of Molecular Genetics of Montpellier, UMR5535 CNRS, University of Montpellier, 34000Montpellier, France
| | | | - Patrick Edery
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Department of Genetics, Clinical Genetics Unit, Centre de Référence Maladies Rares des Anomalies du Développement, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Lydie Burglen
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Tania Attié-Bitach
- Department of Histology Embryology and Cytogenetics, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, University of Paris, 75015Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Sylvie Mazoyer
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Marion Delous
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| |
Collapse
|
22
|
Mann JT, Riley BA, Baker SF. All differential on the splicing front: Host alternative splicing alters the landscape of virus-host conflict. Semin Cell Dev Biol 2023; 146:40-56. [PMID: 36737258 DOI: 10.1016/j.semcdb.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
Alternative RNA splicing is a co-transcriptional process that richly increases proteome diversity, and is dynamically regulated based on cell species, lineage, and activation state. Virus infection in vertebrate hosts results in rapid host transcriptome-wide changes, and regulation of alternative splicing can direct a combinatorial effect on the host transcriptome. There has been a recent increase in genome-wide studies evaluating host alternative splicing during viral infection, which integrates well with prior knowledge on viral interactions with host splicing proteins. A critical challenge remains in linking how these individual events direct global changes, and whether alternative splicing is an overall favorable pathway for fending off or supporting viral infection. Here, we introduce the process of alternative splicing, discuss how to analyze splice regulation, and detail studies on genome-wide and splice factor changes during viral infection. We seek to highlight where the field can focus on moving forward, and how incorporation of a virus-host co-evolutionary perspective can benefit this burgeoning subject.
Collapse
Affiliation(s)
- Joshua T Mann
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Brent A Riley
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Steven F Baker
- Infectious Disease Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA.
| |
Collapse
|
23
|
Turner BRH, Mellor C, McElroy C, Bowen N, Gu W, Knill C, Itasaki N. Non-ubiquitous expression of core spliceosomal protein SmB/B' in chick and mouse embryos. Dev Dyn 2023; 252:276-293. [PMID: 36058892 PMCID: PMC10087933 DOI: 10.1002/dvdy.537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Although splicing is an integral part of the expression of many genes in our body, genetic syndromes with spliceosomal defects affect only specific tissues. To help understand the mechanism, we investigated the expression pattern of a core protein of the major spliceosome, SmB/B' (Small Nuclear Ribonucleoprotein Polypeptides B/B'), which is encoded by SNRPB. Loss-of-function mutations of SNRPB in humans cause cerebro-costo-mandibular syndrome (CCMS) characterized by rib gaps, micrognathia, cleft palate, and scoliosis. Our expression analysis focused on the affected structures as well as non-affected tissues, using chick and mouse embryos as model animals. RESULTS Embryos at young stages (gastrula) showed ubiquitous expression of SmB/B'. However, the level and pattern of expression became tissue-specific as differentiation proceeded. The regions relating to CCMS phenotypes such as cartilages of ribs and vertebrae and palatal mesenchyme express SmB/B' in the nucleus sporadically. However, cartilages that are not affected in CCMS also showed similar expressions. Another spliceosomal gene, SNRNP200, which mutations cause retinitis pigmentosa, was also prominently expressed in cartilages in addition to the retina. CONCLUSION The expression of SmB/B' is spatiotemporally regulated during embryogenesis despite the ubiquitous requirement of the spliceosome, however, the expression pattern is not strictly correlated with the phenotype presentation.
Collapse
Affiliation(s)
| | | | - Clara McElroy
- Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Natalie Bowen
- Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Wenjia Gu
- Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Chris Knill
- Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Nobue Itasaki
- Faculty of Health Sciences, University of Bristol, Bristol, UK
| |
Collapse
|
24
|
Li Z, He Z, Wang J, Kong G. RNA splicing factors in normal hematopoiesis and hematologic malignancies: novel therapeutic targets and strategies. J Leukoc Biol 2023; 113:149-163. [PMID: 36822179 DOI: 10.1093/jleuko/qiac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Indexed: 01/18/2023] Open
Abstract
RNA splicing, a crucial transesterification-based process by which noncoding regions are removed from premature RNA to create mature mRNA, regulates various cellular functions, such as proliferation, survival, and differentiation. Clinical and functional studies over the past 10 y have confirmed that mutations in RNA splicing factors are among the most recurrent genetic abnormalities in hematologic neoplasms, including myeloid malignancies, chronic lymphocytic leukemia, mantle cell lymphoma, and clonal hematopoiesis. These findings indicate an important role for splicing factor mutations in the development of clonal hematopoietic disorders. Mutations in core or accessory components of the RNA spliceosome complex alter splicing sites in a manner of change of function. These changes can result in the dysregulation of cancer-associated gene expression and the generation of novel mRNA transcripts, some of which are not only critical to disease development but may be also serving as potential therapeutic targets. Furthermore, multiple studies have revealed that hematopoietic cells bearing mutations in splicing factors depend on the expression of the residual wild-type allele for survival, and these cells are more sensitive to reduced expression of wild-type splicing factors or chemical perturbations of the splicing machinery. These findings suggest a promising possibility for developing novel therapeutic opportunities in tumor cells based on mutations in splicing factors. Here, we combine current knowledge of the mechanistic and functional effects of frequently mutated splicing factors in normal hematopoiesis and the effects of their mutations in hematologic malignancies. Moreover, we discuss the development of potential therapeutic opportunities based on these mutations.
Collapse
Affiliation(s)
- Zhenzhen Li
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, No. 127 Youyi West Road, Beilin District, Xi'an, Shaanxi 710072, China
| | - Zhongzheng He
- Department of Neurosurgery, Mini-invasive Neurosurgery and Translational Medical Center, Xi'an Central Hospital, Xi'an Jiaotong University, No. 161 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710003, China
| | - Jihan Wang
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, No. 127 Youyi West Road, Beilin District, Xi'an, Shaanxi 710072, China
| | - Guangyao Kong
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 Xiwu Road, Xincheng District, Xi'an, Shaanxi 710004, China
| |
Collapse
|
25
|
Vosseberg J, Stolker D, von der Dunk SHA, Snel B. Integrating Phylogenetics With Intron Positions Illuminates the Origin of the Complex Spliceosome. Mol Biol Evol 2023; 40:6985000. [PMID: 36631250 PMCID: PMC9887622 DOI: 10.1093/molbev/msad011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/09/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Eukaryotic genes are characterized by the presence of introns that are removed from pre-mRNA by a spliceosome. This ribonucleoprotein complex is comprised of multiple RNA molecules and over a hundred proteins, which makes it one of the most complex molecular machines that originated during the prokaryote-to-eukaryote transition. Previous works have established that these introns and the spliceosomal core originated from self-splicing introns in prokaryotes. Yet, how the spliceosomal core expanded by recruiting many additional proteins remains largely elusive. In this study, we use phylogenetic analyses to infer the evolutionary history of 145 proteins that we could trace back to the spliceosome in the last eukaryotic common ancestor. We found that an overabundance of proteins derived from ribosome-related processes was added to the prokaryote-derived core. Extensive duplications of these proteins substantially increased the complexity of the emerging spliceosome. By comparing the intron positions between spliceosomal paralogs, we infer that most spliceosomal complexity postdates the spread of introns through the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insight into the driving forces behind the emergence of complexes with many proteins during eukaryogenesis.
Collapse
Affiliation(s)
- Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands,Laboratory of Microbiology, Wageningen University & Research, 6700 EH Wageningen, the Netherlands
| | - Daan Stolker
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Samuel H A von der Dunk
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | | |
Collapse
|
26
|
Ding Z, Meng YR, Fan YJ, Xu YZ. Roles of minor spliceosome in intron recognition and the convergence with the better understood major spliceosome. Wiley Interdiscip Rev RNA 2023; 14:e1761. [PMID: 36056453 DOI: 10.1002/wrna.1761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/06/2022] [Accepted: 08/06/2022] [Indexed: 01/31/2023]
Abstract
Catalyzed by spliceosomes in the nucleus, RNA splicing removes intronic sequences from precursor RNAs in eukaryotes to generate mature RNA, which also significantly increases proteome complexity and fine-tunes gene expression. Most metazoans have two coexisting spliceosomes; the major spliceosome, which removes >99.5% of introns, and the minor spliceosome, which removes far fewer introns (only 770 at present have been predicted in the human genome). Both spliceosomes are large and dynamic machineries, each consisting of five small nuclear RNAs (snRNAs) and more than 100 proteins. However, the dynamic assembly, catalysis, and protein composition of the minor spliceosome are still poorly understood. With different splicing signals, minor introns are rare and usually distributed alone and flanked by major introns in genes, raising questions of how they are recognized by the minor spliceosome and how their processing deals with the splicing of neighboring major introns. Due to large numbers of introns and close similarities between the two machinery, cooperative, and competitive recognition by the two spliceosomes has been investigated. Functionally, many minor-intron-containing genes are evolutionarily conserved and essential. Mutations in the minor spliceosome exhibit a variety of developmental defects in plants and animals and are linked to numerous human diseases. Here, we review recent progress in the understanding of minor splicing, compare currently known components of the two spliceosomes, survey minor introns in a wide range of organisms, discuss cooperation and competition of the two spliceosomes in splicing of minor-intron-containing genes, and contributions of minor splicing mutations in development and diseases. This article is categorized under: RNA Processing > Processing of Small RNAs RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
Collapse
Affiliation(s)
- Zhan Ding
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan-Ran Meng
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| |
Collapse
|
27
|
Almentina Ramos Shidi F, Cologne A, Delous M, Besson A, Putoux A, Leutenegger AL, Lacroix V, Edery P, Mazoyer S, Bordonné R. Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex. Nucleic Acids Res 2022; 51:712-727. [PMID: 36537210 PMCID: PMC9881141 DOI: 10.1093/nar/gkac1182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Various genetic diseases associated with microcephaly and developmental defects are due to pathogenic variants in the U4atac small nuclear RNA (snRNA), a component of the minor spliceosome essential for the removal of U12-type introns from eukaryotic mRNAs. While it has been shown that a few RNU4ATAC mutations result in impaired binding of essential protein components, the molecular defects of the vast majority of variants are still unknown. Here, we used lymphoblastoid cells derived from RNU4ATAC compound heterozygous (g.108_126del;g.111G>A) twin patients with MOPD1 phenotypes to analyze the molecular consequences of the mutations on small nuclear ribonucleoproteins (snRNPs) formation and on splicing. We found that the U4atac108_126del mutant is unstable and that the U4atac111G>A mutant as well as the minor di- and tri-snRNPs are present at reduced levels. Our results also reveal the existence of 3'-extended snRNA transcripts in patients' cells. Moreover, we show that the mutant cells have alterations in splicing of INTS7 and INTS10 minor introns, contain lower levels of the INTS7 and INTS10 proteins and display changes in the assembly of Integrator subunits. Altogether, our results show that compound heterozygous g.108_126del;g.111G>A mutations induce splicing defects and affect the homeostasis and function of the Integrator complex.
Collapse
Affiliation(s)
- Fatimat Almentina Ramos Shidi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR5535, 34293 Montpellier, France
| | - Audric Cologne
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, 69622 Villeurbanne, France
| | - Marion Delous
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | - Alicia Besson
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | - Audrey Putoux
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France,Clinical Genetics Unit, Department of Genetics, Centre de Référence Anomalies du Développement et Syndromes Polymalformatifs, Hospices Civils de Lyon, University Lyon 1, Bron, France
| | | | - Vincent Lacroix
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, 69622 Villeurbanne, France
| | - Patrick Edery
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France,Clinical Genetics Unit, Department of Genetics, Centre de Référence Anomalies du Développement et Syndromes Polymalformatifs, Hospices Civils de Lyon, University Lyon 1, Bron, France
| | - Sylvie Mazoyer
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | | |
Collapse
|
28
|
Zhang P, Philippot Q, Ren W, Lei W, Li J, Stenson PD, Palacín PS, Colobran R, Boisson B, Zhang S, Puel A, Pan-hammarström Q, Zhang Q, Cooper DN, Abel L, Casanova J. Genome-wide detection of human variants that disrupt intronic branchpoints. Proc Natl Acad Sci U S A 2022; 119. [PMID: 36306325 PMCID: PMC9636908 DOI: 10.1073/pnas.2211194119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pre-messenger RNA splicing is initiated with the recognition of a single-nucleotide intronic branchpoint (BP) within a BP motif by spliceosome elements. Forty-eight rare variants in 43 human genes have been reported to alter splicing and cause disease by disrupting BP. However, until now, no computational approach was available to efficiently detect such variants in massively parallel sequencing data. We established a comprehensive human genome-wide BP database by integrating existing BP data and generating new BP data from RNA sequencing of lariat debranching enzyme DBR1-mutated patients and from machine-learning predictions. We characterized multiple features of BP in major and minor introns and found that BP and BP-2 (two nucleotides upstream of BP) positions exhibit a lower rate of variation in human populations and higher evolutionary conservation than the intronic background, while being comparable to the exonic background. We developed BPHunter as a genome-wide computational approach to systematically and efficiently detect intronic variants that may disrupt BP recognition. BPHunter retrospectively identified 40 of the 48 known pathogenic BP variants, in which we summarized a strategy for prioritizing BP variant candidates. The remaining eight variants all create AG-dinucleotides between the BP and acceptor site, which is the likely reason for missplicing. We demonstrated the practical utility of BPHunter prospectively by using it to identify a novel germline heterozygous BP variant of
STAT2
in a patient with critical COVID-19 pneumonia and a novel somatic intronic 59-nucleotide deletion of
ITPKB
in a lymphoma patient, both of which were validated experimentally. BPHunter is publicly available from
https://hgidsoft.rockefeller.edu/BPHunter
and
https://github.com/casanova-lab/BPHunter
.
Collapse
|
29
|
Cheng X, Zhao C, Gao L, Zeng L, Xu Y, Liu F, Huang J, Liu L, Liu S, Zhang X. Alternative splicing reprogramming in fungal pathogen Sclerotinia sclerotiorum at different infection stages on Brassica napus. Front Plant Sci 2022; 13:1008665. [PMID: 36311105 PMCID: PMC9597501 DOI: 10.3389/fpls.2022.1008665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Alternative splicing (AS) is an important post-transcriptional mechanism promoting the diversity of transcripts and proteins to regulate various life processes in eukaryotes. Sclerotinia stem rot is a major disease of Brassica napus caused by Sclerotinia sclerotiorum, which causes severe yield loss in B. napus production worldwide. Although many transcriptome studies have been carried out on the growth, development, and infection of S. sclerotiorum, the genome-wide AS events of S. sclerotiorum remain poorly understood, particularly at the infection stage. In this study, transcriptome sequencing was performed to systematically explore the genome-scale AS events of S. sclerotiorum at five important infection stages on a susceptible oilseed rape cultivar. A total of 130 genes were predicted to be involved in AS from the S. sclerotiorum genome, among which 98 genes were differentially expressed and may be responsible for AS reprogramming for its successful infection. In addition, 641 differential alternative splicing genes (DASGs) were identified during S. sclerotiorum infection, accounting for 5.76% of all annotated S. sclerotiorum genes, and 71 DASGs were commonly found at all the five infection stages. The most dominant AS type of S. sclerotiorum was found to be retained introns or alternative 3' splice sites. Furthermore, the resultant AS isoforms of 21 DASGs became pseudogenes, and 60 DASGs encoded different putative proteins with different domains. More importantly, 16 DASGs of S. sclerotiorum were found to have signal peptides and possibly encode putative effectors to facilitate the infection of S. sclerotiorum. Finally, about 69.27% of DASGs were found to be non-differentially expressed genes, indicating that AS serves as another important way to regulate the infection of S. sclerotiorum on plants besides the gene expression level. Taken together, this study provides a genome-wide landscape for the AS of S. sclerotiorum during infection as well as an important resource for further elucidating the pathogenic mechanisms of S. sclerotiorum.
Collapse
Affiliation(s)
- Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lixia Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Lingyi Zeng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yu Xu
- Hebei Provincial Academy of Ecological and Environmental Sciences, Shijiazhuang, China
| | - Fan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lijiang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the People’s Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
30
|
Rozza R, Janoš P, Spinello A, Magistrato A. Role of computational and structural biology in the development of small-molecule modulators of the spliceosome. Expert Opin Drug Discov 2022; 17:1095-1109. [PMID: 35983696 DOI: 10.1080/17460441.2022.2114452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION RNA splicing is a pivotal step of eukaryotic gene expression during which the introns are excised from the precursor (pre-)RNA and the exons are joined together to form mature RNA products (i.e a protein-coding mRNA or long non-coding (lnc)RNAs). The spliceosome, a complex ribonucleoprotein machine, performs pre-RNA splicing with extreme precision. Deregulated splicing is linked to cancer, genetic, and neurodegenerative diseases. Hence, the discovery of small-molecules targeting core spliceosome components represents an appealing therapeutic opportunity. AREA COVERED Several atomic-level structures of the spliceosome and distinct splicing-modulators bound to its protein/RNA components have been solved. Here, we review recent advances in the discovery of small-molecule splicing-modulators, discuss opportunities and challenges for their therapeutic applicability, and showcase how structural data and/or all-atom simulations can illuminate key facets of their mechanism, thus contributing to future drug-discovery campaigns. EXPERT OPINION This review highlights the potential of modulating pre-RNA splicing with small-molecules, and anticipates how the synergy of computer and wet-lab experiments will enrich our understanding of splicing regulation/deregulation mechanisms. This information will aid future structure-based drug-discovery efforts aimed to expand the currently limited portfolio of selective splicing-modulators.
Collapse
Affiliation(s)
- Riccardo Rozza
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| | - Pavel Janoš
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| | - Angelo Spinello
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, Palermo, Italy
| | - Alessandra Magistrato
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| |
Collapse
|
31
|
Siebert AE, Corll J, Paige Gronevelt J, Levine L, Hobbs LM, Kenney C, Powell CLE, Battistuzzi FU, Davenport R, Mark Settles A, Brad Barbazuk W, Westrick RJ, Madlambayan GJ, Lal S. Genetic analysis of human RNA binding motif protein 48 (RBM48) reveals an essential role in U12-type intron splicing. Genetics 2022; 222:iyac129. [PMID: 36040194 PMCID: PMC9526058 DOI: 10.1093/genetics/iyac129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
U12-type or minor introns are found in most multicellular eukaryotes and constitute ∼0.5% of all introns in species with a minor spliceosome. Although the biological significance for the evolutionary conservation of U12-type introns is debated, mutations disrupting U12 splicing cause developmental defects in both plants and animals. In human hematopoietic stem cells, U12 splicing defects disrupt proper differentiation of myeloid lineages and are associated with myelodysplastic syndrome, predisposing individuals to acute myeloid leukemia. Mutants in the maize ortholog of RNA binding motif protein 48 (RBM48) have aberrant U12-type intron splicing. Human RBM48 was recently purified biochemically as part of the minor spliceosome and shown to recognize the 5' end of the U6atac snRNA. In this report, we use CRISPR/Cas9-mediated ablation of RBM48 in human K-562 cells to show the genetic function of RBM48. RNA-seq analysis comparing wild-type and mutant K-562 genotypes found that 48% of minor intron-containing genes have significant U12-type intron retention in RBM48 mutants. Comparing these results to maize rbm48 mutants defined a subset of minor intron-containing genes disrupted in both species. Mutations in the majority of these orthologous minor intron-containing genes have been reported to cause developmental defects in both plants and animals. Our results provide genetic evidence that the primary defect of human RBM48 mutants is aberrant U12-type intron splicing, while a comparison of human and maize RNA-seq data identifies candidate genes likely to mediate mutant phenotypes of U12-type splicing defects.
Collapse
Affiliation(s)
- Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Jacob Corll
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - J Paige Gronevelt
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Laurel Levine
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Linzi M Hobbs
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Catalina Kenney
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Christopher L E Powell
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Fabia U Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Ruth Davenport
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - A Mark Settles
- Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - W Brad Barbazuk
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Randal J Westrick
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Gerard J Madlambayan
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Shailesh Lal
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| |
Collapse
|
32
|
Weinstein R, Bishop K, Broadbridge E, Yu K, Carrington B, Elkahloun A, Zhen T, Pei W, Burgess SM, Liu P, Bresciani E, Sood R. Zrsr2 Is Essential for the Embryonic Development and Splicing of Minor Introns in RNA and Protein Processing Genes in Zebrafish. Int J Mol Sci 2022; 23:10668. [PMID: 36142581 PMCID: PMC9501576 DOI: 10.3390/ijms231810668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
ZRSR2 (zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2) is an essential splicing factor involved in 3' splice-site recognition as a component of both the major and minor spliceosomes that mediate the splicing of U2-type (major) and U12-type (minor) introns, respectively. Studies of ZRSR2-depleted cell lines and ZRSR2-mutated patient samples revealed its essential role in the U12-dependent minor spliceosome. However, the role of ZRSR2 during embryonic development is not clear, as its function is compensated for by Zrsr1 in mice. Here, we utilized the zebrafish model to investigate the role of zrsr2 during embryonic development. Using CRISPR/Cas9 technology, we generated a zrsr2-knockout zebrafish line, termed zrsr2hg129/hg129 (p.Trp167Argfs*9) and examined embryo development in the homozygous mutant embryos. zrsr2hg129/hg129 embryos displayed multiple developmental defects starting at 4 days post fertilization (dpf) and died after 8 dpf, suggesting that proper Zrsr2 function is required during embryonic development. The global transcriptome analysis of 3 dpf zrsr2hg129/hg129 embryos revealed that the loss of Zrsr2 results in the downregulation of essential metabolic pathways and the aberrant retention of minor introns in about one-third of all minor intron-containing genes in zebrafish. Overall, our study has demonstrated that the role of Zrsr2 as a component of the minor spliceosome is conserved and critical for proper embryonic development in zebrafish.
Collapse
Affiliation(s)
- Rachel Weinstein
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth Broadbridge
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Yu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdel Elkahloun
- Microarray Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tao Zhen
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wuhong Pei
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn M. Burgess
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Liu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erica Bresciani
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
33
|
Bezen D, Kutlu O, Mouilleron S, Rizzoti K, Dattani M, Guran T, Yeşil G. A homozygous Y443C variant in the RNPC3 is associated with severe syndromic congenital hypopituitarism and diffuse brain atrophy. Am J Med Genet A 2022; 188:2701-2706. [PMID: 35792517 DOI: 10.1002/ajmg.a.62888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 01/25/2023]
Abstract
Biallelic RNPC3 variants have been reported in a few patients with growth hormone deficiency, either in isolation or in association with central hypothyroidism, congenital cataract, neuropathy, developmental delay/intellectual disability, hypogonadism, and pituitary hypoplasia. To describe a new patient with syndromic congenital hypopituitarism and diffuse brain atrophy due to RNPC3 mutations and to compare her clinical and molecular characteristics and pituitary functions with previously published patients. A 20-year-old female presented with severe growth, neuromotor, and developmental delay. Her weight, height, and head circumference were 5135 gr (-25.81 SDS), 68 cm (-16.17 SDS), and 34 cm (-17.03 SDS), respectively. She was prepubertal, and had dysmorphic facies, contractures, and spasticity in the extremities, and severe truncal hypotonia. There were no radiological signs of a skeletal dysplasia. The bone age was extremely delayed at 2 years. Investigation of pituitary function revealed growth hormone, prolactin, and thyroid-stimulating hormone deficiencies. Whole-exome sequencing revealed a novel homozygous missense (c.1328A > G; Y443C) variant in RNPC3. Cranial MRI revealed a hypoplastic anterior pituitary with diffuse cerebral and cerebellar atrophy. The Y443C variant in RNPC3 associated with syndromic congenital hypopituitarism and abnormal brain development. This report extends the RNPC3-related hypopituitarism phenotype with a severe neurodegenerative presentation.
Collapse
Affiliation(s)
- Diğdem Bezen
- Department of Pediatrics, Pediatric Endocrinology, University of Health Sciences, Prof. Dr. Cemil Taşçıoğlu City Hospital, Istanbul, Turkey
| | - Orkide Kutlu
- Department of Internal Medicine, University of Health Sciences, Prof. Dr. Cemil Taşçıoğlu City Hospital, Istanbul, Turkey
| | - Stephane Mouilleron
- Structural Biology Science Technology Platforms, The Francis Crick Institute, London, UK
| | - Karine Rizzoti
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London, UK
| | - Mehul Dattani
- Department and Genetics and Genomic Medicine Research and Teaching, UCL GOS Institute of Child Health, London
| | - Tulay Guran
- Department of Pediatric Endocrinology and Diabetes, School of Medicine, Marmara University, Istanbul, Turkey
| | - Gözde Yeşil
- Department of Medical Genetics, Pediatric Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| |
Collapse
|
34
|
Fort RS, Chavez S, Trinidad Barnech JM, Oliveira-rizzo C, Smircich P, Sotelo-silveira JR, Duhagon MA. Current Status of Regulatory Non-Coding RNAs Research in the Tritryp. Noncoding RNA 2022; 8:54. [PMID: 35893237 PMCID: PMC9326685 DOI: 10.3390/ncrna8040054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.
Collapse
|
35
|
López-Cortés A, Echeverría-Garcés G, Ramos-Medina MJ. Molecular Pathogenesis and New Therapeutic Dimensions for Spinal Muscular Atrophy. Biology 2022; 11:biology11060894. [PMID: 35741415 PMCID: PMC9219894 DOI: 10.3390/biology11060894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 11/16/2022]
Abstract
The condition known as 5q spinal muscular atrophy (SMA) is a devastating autosomal recessive neuromuscular disease caused by a deficiency of the ubiquitous protein survival of motor neuron (SMN), which is encoded by the SMN1 and SMN2 genes. It is one of the most common pediatric recessive genetic diseases, and it represents the most common cause of hereditary infant mortality. After decades of intensive basic and clinical research efforts, and improvements in the standard of care, successful therapeutic milestones have been developed, delaying the progression of 5q SMA and increasing patient survival. At the same time, promising data from early-stage clinical trials have indicated that additional therapeutic options are likely to emerge in the near future. Here, we provide updated information on the molecular underpinnings of SMA; we also provide an overview of the rapidly evolving therapeutic landscape for SMA, including SMN-targeted therapies, SMN-independent therapies, and combinational therapies that are likely to be key for the development of treatments that are effective across a patient’s lifespan.
Collapse
Affiliation(s)
- Andrés López-Cortés
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito 170302, Ecuador
- Facultad de Medicina, Universidad de Las Américas, Quito 170124, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain; (G.E.-G.); (M.J.R.-M.)
- Correspondence:
| | - Gabriela Echeverría-Garcés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain; (G.E.-G.); (M.J.R.-M.)
| | - María José Ramos-Medina
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain; (G.E.-G.); (M.J.R.-M.)
| |
Collapse
|
36
|
Azambuja M, Orane Schemberger M, Nogaroto V, Moreira-Filho O, Martins C, Ricardo Vicari M. Major and minor U small nuclear RNAs genes characterization in a neotropical fish genome: Chromosomal remodeling and repeat units dispersion in Parodontidae. Gene 2022; 826:146459. [PMID: 35358649 DOI: 10.1016/j.gene.2022.146459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/15/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022]
Abstract
In association with many proteins, small nuclear RNAs (snRNAs) organize the spliceosomes that play a significant role in processing precursor mRNAs during gene expression. According to snRNAs genic arrangements, two kinds of spliceosomes (major and minor) can be organized into eukaryotic cells. Although in situ localization of U1 and U2 snDNAs have been performed in fish karyotypes, studies with genomic characterization and functionality of U snRNAs integrated into chromosomal changes on Teleostei are still scarce. This study aimed to achieve a genomic characterization of the U snRNAs genes in Apareiodon sp. (2n = 54, ZZ/ZW), apply these data to recognize functional/defective copies, and map chromosomal changes involving snDNAs in Parodontidae species karyotype diversification. Nine snRNA multigene families (U1, U2, U4, U5, U6, U11, U12, U4atac and U6atac) arranged in putatively functional copies in the genome were analyzed. Proximal Sequence Elements (PSE) and TATA-box promoters occurrence, besides an entire transcribed region and conserved secondary structures, qualify them for spliceosome activity. In addition, several defective copies or pseudogenes were identified for the snRNAs that make up the major spliceosome. In situ localization of snDNAs in five species of Parodontidae demonstrated that U1, U2, and U4 snDNAs were involved in chromosomal location changes or units dispersion. The U snRNAs defective/pseudogenes units dispersion could be favored by the probable occurrence of active retrotransposition enzymes in the Apareiodon genome. The U2 and U4 snDNAs sites were involved in independent events in the differentiation of sex chromosomes among Parodontidae lineages. The study characterized U snRNA genes that compose major and minor spliceosomes in the Apareiodon sp. genome and proposes that their defective copies trigger chromosome differentiation and diversification events in Parodontidae.
Collapse
Affiliation(s)
- Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. dos Santos, 100, 81531-990 Curitiba, Paraná, Brazil.
| | - Michelle Orane Schemberger
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. dos Santos, 100, 81531-990 Curitiba, Paraná, Brazil.
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, Paraná, Brazil.
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Carlos, São Paulo, Brazil.
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Júnior, s/n, 18618-689 Botucatu, São Paulo, Brazil.
| | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Centro Politécnico, Avenida Coronel Francisco H. dos Santos, 100, 81531-990 Curitiba, Paraná, Brazil; Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900 Ponta Grossa, Paraná, Brazil.
| |
Collapse
|
37
|
Yu L, Majerciak V, Zheng ZM. HPV16 and HPV18 Genome Structure, Expression, and Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094943. [PMID: 35563334 PMCID: PMC9105396 DOI: 10.3390/ijms23094943] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/18/2022] Open
Abstract
Human papillomaviruses (HPV) are a group of small non-enveloped DNA viruses whose infection causes benign tumors or cancers. HPV16 and HPV18, the two most common high-risk HPVs, are responsible for ~70% of all HPV-related cervical cancers and head and neck cancers. The expression of the HPV genome is highly dependent on cell differentiation and is strictly regulated at the transcriptional and post-transcriptional levels. Both HPV early and late transcripts differentially expressed in the infected cells are intron-containing bicistronic or polycistronic RNAs bearing more than one open reading frame (ORF), because of usage of alternative viral promoters and two alternative viral RNA polyadenylation signals. Papillomaviruses proficiently engage alternative RNA splicing to express individual ORFs from the bicistronic or polycistronic RNA transcripts. In this review, we discuss the genome structures and the updated transcription maps of HPV16 and HPV18, and the latest research advances in understanding RNA cis-elements, intron branch point sequences, and RNA-binding proteins in the regulation of viral RNA processing. Moreover, we briefly discuss the epigenetic modifications, including DNA methylation and possible APOBEC-mediated genome editing in HPV infections and carcinogenesis.
Collapse
|
38
|
Murphy AJ, Li AH, Li P, Sun H. Therapeutic Targeting of Alternative Splicing: A New Frontier in Cancer Treatment. Front Oncol 2022; 12:868664. [PMID: 35463320 PMCID: PMC9027816 DOI: 10.3389/fonc.2022.868664] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/11/2022] [Indexed: 01/05/2023] Open
Abstract
The ability for cells to harness alternative splicing enables them to diversify their proteome in order to carry out complex biological functions and adapt to external and internal stimuli. The spliceosome is the multiprotein-RNA complex charged with the intricate task of alternative splicing. Aberrant splicing can arise from abnormal spliceosomes or splicing factors and drive cancer development and progression. This review will provide an overview of the alternative splicing process and aberrant splicing in cancer, with a focus on serine/arginine-rich (SR) proteins and their recently reported roles in cancer development and progression and beyond. Recent mapping of the spliceosome, its associated splicing factors, and their relationship to cancer have opened the door to novel therapeutic approaches that capitalize on the widespread influence of alternative splicing. We conclude by discussing small molecule inhibitors of the spliceosome that have been identified in an evolving era of cancer treatment.
Collapse
Affiliation(s)
- Anthony J. Murphy
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| | - Alex H. Li
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| | - Peichao Li
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| |
Collapse
|
39
|
Reinhardt F, Stadler PF. ExceS-A: an exon-centric split aligner. J Integr Bioinform 2022; 19:jib-2021-0040. [PMID: 35254744 PMCID: PMC9069663 DOI: 10.1515/jib-2021-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022] Open
Abstract
Spliced alignments are a key step in the construction of high-quality homology-based annotations of protein sequences. The exon/intron structure, which is computed as part of spliced alignment procedures, often conveys important information for the distinguishing paralogous members of gene families. Here we present an exon-centric pipeline for spliced alignment that is intended in particular for applications that involve exon-by-exon comparisons of coding sequences. We show that the simple, blat-based approach has advantages over established tools in particular for genes with very large introns and applications to fragmented genome assemblies.
Collapse
Affiliation(s)
- Franziska Reinhardt
- Bioinformatics Group, Institute of Computer Science, Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Institute of Computer Science, Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Max-Planck-Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| |
Collapse
|
40
|
Jacquier V, Prévot M, Gostan T, Bordonné R, Benkhelifa-Ziyyat S, Barkats M, Soret J. Splicing efficiency of minor introns in a mouse model of SMA predominantly depends on their branchpoint sequence and can involve the contribution of major spliceosome components. RNA 2022; 28:303-319. [PMID: 34893560 PMCID: PMC8848931 DOI: 10.1261/rna.078329.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Spinal muscular atrophy (SMA) is a devastating neurodegenerative disease caused by reduced amounts of the ubiquitously expressed Survival of Motor Neuron (SMN) protein. In agreement with its crucial role in the biogenesis of spliceosomal snRNPs, SMN-deficiency is correlated to numerous splicing alterations in patient cells and various tissues of SMA mouse models. Among the snRNPs whose assembly is impacted by SMN-deficiency, those involved in the minor spliceosome are particularly affected. Importantly, splicing of several, but not all U12-dependent introns has been shown to be affected in different SMA models. Here, we have investigated the molecular determinants of this differential splicing in spinal cords from SMA mice. We show that the branchpoint sequence (BPS) is a key element controlling splicing efficiency of minor introns. Unexpectedly, splicing of several minor introns with suboptimal BPS is not affected in SMA mice. Using in vitro splicing experiments and oligonucleotides targeting minor or major snRNAs, we show for the first time that splicing of these introns involves both the minor and major machineries. Our results strongly suggest that splicing of a subset of minor introns is not affected in SMA mice because components of the major spliceosome compensate for the loss of minor splicing activity.
Collapse
Affiliation(s)
- Valentin Jacquier
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Manon Prévot
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Thierry Gostan
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Sofia Benkhelifa-Ziyyat
- Centre de Recherche en Myologie (CRM), Institut de Myologie, Sorbonne Universités, UPMC Univ Paris 06, Inserm UMRS974, GH Pitié Salpêtrière, Paris 75013, France
| | - Martine Barkats
- Centre de Recherche en Myologie (CRM), Institut de Myologie, Sorbonne Universités, UPMC Univ Paris 06, Inserm UMRS974, GH Pitié Salpêtrière, Paris 75013, France
| | - Johann Soret
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| |
Collapse
|
41
|
Satou Y, Tokuoka M, Oda-Ishii I, Tokuhiro S, Ishida T, Liu B, Iwamura Y. A Manually Curated Gene Model Set for an Ascidian, Ciona robusta (Ciona intestinalis Type A). Zoolog Sci 2022; 39:253-260. [DOI: 10.2108/zs210102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/15/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Miki Tokuoka
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Sinichi Tokuhiro
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tasuku Ishida
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Boqi Liu
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yuri Iwamura
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| |
Collapse
|
42
|
Levesque L, Salazar N, Roy SW. Distinct Minor Splicing Patterns across Cancers. Genes (Basel) 2022; 13:387. [PMID: 35205431 DOI: 10.3390/genes13020387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 12/21/2022] Open
Abstract
In human cells, the U12 spliceosome, also known as the minor spliceosome, is responsible for the splicing of 0.5% of introns, while the major U2 spliceosome is responsible for the other 99.5%. While many studies have been done to characterize and understand splicing dysregulation in cancer, almost all of them have focused on U2 splicing and ignored U12 splicing, despite evidence suggesting minor splicing is involved in cell cycle regulation. In this study, we analyzed RNA-seq data from The Cancer Genome Atlas for 14 different cohorts to determine differential splicing of minor introns in tumor and adjacent normal tissue. We found that in some cohorts, such as breast cancer, there was a strong skew towards minor introns showing increased splicing in the tumor; in others, such as the renal chromophobe cell carcinoma cohort, the opposite pattern was found, with minor introns being much more likely to have decreased splicing in the tumor. Further analysis of gene expression did not reveal any candidate regulatory mechanisms that could cause these different minor splicing phenotypes between cohorts. Our data suggest context-dependent roles of the minor spliceosome in tumorigenesis and provides a foundation for further investigation of minor splicing in cancer, which could then serve as a basis for novel therapeutic strategies.
Collapse
|
43
|
Gómez-Redondo I, Pericuesta E, Navarrete-Lopez P, Ramos-Ibeas P, Planells B, Fonseca-Balvís N, Vaquero-Rey A, Fernández-González R, Laguna-Barraza R, Horiuchi K, Gutiérrez-Adán A. Zrsr2 and functional U12-dependent spliceosome are necessary for follicular development. iScience 2022; 25:103860. [PMID: 35198906 PMCID: PMC8850803 DOI: 10.1016/j.isci.2022.103860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/26/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
ZRSR2 is a splicing factor involved in recognition of 3′-intron splice sites that is frequently mutated in myeloid malignancies and several tumors; however, the role of mutations of Zrsr2 in other tissues has not been analyzed. To explore the biological role of ZRSR2, we generated three Zrsr2 mutant mouse lines. All Zrsr2 mutant lines exhibited blood cell anomalies, and in two lines, oogenesis was blocked at the secondary follicle stage. RNA-seq of Zrsr2mu secondary follicles showed aberrations in gene expression and showed altered alternative splicing (AS) events involving enrichment of U12-type intron retention (IR), supporting the functional Zrsr2 action in minor spliceosomes. IR events were preferentially associated with centriole replication, protein phosphorylation, and DNA damage checkpoint. Notably, we found alterations in AS events of 50 meiotic genes. These results indicate that ZRSR2 mutations alter splicing mainly in U12-type introns, which may affect peripheral blood cells, and impede oogenesis and female fertility. Zrsr2mu mice allow us to identify functions of Zrsr2 in vivo Minor splicing factor Zrsr2 is essential for oogenesis and peripheral blood cells Zrsr2 impairment affects the splicing of U12-type intron-containing genes Zrsr2mu aberrant splicing causes a global alteration of gene expression
Collapse
Affiliation(s)
- Isabel Gómez-Redondo
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Eva Pericuesta
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Paula Navarrete-Lopez
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Priscila Ramos-Ibeas
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Benjamín Planells
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Noelia Fonseca-Balvís
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Aida Vaquero-Rey
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Raúl Fernández-González
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Ricardo Laguna-Barraza
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Keiko Horiuchi
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, 1-396 Kosugi-cho, Nakahara-ku, Kawasaki, Kanagawa 211-8533, Japan
| | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| |
Collapse
|
44
|
Akin L, Rizzoti K, Gregory LC, Corredor B, Le Quesne Stabej P, Williams H, Buonocore F, Mouilleron S, Capra V, McGlacken-Byrne SM, Martos-Moreno GÁ, Azmanov DN, Kendirci M, Kurtoglu S, Suntharalingham JP, Galichet C, Gustincich S, Tasic V, Achermann JC, Accogli A, Filipovska A, Tuilpakov A, Maghnie M, Gucev Z, Gonen ZB, Pérez-Jurado LA, Robinson I, Lovell-Badge R, Argente J, Dattani MT. Pathogenic variants in RNPC3 are associated with hypopituitarism and primary ovarian insufficiency. Genet Med 2022; 24:384-397. [PMID: 34906446 PMCID: PMC7612377 DOI: 10.1016/j.gim.2021.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/15/2021] [Accepted: 09/27/2021] [Indexed: 11/19/2022] Open
Abstract
PURPOSE We aimed to investigate the molecular basis underlying a novel phenotype including hypopituitarism associated with primary ovarian insufficiency. METHODS We used next-generation sequencing to identify variants in all pedigrees. Expression of Rnpc3/RNPC3 was analyzed by in situ hybridization on murine/human embryonic sections. CRISPR/Cas9 was used to generate mice carrying the p.Leu483Phe pathogenic variant in the conserved murine Rnpc3 RRM2 domain. RESULTS We described 15 patients from 9 pedigrees with biallelic pathogenic variants in RNPC3, encoding a specific protein component of the minor spliceosome, which is associated with a hypopituitary phenotype, including severe growth hormone (GH) deficiency, hypoprolactinemia, variable thyrotropin (also known as thyroid-stimulating hormone) deficiency, and anterior pituitary hypoplasia. Primary ovarian insufficiency was diagnosed in 8 of 9 affected females, whereas males had normal gonadal function. In addition, 2 affected males displayed normal growth when off GH treatment despite severe biochemical GH deficiency. In both mouse and human embryos, Rnpc3/RNPC3 was expressed in the developing forebrain, including the hypothalamus and Rathke's pouch. Female Rnpc3 mutant mice displayed a reduction in pituitary GH content but with no reproductive impairment in young mice. Male mice exhibited no obvious phenotype. CONCLUSION Our findings suggest novel insights into the role of RNPC3 in female-specific gonadal function and emphasize a critical role for the minor spliceosome in pituitary and ovarian development and function.
Collapse
Affiliation(s)
- Leyla Akin
- Department of Paediatric Endocrinology, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey; Department of Paediatric Endocrinology, Faculty of Medicine, Erciyes University, Kayseri, Turkey.
| | - Karine Rizzoti
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London, United Kingdom
| | - Louise C Gregory
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Beatriz Corredor
- Departments of Paediatrics and Paediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Polona Le Quesne Stabej
- GOSgene, Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Hywel Williams
- Division of Cancer and Genetics, Genetics and Genomic Medicine, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Federica Buonocore
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Stephane Mouilleron
- Structural Biology Science Technology Platforms, The Francis Crick Institute, London, United Kingdom
| | - Valeria Capra
- Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Genova, Italy
| | - Sinead M McGlacken-Byrne
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Gabriel Á Martos-Moreno
- Departments of Paediatrics and Paediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Department of Paediatrics, Universidad Autónoma de Madrid, Madrid, Spain; CIBER Fisiopatología Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Dimitar N Azmanov
- Centre of Medical Research, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia; Department of Diagnostic Genomics, PathWest, QEII MedicalCentre, Perth, Western Australia, Australia
| | - Mustafa Kendirci
- Department of Paediatric Endocrinology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Selim Kurtoglu
- Department of Paediatric Endocrinology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Jenifer P Suntharalingham
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Christophe Galichet
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London, United Kingdom
| | | | - Velibor Tasic
- University Children's Hospital, Medical School, Skopje, North Macedonia
| | - John C Achermann
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Aleksandra Filipovska
- Centre of Medical Research, The University of Western Australia and Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia; Telethon Kids Institute, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Anatoly Tuilpakov
- Department of Endocrine Genetics, Research Centre for Medical Genetics, Moscow, Russia; Department of Inherited Endocrine Disorders, Endocrinology Research Centre, Moscow, Russia
| | - Mohamad Maghnie
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy; Department of Paediatrics, IRCCS Giannina Gaslini Institute, Genoa, Italy
| | - Zoran Gucev
- University Children's Hospital, Medical School, Skopje, North Macedonia
| | - Zeynep Burcin Gonen
- Oral and Maxillofacial Surgery, Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey
| | - Luis A Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; South Australian Health and Medical Research Institute (SAHMRI), The University of Adelaide, Adelaide, South Australia, Australia
| | - Iain Robinson
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London, United Kingdom
| | - Robin Lovell-Badge
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London, United Kingdom
| | - Jesús Argente
- Departments of Paediatrics and Paediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Department of Paediatrics, Universidad Autónoma de Madrid, Madrid, Spain; CIBER Fisiopatología Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain; IMDEA Food Institute, Campus of International Excellence UAM+CSIC, Madrid, Spain
| | - Mehul T Dattani
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; South Australian Health and Medical Research Institute (SAHMRI), The University of Adelaide, Adelaide, South Australia, Australia; Department of Paediatric Endocrinology, Great Ormond Street Hospital for Children, London, United Kingdom.
| |
Collapse
|
45
|
Suzuki T, Shinagawa T, Niwa T, Akeda H, Hashimoto S, Tanaka H, Hiroaki Y, Yamasaki F, Mishima H, Kawai T, Higashiyama T, Nakamura K. The DROL1 subunit of U5 snRNP in the spliceosome is specifically required to splice AT-AC-type introns in Arabidopsis. Plant J 2022; 109:633-648. [PMID: 34780096 DOI: 10.1111/tpj.15582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 10/25/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
An Arabidopsis mutant named defective repression of OLE3::LUC 1 (drol1) was originally isolated as a mutant with defects in the repression of OLEOSIN3 (OLE3) after seed germination. In this study, we show that DROL1 is an Arabidopsis homolog of yeast DIB1, a subunit of the U5 small nuclear ribonucleoprotein particle (snRNP) in the spliceosome. It is also part of a new subfamily that is specific to a certain class of eukaryotes. Comprehensive analysis of the intron splicing using RNA sequencing analysis of the drol1 mutants revealed that most of the minor introns with AT-AC dinucleotide termini had reduced levels of splicing. Only two nucleotide substitutions from AT-AC to GT-AG enabled AT-AC-type introns to be spliced in drol1 mutants. Forty-eight genes, including those having important roles in abiotic stress responses and cell proliferation, exhibited reduced splicing of AT-AC-type introns in the drol1 mutants. Additionally, drol1 mutant seedlings showed retarded growth, similar to that caused by the activation of abscisic acid signaling, possibly as a result of reduced AT-AC-type intron splicing in the endosomal Na+ /H+ antiporters and plant-specific histone deacetylases. These results indicate that DROL1 is specifically involved in the splicing of minor introns with AT-AC termini and that this plays an important role in plant growth and development.
Collapse
Affiliation(s)
- Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Tomomi Shinagawa
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Tomoko Niwa
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Hibiki Akeda
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Satoki Hashimoto
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Hideki Tanaka
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Yoko Hiroaki
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Fumiya Yamasaki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Hiroyuki Mishima
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Tsutae Kawai
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bukyo-ku, Tokyo, 113-0033, Japan
| | - Kenzo Nakamura
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| |
Collapse
|
46
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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.
Collapse
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
- *Correspondence: Niall P. Keegan,
| | - 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
| |
Collapse
|
47
|
Bando H, Urai S, Kanie K, Sasaki Y, Yamamoto M, Fukuoka H, Iguchi G, Camper SA. Novel genes and variants associated with congenital pituitary hormone deficiency in the era of next-generation sequencing. Front Endocrinol (Lausanne) 2022; 13:1008306. [PMID: 36237189 PMCID: PMC9551393 DOI: 10.3389/fendo.2022.1008306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/09/2022] [Indexed: 01/07/2023] Open
Abstract
Combined pituitary hormone deficiency (CPHD) is not a rare disorder, with a frequency of approximately 1 case per 4,000 live births. However, in most cases, a genetic diagnosis is not available. Furthermore, the diagnosis is challenging because no clear correlation exists between the pituitary hormones affected and the gene(s) responsible for the disorder. Next-generation sequencing (NGS) has recently been widely used to identify novel genes that cause (or putatively cause) CPHD. This review outlines causative genes for CPHD that have been newly reported in recent years. Moreover, novel variants of known CPHD-related genes (POU1F1 and GH1 genes) that contribute to CPHD through unique mechanisms are also discussed in this review. From a clinical perspective, variants in some of the recently identified causative genes result in extra-pituitary phenotypes. Clinical research on the related symptoms and basic research on pituitary formation may help in inferring the causative gene(s) of CPHD. Future NGS analysis of a large number of CPHD cases may reveal new genes related to pituitary development. Clarifying the causative genes of CPHD may help to understand the process of pituitary development. We hope that future innovations will lead to the identification of genes responsible for CPHD and pituitary development.
Collapse
Affiliation(s)
- Hironori Bando
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
- *Correspondence: Hironori Bando,
| | - Shin Urai
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University School of Medicine, Kobe, Japan
| | - Keitaro Kanie
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
| | - Yuriko Sasaki
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University School of Medicine, Kobe, Japan
| | - Masaaki Yamamoto
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
| | - Hidenori Fukuoka
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
| | - Genzo Iguchi
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
- Division of Biosignal Pathophysiology, Kobe University Graduate School of Medicine, Kobe, Japan
- Medical Center for Student Health, Kobe University, Kobe, Japan
| | - Sally A. Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
| |
Collapse
|
48
|
Jutzi D, Ruepp MD. Alternative Splicing in Human Biology and Disease. Methods Mol Biol 2022; 2537:1-19. [PMID: 35895255 DOI: 10.1007/978-1-0716-2521-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Alternative pre-mRNA splicing allows for the production of multiple mRNAs from an individual gene, which not only expands the protein-coding potential of the genome but also enables complex mechanisms for the post-transcriptional control of gene expression. Regulation of alternative splicing entails a combinatorial interplay between an abundance of trans-acting splicing factors, cis-acting regulatory sequence elements and their concerted effects on the core splicing machinery. Given the extent and biological significance of alternative splicing in humans, it is not surprising that aberrant splicing patterns can cause or contribute to a wide range of diseases. In this introductory chapter, we outline the mechanisms that govern alternative pre-mRNA splicing and its regulation and discuss how dysregulated splicing contributes to human diseases affecting the motor system and the brain.
Collapse
Affiliation(s)
- Daniel Jutzi
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK.
| | - Marc-David Ruepp
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK.
| |
Collapse
|
49
|
Mars JC, Ghram M, Culjkovic-Kraljacic B, Borden KLB. The Cap-Binding Complex CBC and the Eukaryotic Translation Factor eIF4E: Co-Conspirators in Cap-Dependent RNA Maturation and Translation. Cancers (Basel) 2021; 13:6185. [PMID: 34944805 PMCID: PMC8699206 DOI: 10.3390/cancers13246185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/26/2022] Open
Abstract
The translation of RNA into protein is a dynamic process which is heavily regulated during normal cell physiology and can be dysregulated in human malignancies. Its dysregulation can impact selected groups of RNAs, modifying protein levels independently of transcription. Integral to their suitability for translation, RNAs undergo a series of maturation steps including the addition of the m7G cap on the 5' end of RNAs, splicing, as well as cleavage and polyadenylation (CPA). Importantly, each of these steps can be coopted to modify the transcript signal. Factors that bind the m7G cap escort these RNAs through different steps of maturation and thus govern the physical nature of the final transcript product presented to the translation machinery. Here, we describe these steps and how the major m7G cap-binding factors in mammalian cells, the cap binding complex (CBC) and the eukaryotic translation initiation factor eIF4E, are positioned to chaperone transcripts through RNA maturation, nuclear export, and translation in a transcript-specific manner. To conceptualize a framework for the flow and integration of this genetic information, we discuss RNA maturation models and how these integrate with translation. Finally, we discuss how these processes can be coopted by cancer cells and means to target these in malignancy.
Collapse
Affiliation(s)
- Jean-Clement Mars
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Mehdi Ghram
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| |
Collapse
|
50
|
Montañés-Agudo P, Casini S, Aufiero S, Ernault AC, van der Made I, Pinto YM, Remme CA, Creemers EE. Inhibition of minor intron splicing reduces Na+ and Ca2+ channel expression and function in cardiomyocytes. J Cell Sci 2021; 135:273616. [PMID: 34859816 PMCID: PMC8767276 DOI: 10.1242/jcs.259191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
Eukaryotic genomes contain a tiny subset of ‘minor class’ introns with unique sequence elements that require their own splicing machinery. These minor introns are present in certain gene families with specific functions, such as voltage-gated Na+ and voltage-gated Ca2+ channels. Removal of minor introns by the minor spliceosome has been proposed as a post-transcriptional regulatory layer, which remains unexplored in the heart. Here, we investigate whether the minor spliceosome regulates electrophysiological properties of cardiomyocytes by knocking down the essential minor spliceosome small nuclear snRNA component U6atac in neonatal rat ventricular myocytes. Loss of U6atac led to robust minor intron retention within Scn5a and Cacna1c, resulting in reduced protein levels of Nav1.5 and Cav1.2 channels. Functional consequences were studied through patch-clamp analysis, and revealed reduced Na+ and L-type Ca2+ currents after loss of U6atac. In conclusion, minor intron splicing modulates voltage-dependent ion channel expression and function in cardiomyocytes. This may be of particular relevance in situations in which minor splicing activity changes, such as in genetic diseases affecting minor spliceosome components, or in acquired diseases in which minor spliceosome components are dysregulated, such as heart failure. Summary: Knockdown of minor spliceosome component U6atac in cardiomyocytes reveals that expression of the Na+ channel Scn5a and the L-type Ca2+ channel Cacna1c critically depend on minor intron splicing.
Collapse
Affiliation(s)
- Pablo Montañés-Agudo
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Simona Casini
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Simona Aufiero
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands.,Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Auriane C Ernault
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Ingeborg van der Made
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Yigal M Pinto
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Carol Ann Remme
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Esther E Creemers
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| |
Collapse
|