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Chen G, Chen J, Qi L, Yin Y, Lin Z, Wen H, Zhang S, Xiao C, Bello SF, Zhang X, Nie Q, Luo W. Bulk and single-cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation. Cell Prolif 2024; 57:e13545. [PMID: 37705195 PMCID: PMC10849790 DOI: 10.1111/cpr.13545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/08/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023] Open
Abstract
Alternative splicing (AS) disruption has been linked to disorders of muscle development, as well as muscular atrophy. However, the precise changes in AS patterns that occur during myogenesis are not well understood. Here, we employed isoform long-reads RNA-seq (Iso-seq) and single-cell RNA-seq (scRNA-seq) to investigate the AS landscape during myogenesis. Our Iso-seq data identified 61,146 full-length isoforms representing 11,682 expressed genes, of which over 52% were novel. We identified 38,022 AS events, with most of these events altering coding sequences and exhibiting stage-specific splicing patterns. We identified AS dynamics in different types of muscle cells through scRNA-seq analysis, revealing genes essential for the contractile muscle system and cytoskeleton that undergo differential splicing across cell types. Gene-splicing analysis demonstrated that AS acts as a regulator, independent of changes in overall gene expression. Two isoforms of splicing factor TRA2B play distinct roles in myogenic differentiation by triggering AS of TGFBR2 to regulate canonical TGF-β signalling cascades differently. Our study provides a valuable transcriptome resource for myogenesis and reveals the complexity of AS and its regulation during myogenesis.
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Affiliation(s)
- Genghua Chen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jiahui Chen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lin Qi
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Yunqian Yin
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Zetong Lin
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Huaqiang Wen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Shuai Zhang
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Chuanyun Xiao
- Human and Animal PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Semiu Folaniyi Bello
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Xiquan Zhang
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Qinghua Nie
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Wen Luo
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
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Shatokhina O, Kovalskaia V, Sparber P, Sharkova I, Mishina I, Kuznetsova V, Ryzhkova O. TRA2B Gene Splice Variant Linked to Seizures and Neurodevelopmental Delay: A Second Case Study. Int J Mol Sci 2023; 24:15572. [PMID: 37958557 PMCID: PMC10648248 DOI: 10.3390/ijms242115572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
In this study, we report a novel splice variant in the TRA2B gene identified in a patient presenting with seizures and neurodevelopmental delay. This paper represents the second investigation of pathogenic variants in the TRA2B gene in humans, reaffirming the conclusions of the initial study and underscoring the importance of this research. Comprehensive genetic testing, including whole genome sequencing, Sanger sequencing, and mRNA analysis, was performed on the proband and her parents. The proband harbored a de novo c.170+1G>A variant in the RS1 domain of Tra2β, which was confirmed to be pathogenic through mRNA analysis, resulting in exon 2 deletion and a frameshift (p.Glu13Valfs*2). The clinical presentation of the patient was consistent with phenotypes described in one of the previous studies. These findings contribute to the dissemination and reinforcement of prior discoveries in the context of TRA2B-related syndrome and highlight the need for further investigation into the functional consequences and underlying pathogenic mechanisms associated with TRA2B mutations.
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Affiliation(s)
- Olga Shatokhina
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia; (O.S.); (V.K.); (P.S.); (I.S.); (I.M.)
| | - Valeriia Kovalskaia
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia; (O.S.); (V.K.); (P.S.); (I.S.); (I.M.)
| | - Peter Sparber
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia; (O.S.); (V.K.); (P.S.); (I.S.); (I.M.)
| | - Inna Sharkova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia; (O.S.); (V.K.); (P.S.); (I.S.); (I.M.)
| | - Irina Mishina
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia; (O.S.); (V.K.); (P.S.); (I.S.); (I.M.)
| | | | - Oxana Ryzhkova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia; (O.S.); (V.K.); (P.S.); (I.S.); (I.M.)
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3
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Capuz A, Osien S, Cardon T, Karnoub MA, Aboulouard S, Raffo-Romero A, Duhamel M, Cizkova D, Trerotola M, Devos D, Kobeissy F, Vanden Abeele F, Bonnefond A, Fournier I, Rodet F, Salzet M. Heimdall, an alternative protein issued from a ncRNA related to kappa light chain variable region of immunoglobulins from astrocytes: a new player in neural proteome. Cell Death Dis 2023; 14:526. [PMID: 37587118 PMCID: PMC10432539 DOI: 10.1038/s41419-023-06037-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
The dogma "One gene, one protein" is clearly obsolete since cells use alternative splicing and generate multiple transcripts which are translated into protein isoforms, but also use alternative translation initiation sites (TISs) and termination sites on a given transcript. Alternative open reading frames for individual transcripts give proteins originate from the 5'- and 3'-UTR mRNA regions, frameshifts of mRNA ORFs or from non-coding RNAs. Longtime considered as non-coding, recent in-silico translation prediction methods enriched the protein databases allowing the identification of new target structures that have not been identified previously. To gain insight into the role of these newly identified alternative proteins in the regulation of cellular functions, it is crucial to assess their dynamic modulation within a framework of altered physiological modifications such as experimental spinal cord injury (SCI). Here, we carried out a longitudinal proteomic study on rat SCI from 12 h to 10 days. Based on the alternative protein predictions, it was possible to identify a plethora of newly predicted protein hits. Among these proteins, some presented a special interest due to high homology with variable chain regions of immunoglobulins. We focus our interest on the one related to Kappa variable light chains which is similarly highly produced by B cells in the Bence jones disease, but here expressed in astrocytes. This protein, name Heimdall is an Intrinsically disordered protein which is secreted under inflammatory conditions. Immunoprecipitation experiments showed that the Heimdall interactome contained proteins related to astrocyte fate keepers such as "NOTCH1, EPHA3, IPO13" as well as membrane receptor protein including "CHRNA9; TGFBR, EPHB6, and TRAM". However, when Heimdall protein was neutralized utilizing a specific antibody or its gene knocked out by CRISPR-Cas9, sprouting elongations were observed in the corresponding astrocytes. Interestingly, depolarization assays and intracellular calcium measurements in Heimdall KO, established a depolarization effect on astrocyte membranes KO cells were more likely that the one found in neuroprogenitors. Proteomic analyses performed under injury conditions or under lipopolysaccharides (LPS) stimulation, revealed the expression of neuronal factors, stem cell proteins, proliferation, and neurogenesis of astrocyte convertor factors such as EPHA4, NOTCH2, SLIT3, SEMA3F, suggesting a role of Heimdall could regulate astrocytic fate. Taken together, Heimdall could be a novel member of the gatekeeping astrocyte-to-neuroprogenitor conversion factors.
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Affiliation(s)
- Alice Capuz
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Sylvain Osien
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Tristan Cardon
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Mélodie Anne Karnoub
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Antonella Raffo-Romero
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Marie Duhamel
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Dasa Cizkova
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 10, Bratislava, Slovakia
- Centre for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Marco Trerotola
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), University 'G. d'Annunzio', Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, University 'G. d'Annunzio', Chieti, Italy
| | - David Devos
- Université de Lille, INSERM, U1172, CHU-Lille, Lille Neuroscience Cognition Research Centre, 1 place de Verdun, 59000, Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Fabien Vanden Abeele
- Université de Lille, INSERM U1003, Laboratory of Cell Physiology, 59650, Villeneuve d'Ascq, France
| | - Amélie Bonnefond
- Univ. Lille, Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, CHU de Lille, 1 place de Verdun, 59000, Lille, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
- Institut Universitaire de France, 75005, Paris, France
| | - Franck Rodet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France.
| | - Michel Salzet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75005, Paris, France.
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4
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Xue J, Ma T, Zhang X. TRA2: The dominant power of alternative splicing in tumors. Heliyon 2023; 9:e15516. [PMID: 37151663 PMCID: PMC10161706 DOI: 10.1016/j.heliyon.2023.e15516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023] Open
Abstract
The dysregulation of alternative splicing (AS) is frequently found in cancer and considered as key markers for cancer progression and therapy. Transformer 2 (TRA2), a nuclear RNA binding protein, consists of transformer 2 alpha homolog (TRA2A) and transformer 2 beta homolog (TRA2B), and plays a role in the regulation of pre-mRNA splicing. Growing evidence has been provided that TRA2A and TRA2B are dysregulated in several types of tumors, and participate in the regulation of proliferation, migration, invasion, and chemotherapy resistance in cancer cells through alteration of AS of cancer-related genes. In this review, we highlight the role of TRA2 in tumorigenesis and metastasis, and discuss potential molecular mechanisms how TRA2 influences tumorigenesis and metastasis via controlling AS of pre-mRNA. We propose that TRA2Ais a novel biomarker and therapeutic target for cancer progression and therapy.
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Affiliation(s)
- Jiancheng Xue
- Medical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Shenyang, China
| | - Tie Ma
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, China
- Corresponding author.
| | - Xiaowen Zhang
- Medical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Research and Application of Animal Model for Environmental and Metabolic Diseases, Shenyang, China
- Corresponding author. Medical Research Center, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, China.
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5
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Ramond F, Dalgliesh C, Grimmel M, Wechsberg O, Vetro A, Guerrini R, FitzPatrick D, Poole RL, Lebrun M, Bayat A, Grasshoff U, Bertrand M, Witt D, Turnpenny PD, Faundes V, Santa María L, Mendoza Fuentes C, Mabe P, Hussain SA, Mullegama SV, Torti E, Oehl-Jaschkowitz B, Salmon LB, Orenstein N, Shahar NR, Hagari O, Bazak L, Hoffjan S, Prada CE, Haack T, Elliott DJ. Clustered variants in the 5' coding region of TRA2B cause a distinctive neurodevelopmental syndrome. Genet Med 2022; 25:100003. [PMID: 36549593 DOI: 10.1016/j.gim.2022.100003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Transformer2 proteins (Tra2α and Tra2β) control splicing patterns in human cells, and no human phenotypes have been associated with germline variants in these genes. The aim of this work was to associate germline variants in the TRA2B gene to a novel neurodevelopmental disorder. METHODS A total of 12 individuals from 11 unrelated families who harbored predicted loss-of-function monoallelic variants, mostly de novo, were recruited. RNA sequencing and western blot analyses of Tra2β-1 and Tra2β-3 isoforms from patient-derived cells were performed. Tra2β1-GFP, Tra2β3-GFP and CHEK1 exon 3 plasmids were transfected into HEK-293 cells. RESULTS All variants clustered in the 5' part of TRA2B, upstream of an alternative translation start site responsible for the expression of the noncanonical Tra2β-3 isoform. All affected individuals presented intellectual disability and/or developmental delay, frequently associated with infantile spasms, microcephaly, brain anomalies, autism spectrum disorder, feeding difficulties, and short stature. Experimental studies showed that these variants decreased the expression of the canonical Tra2β-1 isoform, whereas they increased the expression of the Tra2β-3 isoform, which is shorter and lacks the N-terminal RS1 domain. Increased expression of Tra2β-3-GFP were shown to interfere with the incorporation of CHEK1 exon 3 into its mature transcript, normally incorporated by Tra2β-1. CONCLUSION Predicted loss-of-function variants clustered in the 5' portion of TRA2B cause a new neurodevelopmental syndrome through an apparently dominant negative disease mechanism involving the use of an alternative translation start site and the overexpression of a shorter, repressive Tra2β protein.
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Affiliation(s)
- Francis Ramond
- Service de Génétique, Hôpital Nord, CHU Saint-Etienne, Saint-Etienne, France.
| | - Caroline Dalgliesh
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - Oded Wechsberg
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Maccabi Healthcare Services, Tel Aviv, Israel
| | - Annalisa Vetro
- Neuroscience Department, Meyer Children's Hospital and University of Florence, Florence, Italy
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital and University of Florence, Florence, Italy
| | - David FitzPatrick
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Rebecca L Poole
- NHS Education for Scotland South East Region, South East of Scotland Clinical Genetics Service, Edinburgh, United Kingdom
| | - Marine Lebrun
- Service de Génétique, Hôpital Nord, CHU Saint-Etienne, Saint-Etienne, France
| | - Allan Bayat
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark; Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Center, Dianalund, Denmark
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - Dennis Witt
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany
| | - Peter D Turnpenny
- Clinical Genetics, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Víctor Faundes
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Lorena Santa María
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Carolina Mendoza Fuentes
- Unidad de Endocrinología, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paulina Mabe
- Unidad de Neurología, Hospital de Niños Dr. Exequiel González Cortés, Santiago, Chile
| | - Shaun A Hussain
- Division of Pediatric Neurology, University of California, Los Angeles, Los Angeles, CA
| | | | | | | | - Lina Basel Salmon
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel; Pediatric Immunogenetics, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Naama Orenstein
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noa Ruhrman Shahar
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Ofir Hagari
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Lily Bazak
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel
| | - Sabine Hoffjan
- Abteilung für Humangenetik, Ruhr-Universitat Bochum, Bochum, Germany
| | - Carlos E Prada
- Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL; Department of Pediatrics, Feinberg School of Medicine of Northwestern University, Chicago, IL
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany; Centre for Rare Diseases, University of Tuebingen, Tuebingen, Germany
| | - David J Elliott
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.
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6
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Tang YL, Liu AL, Lv SS, Zhou ZR, Cao H, Weng SJ, Zhang YQ. Green light analgesia in mice is mediated by visual activation of enkephalinergic neurons in the ventrolateral geniculate nucleus. Sci Transl Med 2022; 14:eabq6474. [PMID: 36475906 DOI: 10.1126/scitranslmed.abq6474] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Green light exposure has been shown to reduce pain in animal models. Here, we report a vision-associated enkephalinergic neural circuit responsible for green light-mediated analgesia. Full-field green light exposure at an intensity of 10 lux produced analgesic effects in healthy mice and in a model of arthrosis. Ablation of cone photoreceptors completely inhibited the analgesic effect, whereas rod ablation only partially reduced pain relief. The analgesic effect was not modulated by the ablation of intrinsically photosensitive retinal ganglion cells (ipRGCs), which are atypical photoreceptors that control various nonvisual effects of light. Inhibition of the retino-ventrolateral geniculate nucleus (vLGN) pathway completely abolished the analgesic effects. Activation of this pathway reduced nociceptive behavioral responses; such activation was blocked by the inhibition of proenkephalin (Penk)-positive neurons in the vLGN (vLGNPenk). Moreover, green light analgesia was prevented by knockdown of Penk in the vLGN or by ablation of vLGNPenk neurons. In addition, activation of the projections from vLGNPenk neurons to the dorsal raphe nucleus (DRN) was sufficient to suppress nociceptive behaviors, whereas its inhibition abolished the green light analgesia. Our findings indicate that cone-dominated retinal inputs mediated green light analgesia through the vLGNPenk-DRN pathway and suggest that this signaling pathway could be exploited for reducing pain.
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Affiliation(s)
- Yu-Long Tang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Ai-Lin Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Su-Su Lv
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zi-Rui Zhou
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Hong Cao
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Shi-Jun Weng
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Yu-Qiu Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
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7
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Leclair NK, Brugiolo M, Urbanski L, Lawson SC, Thakar K, Yurieva M, George J, Hinson JT, Cheng A, Graveley BR, Anczuków O. Poison Exon Splicing Regulates a Coordinated Network of SR Protein Expression during Differentiation and Tumorigenesis. Mol Cell 2020; 80:648-665.e9. [PMID: 33176162 PMCID: PMC7680420 DOI: 10.1016/j.molcel.2020.10.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022]
Abstract
The RNA isoform repertoire is regulated by splicing factor (SF) expression, and alterations in SF levels are associated with disease. SFs contain ultraconserved poison exon (PE) sequences that exhibit greater identity across species than nearby coding exons, but their physiological role and molecular regulation is incompletely understood. We show that PEs in serine-arginine-rich (SR) proteins, a family of 14 essential SFs, are differentially spliced during induced pluripotent stem cell (iPSC) differentiation and in tumors versus normal tissues. We uncover an extensive cross-regulatory network of SR proteins controlling their expression via alternative splicing coupled to nonsense-mediated decay. We define sequences that regulate PE inclusion and protein expression of the oncogenic SF TRA2β using an RNA-targeting CRISPR screen. We demonstrate location dependency of RS domain activity on regulation of TRA2β-PE using CRISPR artificial SFs. Finally, we develop splice-switching antisense oligonucleotides to reverse the increased skipping of TRA2β-PE detected in breast tumors, altering breast cancer cell viability, proliferation, and migration.
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Affiliation(s)
- Nathan K Leclair
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | - Mattia Brugiolo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Laura Urbanski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | - Shane C Lawson
- Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Ketan Thakar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Marina Yurieva
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - John Travis Hinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Albert Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA; Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA; Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA; Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
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8
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Schieweck R, Ninkovic J, Kiebler MA. RNA-binding proteins balance brain function in health and disease. Physiol Rev 2020; 101:1309-1370. [PMID: 33000986 DOI: 10.1152/physrev.00047.2019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Posttranscriptional gene expression including splicing, RNA transport, translation, and RNA decay provides an important regulatory layer in many if not all molecular pathways. Research in the last decades has positioned RNA-binding proteins (RBPs) right in the center of posttranscriptional gene regulation. Here, we propose interdependent networks of RBPs to regulate complex pathways within the central nervous system (CNS). These are involved in multiple aspects of neuronal development and functioning, including higher cognition. Therefore, it is not sufficient to unravel the individual contribution of a single RBP and its consequences but rather to study and understand the tight interplay between different RBPs. In this review, we summarize recent findings in the field of RBP biology and discuss the complex interplay between different RBPs. Second, we emphasize the underlying dynamics within an RBP network and how this might regulate key processes such as neurogenesis, synaptic transmission, and synaptic plasticity. Importantly, we envision that dysfunction of specific RBPs could lead to perturbation within the RBP network. This would have direct and indirect (compensatory) effects in mRNA binding and translational control leading to global changes in cellular expression programs in general and in synaptic plasticity in particular. Therefore, we focus on RBP dysfunction and how this might cause neuropsychiatric and neurodegenerative disorders. Based on recent findings, we propose that alterations in the entire regulatory RBP network might account for phenotypic dysfunctions observed in complex diseases including neurodegeneration, epilepsy, and autism spectrum disorders.
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Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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9
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Marshall CJ, Prescott M, Campbell RE. Investigating the NPY/AgRP/GABA to GnRH Neuron Circuit in Prenatally Androgenized PCOS-Like Mice. J Endocr Soc 2020; 4:bvaa129. [PMID: 33094210 PMCID: PMC7566551 DOI: 10.1210/jendso/bvaa129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Polycystic ovary syndrome (PCOS), the most common form of anovulatory infertility, is associated with altered signaling within the hormone-sensitive neuronal network that regulates gonadotropin-releasing hormone (GnRH) neurons, leading to a pathological increase in GnRH secretion. Circuit remodeling is evident between GABAergic neurons in the arcuate nucleus (ARN) and GnRH neurons in a murine model of PCOS. One-third of ARN GABA neurons co-express neuropeptide Y (NPY), which has a known yet complex role in regulating GnRH neurons and reproductive function. Here, we investigated whether the NPY-expressing subpopulation (NPYARN) of ARN GABA neurons (GABAARN) is also affected in prenatally androgenized (PNA) PCOS-like NPYARN reporter mice [Agouti-related protein (AgRP)-Cre;τGFP]. PCOS-like mice and controls were generated by exposure to di-hydrotestosterone or vehicle (VEH) in late gestation. τGFP-expressing NPYARN neuron fiber appositions with GnRH neurons and gonadal steroid hormone receptor expression in τGFP-expressing NPYARN neurons were assessed using confocal microscopy. Although GnRH neurons received abundant close contacts from τGFP-expressing NPYARN neuron fibers, the number and density of putative inputs was not affected by prenatal androgen excess. NPYARN neurons did not co-express progesterone receptor or estrogen receptor α in either PNA or VEH mice. However, the proportion of NPYARN neurons co-expressing the androgen receptor was significantly elevated in PNA mice. Therefore, NPYARN neurons are not remodeled by prenatal androgen excess like the wider GABAARN population, indicating GABA-to-GnRH neuron circuit remodeling occurs in a presently unidentified non-NPY/AgRP population of GABAARN neurons. NPYARN neurons do, however, show independent changes in the form of elevated androgen sensitivity.
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Affiliation(s)
- Christopher J Marshall
- Centre for Neuroendocrinology and Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Melanie Prescott
- Centre for Neuroendocrinology and Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Rebecca E Campbell
- Centre for Neuroendocrinology and Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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10
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Medvedev A, Kopylov A, Buneeva O, Kurbatov L, Tikhonova O, Ivanov A, Zgoda V. A Neuroprotective Dose of Isatin Causes Multilevel Changes Involving the Brain Proteome: Prospects for Further Research. Int J Mol Sci 2020; 21:ijms21114187. [PMID: 32545384 PMCID: PMC7313464 DOI: 10.3390/ijms21114187] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/18/2022] Open
Abstract
Isatin (indole-2,3-dione) is an endogenous regulator, exhibiting a wide range of biological and pharmacological activities. At doses of 100 mg/kg and above, isatin is neuroprotective in different experimental models of neurodegeneration. Good evidence exists that its effects are realized via interaction with numerous isatin-binding proteins identified in the brain and peripheral tissues studied. In this study, we investigated the effect of a single dose administration of isatin to mice (100 mg/kg, 24 h) on differentially expressed proteins and a profile of the isatin-binding proteins in brain hemispheres. Isatin administration to mice caused downregulation of 31 proteins. However, these changes cannot be attributed to altered expression of corresponding genes. Although at this time point isatin influenced the expression of more than 850 genes in brain hemispheres (including 433 upregulated and 418 downregulated genes), none of them could account for the changes in the differentially expressed proteins. Comparative proteomic analysis of brain isatin-binding proteins of control and isatin-treated mice revealed representative groups of proteins sensitive to isatin administration. Control-specific proteins (n = 55) represent specific targets that interact directly with isatin. Appearance of brain isatin-binding proteins specific to isatin-treated mice (n = 94) may be attributed to the formation of new clusters of protein–protein interactions and/or novel binding sites induced by a high concentration of this regulator (ligand-induced binding sites). Thus, isatin administration produces multiple effects in the brain, which include changes in gene expression and also profiles of isatin-binding proteins and their interactomes. Further studies are needed for deeper insight into the mechanisms of the multilevel changes in the brain proteome induced by isatin. In the context of the neuroprotective action, these changes may be aimed at interruption of pathological links that begin to form after initiation of pathological processes.
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11
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Proteomic sift through serum and endometrium profiles unraveled signature proteins associated with subdued fertility and dampened endometrial receptivity in women with polycystic ovary syndrome. Cell Tissue Res 2020; 380:593-614. [PMID: 32052139 DOI: 10.1007/s00441-020-03171-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 01/10/2020] [Indexed: 01/20/2023]
Abstract
The objective of this study is to discern the proteomic differences responsible for hampering the receptivity of endometrium and subduing the fertility of females with polycystic ovary syndrome in analogy to healthy fertile females. This study was designed in collaboration with Hakeem Abdul Hameed Centenary Hospital affiliated to Jamia Hamdard, New Delhi, India. Serum samples were taken from infertile PCOS subjects (n = 6) and fertile control subjects (n = 6) whereas endometrial tissue samples were recruited from ovulatory PCOS (n = 4), anovulatory PCOS (n = 4) and normal healthy fertile control subjects (n = 4) for proteomic studies. Additionally, endometrial biopsies from healthy fertile control (n = 8), PCOS with infertility (n = 6), unexplained infertility (n = 3) and endometrial hyperplasia (n = 3) were taken for validation studies. Anthropometric, biochemical and hormonal evaluation was done for all the subjects enrolled in this study. Protein profiles were generated through 2D-PAGE and differential proteins analyzed with PD-QUEST software followed by identification with MALDI-TOF MS protein mass fingerprinting. Validation of identified proteins was done through RT-PCR relative expression analysis. Protein profiling of serum revealed differential expression of proteins involved in transcriptional regulation, embryogenesis, DNA repair, decidual cell ploidy, immunomodulation, intracellular trafficking and degradation processes. Proteins involved in cell cycle regulation, cellular transport and signaling, DNA repair, apoptotic processes and mitochondrial metabolism were found to be differentially expressed in endometrium. The findings of this study revealed proteins that hold strong candidature as potential drug targets to regulate the cellular processes implicating infertility and reduced receptivity of endometrium in women with polycystic ovary syndrome.
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12
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Translating neural stem cells to neurons in the mammalian brain. Cell Death Differ 2019; 26:2495-2512. [PMID: 31551564 DOI: 10.1038/s41418-019-0411-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/05/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
The mammalian neocortex underlies our perception of sensory information, performance of motor activities, and higher-order cognition. During mammalian embryogenesis, radial glial precursor cells sequentially give rise to diverse populations of excitatory cortical neurons, followed by astrocytes and oligodendrocytes. A subpopulation of these embryonic neural precursors persists into adulthood as neural stem cells, which give rise to inhibitory interneurons and glia. Although the intrinsic mechanisms instructing the genesis of these distinct progeny have been well-studied, most work to date has focused on transcriptional, epigenetic, and cell-cycle control. Recent studies, however, have shown that posttranscriptional mechanisms also regulate the cell fate choices of transcriptionally primed neural precursors during cortical development. These mechanisms are mediated primarily by RNA-binding proteins and microRNAs that coordinately regulate mRNA translation, stability, splicing, and localization. Together, these findings point to an extensive network of posttranscriptional control and provide insight into both normal cortical development and disease. They also add another layer of complexity to brain development and raise important biological questions for future investigation.
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13
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Alternatively spliced variants in Atlantic cod (Gadus morhua) support response to variable salinity environment. Sci Rep 2018; 8:11607. [PMID: 30072755 PMCID: PMC6072735 DOI: 10.1038/s41598-018-29723-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 07/14/2018] [Indexed: 12/21/2022] Open
Abstract
Analysis of gill transcriptome of the Atlantic cod from the Baltic Sea demonstrated that alternatively spliced (AS) variants may be actively involved in the process of adaptation to altered salinity. Some AS variants of different genes, like phospholipase A2 group IVC (PLA2G4C), appeared only in fish exposed to altered salinity, while other isoforms of the same genes were present in all experimental groups. Novel sequence arrangements represent 89% of all AS in the Baltic cod compared to the Atlantic population. Profiles of modified pathways suggest that regulation by AS can afford specific changes of genes expressed in response to the environment. The AS variants appear to be involved in the response to stress by modifications of signalling in apoptosis pathways, an innate immunological response and pro-inflammatory process. Present results support the hypothesis that developing new AS variants could support genome complexity and reinforce the ability to fast adapt to local environments.
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14
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Diao Y, Cui L, Chen Y, Burbridge TJ, Han W, Wirth B, Sestan N, Crair MC, Zhang J. Reciprocal Connections Between Cortex and Thalamus Contribute to Retinal Axon Targeting to Dorsal Lateral Geniculate Nucleus. Cereb Cortex 2018; 28:1168-1182. [PMID: 28334242 PMCID: PMC6059179 DOI: 10.1093/cercor/bhx028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/30/2016] [Accepted: 01/19/2017] [Indexed: 12/24/2022] Open
Abstract
The dorsal Lateral Geniculate Nucleus (dLGN) is the primary image-forming target of the retina and shares a reciprocal connection with primary visual cortex (V1). Previous studies showed that corticothalamic input is essential for the development of thalamocortical projections, but less is known about the potential role of this reciprocal connection in the development of retinal projections. Here, we show a deficit of retinal innervation in the dLGN around E18.5 in Tra2β conditional knockout (cKO) "cortexless" mice, an age when apoptosis occurs along the thalamocortical tract and in some dLGN neurons. In vivo electrophysiology experiments in the dLGN further confirmed the loss of functional retinal input. Experiments with N-methyl-d-aspartic acid-induced V1 lesion as well as Fezf2 cKO mice confirmed that the disruption of connections between the dLGN and V1 lead to abnormal retinal projections to the dLGN. Interestingly, retinal projections to the ventral Lateral Geniculate Nucleus (vLGN) and Superior Colliculus (SC) were normal in all 3 mice models. Finally, we show that the cortexless mice had worse performance than control mice in a go-no go task with visual cues. Our results provide evidence that the wiring of visual circuit from the retina to the dLGN and V1 thereafter is coordinated at a surprisingly early stage of circuit development.
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Affiliation(s)
- Yupu Diao
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Liyuan Cui
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Yuqing Chen
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | | | - Wenqi Han
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Brunhilde Wirth
- Institute of Human Genetics, Institute for Genetics, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Michael C Crair
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Jiayi Zhang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
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15
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Liu J, Bian T, Feng J, Qian L, Zhang J, Jiang D, Zhang Q, Li X, Liu Y, Shi J. miR-335 inhibited cell proliferation of lung cancer cells by target Tra2β. Cancer Sci 2017; 109:289-296. [PMID: 29161765 PMCID: PMC5797811 DOI: 10.1111/cas.13452] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/31/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
Accumulating evidence has suggested that the dysregulation of miRNA is an important factor in the pathogenesis of lung cancer. Here, we demonstrate that miR-335 expression is reduced in non-small cell lung cancer (NSCLC) tumors relative to non-cancerous adjacent tissues, while the expression of Tra2β is increased. In addition, clinical data revealed that the increased Tra2β and decreased miR-335 expression observed in NSCLC cells was associated with poor patient survival rates. In vitro experimentation showed that the overexpression of miR-335 inhibited the growth, invasion and migration capabilities of A459 lung cancer cells, by targeting Tra2β. In contrast, inhibition of miR-335 or overexpression of the Tra2β target gene stimulated the growth, invasion and migratory capabilities of A459 lung cancer cells in vitro. Furthermore, overexpression of miR-335 or inhibition of Tra2β decreased the phosphorylation of Rb-S780 and Rb-AKT. Overall, these findings suggest that the downregulation of miR-335 in A459 lung cancer cells promoted cell proliferation through upregulation of Tra2β, mediated via activation of the AKT/mTOR signaling pathway, and suggest that miR-335 may have potential as a novel therapeutic target for NSCLC.
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Affiliation(s)
- Jian Liu
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Tingting Bian
- Departments of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jia Feng
- Departments of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Li Qian
- Departments of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jianguo Zhang
- Departments of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Daishan Jiang
- Departments of Emergency medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Qing Zhang
- Departments of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xiaoli Li
- Departments of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yifei Liu
- Departments of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jiahai Shi
- Departments of Cardio-Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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16
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Lennox AL, Mao H, Silver DL. RNA on the brain: emerging layers of post-transcriptional regulation in cerebral cortex development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 7. [PMID: 28837264 DOI: 10.1002/wdev.290] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Embryonic development is a critical period during which neurons of the brain are generated and organized. In the developing cerebral cortex, this requires complex processes of neural progenitor proliferation, neuronal differentiation, and migration. Each step relies upon highly regulated control of gene expression. In particular, RNA splicing, stability, localization, and translation have emerged as key post-transcriptional regulatory nodes of mouse corticogenesis. Trans-regulators of RNA metabolism, including microRNAs (miRs) and RNA-binding proteins (RBPs), orchestrate diverse steps of cortical development. These trans-factors function either individually or cooperatively to influence RNAs, often of similar classes, termed RNA regulons. New technological advances raise the potential for an increasingly sophisticated understanding of post-transcriptional control in the developing neocortex. Many RNA-binding factors are also implicated in neurodevelopmental diseases of the cortex. Therefore, elucidating how RBPs and miRs converge to influence mRNA expression in progenitors and neurons will give valuable insights into mechanisms of cortical development and disease. WIREs Dev Biol 2018, 7:e290. doi: 10.1002/wdev.290 This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory RNA Nervous System Development > Vertebrates: Regional Development Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cells and Disease.
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Affiliation(s)
- Ashley L Lennox
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Hanqian Mao
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.,Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
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17
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Corticothalamic Axons Are Essential for Retinal Ganglion Cell Axon Targeting to the Mouse Dorsal Lateral Geniculate Nucleus. J Neurosci 2017; 36:5252-63. [PMID: 27170123 DOI: 10.1523/jneurosci.4599-15.2016] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/25/2016] [Indexed: 01/21/2023] Open
Abstract
UNLABELLED Retinal ganglion cells (RGCs) relay information about the outside world to multiple subcortical targets within the brain. This information is either used to dictate reflexive behaviors or relayed to the visual cortex for further processing. Many subcortical visual nuclei also receive descending inputs from projection neurons in the visual cortex. Most areas receive inputs from layer 5 cortical neurons in the visual cortex but one exception is the dorsal lateral geniculate nucleus (dLGN), which receives layer 6 inputs and is also the only RGC target that sends direct projections to the cortex. Here we ask how visual system development and function changes in mice that develop without a cortex. We find that the development of a cortex is essential for RGC axons to terminate in the dLGN, but is not required for targeting RGC axons to other subcortical nuclei. RGC axons also fail to target to the dLGN in mice that specifically lack cortical layer 6 projections to the dLGN. Finally, we show that when mice develop without a cortex they can still perform a number of vision-dependent tasks. SIGNIFICANCE STATEMENT The dorsal lateral geniculate nucleus (dLGN) is a sensory thalamic relay area that receives feedforward inputs from retinal ganglion cells (RGCs) in the retina, and feed back inputs from layer 6 neurons in the visual cortex. In this study we examined genetically manipulated mice that develop without a cortex or without cortical layer 6 axonal projections, and find that RGC axons fail to project to the dLGN. Other RGC recipient areas, such as the superior colliculus and suprachiasmatic nucleus, are targeted normally. These results provide support for a new mechanism of target selection that may be specific to the thalamus, whereby descending cortical axons provide an activity that promotes feedforward targeting of RGC axons to the dLGN.
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18
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Kanemitsu Y, Fujitani M, Fujita Y, Zhang S, Su YQ, Kawahara Y, Yamashita T. The RNA-binding protein MARF1 promotes cortical neurogenesis through its RNase activity domain. Sci Rep 2017; 7:1155. [PMID: 28442784 PMCID: PMC5430739 DOI: 10.1038/s41598-017-01317-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/27/2017] [Indexed: 01/14/2023] Open
Abstract
Cortical neurogenesis is a fundamental process of brain development that is spatiotemporally regulated by both intrinsic and extrinsic cues. Although recent evidence has highlighted the significance of transcription factors in cortical neurogenesis, little is known regarding the role of RNA-binding proteins (RBPs) in the post-transcriptional regulation of cortical neurogenesis. Here, we report that meiosis arrest female 1 (MARF1) is an RBP that is expressed during neuronal differentiation. Cortical neurons expressed the somatic form of MARF1 (sMARF1) but not the oocyte form (oMARF1). sMARF1 was enriched in embryonic brains, and its expression level decreased as brain development progressed. Overexpression of sMARF1 in E12.5 neuronal progenitor cells promoted neuronal differentiation, whereas sMARF1 knockdown decreased neuronal progenitor differentiation in vitro. We also examined the function of sMARF1 in vivo using an in utero electroporation technique. Overexpression of sMARF1 increased neuronal differentiation, whereas knockdown of sMARF1 inhibited differentiation in vivo. Moreover, using an RNase domain deletion mutant of sMARF1, we showed that the RNase domain is required for the effects of sMARF1 on cortical neurogenesis in vitro. Our results further elucidate the mechanisms of post-transcriptional regulation of cortical neurogenesis by RBPs.
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Affiliation(s)
- Yoshitaka Kanemitsu
- Department of Molecular Neuroscience, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Interdisciplinary Program for Biomedical Sciences, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masashi Fujitani
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0872, Japan. .,Department of Anatomy and Neuroscience, Hyogo College of Medicine, 1-1, Mukogawa-cho, Nishinomiya, Hyogo, 663-8501, Japan.
| | - Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Suxiang Zhang
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - You-Qiang Su
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 140 Hanzhong Road, Nanjing, 210029, Jiangsu Province, China
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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19
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Abstract
Tumor-associated alterations in RNA splicing result either from mutations in splicing-regulatory elements or changes in components of the splicing machinery. This review summarizes our current understanding of the role of splicing-factor alterations in human cancers. We describe splicing-factor alterations detected in human tumors and the resulting changes in splicing, highlighting cell-type-specific similarities and differences. We review the mechanisms of splicing-factor regulation in normal and cancer cells. Finally, we summarize recent efforts to develop novel cancer therapies, based on targeting either the oncogenic splicing events or their upstream splicing regulators.
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Affiliation(s)
- Olga Anczuków
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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Shanks JA, Ito S, Schaevitz L, Yamada J, Chen B, Litke A, Feldheim DA. Corticothalamic Axons Are Essential for Retinal Ganglion Cell Axon Targeting to the Mouse Dorsal Lateral Geniculate Nucleus. J Neurosci 2016. [PMID: 27170123 DOI: 10.6080/k07d2s2f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023] Open
Abstract
UNLABELLED Retinal ganglion cells (RGCs) relay information about the outside world to multiple subcortical targets within the brain. This information is either used to dictate reflexive behaviors or relayed to the visual cortex for further processing. Many subcortical visual nuclei also receive descending inputs from projection neurons in the visual cortex. Most areas receive inputs from layer 5 cortical neurons in the visual cortex but one exception is the dorsal lateral geniculate nucleus (dLGN), which receives layer 6 inputs and is also the only RGC target that sends direct projections to the cortex. Here we ask how visual system development and function changes in mice that develop without a cortex. We find that the development of a cortex is essential for RGC axons to terminate in the dLGN, but is not required for targeting RGC axons to other subcortical nuclei. RGC axons also fail to target to the dLGN in mice that specifically lack cortical layer 6 projections to the dLGN. Finally, we show that when mice develop without a cortex they can still perform a number of vision-dependent tasks. SIGNIFICANCE STATEMENT The dorsal lateral geniculate nucleus (dLGN) is a sensory thalamic relay area that receives feedforward inputs from retinal ganglion cells (RGCs) in the retina, and feed back inputs from layer 6 neurons in the visual cortex. In this study we examined genetically manipulated mice that develop without a cortex or without cortical layer 6 axonal projections, and find that RGC axons fail to project to the dLGN. Other RGC recipient areas, such as the superior colliculus and suprachiasmatic nucleus, are targeted normally. These results provide support for a new mechanism of target selection that may be specific to the thalamus, whereby descending cortical axons provide an activity that promotes feedforward targeting of RGC axons to the dLGN.
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Affiliation(s)
- James A Shanks
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Shinya Ito
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, Santa Cruz, California 95064, and
| | - Laura Schaevitz
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064, Department of Biology, Trinity College, Hartford, Connecticut 06106
| | - Jena Yamada
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Alan Litke
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, Santa Cruz, California 95064, and
| | - David A Feldheim
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064,
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21
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Pilaz LJ, Silver DL. Post-transcriptional regulation in corticogenesis: how RNA-binding proteins help build the brain. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:501-15. [PMID: 26088328 DOI: 10.1002/wrna.1289] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/01/2015] [Accepted: 05/01/2015] [Indexed: 12/17/2022]
Abstract
The cerebral cortex, the brain structure responsible for our higher cognitive functions, is built during embryonic development in a process called corticogenesis. During corticogenesis, neural stem cells generate distinct populations of progenitors and excitatory neurons. These new neurons migrate radially in the cortex, eventually forming neuronal layers and establishing synaptic connections with other neurons both within and outside the cortex. Perturbations to corticogenesis can result in severe neurodevelopmental disorders, thus emphasizing the need to better understand molecular regulation of brain development. Recent studies in both model organisms and humans have collectively highlighted roles for post-transcriptional regulation in virtually all steps of corticogenesis. Genomic approaches have revealed global RNA changes associated with spatial and temporal regulation of cortical development. Additionally, genetic studies have uncovered RNA-binding proteins (RBPs) critical for cell proliferation, differentiation, and migration within the developing neocortex. Many of these same RBPs play causal roles in neurodevelopmental pathologies. In the developing neocortex, RBPs influence diverse steps of mRNA metabolism, including splicing, stability, translation, and localization. With the advent of new technologies, researchers have begun to uncover key transcripts regulated by these RBPs. Given the complexity of the developing mammalian cortex, a major challenge for the future will be to understand how dynamic RNA regulation occurs within heterogeneous cell populations, across space and time. In sum, post-transcriptional regulation has emerged as a critical mechanism for driving corticogenesis and exciting direction of future research.
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Affiliation(s)
- Louis-Jan Pilaz
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.,Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.,Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
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22
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Diao Y, Wu D, Dai Z, Kang H, Wang Z, Wang X. Prognostic value of transformer 2β expression in prostate cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:6967-6973. [PMID: 26261585 PMCID: PMC4525919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/17/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Deregulation of transformer 2β (Tra2β) has been implicated in several cancers. However, the role of Tra2β expression in prostate cancer (PCa) is unclear. Therefore, this study was to investigate the expression of Tra2β in PCa and evaluated its association with clinicopathological variables and prognosis. METHODS Thirty paired fresh PCa samples were analyzed for Tra2β expression by Western blot analysis. Immunohistochemistry (IHC) assay was performed in 160 PCa samples after radical prostatectomy and adjacent non-cancerous tissues. Tra2β protein expression was divided into high expression group and low expression group by IHC. We also investigated the association of Tra2β expression with clinical and pathologic parameters. Kaplan-Meier plots and Cox proportional hazards regression model were used to analyze the association between Tra2β protein expression and prognosis of PCa patients. Our results showed that Tra2β was significantly upregulated in PCa tissues by western blot and IHC. RESULTS Our data indicated that high expression of Tra2β was significantly associated with lymph node metastasis (P=0.002), clinical stage (P=0.015), preoperative prostate-specific antigen (P=0.003), Gleason score (P=0.001), and biochemical recurrence (P=0.021). High Tra2β expression was a significant predictor of poor biochemical recurrence free survival and overall survival both in univariate and multivariate analysis. CONCLUSION We show that Tra2β was significantly upregulated in PCa patients after radical prostatectomy, and multivariate analysis confirmed Tra2β as an independent prognostic factor.
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Affiliation(s)
- Yan Diao
- Department of Oncology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong UniversityXi’an, People’s Republic of China
| | - Dong Wu
- Department of Emergency, Shaanxi Provincial People’s HospitalXi’an, People’s Republic of China
| | - Zhijun Dai
- Department of Oncology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong UniversityXi’an, People’s Republic of China
| | - Huafeng Kang
- Department of Oncology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong UniversityXi’an, People’s Republic of China
| | - Ziming Wang
- Department of Urology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong UniversityXi’an, People’s Republic of China
| | - Xijing Wang
- Department of Oncology, Second Affiliated Hospital, Medical School of Xi’an Jiaotong UniversityXi’an, People’s Republic of China
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23
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Abstract
Tra2 proteins regulate pre-mRNA splicing in vertebrates and invertebrates, and are involved in important processes ranging from brain development in mice to sex determination in fruitflies. In structure Tra2 proteins contain two RS domains (domains enriched in arginine and serine residues) flanking a central RRM (RNA recognition motif). Understanding the mechanisms of how Tra2 proteins work to control splicing is one of the key requirements to understand their biology. In the present article, we review what is known about how Tra2 proteins regulate splicing decisions in mammals and fruitflies.
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24
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Dichmann DS, Walentek P, Harland RM. The alternative splicing regulator Tra2b is required for somitogenesis and regulates splicing of an inhibitory Wnt11b isoform. Cell Rep 2015; 10:527-36. [PMID: 25620705 DOI: 10.1016/j.celrep.2014.12.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/25/2014] [Accepted: 12/18/2014] [Indexed: 11/18/2022] Open
Abstract
Alternative splicing is pervasive in vertebrates, yet little is known about most isoforms or their regulation. transformer-2b (tra2b) encodes a splicing regulator whose endogenous function is poorly understood. Tra2b knockdown in Xenopus results in embryos with multiple defects, including defective somitogenesis. Using RNA sequencing, we identify 142 splice changes (mostly intron retention and exon skipping), 89% of which are not in current annotations. A previously undescribed isoform of wnt11b retains the last intron, resulting in a truncated ligand (Wnt11b-short). We show that this isoform acts as a dominant-negative ligand in cardiac gene induction and pronephric tubule formation. To determine the contribution of Wnt11b-short to the tra2b phenotype, we induce retention of intron 4 in wnt11b, which recapitulates the failure to form somites but not other tra2b morphant defects. This alternative splicing of a Wnt ligand adds intricacy to a complex signaling pathway and highlights intron retention as a regulatory mechanism.
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Affiliation(s)
- Darwin S Dichmann
- Department of Molecular & Cell Biology, 142 Life Sciences Addition #3200, University of California, Berkeley, Berkeley, CA 94720-3200, USA.
| | - Peter Walentek
- Department of Molecular & Cell Biology, 142 Life Sciences Addition #3200, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Richard M Harland
- Department of Molecular & Cell Biology, 142 Life Sciences Addition #3200, University of California, Berkeley, Berkeley, CA 94720-3200, USA.
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25
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Best A, James K, Dalgliesh C, Hong E, Kheirolahi-Kouhestani M, Curk T, Xu Y, Danilenko M, Hussain R, Keavney B, Wipat A, Klinck R, Cowell IG, Cheong Lee K, Austin CA, Venables JP, Chabot B, Santibanez Koref M, Tyson-Capper A, Elliott DJ. Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons. Nat Commun 2014; 5:4760. [PMID: 25208576 PMCID: PMC4175592 DOI: 10.1038/ncomms5760] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/22/2014] [Indexed: 01/11/2023] Open
Abstract
Alternative splicing--the production of multiple messenger RNA isoforms from a single gene--is regulated in part by RNA binding proteins. While the RBPs transformer2 alpha (Tra2α) and Tra2β have both been implicated in the regulation of alternative splicing, their relative contributions to this process are not well understood. Here we find simultaneous--but not individual--depletion of Tra2α and Tra2β induces substantial shifts in splicing of endogenous Tra2β target exons, and that both constitutive and alternative target exons are under dual Tra2α-Tra2β control. Target exons are enriched in genes associated with chromosome biology including CHEK1, which encodes a key DNA damage response protein. Dual Tra2 protein depletion reduces expression of full-length CHK1 protein, results in the accumulation of the DNA damage marker γH2AX and decreased cell viability. We conclude Tra2 proteins jointly control constitutive and alternative splicing patterns via paralog compensation to control pathways essential to the maintenance of cell viability.
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Affiliation(s)
- Andrew Best
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Katherine James
- School of Computing Science, Claremont Tower, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Caroline Dalgliesh
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Elaine Hong
- Institute for Cellular Medicine, Newcastle University, Framlington Place, Newcastle NE2 4HH, UK
| | | | - Tomaz Curk
- Faculty of Computer and Information Science, University of Ljubljana, Trzaska cesta 25, SI-1000, Ljubljana, Slovenia
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Marina Danilenko
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Rafiq Hussain
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Bernard Keavney
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
- Institute of Cardiovascular Sciences, The University of Manchester, Manchester M13 9NT, UK
| | - Anil Wipat
- School of Computing Science, Claremont Tower, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Roscoe Klinck
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Ian G. Cowell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle NE2 4HH, UK
| | - Ka Cheong Lee
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle NE2 4HH, UK
| | - Caroline A. Austin
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle NE2 4HH, UK
| | - Julian P. Venables
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Mauro Santibanez Koref
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Alison Tyson-Capper
- Institute for Cellular Medicine, Newcastle University, Framlington Place, Newcastle NE2 4HH, UK
| | - David J. Elliott
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
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26
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Liu SM, Chen W, Wang J. Distinguishing between cancer cell differentiation and resistance induced by all-trans retinoic acid using transcriptional profiles and functional pathway analysis. Sci Rep 2014; 4:5577. [PMID: 24993014 PMCID: PMC4894425 DOI: 10.1038/srep05577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/18/2014] [Indexed: 11/03/2022] Open
Abstract
All-trans retinoic acid (ATRA) induces differentiation in various cell types and has been investigated extensively for its effective use in cancer prevention and treatment. Relapsed or refractory disease that is resistant to ATRA is a clinically significant problem. To identify the molecular mechanism that bridges ATRA differentiation and resistance in cancer, we selected the multidrug-resistant leukemia cell line HL-60[R] by exposing it to ATRA, followed by sequential increases of one-half log concentration. A cytotoxicity analysis revealed that HL-60[R] cells were highly resistant to ATRA, doxorubicin, and etoposide. A comparative genome hybridization analysis of HL-60[R] cells identified gains of 4q34, 9q12, and 19q13 and a loss of Yq12 compared with in the parental HL-60 cell line. Transcriptional profiles and functional pathway analyses further demonstrated that 7 genes (FEN1, RFC5, EXO1, XRCC5, PARP1, POLR2F, and GTF2H3) that were relatively up-regulated in HL-60[R] cells and repressed in cells with ATRA-induced differentiation were related to mismatch repair in eukaryotes, DNA double-strand break repair, and nucleotide excision repair pathways. Our results suggest that transcriptional time series profiles and a functional pathway analysis of drug resistance and ATRA-induced cell differentiation will be useful for identifying promyelocytic leukemia patients who are eligible for new therapeutic strategies.
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Affiliation(s)
- Song-Mei Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Weiping Chen
- Microarray Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jin Wang
- Department of Translational Molecular Pathology, The University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Transformer 2β (Tra2β/SFRS10) positively regulates the progression of NSCLC via promoting cell proliferation. J Mol Histol 2014; 45:573-82. [DOI: 10.1007/s10735-014-9582-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
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28
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Storbeck M, Hupperich K, Gaspar JA, Meganathan K, Martínez Carrera L, Wirth R, Sachinidis A, Wirth B. Neuronal-specific deficiency of the splicing factor Tra2b causes apoptosis in neurogenic areas of the developing mouse brain. PLoS One 2014; 9:e89020. [PMID: 24586484 PMCID: PMC3929626 DOI: 10.1371/journal.pone.0089020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/13/2014] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) increases the informational content of the genome and is more prevalent in the brain than in any other tissue. The splicing factor Tra2b (Sfrs10) can modulate splicing inclusion of exons by specifically detecting GAA-rich binding motifs and its absence causes early embryonic lethality in mice. TRA2B has been shown to be involved in splicing processes of Nasp (nuclear autoantigenic sperm protein), MAPT (microtubule associated protein tau) and SMN (survival motor neuron), and is therefore implicated in spermatogenesis and neurological diseases like Alzheimer’s disease, dementia, Parkinson’s disease and spinal muscular atrophy. Here we generated a neuronal-specific Tra2b knock-out mouse that lacks Tra2b expression in neuronal and glial precursor cells by using the Nestin-Cre. Neuronal-specific Tra2b knock-out mice die immediately after birth and show severe abnormalities in cortical development, which are caused by massive apoptotic events in the ventricular layers of the cortex, demonstrating a pivotal role of Tra2b for the developing central nervous system. Using whole brain RNA on exon arrays we identified differentially expressed alternative exons of Tubulinδ1 and Shugoshin-like2 as in vivo targets of Tra2b. Most interestingly, we found increased expression of the cyclin dependent kinase inhibitor 1a (p21) which we could functionally link to neuronal precursor cells in the affected brain regions. We provide further evidence that the absence of Tra2b causes p21 upregulation and ultimately cell death in NSC34 neuronal-like cells. These findings demonstrate that Tra2b regulates splicing events essential for maintaining neuronal viability during development. Apoptotic events triggered via p21 might not be restricted to the developing brain but could possibly be generalized to the whole organism and explain early embryonic lethality in Tra2b-depleted mice.
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Affiliation(s)
- Markus Storbeck
- Institute of Human Genetics, University of Cologne, Cologne, Germany
- Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Kristina Hupperich
- Institute of Human Genetics, University of Cologne, Cologne, Germany
- Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | | | | | - Lilian Martínez Carrera
- Institute of Human Genetics, University of Cologne, Cologne, Germany
- Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Radu Wirth
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | | | - Brunhilde Wirth
- Institute of Human Genetics, University of Cologne, Cologne, Germany
- Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- * E-mail:
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29
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Genomics of alternative splicing: evolution, development and pathophysiology. Hum Genet 2014; 133:679-87. [PMID: 24378600 DOI: 10.1007/s00439-013-1411-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/15/2013] [Indexed: 12/11/2022]
Abstract
Alternative splicing is a major cellular mechanism in metazoans for generating proteomic diversity. A large proportion of protein-coding genes in multicellular organisms undergo alternative splicing, and in humans, it has been estimated that nearly 90 % of protein-coding genes-much larger than expected-are subject to alternative splicing. Genomic analyses of alternative splicing have illuminated its universal role in shaping the evolution of genomes, in the control of developmental processes, and in the dynamic regulation of the transcriptome to influence phenotype. Disruption of the splicing machinery has been found to drive pathophysiology, and indeed reprogramming of aberrant splicing can provide novel approaches to the development of molecular therapy. This review focuses on the recent progress in our understanding of alternative splicing brought about by the unprecedented explosive growth of genomic data and highlights the relevance of human splicing variation on disease and therapy.
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