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Anczukow O, Allain FHT, Angarola BL, Black DL, Brooks AN, Cheng C, Conesa A, Crosse EI, Eyras E, Guccione E, Lu SX, Neugebauer KM, Sehgal P, Song X, Tothova Z, Valcárcel J, Weeks KM, Yeo GW, Thomas-Tikhonenko A. Steering research on mRNA splicing in cancer towards clinical translation. Nat Rev Cancer 2024:10.1038/s41568-024-00750-2. [PMID: 39384951 DOI: 10.1038/s41568-024-00750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 10/11/2024]
Abstract
Splicing factors are affected by recurrent somatic mutations and copy number variations in several types of haematologic and solid malignancies, which is often seen as prima facie evidence that splicing aberrations can drive cancer initiation and progression. However, numerous spliceosome components also 'moonlight' in DNA repair and other cellular processes, making their precise role in cancer difficult to pinpoint. Still, few would deny that dysregulated mRNA splicing is a pervasive feature of most cancers. Correctly interpreting these molecular fingerprints can reveal novel tumour vulnerabilities and untapped therapeutic opportunities. Yet multiple technological challenges, lingering misconceptions, and outstanding questions hinder clinical translation. To start with, the general landscape of splicing aberrations in cancer is not well defined, due to limitations of short-read RNA sequencing not adept at resolving complete mRNA isoforms, as well as the shallow read depth inherent in long-read RNA-sequencing, especially at single-cell level. Although individual cancer-associated isoforms are known to contribute to cancer progression, widespread splicing alterations could be an equally important and, perhaps, more readily actionable feature of human cancers. This is to say that in addition to 'repairing' mis-spliced transcripts, possible therapeutic avenues include exacerbating splicing aberration with small-molecule spliceosome inhibitors, targeting recurrent splicing aberrations with synthetic lethal approaches, and training the immune system to recognize splicing-derived neoantigens.
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Affiliation(s)
- Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
| | - Frédéric H-T Allain
- Department of Biology, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | | | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Chonghui Cheng
- Department of Molecular and Human Genetics, Lester & Sue Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Spain
| | - Edie I Crosse
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Eduardo Eyras
- Shine-Dalgarno Centre for RNA Innovation, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Ernesto Guccione
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY, USA
| | - Sydney X Lu
- Department of Medicine, Stanford Medical School, Palo Alto, CA, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Priyanka Sehgal
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiao Song
- Department of Neurology, Northwestern University, Chicago, IL, USA
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Juan Valcárcel
- Centre for Genomic Regulation, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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2
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Karasu ME, Jahnke L, Joseph BJ, Amerzhanova Y, Mironov A, Shu X, Schröder MS, Gvozdenovic A, Sala I, Zavolan M, Jonas S, Corn JE. CCAR1 promotes DNA repair via alternative splicing. Mol Cell 2024; 84:2634-2647.e9. [PMID: 38964321 DOI: 10.1016/j.molcel.2024.06.011] [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: 04/29/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024]
Abstract
DNA repair is directly performed by hundreds of core factors and indirectly regulated by thousands of others. We massively expanded a CRISPR inhibition and Cas9-editing screening system to discover factors indirectly modulating homology-directed repair (HDR) in the context of ∼18,000 individual gene knockdowns. We focused on CCAR1, a poorly understood gene that we found the depletion of reduced both HDR and interstrand crosslink repair, phenocopying the loss of the Fanconi anemia pathway. CCAR1 loss abrogated FANCA protein without substantial reduction in the level of its mRNA or that of other FA genes. We instead found that CCAR1 prevents inclusion of a poison exon in FANCA. Transcriptomic analysis revealed that the CCAR1 splicing modulatory activity is not limited to FANCA, and it instead regulates widespread changes in alternative splicing that would damage coding sequences in mouse and human cells. CCAR1 therefore has an unanticipated function as a splicing fidelity factor.
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Affiliation(s)
- Mehmet E Karasu
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Leonard Jahnke
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Brian J Joseph
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Yerkezhan Amerzhanova
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Aleksei Mironov
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Xuan Shu
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Markus S Schröder
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Ana Gvozdenovic
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Irene Sala
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Jacob E Corn
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland.
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3
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Harada N, Asada S, Jiang L, Nguyen H, Moreau L, Marina RJ, Adelman K, Iyer DR, D'Andrea AD. The splicing factor CCAR1 regulates the Fanconi anemia/BRCA pathway. Mol Cell 2024; 84:2618-2633.e10. [PMID: 39025073 PMCID: PMC11321822 DOI: 10.1016/j.molcel.2024.06.031] [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: 09/06/2023] [Revised: 05/15/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
The twenty-three Fanconi anemia (FA) proteins cooperate in the FA/BRCA pathway to repair DNA interstrand cross-links (ICLs). The cell division cycle and apoptosis regulator 1 (CCAR1) protein is also a regulator of ICL repair, though its possible function in the FA/BRCA pathway remains unknown. Here, we demonstrate that CCAR1 plays a unique upstream role in the FA/BRCA pathway and is required for FANCA protein expression in human cells. Interestingly, CCAR1 co-immunoprecipitates with FANCA pre-mRNA and is required for FANCA mRNA processing. Loss of CCAR1 results in retention of a poison exon in the FANCA transcript, thereby leading to reduced FANCA protein expression. A unique domain of CCAR1, the EF hand domain, is required for interaction with the U2AF heterodimer of the spliceosome and for excision of the poison exon. Taken together, CCAR1 is a splicing modulator required for normal splicing of the FANCA mRNA and other mRNAs involved in various cellular pathways.
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Affiliation(s)
- Naoya Harada
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Shuhei Asada
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Lige Jiang
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Huy Nguyen
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Lisa Moreau
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ryan J Marina
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Divya R Iyer
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
| | - Alan D D'Andrea
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
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Shirakawa Y, Li H, Inoue Y, Izumi H, Kaga Y, Goto YI, Inoue K, Inagaki M. Abnormality in GABAergic postsynaptic transmission associated with anxiety in Bronx waltzer mice with an Srrm4 mutation. IBRO Neurosci Rep 2024; 16:67-77. [PMID: 38229888 PMCID: PMC10790029 DOI: 10.1016/j.ibneur.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024] Open
Abstract
The homozygous Bronx waltzer (bv) mouse, which shows hearing impairment, also exhibits anxiety accompanied by a reduction in cortical parvalbumin (PV)-positive GABAergic interneurons. Recently, a mutation in splicing factor Ser/Arg repetitive matrix 4 (Srrm4) was found in bv mice. However, the cellular consequences of the Srrm4 mutation for anxiety remain unknown. Here, we tested our hypothesis that bv mutant primarily affects interneurons through a cell-intrinsic pathology that leads to a reduction of interneurons and consequently causes anxiety. We found that the anxiety becomes apparent at 6 weeks of age in bv/bv mice. However, in situ hybridization revealed that Srrm4 is not expressed in interneurons, but rather dominates in pyramidal neurons. In addition, the PV-positive GABAergic interneurons were not reduced in number in the bv/bv cortex when anxiety became evident. However, electrophysiological abnormality of GABAergic transmission from interneurons was concomitantly present. Pharmacological blockage of GABAA receptors revealed increased excitability in bv/bv mice, although no gross change occurred in the expression of an Srrm4-downstream gene, Kcc2, which regulates chloride flux upon GABAergic transmission. These findings suggest that the bv-associated Srrm4 mutation mainly involves post-synaptic GABAergic transmission in the central nervous system, which may be associated with the anxiety phenotype in bv/bv mice.
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Affiliation(s)
- Yuka Shirakawa
- Department of Developmental Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4–1-1 Ogawa Higashi, Kodaira, Tokyo 187–8553, Japan
| | - Heng Li
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4–1-1 Ogawa Higashi, Kodaira, Tokyo 187–8553, Japan
| | - Yuki Inoue
- Department of Developmental Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4–1-1 Ogawa Higashi, Kodaira, Tokyo 187–8553, Japan
| | - Hitomi Izumi
- Department of Developmental Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4–1-1 Ogawa Higashi, Kodaira, Tokyo 187–8553, Japan
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4–1-1 Ogawa Higashi, Kodaira, Tokyo 187–8553, Japan
| | - Yoshimi Kaga
- Department of Developmental Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4–1-1 Ogawa Higashi, Kodaira, Tokyo 187–8553, Japan
| | - Yu-ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4–1-1 Ogawa Higashi, Kodaira, Tokyo 187–8553, Japan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4–1-1 Ogawa Higashi, Kodaira, Tokyo 187–8553, Japan
| | - Masumi Inagaki
- Department of Developmental Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4–1-1 Ogawa Higashi, Kodaira, Tokyo 187–8553, Japan
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Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science 2024; 384:eadh7688. [PMID: 38781356 DOI: 10.1126/science.adh7688] [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: 03/15/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders; yet, the role of cell type-specific splicing and transcript-isoform diversity during human brain development has not been systematically investigated. In this work, we leveraged single-molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone and cortical plate regions of the developing human neocortex at tissue and single-cell resolution. We identified 214,516 distinct isoforms, of which 72.6% were novel (not previously annotated in Gencode version 33), and uncovered a substantial contribution of transcript-isoform diversity-regulated by RNA binding proteins-in defining cellular identity in the developing neocortex. We leveraged this comprehensive isoform-centric gene annotation to reprioritize thousands of rare de novo risk variants and elucidate genetic risk mechanisms for neuropsychiatric disorders.
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Affiliation(s)
- Ashok Patowary
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Pan Zhang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Connor Jops
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Celine K Vuong
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xinzhou Ge
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Minsoo Kim
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Naihua Gong
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Margolis
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Vo
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jingyi Jessica Li
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Luis de la Torre-Ubieta
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
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Ciampi L, Serrano L, Irimia M. Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States. Mol Syst Biol 2024; 20:296-310. [PMID: 38438733 PMCID: PMC10987577 DOI: 10.1038/s44320-024-00020-1] [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: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 03/06/2024] Open
Abstract
Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.
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Affiliation(s)
- Ludovica Ciampi
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Luis Serrano
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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7
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Engal E, Zhang Z, Geminder O, Jaffe-Herman S, Kay G, Ben-Hur A, Salton M. The spectrum of pre-mRNA splicing in autism. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1838. [PMID: 38509732 DOI: 10.1002/wrna.1838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Disruptions in spatiotemporal gene expression can result in atypical brain function. Specifically, autism spectrum disorder (ASD) is characterized by abnormalities in pre-mRNA splicing. Abnormal splicing patterns have been identified in the brains of individuals with ASD, and mutations in splicing factors have been found to contribute to neurodevelopmental delays associated with ASD. Here we review studies that shed light on the importance of splicing observed in ASD and that explored the intricate relationship between splicing factors and ASD, revealing how disruptions in pre-mRNA splicing may underlie ASD pathogenesis. We provide an overview of the research regarding all splicing factors associated with ASD and place a special emphasis on five specific splicing factors-HNRNPH2, NOVA2, WBP4, SRRM2, and RBFOX1-known to impact the splicing of ASD-related genes. In the discussion of the molecular mechanisms influenced by these splicing factors, we lay the groundwork for a deeper understanding of ASD's complex etiology. Finally, we discuss the potential benefit of unraveling the connection between splicing and ASD for the development of more precise diagnostic tools and targeted therapeutic interventions. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Evolution and Genomics > Computational Analyses of RNA RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
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Affiliation(s)
- Eden Engal
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zhenwei Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Jaffe-Herman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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8
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Han KA, Yoon TH, Kim J, Lee J, Lee JY, Jang G, Um JW, Kim JK, Ko J. Specification of neural circuit architecture shaped by context-dependent patterned LAR-RPTP microexons. Nat Commun 2024; 15:1624. [PMID: 38388459 PMCID: PMC10883964 DOI: 10.1038/s41467-024-45695-0] [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: 07/13/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
LAR-RPTPs are evolutionarily conserved presynaptic cell-adhesion molecules that orchestrate multifarious synaptic adhesion pathways. Extensive alternative splicing of LAR-RPTP mRNAs may produce innumerable LAR-RPTP isoforms that act as regulatory "codes" for determining the identity and strength of specific synapse signaling. However, no direct evidence for this hypothesis exists. Here, using targeted RNA sequencing, we detected LAR-RPTP mRNAs in diverse cell types across adult male mouse brain areas. We found pronounced cell-type-specific patterns of two microexons, meA and meB, in Ptprd mRNAs. Moreover, diverse neural circuits targeting the same neuronal populations were dictated by the expression of different Ptprd variants with distinct inclusion patterns of microexons. Furthermore, conditional ablation of Ptprd meA+ variants at presynaptic loci of distinct hippocampal circuits impaired distinct modes of synaptic transmission and objection-location memory. Activity-triggered alterations of the presynaptic Ptprd meA code in subicular neurons mediates NMDA receptor-mediated postsynaptic responses in CA1 neurons and objection-location memory. Our data provide the evidence of cell-type- and/or circuit-specific expression patterns in vivo and physiological functions of LAR-RPTP microexons that are dynamically regulated.
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Affiliation(s)
- Kyung Ah Han
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
- Center for Synapse Diversity and Specificity, DGIST, Daegu, 42988, Korea
| | - Taek-Han Yoon
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
| | - Jinhu Kim
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
| | - Jusung Lee
- Department of New Biology, DGIST, Daegu, 42988, Korea
| | - Ju Yeon Lee
- Korea Basic Science Institute, Research Center for Bioconvergence Analysis, Cheongju, 28119, Korea
| | - Gyubin Jang
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
- Center for Synapse Diversity and Specificity, DGIST, Daegu, 42988, Korea
| | - Ji Won Um
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
- Center for Synapse Diversity and Specificity, DGIST, Daegu, 42988, Korea
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu, 42988, Korea
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Jaewon Ko
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea.
- Center for Synapse Diversity and Specificity, DGIST, Daegu, 42988, Korea.
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9
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Lee S, Aubee JI, Lai EC. Regulation of alternative splicing and polyadenylation in neurons. Life Sci Alliance 2023; 6:e202302000. [PMID: 37793776 PMCID: PMC10551640 DOI: 10.26508/lsa.202302000] [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: 02/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Cell-type-specific gene expression is a fundamental feature of multicellular organisms and is achieved by combinations of regulatory strategies. Although cell-restricted transcription is perhaps the most widely studied mechanism, co-transcriptional and post-transcriptional processes are also central to the spatiotemporal control of gene functions. One general category of expression control involves the generation of multiple transcript isoforms from an individual gene, whose balance and cell specificity are frequently tightly regulated via diverse strategies. The nervous system makes particularly extensive use of cell-specific isoforms, specializing the neural function of genes that are expressed more broadly. Here, we review regulatory strategies and RNA-binding proteins that direct neural-specific isoform processing. These include various classes of alternative splicing and alternative polyadenylation events, both of which broadly diversify the neural transcriptome. Importantly, global alterations of splicing and alternative polyadenylation are characteristic of many neural pathologies, and recent genetic studies demonstrate how misregulation of individual neural isoforms can directly cause mutant phenotypes.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Joseph I Aubee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
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10
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Porter RS, Nagai M, An S, Gavilan MC, Murata-Nakamura Y, Bonefas KM, Zhou B, Dionne O, Manuel JM, St-Germain J, Browning L, Laurent B, Cho US, Iwase S. A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563357. [PMID: 37904995 PMCID: PMC10614952 DOI: 10.1101/2023.10.20.563357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
How cell-type-specific chromatin landscapes emerge and progress during metazoan ontogenesis remains an important question. Transcription factors are expressed in a cell-type-specific manner and recruit chromatin-regulatory machinery to specific genomic loci. In contrast, chromatin-regulatory proteins are expressed broadly and are assumed to exert the same intrinsic function across cell types. However, human genetics studies have revealed an unexpected vulnerability of neurodevelopment to chromatin factor mutations with unknown mechanisms. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Of the 14 chromatin regulators, two are integral components of a histone H3K4 demethylase complex; the catalytic subunit LSD1 and an H3K4me0-reader protein PHF21A adopt neuron-specific forms. We found that canonical PHF21A (PHF21A-c) binds to DNA by AT-hook motif, and the neuronal counterpart PHF21A-n lacks this DNA-binding function yet maintains H3K4me0 recognition intact. In-vitro reconstitution of the canonical and neuronal PHF21A-LSD1 complexes identified the neuronal complex as a hypomorphic H3K4 demethylating machinery with reduced nucleosome engagement. Furthermore, an autism-associated PHF21A missense mutation, 1285 G>A, at the last nucleotide of the common exon immediately upstream of the neuronal microexon led to impaired splicing of PHF21A -n. Thus, ubiquitous chromatin regulatory complexes exert unique intrinsic functions in neurons via alternative splicing of their subunits and potentially contribute to faithful human brain development.
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11
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Yang Y, Lee GC, Nakagaki-Silva E, Huang Y, Peacey M, Partridge R, Gooding C, Smith CJ. Cell-type specific regulator RBPMS switches alternative splicing via higher-order oligomerization and heterotypic interactions with other splicing regulators. Nucleic Acids Res 2023; 51:9961-9982. [PMID: 37548402 PMCID: PMC10570038 DOI: 10.1093/nar/gkad652] [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: 02/01/2023] [Revised: 06/28/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
Alternative pre-mRNA splicing decisions are regulated by RNA binding proteins (RBPs) that can activate or repress regulated splice sites. Repressive RBPs typically harness multivalent interactions to bind stably to target RNAs. Multivalency can be achieved by homomeric oligomerization and heteromeric interactions with other RBPs, often mediated by intrinsically disordered regions (IDRs), and by possessing multiple RNA binding domains. Cell-specific splicing decisions often involve the action of widely expressed RBPs, which are able to bind multivalently around target exons, but without effect in the absence of a cell-specific regulator. To address how cell-specific regulators can collaborate with constitutive RBPs in alternative splicing regulation, we used the smooth-muscle specific regulator RBPMS. Recombinant RBPMS is sufficient to confer smooth muscle cell specific alternative splicing of Tpm1 exon 3 in cell-free assays by preventing assembly of ATP-dependent splicing complexes. This activity depends upon a C-terminal IDR that facilitates dynamic higher-order self-assembly, cooperative binding to multivalent RNA and interactions with widely expressed splicing co-regulators, including MBNL1 and RBFOX2, allowing cooperative assembly of stable cell-specific regulatory complexes.
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Affiliation(s)
- Yi Yang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Giselle C Lee
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | | | - Yuling Huang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Matthew Peacey
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ruth Partridge
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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12
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Xie D, Wang Z, Sun B, Qu L, Zeng M, Feng L, Guo M, Wang G, Hao J, Zhou G. High frequency of alternative splicing variants of the oncogene Focal Adhesion Kinase in neuroendocrine tumors of the pancreas and breast. Front Med 2023; 17:907-923. [PMID: 37682378 DOI: 10.1007/s11684-023-1009-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2023] [Indexed: 09/09/2023]
Abstract
The characteristic genetic abnormality of neuroendocrine neoplasms (NENs), a heterogeneous group of tumors found in various organs, remains to be identified. Here, based on the analysis of the splicing variants of an oncogene Focal Adhesion Kinase (FAK) in The Cancer Genome Atlas datasets that contain 9193 patients of 33 cancer subtypes, we found that Box 6/Box 7-containing FAK variants (FAK6/7) were observed in 7 (87.5%) of 8 pancreatic neuroendocrine carcinomas and 20 (11.76%) of 170 pancreatic ductal adenocarcinomas (PDACs). We tested FAK variants in 157 tumor samples collected from Chinese patients with pancreatic tumors, and found that FAK6/7 was positive in 34 (75.6%) of 45 pancreatic NENs, 19 (47.5%) of 40 pancreatic solid pseudopapillary neoplasms, and 2 (2.9%) of 69 PDACs. We further tested FAK splicing variants in breast neuroendocrine carcinoma (BrNECs), and found that FAK6/7 was positive in 14 (93.3%) of 15 BrNECs but 0 in 23 non-NEC breast cancers. We explored the underlying mechanisms and found that a splicing factor serine/arginine repetitive matrix protein 4 (SRRM4) was overexpressed in FAK6/7-positive pancreatic tumors and breast tumors, which promoted the formation of FAK6/7 in cells. These results suggested that FAK6/7 could be a biomarker of NENs and represent a potential therapeutic target for these orphan diseases.
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Affiliation(s)
- Dawei Xie
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zheng Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Beibei Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Liwei Qu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Musheng Zeng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Lin Feng
- Department of Gastroenterology & Hepatology and Department of Pathology, Chinese People's Liberation Army General Hospital, Beijing, 100853, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology and Department of Pathology, Chinese People's Liberation Army General Hospital, Beijing, 100853, China.
| | - Guizhen Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jihui Hao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| | - Guangbiao Zhou
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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13
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Sznajder L, Khan M, Tadross M, Ciesiołka A, Nutter C, Taylor K, Pearson C, Sobczak K, Lewis M, Swanson M, Yuen R. Autistic traits in myotonic dystrophy type 1 due to MBNL inhibition and RNA mis-splicing. RESEARCH SQUARE 2023:rs.3.rs-3221704. [PMID: 37645891 PMCID: PMC10462192 DOI: 10.21203/rs.3.rs-3221704/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tandem repeat expansions are enriched in autism spectrum disorder, including CTG expansion in the DMPK gene that underlines myotonic muscular dystrophy type 1. Although the clinical connection of autism to myotonic dystrophy is corroborated, the molecular links remained unknown. Here, we show a mechanistic path of autism via repeat expansion in myotonic dystrophy. We found that inhibition of muscleblind-like (MBNL) splicing factors by expanded CUG RNAs alerts the splicing of autism-risk genes during brain development especially a class of autism-relevant microexons. To provide in vivo evidence that the CTG expansion and MBNL inhibition axis leads to the presentation of autistic traits, we demonstrate that CTG expansion and MBNL-null mouse models recapitulate autism-relevant mis-splicing profiles and demonstrate social deficits. Our findings indicate that DMPK CTG expansion-associated autism arises from developmental mis-splicing. Understanding this pathomechanistic connection provides an opportunity for greater in-depth investigations of mechanistic threads in autism.
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14
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Gohr A, Iñiguez LP, Torres-Méndez A, Bonnal S, Irimia M. Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads. Nucleic Acids Res 2023; 51:e56. [PMID: 37026474 PMCID: PMC10250204 DOI: 10.1093/nar/gkad244] [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: 07/19/2022] [Revised: 03/13/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence whether or not an intron is spliced before its downstream neighbor, multiple questions related to adjacent introns' splicing order (AISO) remain unanswered. Here, we present Insplico, the first standalone software for quantifying AISO that works with both short and long read sequencing technologies. We first demonstrate its applicability and effectiveness using simulated reads and by recapitulating previously reported AISO patterns, which unveiled overlooked biases associated with long read sequencing. We next show that AISO around individual exons is remarkably constant across cell and tissue types and even upon major spliceosomal disruption, and it is evolutionarily conserved between human and mouse brains. We also establish a set of universal features associated with AISO patterns across various animal and plant species. Finally, we used Insplico to investigate AISO in the context of tissue-specific exons, particularly focusing on SRRM4-dependent microexons. We found that the majority of such microexons have non-canonical AISO, in which the downstream intron is spliced first, and we suggest two potential modes of SRRM4 regulation of microexons related to their AISO and various splicing-related features. Insplico is available on gitlab.com/aghr/insplico.
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Affiliation(s)
- André Gohr
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis P Iñiguez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Méndez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
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15
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Vaquero-Garcia J, Aicher JK, Jewell S, Gazzara MR, Radens CM, Jha A, Norton SS, Lahens NF, Grant GR, Barash Y. RNA splicing analysis using heterogeneous and large RNA-seq datasets. Nat Commun 2023; 14:1230. [PMID: 36869033 PMCID: PMC9984406 DOI: 10.1038/s41467-023-36585-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/06/2023] [Indexed: 03/05/2023] Open
Abstract
The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples across dozens of experimental conditions, exhibit increased variability compared to biological replicates, and involve thousands of unannotated splice variants resulting in increased transcriptome complexity. We describe here a suite of algorithms and tools implemented in the MAJIQ v2 package to address challenges in detection, quantification, and visualization of splicing variations from such datasets. Using both large scale synthetic data and GTEx v8 as benchmark datasets, we assess the advantages of MAJIQ v2 compared to existing methods. We then apply MAJIQ v2 package to analyze differential splicing across 2,335 samples from 13 brain subregions, demonstrating its ability to offer insights into brain subregion-specific splicing regulation.
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Affiliation(s)
| | - Joseph K Aicher
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - San Jewell
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew R Gazzara
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Caleb M Radens
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Anupama Jha
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott S Norton
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory R Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yoseph Barash
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Juan-Mateu J, Bajew S, Miret-Cuesta M, Íñiguez LP, Lopez-Pascual A, Bonnal S, Atla G, Bonàs-Guarch S, Ferrer J, Valcárcel J, Irimia M. Pancreatic microexons regulate islet function and glucose homeostasis. Nat Metab 2023; 5:219-236. [PMID: 36759540 DOI: 10.1038/s42255-022-00734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/21/2022] [Indexed: 02/11/2023]
Abstract
Pancreatic islets control glucose homeostasis by the balanced secretion of insulin and other hormones, and their abnormal function causes diabetes or hypoglycaemia. Here we uncover a conserved programme of alternative microexons included in mRNAs of islet cells, particularly in genes involved in vesicle transport and exocytosis. Islet microexons (IsletMICs) are regulated by the RNA binding protein SRRM3 and represent a subset of the larger neural programme that are particularly sensitive to SRRM3 levels. Both SRRM3 and IsletMICs are induced by elevated glucose levels, and depletion of SRRM3 in human and rat beta cell lines and mouse islets, or repression of particular IsletMICs using antisense oligonucleotides, leads to inappropriate insulin secretion. Consistently, mice harbouring mutations in Srrm3 display defects in islet cell identity and function, leading to hyperinsulinaemic hypoglycaemia. Importantly, human genetic variants that influence SRRM3 expression and IsletMIC inclusion in islets are associated with fasting glucose variation and type 2 diabetes risk. Taken together, our data identify a conserved microexon programme that regulates glucose homeostasis.
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Affiliation(s)
- Jonàs Juan-Mateu
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Simon Bajew
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Miret-Cuesta
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis P Íñiguez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amaya Lopez-Pascual
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Goutham Atla
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Sílvia Bonàs-Guarch
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jorge Ferrer
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Juan Valcárcel
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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17
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Rogalska ME, Vafiadaki E, Erpapazoglou Z, Haghighi K, Green L, Mantzoros CS, Hajjar RJ, Tranter M, Karakikes I, Kranias EG, Stillitano F, Kafasla P, Sanoudou D. Isoform changes of action potential regulators in the ventricles of arrhythmogenic phospholamban-R14del humanized mouse hearts. Metabolism 2023; 138:155344. [PMID: 36375644 DOI: 10.1016/j.metabol.2022.155344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]
Abstract
Arrhythmogenic cardiomyopathy (ACM) is characterized by life-threatening ventricular arrhythmias and sudden cardiac death and affects hundreds of thousands of patients worldwide. The deletion of Arginine 14 (p.R14del) in the phospholamban (PLN) gene has been implicated in the pathogenesis of ACM. PLN is a key regulator of sarcoplasmic reticulum (SR) Ca2+ cycling and cardiac contractility. Despite global gene and protein expression studies, the molecular mechanisms of PLN-R14del ACM pathogenesis remain unclear. Using a humanized PLN-R14del mouse model and human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs), we investigated the transcriptome-wide mRNA splicing changes associated with the R14del mutation. We identified >200 significant alternative splicing (AS) events and distinct AS profiles were observed in the right (RV) and left (LV) ventricles in PLN-R14del compared to WT mouse hearts. Enrichment analysis of the AS events showed that the most affected biological process was associated with "cardiac cell action potential", specifically in the RV. We found that splicing of 2 key genes, Trpm4 and Camk2d, which encode proteins regulating calcium homeostasis in the heart, were altered in PLN-R14del mouse hearts and human iPSC-CMs. Bioinformatical analysis pointed to the tissue-specific splicing factors Srrm4 and Nova1 as likely upstream regulators of the observed splicing changes in the PLN-R14del cardiomyocytes. Our findings suggest that aberrant splicing may affect Ca2+-homeostasis in the heart, contributing to the increased risk of arrythmogenesis in PLN-R14del ACM.
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Affiliation(s)
- Malgorzata E Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Elizabeth Vafiadaki
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Zoi Erpapazoglou
- Institute for Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming", 16672 Athens, Greece
| | - Kobra Haghighi
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Lisa Green
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Christos S Mantzoros
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Section of Endocrinology, Boston VA Healthcare System, Harvard Medical School, Boston, MA 02215, USA
| | | | - Michael Tranter
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Ioannis Karakikes
- Department of Cardiothoracic Surgery and Cardiovascular Institute, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, USA
| | - Evangelia G Kranias
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Francesca Stillitano
- Division Heart and Lung, Department of Cardiology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Panagiota Kafasla
- Institute for Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming", 16672 Athens, Greece
| | - Despina Sanoudou
- Molecular Biology Division, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece; Clinical Genomics and Pharmacogenomics Unit, 4(th) Department of Internal Medicine, Attikon Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Center for New Biotechnologies and Precision Medicine, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece.
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18
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Liu S, Alabi BR, Yin Q, Stoyanova T. Molecular mechanisms underlying the development of neuroendocrine prostate cancer. Semin Cancer Biol 2022; 86:57-68. [PMID: 35597438 DOI: 10.1016/j.semcancer.2022.05.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/19/2022] [Accepted: 05/14/2022] [Indexed: 01/27/2023]
Abstract
Prostate cancer is the most common non-cutaneous cancer and the second leading cause of cancer-associated deaths among men in the United States. Androgen deprivation therapy (ADT) is the standard of care for advanced prostate cancer. While patients with advanced prostate cancer initially respond to ADT, the disease frequently progresses to a lethal metastatic form, defined as castration-resistant prostate cancer (CRPC). After multiple rounds of anti-androgen therapies, 20-25% of metastatic CRPCs develop a neuroendocrine (NE) phenotype. These tumors are classified as neuroendocrine prostate cancer (NEPC). De novo NEPC is rare and accounts for less than 2% of all prostate cancers at diagnosis. NEPC is commonly characterized by the expression of NE markers and the absence of androgen receptor (AR) expression. NEPC is usually associated with tumor aggressiveness, hormone therapy resistance, and poor clinical outcome. Here, we review the molecular mechanisms underlying the emergence of NEPC and provide insights into the future perspectives on potential therapeutic strategies for NEPC.
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Affiliation(s)
- Shiqin Liu
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA, USA
| | - Busola Ruth Alabi
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA, USA
| | - Qingqing Yin
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA, USA
| | - Tanya Stoyanova
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA, USA.
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19
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Emerging Roles of RNA-Binding Proteins in Inner Ear Hair Cell Development and Regeneration. Int J Mol Sci 2022; 23:ijms232012393. [PMID: 36293251 PMCID: PMC9604452 DOI: 10.3390/ijms232012393] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
RNA-binding proteins (RBPs) regulate gene expression at the post-transcriptional level. They play major roles in the tissue- and stage-specific expression of protein isoforms as well as in the maintenance of protein homeostasis. The inner ear is a bi-functional organ, with the cochlea and the vestibular system required for hearing and for maintaining balance, respectively. It is relatively well documented that transcription factors and signaling pathways are critically involved in the formation of inner ear structures and in the development of hair cells. Accumulating evidence highlights emerging functions of RBPs in the post-transcriptional regulation of inner ear development and hair cell function. Importantly, mutations of splicing factors of the RBP family and defective alternative splicing, which result in inappropriate expression of protein isoforms, lead to deafness in both animal models and humans. Because RBPs are critical regulators of cell proliferation and differentiation, they present the potential to promote hair cell regeneration following noise- or ototoxin-induced damage through mitotic and non-mitotic mechanisms. Therefore, deciphering RBP-regulated events during inner ear development and hair cell regeneration can help define therapeutic strategies for treatment of hearing loss. In this review, we outline our evolving understanding of the implications of RBPs in hair cell formation and hearing disease with the aim of promoting future research in this field.
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20
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Han H, Best AJ, Braunschweig U, Mikolajewicz N, Li JD, Roth J, Chowdhury F, Mantica F, Nabeel-Shah S, Parada G, Brown KR, O'Hanlon D, Wei J, Yao Y, Zid AA, Comsa LC, Jen M, Wang J, Datti A, Gonatopoulos-Pournatzis T, Weatheritt RJ, Greenblatt JF, Wrana JL, Irimia M, Gingras AC, Moffat J, Blencowe BJ. Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis. Mol Cell 2022; 82:2982-2999.e14. [PMID: 35914530 PMCID: PMC10686216 DOI: 10.1016/j.molcel.2022.06.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/16/2022] [Accepted: 06/29/2022] [Indexed: 11/19/2022]
Abstract
Alternative splicing (AS) is a critical regulatory layer; yet, factors controlling functionally coordinated splicing programs during developmental transitions are poorly understood. Here, we employ a screening strategy to identify factors controlling dynamic splicing events important for mammalian neurogenesis. Among previously unknown regulators, Rbm38 acts widely to negatively control neural AS, in part through interactions mediated by the established repressor of splicing, Ptbp1. Puf60, a ubiquitous factor, is surprisingly found to promote neural splicing patterns. This activity requires a conserved, neural-differential exon that remodels Puf60 co-factor interactions. Ablation of this exon rewires distinct AS networks in embryonic stem cells and at different stages of mouse neurogenesis. Single-cell transcriptome analyses further reveal distinct roles for Rbm38 and Puf60 isoforms in establishing neuronal identity. Our results describe important roles for previously unknown regulators of neurogenesis and establish how an alternative exon in a widely expressed splicing factor orchestrates temporal control over cell differentiation.
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Affiliation(s)
- Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Andrew J Best
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | | | | | - Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jonathan Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Fuad Chowdhury
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, Barcelona 08003, Spain
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Guillermo Parada
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Dave O'Hanlon
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jiarun Wei
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Yuxi Yao
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Abdelrahman Abou Zid
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Lim Caden Comsa
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mark Jen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jenny Wang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Alessandro Datti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Thomas Gonatopoulos-Pournatzis
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Center for Cancer Research National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert J Weatheritt
- EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, Barcelona 08003, Spain; Universitat Pompeu Fabra, Barcelona, Spain; ICREA, Barcelona, Spain
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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21
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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22
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Irie K, Doi M, Usui N, Shimada S. Evolution of the Human Brain Can Help Determine Pathophysiology of Neurodevelopmental Disorders. Front Neurosci 2022; 16:871979. [PMID: 35431788 PMCID: PMC9010664 DOI: 10.3389/fnins.2022.871979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 02/03/2023] Open
Abstract
The evolution of humans brought about a co-occurring evolution of the human brain, which is far larger and more complex than that of many other organisms. The brain has evolved characteristically in humans in many respects, including macro-and micro-anatomical changes in the brain structure, changes in gene expression, and cell populations and ratios. These characteristics are essential for the execution of higher functions, such as sociality, language, and cognition, which express humanity, and are thought to have been acquired over evolutionary time. However, with the acquisition of higher functions also comes the risk of the disease in which they fail. This review focuses on human brain evolution and neurodevelopmental disorders (NDDs) and discusses brain development, molecular evolution, and human brain evolution. Discussing the potential for the development and pathophysiology of NDDs acquired by human brain evolution will provide insights into the acquisition and breakdown of higher functions from a new perspective.
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Affiliation(s)
- Koichiro Irie
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- Center for Medical Research and Education, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Miyuki Doi
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Noriyoshi Usui
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- United Graduate School of Child Development, Osaka University, Suita, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
- *Correspondence: Noriyoshi Usui,
| | - Shoichi Shimada
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- United Graduate School of Child Development, Osaka University, Suita, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
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23
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Pitolli C, Marini A, Sette C, Pagliarini V. Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer. Int J Mol Sci 2022; 23:ijms23052811. [PMID: 35269953 PMCID: PMC8911335 DOI: 10.3390/ijms23052811] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
The advance of experimental and computational techniques has allowed us to highlight the existence of numerous different mechanisms of RNA maturation, which have been so far unknown. Besides canonical splicing, consisting of the removal of introns from pre-mRNA molecules, non-canonical splicing events may occur to further increase the regulatory and coding potential of the human genome. Among these, splicing of microexons, recursive splicing and biogenesis of circular and chimeric RNAs through back-splicing and trans-splicing processes, respectively, all contribute to expanding the repertoire of RNA transcripts with newly acquired regulatory functions. Interestingly, these non-canonical splicing events seem to occur more frequently in the central nervous system, affecting neuronal development and differentiation programs with important implications on brain physiology. Coherently, dysregulation of non-canonical RNA processing events is associated with brain disorders, including brain tumours. Herein, we summarize the current knowledge on molecular and regulatory mechanisms underlying canonical and non-canonical splicing events with particular emphasis on cis-acting elements and trans-acting factors that all together orchestrate splicing catalysis reactions and decisions. Lastly, we review the impact of non-canonical splicing on brain physiology and pathology and how unconventional splicing mechanisms may be targeted or exploited for novel therapeutic strategies in cancer.
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Affiliation(s)
- Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Alberto Marini
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
- Correspondence:
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24
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Torres-Méndez A, Pop S, Bonnal S, Almudi I, Avola A, Roberts RJV, Paolantoni C, Alcaina-Caro A, Martín-Anduaga A, Haussmann IU, Morin V, Casares F, Soller M, Kadener S, Roignant JY, Prieto-Godino L, Irimia M. Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals. SCIENCE ADVANCES 2022; 8:eabk0445. [PMID: 35089784 PMCID: PMC8797185 DOI: 10.1126/sciadv.abk0445] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/08/2021] [Indexed: 05/08/2023]
Abstract
Alternative splicing increases neuronal transcriptomic complexity throughout animal phylogeny. To delve into the mechanisms controlling the assembly and evolution of this regulatory layer, we characterized the neuronal microexon program in Drosophila and compared it with that of mammals. In nonvertebrate bilaterians, this splicing program is restricted to neurons by the posttranscriptional processing of the enhancer of microexons (eMIC) domain in Srrm234. In Drosophila, this processing is dependent on regulation by Elav/Fne. eMIC deficiency or misexpression leads to widespread neurological alterations largely emerging from impaired neuronal activity, as revealed by a combination of neuronal imaging experiments and cell type-specific rescues. These defects are associated with the genome-wide skipping of short neural exons, which are strongly enriched in ion channels. We found no overlap of eMIC-regulated exons between flies and mice, illustrating how ancient posttranscriptional programs can evolve independently in different phyla to affect distinct cellular modules while maintaining cell-type specificity.
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Affiliation(s)
- Antonio Torres-Méndez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
- Francis Crick Institute, London, UK
| | | | - Sophie Bonnal
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Isabel Almudi
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Department of Genetics, Microbiology and Statistics and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | | | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | | | - Irmgard U. Haussmann
- Department of Life Science, School of Health Sciences, Birmingham City University, Birmingham B5 3TN, UK
| | - Violeta Morin
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Fernando Casares
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | | | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- ICREA, Barcelona, Spain
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25
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Gohr A, Mantica F, Hermoso-Pulido A, Tapial J, Márquez Y, Irimia M. Computational Analysis of Alternative Splicing Using VAST-TOOLS and the VastDB Framework. Methods Mol Biol 2022; 2537:97-128. [PMID: 35895261 DOI: 10.1007/978-1-0716-2521-7_7] [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] [Indexed: 06/15/2023]
Abstract
Alternative splicing (AS) can vastly expand animal transcriptomes and proteomes. Two main open questions in the field are how AS is regulated across cell/tissue types and disease, and what roles different AS events play. To facilitate AS research, we have created the computational VastDB framework, which comprises a series of complementary software and resources that we describe in this chapter. The VastDB framework is especially designed to aid biomedical researchers without a strong computational background. It offers tools and resources to: (a) quantify AS and identify differentially spliced AS events using RNA-seq data (vast-tools), (b) perform multiple genomic and sequence analyses for investigating AS events (Matt), (c) identify AS events with genomic and regulatory conservation among species (ExOrthist), and (d) help with the biological interpretation of the results, and, ultimately, with the identification of interesting AS events to design wet-lab experiments (VastDB and PastDB).
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Affiliation(s)
- André Gohr
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Hermoso-Pulido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Javier Tapial
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yamile Márquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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26
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Li D, McIntosh CS, Mastaglia FL, Wilton SD, Aung-Htut MT. Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Transl Neurodegener 2021; 10:16. [PMID: 34016162 PMCID: PMC8136212 DOI: 10.1186/s40035-021-00240-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is a fundamental step in eukaryotic gene expression that systematically removes non-coding regions (introns) and ligates coding regions (exons) into a continuous message (mature mRNA). This process is highly regulated and can be highly flexible through a process known as alternative splicing, which allows for several transcripts to arise from a single gene, thereby greatly increasing genetic plasticity and the diversity of proteome. Alternative splicing is particularly prevalent in neuronal cells, where the splicing patterns are continuously changing to maintain cellular homeostasis and promote neurogenesis, migration and synaptic function. The continuous changes in splicing patterns and a high demand on many cis- and trans-splicing factors contribute to the susceptibility of neuronal tissues to splicing defects. The resultant neurodegenerative diseases are a large group of disorders defined by a gradual loss of neurons and a progressive impairment in neuronal function. Several of the most common neurodegenerative diseases involve some form of splicing defect(s), such as Alzheimer's disease, Parkinson's disease and spinal muscular atrophy. Our growing understanding of RNA splicing has led to the explosion of research in the field of splice-switching antisense oligonucleotide therapeutics. Here we review our current understanding of the effects alternative splicing has on neuronal differentiation, neuronal migration, synaptic maturation and regulation, as well as the impact on neurodegenerative diseases. We will also review the current landscape of splice-switching antisense oligonucleotides as a therapeutic strategy for a number of common neurodegenerative disorders.
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Affiliation(s)
- Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Craig Stewart McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Frank Louis Mastaglia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Steve Donald Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia. .,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia.
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27
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Frankowski H, Yeboah F, Berry BJ, Kinoshita C, Lee M, Evitts K, Davis J, Kinoshita Y, Morrison RS, Young JE. Knock-Down of HDAC2 in Human Induced Pluripotent Stem Cell Derived Neurons Improves Neuronal Mitochondrial Dynamics, Neuronal Maturation and Reduces Amyloid Beta Peptides. Int J Mol Sci 2021; 22:ijms22052526. [PMID: 33802405 PMCID: PMC7959288 DOI: 10.3390/ijms22052526] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylase 2 (HDAC2) is a major HDAC protein in the adult brain and has been shown to regulate many neuronal genes. The aberrant expression of HDAC2 and subsequent dysregulation of neuronal gene expression is implicated in neurodegeneration and brain aging. Human induced pluripotent stem cell-derived neurons (hiPSC-Ns) are widely used models for studying neurodegenerative disease mechanisms, but the role of HDAC2 in hiPSC-N differentiation and maturation has not been explored. In this study, we show that levels of HDAC2 progressively decrease as hiPSCs are differentiated towards neurons. This suppression of HDAC2 inversely corresponds to an increase in neuron-specific isoforms of Endophilin-B1, a multifunctional protein involved in mitochondrial dynamics. Expression of neuron-specific isoforms of Endophilin-B1 is accompanied by concomitant expression of a neuron-specific alternative splicing factor, SRRM4. Manipulation of HDAC2 and Endophilin-B1 using lentiviral approaches shows that the knock-down of HDAC2 or the overexpression of a neuron-specific Endophilin-B1 isoform promotes mitochondrial elongation and protects against cytotoxic stress in hiPSC-Ns, while HDAC2 knock-down specifically influences genes regulating mitochondrial dynamics and synaptogenesis. Furthermore, HDAC2 knock-down promotes enhanced mitochondrial respiration and reduces levels of neurotoxic amyloid beta peptides. Collectively, our study demonstrates a role for HDAC2 in hiPSC-neuronal differentiation, highlights neuron-specific isoforms of Endophilin-B1 as a marker of differentiating hiPSC-Ns and demonstrates that HDAC2 regulates key neuronal and mitochondrial pathways in hiPSC-Ns.
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Affiliation(s)
- Harald Frankowski
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (H.F.); (F.Y.); (B.J.B.); (C.K.); (M.L.); (K.E.); (J.D.); (Y.K.)
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Fred Yeboah
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (H.F.); (F.Y.); (B.J.B.); (C.K.); (M.L.); (K.E.); (J.D.); (Y.K.)
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Bonnie J. Berry
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (H.F.); (F.Y.); (B.J.B.); (C.K.); (M.L.); (K.E.); (J.D.); (Y.K.)
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Chizuru Kinoshita
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (H.F.); (F.Y.); (B.J.B.); (C.K.); (M.L.); (K.E.); (J.D.); (Y.K.)
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Michelle Lee
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (H.F.); (F.Y.); (B.J.B.); (C.K.); (M.L.); (K.E.); (J.D.); (Y.K.)
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Kira Evitts
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (H.F.); (F.Y.); (B.J.B.); (C.K.); (M.L.); (K.E.); (J.D.); (Y.K.)
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Joshua Davis
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (H.F.); (F.Y.); (B.J.B.); (C.K.); (M.L.); (K.E.); (J.D.); (Y.K.)
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Yoshito Kinoshita
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (H.F.); (F.Y.); (B.J.B.); (C.K.); (M.L.); (K.E.); (J.D.); (Y.K.)
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Richard S. Morrison
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA;
| | - Jessica E. Young
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; (H.F.); (F.Y.); (B.J.B.); (C.K.); (M.L.); (K.E.); (J.D.); (Y.K.)
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Correspondence:
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28
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Cheng WC, Wang HJ. Current advances of targeting epigenetic modifications in neuroendocrine prostate cancer. Tzu Chi Med J 2021; 33:224-232. [PMID: 34386358 PMCID: PMC8323647 DOI: 10.4103/tcmj.tcmj_220_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/05/2020] [Accepted: 10/06/2020] [Indexed: 11/15/2022] Open
Abstract
Neuroendocrine prostate cancer (NEPC) is the most lethal malignancy of prostate cancer (PCa). Treatment with next-generation androgen receptor (AR) pathway inhibitors (ARPIs) has successfully extended patients' lifespan. However, with the emergence of drug resistance, PCa tumors increasingly adapt to potent ARPI therapies by transitioning to alternative cellular lineage. Such therapy-induced drug resistance is largely driven from the cellular plasticity of PCa cells to alter their phenotypes of AR independence for cell growth and survival. Some of the resistant PCa cells undergo cellular reprogramming to form neuroendocrine phenotypes. Recent evidences suggest that this cellular reprogramming or the lineage plasticity is driven by dysregulation of the epigenome and transcriptional networks. Aberrant DNA methylation and altered expression of epigenetic modifiers, such as enhancer of zeste-homolog 2, transcription factors, histone demethylases, are hallmarks of NEPC. In this review, we discuss the nature of the epigenetic and transcriptional landscapes of PCa cells which lose their AR independence and transition to the neuroendocrine lineage. We also discuss how oncogenic signaling and metabolic reprogramming fuel epigenetic and transcriptional alterations. In addition, the current state of epigenetic therapies for NEPC is addressed.
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Affiliation(s)
- Wen-Chi Cheng
- SDGs Teaching and Research Headquarters, Tzu Chi University, Hualien, Taiwan
| | - Hung-Jung Wang
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan.,Doctoral Degree Program in Translational Medicine, Tzu Chi University and Academia Sinica, Hualien, Taiwan
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Kaarijärvi R, Kaljunen H, Ketola K. Molecular and Functional Links between Neurodevelopmental Processes and Treatment-Induced Neuroendocrine Plasticity in Prostate Cancer Progression. Cancers (Basel) 2021; 13:cancers13040692. [PMID: 33572108 PMCID: PMC7915380 DOI: 10.3390/cancers13040692] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Treatment-induced neuroendocrine prostate cancer (t-NEPC) is a subtype of castration-resistant prostate cancer (CRPC) which develops under prolonged androgen deprivation therapy. The mechanisms and pathways underlying the t-NEPC are still poorly understood and there are no effective treatments available. Here, we summarize the literature on the molecules and pathways contributing to neuroendocrine phenotype in prostate cancer in the context of their known cellular neurodevelopmental processes. We also discuss the role of tumor microenvironment in neuroendocrine plasticity, future directions, and therapeutic options under clinical investigation for neuroendocrine prostate cancer. Abstract Neuroendocrine plasticity and treatment-induced neuroendocrine phenotypes have recently been proposed as important resistance mechanisms underlying prostate cancer progression. Treatment-induced neuroendocrine prostate cancer (t-NEPC) is highly aggressive subtype of castration-resistant prostate cancer which develops for one fifth of patients under prolonged androgen deprivation. In recent years, understanding of molecular features and phenotypic changes in neuroendocrine plasticity has been grown. However, there are still fundamental questions to be answered in this emerging research field, for example, why and how do the prostate cancer treatment-resistant cells acquire neuron-like phenotype. The advantages of the phenotypic change and the role of tumor microenvironment in controlling cellular plasticity and in the emergence of treatment-resistant aggressive forms of prostate cancer is mostly unknown. Here, we discuss the molecular and functional links between neurodevelopmental processes and treatment-induced neuroendocrine plasticity in prostate cancer progression and treatment resistance. We provide an overview of the emergence of neurite-like cells in neuroendocrine prostate cancer cells and whether the reported t-NEPC pathways and proteins relate to neurodevelopmental processes like neurogenesis and axonogenesis during the development of treatment resistance. We also discuss emerging novel therapeutic targets modulating neuroendocrine plasticity.
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SRRM4 Expands the Repertoire of Circular RNAs by Regulating Microexon Inclusion. Cells 2020; 9:cells9112488. [PMID: 33207694 PMCID: PMC7697094 DOI: 10.3390/cells9112488] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/27/2020] [Accepted: 11/13/2020] [Indexed: 12/25/2022] Open
Abstract
High-throughput RNA sequencing (RNA-seq) and dedicated bioinformatics pipelines have synergized to identify an expansive repertoire of unique circular RNAs (circRNAs), exceeding 100,000 variants. While the vast majority of these circRNAs comprise canonical exonic and intronic sequences, microexons (MEs)-which occur in 30% of functional mRNA transcripts-have been entirely overlooked. CircRNAs which contain these known MEs (ME-circRNAs) could be identified with commonly utilized circRNA prediction pipelines, CIRCexplorer2 and CIRI2, but were not previously recognized as ME-circRNAs. In addition, when employing a bespoke bioinformatics pipeline for identifying RNA chimeras, called Hyb, we could also identify over 2000 ME-circRNAs which contain novel MEs at their backsplice junctions, that are uncalled by either CIRCexplorer2 or CIRI2. Analysis of circRNA-seq datasets from gliomas of varying clinical grades compared with matched control tissue has shown circRNAs have potential as prognostic markers for stratifying tumor from healthy tissue. Furthermore, the abundance of microexon-containing circRNAs (ME-circRNAs) between tumor and normal tissues is correlated with the expression of a splicing associated factor, Serine/arginine repetitive matrix 4 (SRRM4). Overexpressing SRRM4, known for regulating ME inclusion in mRNAs critical for neural differentiation, in human HEK293 cells resulted in the biogenesis of over 2000 novel ME-circRNAs, including ME-circEIF4G3, and changes in the abundance of many canonical circRNAs, including circSETDB2 and circLBRA. This shows SRRM4, in which its expression is correlated with poor prognosis in gliomas, acts as a bona fide circRNA biogenesis factor. Given the known roles of MEs and circRNAs in oncogenesis, the identification of these previously unrecognized ME-circRNAs further increases the complexity and functional purview of this non-coding RNA family.
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31
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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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32
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Keene KL, Hyacinth HI, Bis JC, Kittner SJ, Mitchell BD, Cheng YC, Pare G, Chong M, O’Donnell M, Meschia JF, Chen WM, Sale MM, Rich SS, Nalls MA, Zonderman AB, Evans MK, Wilson JG, Correa A, Markus HS, Traylor M, Lewis CM, Carty CL, Reiner A, Haessler J, Langefeld CD, Gottesman R, Mosley TH, Woo D, Yaffe K, Liu Y, Longstreth WT, Psaty BM, Kooperberg C, Lange LA, Sacco R, Rundek T, Lee JM, Cruchaga C, Furie KL, Arnett DK, Benavente OR, Grewal RP, Peddareddygari LR, Dichgans M, Malik R, Worrall BB, Fornage M. Genome-Wide Association Study Meta-Analysis of Stroke in 22 000 Individuals of African Descent Identifies Novel Associations With Stroke. Stroke 2020; 51:2454-2463. [PMID: 32693751 PMCID: PMC7387190 DOI: 10.1161/strokeaha.120.029123] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND PURPOSE Stroke is a complex disease with multiple genetic and environmental risk factors. Blacks endure a nearly 2-fold greater risk of stroke and are 2× to 3× more likely to die from stroke than European Americans. METHODS The COMPASS (Consortium of Minority Population Genome-Wide Association Studies of Stroke) has conducted a genome-wide association meta-analysis of stroke in >22 000 individuals of African ancestry (3734 cases, 18 317 controls) from 13 cohorts. RESULTS In meta-analyses, we identified one single nucleotide polymorphism (rs55931441) near the HNF1A gene that reached genome-wide significance (P=4.62×10-8) and an additional 29 variants with suggestive evidence of association (P<1×10-6), representing 24 unique loci. For validation, a look-up analysis for a 100 kb region flanking the COMPASS single nucleotide polymorphism was performed in SiGN (Stroke Genetics Network) Europeans, SiGN Hispanics, and METASTROKE (Europeans). Using a stringent Bonferroni correction P value of 2.08×10-3 (0.05/24 unique loci), we were able to validate associations at the HNF1A locus in both SiGN (P=8.18×10-4) and METASTROKE (P=1.72×10-3) European populations. Overall, 16 of 24 loci showed evidence for validation across multiple populations. Previous studies have reported associations between variants in the HNF1A gene and lipids, C-reactive protein, and risk of coronary artery disease and stroke. Suggestive associations with variants in the SFXN4 and TMEM108 genes represent potential novel ischemic stroke loci. CONCLUSIONS These findings represent the most thorough investigation of genetic determinants of stroke in individuals of African descent, to date.
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Affiliation(s)
- Keith L. Keene
- Department of Biology; Brody School of Medicine Center for Health Disparities, East Carolina University, Greenville, NC
| | - Hyacinth I. Hyacinth
- Aflac Cancer and Blood Disorder Center of Emory University and Children’s Healthcare of Atlanta University, Atlanta, GA
| | | | - Steven J. Kittner
- Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Braxton D. Mitchell
- Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Yu-Ching Cheng
- Baltimore Veterans Administration Medical Center and University of Maryland School of Medicine, Baltimore, MD
| | - Guillaume Pare
- McMaster University and Population Health Research Institute, Hamilton Ontario
| | - Michael Chong
- McMaster University and Population Health Research Institute, Hamilton Ontario
| | | | | | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Michele M. Sale
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD
- Data Tecnica International, Glen Echo, MD
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Baltimore, MD
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Baltimore, MD
| | | | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, MS
| | | | - Matthew Traylor
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
| | - Cathryn M. Lewis
- Social, Genetic and Developmental Psychiatry Centre, King’s College London, London, United Kingdom
| | - Cara L. Carty
- Initiative for Research and Education to Advance Community Health, Washington State University, Seattle, WA
| | - Alexander Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jeff Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Carl D. Langefeld
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | | | | | - Daniel Woo
- Department of Neurology, University of Cincinnati, Cincinnati, OH
| | | | - YongMei Liu
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA; Kaiser Permanente Washington Health Research Institute, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Ralph Sacco
- University of Miami, Miller School of Medicine, Miami, FL
| | - Tatjana Rundek
- University of Miami, Miller School of Medicine, Miami, FL
| | - Jin-Moo Lee
- Washington University School of Medicine, St. Louis, MO
| | | | - Karen L. Furie
- Brown University Warren Alpert Medical School, Providence, RI
| | - Donna K. Arnett
- University of Kentucky, College of Public Health, Lexington, KY
| | | | - Raji P. Grewal
- Neuroscience Institute, Saint Francis Medical Center, Trenton, NJ
| | | | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | | | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX
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Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder. Curr Opin Genet Dev 2020; 65:22-33. [PMID: 32535349 DOI: 10.1016/j.gde.2020.03.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022]
Abstract
The discovery and characterization of a network of highly conserved neuronal microexons has provided fundamental new insight into mechanisms underlying nervous system development and function, as well as an important basis for pathway convergence in autism spectrum disorder. In the past few years, considerable progress has been made in comprehensively determining the repertoires of factors that control neuronal microexons. These results have illuminated molecular mechanisms that activate the splicing of microexons, including those that control gene expression programs critical for neurogenesis, as well as synaptic protein translation and neuronal activity. Remarkably, individual disruption of specific microexons in these pathways results in autism-like phenotypes and cognitive impairment in mice. This review discusses these findings and their implications for delivering new therapeutic strategies for neurological disorders.
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34
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Coleman DJ, Sampson DA, Sehrawat A, Kumaraswamy A, Sun D, Wang Y, Schwartzman J, Urrutia J, Lee AR, Coleman IM, Nelson PS, Dong X, Morrissey C, Corey E, Xia Z, Yates JA, Alumkal JJ. Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4. Neoplasia 2020; 22:253-262. [PMID: 32403054 PMCID: PMC7218227 DOI: 10.1016/j.neo.2020.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 04/06/2020] [Indexed: 02/06/2023] Open
Abstract
Neuroendocrine prostate cancer (NEPC) is the most virulent form of prostate cancer. Importantly, our recent work examining metastatic biopsy samples demonstrates NEPC is increasing in frequency. In contrast to prostate adenocarcinomas that express a luminal gene expression program, NEPC tumors express a neuronal gene expression program. Despite this distinction, the diagnosis of NEPC is often challenging, demonstrating an urgent need to identify new biomarkers and therapeutic targets. Our prior work demonstrated that the histone demethylase LSD1 (KDM1A) is important for survival of prostate adenocarcinomas, but little was known about LSD1's role in NEPC. Recently, a neural-specific transcript variant of LSD1-LSD1+8a-was discovered and demonstrated to activate neuronal gene expression in neural cells. The splicing factor SRRM4 was previously shown to promote LSD1+8a splicing in neuronal cells, and SRRM4 promotes NEPC differentiation and cell survival. Therefore, we sought to determine if LSD1+8a might play a role in NEPC and whether LSD1+8a splicing was linked to SRRM4. To investigate a potential role for LSD1+8a in NEPC, we examined a panel of prostate adenocarcinoma and NEPC patient-derived xenografts and metastatic biopsies. LSD1+8a was expressed exclusively in NEPC samples and correlated significantly with elevated expression of SRRM4. Using SRRM4-overexpressing cell lines, we determined that SRRM4 mediates alternative splicing of LSD1+8a. Finally, using gain of function studies, we confirmed that LSD1+8a and SRRM4 co-regulate target genes distinct from canonical LSD1. Our findings suggest further study of the interplay between SRRM4 and LSD1+8a and mechanisms by which LSD1+8a regulates gene expression in NEPC is warranted.
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Affiliation(s)
- Daniel J Coleman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - David A Sampson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Archana Sehrawat
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Anbarasu Kumaraswamy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Duanchen Sun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Jacob Schwartzman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Joshua Urrutia
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Ilsa M Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Zheng Xia
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA
| | - Joel A Yates
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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35
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Martí-Gómez C, Lara-Pezzi E, Sánchez-Cabo F. dSreg: a Bayesian model to integrate changes in splicing and RNA-binding protein activity. Bioinformatics 2020; 36:2134-2141. [PMID: 31834368 PMCID: PMC7141860 DOI: 10.1093/bioinformatics/btz915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 09/09/2019] [Accepted: 12/10/2019] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION Alternative splicing (AS) is an important mechanism in the generation of transcript diversity across mammals. AS patterns are dynamically regulated during development and in response to environmental changes. Defects or perturbations in its regulation may lead to cancer or neurological disorders, among other pathological conditions. The regulatory mechanisms controlling AS in a given biological context are typically inferred using a two-step framework: differential AS analysis followed by enrichment methods. These strategies require setting rather arbitrary thresholds and are prone to error propagation along the analysis. RESULTS To overcome these limitations, we propose dSreg, a Bayesian model that integrates RNA-seq with data from regulatory features, e.g. binding sites of RNA-binding proteins. dSreg identifies the key underlying regulators controlling AS changes and quantifies their activity while simultaneously estimating the changes in exon inclusion rates. dSreg increased both the sensitivity and the specificity of the identified AS changes in simulated data, even at low read coverage. dSreg also showed improved performance when analyzing a collection of knock-down RNA-binding proteins' experiments from ENCODE, as opposed to traditional enrichment methods, such as over-representation analysis and gene set enrichment analysis. dSreg opens the possibility to integrate a large amount of readily available RNA-seq datasets at low coverage for AS analysis and allows more cost-effective RNA-seq experiments. AVAILABILITY AND IMPLEMENTATION dSreg was implemented in python using stan and is freely available to the community at https://bitbucket.org/cmartiga/dsreg. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Carlos Martí-Gómez
- Molecular Regulation of Heart Failure (CMG and ELP); Bioinformatics Unit (FSC), Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Enrique Lara-Pezzi
- Molecular Regulation of Heart Failure (CMG and ELP); Bioinformatics Unit (FSC), Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Fátima Sánchez-Cabo
- Molecular Regulation of Heart Failure (CMG and ELP); Bioinformatics Unit (FSC), Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
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36
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Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, Ha KCH, Weiss A, Billmann M, Durbic T, Myers CL, Blencowe BJ, Moffat J. Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform. Nat Biotechnol 2020; 38:638-648. [PMID: 32249828 DOI: 10.1038/s41587-020-0437-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Systematic mapping of genetic interactions (GIs) and interrogation of the functions of sizable genomic segments in mammalian cells represent important goals of biomedical research. To advance these goals, we present a CRISPR (clustered regularly interspaced short palindromic repeats)-based screening system for combinatorial genetic manipulation that employs coexpression of CRISPR-associated nucleases 9 and 12a (Cas9 and Cas12a) and machine-learning-optimized libraries of hybrid Cas9-Cas12a guide RNAs. This system, named Cas Hybrid for Multiplexed Editing and screening Applications (CHyMErA), outperforms genetic screens using Cas9 or Cas12a editing alone. Application of CHyMErA to the ablation of mammalian paralog gene pairs reveals extensive GIs and uncovers phenotypes normally masked by functional redundancy. Application of CHyMErA in a chemogenetic interaction screen identifies genes that impact cell growth in response to mTOR pathway inhibition. Moreover, by systematically targeting thousands of alternative splicing events, CHyMErA identifies exons underlying human cell line fitness. CHyMErA thus represents an effective screening approach for GI mapping and the functional analysis of sizable genomic regions, such as alternative exons.
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Affiliation(s)
| | - Michael Aregger
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Tanja Durbic
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Chad L Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Institute for Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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37
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Abstract
High-throughput sequencing-based methods and their applications in the study of transcriptomes have revolutionized our understanding of alternative splicing. Networks of functionally coordinated and biologically important alternative splicing events continue to be discovered in an ever-increasing diversity of cell types in the context of physiologically normal and disease states. These studies have been complemented by efforts directed at defining sequence codes governing splicing and their cognate trans-acting factors, which have illuminated important combinatorial principles of regulation. Additional studies have revealed critical roles of position-dependent, multivalent protein-RNA interactions that direct splicing outcomes. Investigations of evolutionary changes in RNA binding proteins, splice variants, and associated cis elements have further shed light on the emergence, mechanisms, and functions of splicing networks. Progress in these areas has emphasized the need for a coordinated, community-based effort to systematically address the functions of individual splice variants associated with normal and disease biology.
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38
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Epigenetic modulations and lineage plasticity in advanced prostate cancer. Ann Oncol 2020; 31:470-479. [PMID: 32139297 DOI: 10.1016/j.annonc.2020.02.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 12/25/2022] Open
Abstract
Prostate cancer is the most common cancer and second leading cause of cancer-related death in American men. Antiandrogen therapies are part of the standard of therapeutic regimen for advanced or metastatic prostate cancers; however, patients who receive these treatments are more likely to develop castration-resistant prostate cancer (CRPC) or neuroendocrine prostate cancer (NEPC). In the development of CRPC or NEPC, numerous genetic signaling pathways have been under preclinical investigations and in clinical trials. Accumulated evidence shows that DNA methylation, chromatin integrity, and accessibility for transcriptional regulation still play key roles in prostate cancer initiation and progression. Better understanding of how epigenetic change regulates the progression of prostate cancer and the interaction between epigenetic and genetic modulators driving NEPC may help develop a better risk stratification and more effective treatment regimens for prostate cancer patients.
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39
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Gonatopoulos-Pournatzis T, Niibori R, Salter EW, Weatheritt RJ, Tsang B, Farhangmehr S, Liang X, Braunschweig U, Roth J, Zhang S, Henderson T, Sharma E, Quesnel-Vallières M, Permanyer J, Maier S, Georgiou J, Irimia M, Sonenberg N, Forman-Kay JD, Gingras AC, Collingridge GL, Woodin MA, Cordes SP, Blencowe BJ. Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions. Mol Cell 2020; 77:1176-1192.e16. [PMID: 31999954 DOI: 10.1016/j.molcel.2020.01.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 08/15/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022]
Abstract
Microexons represent the most highly conserved class of alternative splicing, yet their functions are poorly understood. Here, we focus on closely related neuronal microexons overlapping prion-like domains in the translation initiation factors, eIF4G1 and eIF4G3, the splicing of which is activity dependent and frequently disrupted in autism. CRISPR-Cas9 deletion of these microexons selectively upregulates synaptic proteins that control neuronal activity and plasticity and further triggers a gene expression program mirroring that of activated neurons. Mice lacking the Eif4g1 microexon display social behavior, learning, and memory deficits, accompanied by altered hippocampal synaptic plasticity. We provide evidence that the eIF4G microexons function as a translational brake by causing ribosome stalling, through their propensity to promote the coalescence of cytoplasmic granule components associated with translation repression, including the fragile X mental retardation protein FMRP. The results thus reveal an autism-disrupted mechanism by which alternative splicing specializes neuronal translation to control higher order cognitive functioning.
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Affiliation(s)
| | - Rieko Niibori
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Eric W Salter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Brian Tsang
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xinyi Liang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | | | - Jonathan Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shen Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Tyler Henderson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eesha Sharma
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mathieu Quesnel-Vallières
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona 08003, Spain
| | - Stefan Maier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - John Georgiou
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain; ICREA, Barcelona 08010, Spain
| | - Nahum Sonenberg
- Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Graham L Collingridge
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Melanie A Woodin
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Sabine P Cordes
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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Andersen RE, Hong SJ, Lim JJ, Cui M, Harpur BA, Hwang E, Delgado RN, Ramos AD, Liu SJ, Blencowe BJ, Lim DA. The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo. Dev Cell 2020; 49:632-642.e7. [PMID: 31112699 DOI: 10.1016/j.devcel.2019.04.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/15/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
While it is now appreciated that certain long noncoding RNAs (lncRNAs) have important functions in cell biology, relatively few have been shown to regulate development in vivo, particularly with genetic strategies that establish cis versus trans mechanisms. Pnky is a nuclear-enriched lncRNA that is transcribed divergently from the neighboring proneural transcription factor Pou3f2. Here, we show that conditional deletion of Pnky from the developing cortex regulates the production of projection neurons from neural stem cells (NSCs) in a cell-autonomous manner, altering postnatal cortical lamination. Surprisingly, Pou3f2 expression is not disrupted by deletion of the entire Pnky gene. Moreover, expression of Pnky from a BAC transgene rescues the differential gene expression and increased neurogenesis of Pnky-knockout NSCs, as well as the developmental phenotypes of Pnky-deletion in vivo. Thus, despite being transcribed divergently from a key developmental transcription factor, the lncRNA Pnky regulates development in trans.
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Affiliation(s)
- Rebecca E Andersen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sung Jun Hong
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Justin J Lim
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Miao Cui
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brock A Harpur
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Elizabeth Hwang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryan N Delgado
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander D Ramos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Siyuan John Liu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA.
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41
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Walker RL, Ramaswami G, Hartl C, Mancuso N, Gandal MJ, de la Torre-Ubieta L, Pasaniuc B, Stein JL, Geschwind DH. Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms. Cell 2019; 179:750-771.e22. [PMID: 31626773 PMCID: PMC8963725 DOI: 10.1016/j.cell.2019.09.021] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/06/2019] [Accepted: 09/20/2019] [Indexed: 02/08/2023]
Abstract
Tissue-specific regulatory regions harbor substantial genetic risk for disease. Because brain development is a critical epoch for neuropsychiatric disease susceptibility, we characterized the genetic control of the transcriptome in 201 mid-gestational human brains, identifying 7,962 expression quantitative trait loci (eQTL) and 4,635 spliceQTL (sQTL), including several thousand prenatal-specific regulatory regions. We show that significant genetic liability for neuropsychiatric disease lies within prenatal eQTL and sQTL. Integration of eQTL and sQTL with genome-wide association studies (GWAS) via transcriptome-wide association identified dozens of novel candidate risk genes, highlighting shared and stage-specific mechanisms in schizophrenia (SCZ). Gene network analysis revealed that SCZ and autism spectrum disorder (ASD) affect distinct developmental gene co-expression modules. Yet, in each disorder, common and rare genetic variation converges within modules, which in ASD implicates superficial cortical neurons. More broadly, these data, available as a web browser and our analyses, demonstrate the genetic mechanisms by which developmental events have a widespread influence on adult anatomical and behavioral phenotypes.
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Affiliation(s)
- Rebecca L Walker
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA; Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gokul Ramaswami
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Christopher Hartl
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA; Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Michael J Gandal
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Luis de la Torre-Ubieta
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA; Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jason L Stein
- Department of Genetics and UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel H Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA; Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA.
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Capponi S, Stöffler N, Irimia M, Van Schaik FMA, Ondik MM, Biniossek ML, Lehmann L, Mitschke J, Vermunt MW, Creyghton MP, Graybiel AM, Reinheckel T, Schilling O, Blencowe BJ, Crittenden JR, Timmers HTM. Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100. RNA Biol 2019; 17:62-74. [PMID: 31559909 PMCID: PMC6948980 DOI: 10.1080/15476286.2019.1667214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Neuronal microexons represent the most highly conserved class of alternative splicing events and their timed expression shapes neuronal biology, including neuronal commitment and differentiation. The six-nt microexon 34ʹ is included in the neuronal form of TAF1 mRNA, which encodes the largest subunit of the basal transcription factor TFIID. In this study, we investigate the tissue distribution of TAF1-34ʹ mRNA and protein and the mechanism responsible for its neuronal-specific splicing. Using isoform-specific RNA probes and antibodies, we observe that canonical TAF1 and TAF1-34ʹ have different distributions in the brain, which distinguish proliferating from post-mitotic neurons. Knockdown and ectopic expression experiments demonstrate that the neuronal-specific splicing factor SRRM4/nSR100 promotes the inclusion of microexon 34ʹ into TAF1 mRNA, through the recognition of UGC sequences in the poly-pyrimidine tract upstream of the regulated microexon. These results show that SRRM4 regulates temporal and spatial expression of alternative TAF1 mRNAs to generate a neuronal-specific TFIID complex.
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Affiliation(s)
- Simona Capponi
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Nadja Stöffler
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Manuel Irimia
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frederik M A Van Schaik
- Molecular Cancer Research and Stem Cells, Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mercedes M Ondik
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lisa Lehmann
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Mitschke
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marit W Vermunt
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Menno P Creyghton
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ann M Graybiel
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) partner site Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine-University of Freiburg, Freiburg, Germany
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jill R Crittenden
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - H Th Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
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43
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Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice. Cell 2019; 177:1600-1618.e17. [PMID: 31150625 PMCID: PMC6993574 DOI: 10.1016/j.cell.2019.05.004] [Citation(s) in RCA: 630] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/11/2019] [Accepted: 04/30/2019] [Indexed: 01/02/2023]
Abstract
Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors including social communication and stereotypies. In addition to genetic risks, the gut microbiome differs between typically developing (TD) and ASD individuals, though it remains unclear whether the microbiome contributes to symptoms. We transplanted gut microbiota from human donors with ASD or TD controls into germ-free mice and reveal that colonization with ASD microbiota is sufficient to induce hallmark autistic behaviors. The brains of mice colonized with ASD microbiota display alternative splicing of ASD-relevant genes. Microbiome and metabolome profiles of mice harboring human microbiota predict that specific bacterial taxa and their metabolites modulate ASD behaviors. Indeed, treatment of an ASD mouse model with candidate microbial metabolites improves behavioral abnormalities and modulates neuronal excitability in the brain. We propose that the gut microbiota regulates behaviors in mice via production of neuroactive metabolites, suggesting that gut-brain connections contribute to the pathophysiology of ASD.
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Affiliation(s)
- Gil Sharon
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Nikki Jamie Cruz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dae-Wook Kang
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287, USA; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Michael J Gandal
- Center for Autism Research and Treatment, Program in Neurobehavioral Genetics, Semel Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, Semel Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bo Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Erika M Zink
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Cameron P Casey
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Bryn C Taylor
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christianne J Lane
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Lisa M Bramer
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Nancy G Isern
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - David W Hoyt
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael J Sweredoski
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Biongineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Program in Neurobehavioral Genetics, Semel Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, Semel Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287, USA; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Blee AM, Huang H. Lineage plasticity-mediated therapy resistance in prostate cancer. Asian J Androl 2019; 21:241-248. [PMID: 29900883 PMCID: PMC6498731 DOI: 10.4103/aja.aja_41_18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/08/2018] [Indexed: 12/21/2022] Open
Abstract
Therapy resistance is a significant challenge for prostate cancer treatment in clinic. Although targeted therapies such as androgen deprivation and androgen receptor (AR) inhibition are effective initially, tumor cells eventually evade these strategies through multiple mechanisms. Lineage reprogramming in response to hormone therapy represents a key mechanism that is increasingly observed. The studies in this area have revealed specific combinations of alterations present in adenocarcinomas that provide cells with the ability to transdifferentiate and perpetuate AR-independent tumor growth after androgen-based therapies. Interestingly, several master regulators have been identified that drive plasticity, some of which also play key roles during development and differentiation of the cell lineages in the normal prostate. Thus, further study of each AR-independent tumor type and understanding underlying mechanisms are warranted to develop combinational therapies that combat lineage plasticity in prostate cancer.
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Affiliation(s)
- Alexandra M Blee
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Department of Urology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Mayo Clinic Cancer Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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45
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Nakano Y, Wiechert S, Bánfi B. Overlapping Activities of Two Neuronal Splicing Factors Switch the GABA Effect from Excitatory to Inhibitory by Regulating REST. Cell Rep 2019; 27:860-871.e8. [PMID: 30995482 PMCID: PMC6556397 DOI: 10.1016/j.celrep.2019.03.072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 01/22/2019] [Accepted: 03/18/2019] [Indexed: 11/23/2022] Open
Abstract
A truncating mutation in the mouse Srrm4 gene, which encodes a neuronal splicing factor, causes alternative splicing defects selectively in the ear. The mechanism by which splicing is preserved in the brain of these mice is not known. Here, we show that SRRM3 limits the Srrm4 mutation-associated defects to the ear and that, in cortical neurons, overlapping SRRM3-SRRM4 activity regulates the development of interneuronal inhibition. In vitro, SRRM3 and SRRM4 regulate the same splicing events, but a mutation in mouse Srrm3 causes tremors and mild defects in neuronal alternative splicing, demonstrating unique SRRM3 roles in vivo. Mice harboring mutations in both Srrm3 and Srrm4 die neonatally and exhibit severe splicing defects. In these mice, splicing alterations prevent inactivation of the gene repressor REST, which maintains immature excitatory GABAergic neurotransmission by repressing K-Cl cotransporter 2. Thus, our data reveal that SRRM3 and SRRM4 act redundantly to regulate GABAergic neurotransmission by inactivating REST.
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Affiliation(s)
- Yoko Nakano
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Inflammation Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Susan Wiechert
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Inflammation Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Botond Bánfi
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Inflammation Program, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Otolaryngology-Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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47
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Li Y, Xie N, Chen R, Lee AR, Lovnicki J, Morrison EA, Fazli L, Zhang Q, Musselman CA, Wang Y, Huang J, Gleave ME, Collins C, Dong X. RNA Splicing of the BHC80 Gene Contributes to Neuroendocrine Prostate Cancer Progression. Eur Urol 2019; 76:157-166. [PMID: 30910347 DOI: 10.1016/j.eururo.2019.03.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/08/2019] [Indexed: 02/01/2023]
Abstract
BACKGROUND Prostate adenocarcinoma (AdPC) progression to treatment-induced neuroendocrine prostate cancer (t-NEPC) is associated with poor patient survival. While AdPC and t-NEPC share similar genomes, they possess distinct transcriptomes, suggesting that RNA splicing and epigenetic mechanisms may regulate t-NEPC development. OBJECTIVE To characterize the role of alternative RNA splicing of the histone demethylase BHC80 during t-NEPC progression. DESIGN, SETTING, AND PARTICIPANTS The expression of BHC80 splice variants (BHC80-1 and BHC80-2) were compared between AdPC and t-NEPC patient tumors. Regulatory mechanisms of RNA splicing of the BHC80 gene were studied, and the signal pathways mediated by BHC80 splice variants were investigated in t-NEPC cell and xenograft models. RESULTS Global transcriptome analyses identified that the BHC80-2 variant is highly expressed in t-NEPC. Compared with the known histone demethylation activities of the BHC80 gene, we discovered a novel nonepigenetic action of BHC80-2, whereby BHC80-2 is localized in the cytoplasm to trigger the MyD88-p38-TTP pathway, which results in increased RNA stability of multiple tumor-promoting cytokines. While BHC80-2 does not induce neuroendocrine differentiation of cancer cells, it stimulates cell proliferation and tumor progression independent of androgen receptor signaling. Blockade of BHC80-2-regulated MyD88 signaling suppresses growth of several t-NEPC cell spheroid and xenograft models. CONCLUSIONS Gain of function of BHC80-2 through alternative RNA splicing activates immune responses of cancer cells to promote t-NEPC development. PATIENT SUMMARY The main obstacle to develop effective therapies for patients with t-NEPC is the lack of understanding on how t-NEPC is developed. Our study not only identifies a previously unknown BHC80-2-MyD88 signaling pathway that plays an important role during t-NEPC development, but also provides a proof of principle that targeting this signal pathway may offer an avenue to treat t-NEPC.
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Affiliation(s)
- Yinan Li
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ning Xie
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ruiqi Chen
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jessica Lovnicki
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ladan Fazli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Qingfu Zhang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA; China Medical University, Shenyang, China
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colin Collins
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
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A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nat Ecol Evol 2019; 3:691-701. [DOI: 10.1038/s41559-019-0813-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/16/2019] [Indexed: 02/02/2023]
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Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons. Mol Cell 2018; 72:510-524.e12. [DOI: 10.1016/j.molcel.2018.10.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/27/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022]
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Sterne-Weiler T, Weatheritt RJ, Best AJ, Ha KC, Blencowe BJ. Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop. Mol Cell 2018; 72:187-200.e6. [DOI: 10.1016/j.molcel.2018.08.018] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/24/2018] [Accepted: 08/09/2018] [Indexed: 01/08/2023]
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