1
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Shender VO, Anufrieva KS, Shnaider PV, Arapidi GP, Pavlyukov MS, Ivanova OM, Malyants IK, Stepanov GA, Zhuravlev E, Ziganshin RH, Butenko IO, Bukato ON, Klimina KM, Veselovsky VA, Grigorieva TV, Malanin SY, Aleshikova OI, Slonov AV, Babaeva NA, Ashrafyan LA, Khomyakova E, Evtushenko EG, Lukina MM, Wang Z, Silantiev AS, Nushtaeva AA, Kharlampieva DD, Lazarev VN, Lashkin AI, Arzumanyan LK, Petrushanko IY, Makarov AA, Lebedeva OS, Bogomazova AN, Lagarkova MA, Govorun VM. Therapy-induced secretion of spliceosomal components mediates pro-survival crosstalk between ovarian cancer cells. Nat Commun 2024; 15:5237. [PMID: 38898005 PMCID: PMC11187153 DOI: 10.1038/s41467-024-49512-6] [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: 02/04/2022] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
Ovarian cancer often develops resistance to conventional therapies, hampering their effectiveness. Here, using ex vivo paired ovarian cancer ascites obtained before and after chemotherapy and in vitro therapy-induced secretomes, we show that molecules secreted by ovarian cancer cells upon therapy promote cisplatin resistance and enhance DNA damage repair in recipient cancer cells. Even a short-term incubation of chemonaive ovarian cancer cells with therapy-induced secretomes induces changes resembling those that are observed in chemoresistant patient-derived tumor cells after long-term therapy. Using integrative omics techniques, we find that both ex vivo and in vitro therapy-induced secretomes are enriched with spliceosomal components, which relocalize from the nucleus to the cytoplasm and subsequently into the extracellular vesicles upon treatment. We demonstrate that these molecules substantially contribute to the phenotypic effects of therapy-induced secretomes. Thus, SNU13 and SYNCRIP spliceosomal proteins promote therapy resistance, while the exogenous U12 and U6atac snRNAs stimulate tumor growth. These findings demonstrate the significance of spliceosomal network perturbation during therapy and further highlight that extracellular signaling might be a key factor contributing to the emergence of ovarian cancer therapy resistance.
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Affiliation(s)
- Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology; Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Georgij P Arapidi
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Marat S Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Irina K Malyants
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Evgenii Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Ivan O Butenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Olga N Bukato
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Ksenia M Klimina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Vladimir A Veselovsky
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | | | | | - Olga I Aleshikova
- National Medical Scientific Centre of Obstetrics, Gynaecology and Perinatal Medicine named after V.I. Kulakov, Moscow, 117198, Russian Federation
- Russian Research Center of Roentgenology and Radiology, Moscow, 117997, Russian Federation
| | - Andrey V Slonov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Nataliya A Babaeva
- National Medical Scientific Centre of Obstetrics, Gynaecology and Perinatal Medicine named after V.I. Kulakov, Moscow, 117198, Russian Federation
- Russian Research Center of Roentgenology and Radiology, Moscow, 117997, Russian Federation
| | - Lev A Ashrafyan
- National Medical Scientific Centre of Obstetrics, Gynaecology and Perinatal Medicine named after V.I. Kulakov, Moscow, 117198, Russian Federation
- Russian Research Center of Roentgenology and Radiology, Moscow, 117997, Russian Federation
| | | | - Evgeniy G Evtushenko
- Faculty of Chemistry; Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Zixiang Wang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Jinan, 250012, Shandong, China
| | - Artemiy S Silantiev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anna A Nushtaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation
| | - Daria D Kharlampieva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Vassili N Lazarev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Arseniy I Lashkin
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Lorine K Arzumanyan
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Irina Yu Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Olga S Lebedeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Alexandra N Bogomazova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Maria A Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Vadim M Govorun
- Research Institute for Systems Biology and Medicine, Moscow, 117246, Russian Federation
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2
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Zhang Q, Chen Y, Teng Z, Lin Z, Liu H. CDK11 facilitates centromeric transcription to maintain centromeric cohesion during mitosis. Mol Biol Cell 2024; 35:ar18. [PMID: 38019613 PMCID: PMC10881149 DOI: 10.1091/mbc.e23-08-0303] [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: 08/07/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
Actively-transcribing RNA polymerase (RNAP)II is remained on centromeres to maintain centromeric cohesion during mitosis, although it is largely released from chromosome arms. This pool of RNAPII plays an important role in centromere functions. However, the mechanism of RNAPII retention on mitotic centromeres is poorly understood. We here demonstrate that Cyclin-dependent kinase (Cdk)11 is involved in RNAPII regulation on mitotic centromeres. Consistently, we show that Cdk11 knockdown induces centromeric cohesion defects and decreases Bub1 on kinetochores, but the centromeric cohesion defects are partially attributed to Bub1. Furthermore, Cdk11 knockdown and the expression of its kinase-dead version significantly reduce both RNAPII and elongating RNAPII (pSer2) levels on centromeres and decrease centromeric transcription. Importantly, the overexpression of centromeric α-satellite RNAs fully rescues Cdk11-knockdown defects. These results suggest that the maintenance of centromeric cohesion requires Cdk11-facilitated centromeric transcription. Mechanistically, Cdk11 localizes on centromeres where it binds and phosphorylates RNAPII to promote transcription. Remarkably, mitosis-specific degradation of G2/M Cdk11-p58 recapitulates Cdk11-knockdown defects. Altogether, our findings establish Cdk11 as an important regulator of centromeric transcription and as part of the mechanism for retaining RNAPII on centromeres during mitosis.
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Affiliation(s)
- Qian Zhang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Yujue Chen
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Teng
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Hong Liu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA 70112
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3
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López-Oreja I, Gohr A, Playa-Albinyana H, Giró A, Arenas F, Higashi M, Tripathi R, López-Guerra M, Irimia M, Aymerich M, Valcárcel J, Bonnal S, Colomer D. SF3B1 mutation-mediated sensitization to H3B-8800 splicing inhibitor in chronic lymphocytic leukemia. Life Sci Alliance 2023; 6:e202301955. [PMID: 37562845 PMCID: PMC10415613 DOI: 10.26508/lsa.202301955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Splicing factor 3B subunit 1 (SF3B1) is involved in pre-mRNA branch site recognition and is the target of antitumor-splicing inhibitors. Mutations in SF3B1 are observed in 15% of patients with chronic lymphocytic leukemia (CLL) and are associated with poor prognosis, but their pathogenic mechanisms remain poorly understood. Using deep RNA-sequencing data from 298 CLL tumor samples and isogenic SF3B1 WT and K700E-mutated CLL cell lines, we characterize targets and pre-mRNA sequence features associated with the selection of cryptic 3' splice sites upon SF3B1 mutation, including an event in the MAP3K7 gene relevant for activation of NF-κB signaling. Using the H3B-8800 splicing modulator, we show, for the first time in CLL, cytotoxic effects in vitro in primary CLL samples and in SF3B1-mutated isogenic CLL cell lines, accompanied by major splicing changes and delayed leukemic infiltration in a CLL xenotransplant mouse model. H3B-8800 displayed preferential lethality towards SF3B1-mutated cells and synergism with the BCL2 inhibitor venetoclax, supporting the potential use of SF3B1 inhibitors as a novel therapeutic strategy in CLL.
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Affiliation(s)
- Irene López-Oreja
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - André Gohr
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Ariadna Giró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Fabian Arenas
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Morihiro Higashi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Rupal Tripathi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Mònica López-Guerra
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
- Universitat Barcelona, Barcelona, Spain
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4
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Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
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Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
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5
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Kontandreopoulou CN, Kalopisis K, Viniou NA, Diamantopoulos P. The genetics of myelodysplastic syndromes and the opportunities for tailored treatments. Front Oncol 2022; 12:989483. [PMID: 36338673 PMCID: PMC9630842 DOI: 10.3389/fonc.2022.989483] [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: 07/08/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic instability, microenvironmental aberrations, and somatic mutations contribute to the phenotype of myelodysplastic syndrome and the risk for transformation to AML. Genes involved in RNA splicing, DNA methylation, histone modification, the cohesin complex, transcription, DNA damage response pathway, signal transduction and other pathways constitute recurrent mutational targets in MDS. RNA-splicing and DNA methylation mutations seem to occur early and are reported as driver mutations in over 50% of MDS patients. The improved understanding of the molecular landscape of MDS has led to better disease and risk classification, leading to novel therapeutic opportunities. Based on these findings, novel agents are currently under preclinical and clinical development and expected to improve the clinical outcome of patients with MDS in the upcoming years. This review provides a comprehensive update of the normal gene function as well as the impact of mutations in the pathogenesis, deregulation, diagnosis, and prognosis of MDS, focuses on the most recent advances of the genetic basis of myelodysplastic syndromes and their clinical relevance, and the latest targeted therapeutic approaches including investigational and approved agents for MDS.
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6
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Olthof AM, White AK, Kanadia RN. The emerging significance of splicing in vertebrate development. Development 2022; 149:dev200373. [PMID: 36178052 PMCID: PMC9641660 DOI: 10.1242/dev.200373] [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] [Indexed: 01/19/2023]
Abstract
Splicing is a crucial regulatory node of gene expression that has been leveraged to expand the proteome from a limited number of genes. Indeed, the vast increase in intron number that accompanied vertebrate emergence might have aided the evolution of developmental and organismal complexity. Here, we review how animal models for core spliceosome components have provided insights into the role of splicing in vertebrate development, with a specific focus on neuronal, neural crest and skeletal development. To this end, we also discuss relevant spliceosomopathies, which are developmental disorders linked to mutations in spliceosome subunits. Finally, we discuss potential mechanisms that could underlie the tissue-specific phenotypes often observed upon spliceosome inhibition and identify gaps in our knowledge that, we hope, will inspire further research.
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Affiliation(s)
- Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Alisa K. White
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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7
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Imbriano C, Belluti S. Histone Marks-Dependent Effect on Alternative Splicing: New Perspectives for Targeted Splicing Modulation in Cancer? Int J Mol Sci 2022; 23:ijms23158304. [PMID: 35955433 PMCID: PMC9368390 DOI: 10.3390/ijms23158304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) is a tightly regulated mechanism that generates the complex human proteome from a small number of genes. Cis-regulatory RNA motifs in exons and introns control AS, recruiting positive and negative trans-acting splicing regulators. At a higher level, chromatin affects splicing events. Growing evidence indicates that the popular histone code hypothesis can be extended to RNA-level processes, such as AS. In addition to nucleosome positioning, which can generate transcriptional barriers to shape the final splicing outcome, histone post-translational modifications can contribute to the detailed regulation of single exon inclusion/exclusion. A histone-based system can identify alternatively spliced chromatin stretches, affecting RNAPII elongation locally or recruiting splicing components via adaptor complexes. In tumor cells, several mechanisms trigger misregulated AS events and produce cancer-associated transcripts. On a genome-wide level, aberrant AS can be the consequence of dysfunctional epigenetic splicing code, including altered enrichment in histone post-translational modifications. This review describes the main findings related to the effect of histone modifications and variants on splicing outcome and how a dysfunctional epigenetic splicing code triggers aberrant AS in cancer. In addition, it highlights recent advances in programmable DNA-targeting technologies and their possible application for AS targeted epigenetic modulation.
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8
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Identification of Three Genes Associated with Metastasis in Melanoma and Construction of a Predictive Model: A Multiracial Identification. JOURNAL OF ONCOLOGY 2022; 2022:4567063. [PMID: 35637857 PMCID: PMC9148232 DOI: 10.1155/2022/4567063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022]
Abstract
The aim of this study was to identify hub genes associated with metastasis and prognosis in melanoma. Weighted gene coexpression network analysis (WGCNA) was performed to screen and identify hub genes. ROC and K-M analyses were used to verify the hub genes in the internal and external data sets. The risk score model and nomogram model were constructed based on the IHC result. Through WGCNA, the three hub genes, SNRPD2, SNRPD3, and EIF4A3, were identified. In the external data set, the hub genes identified were associated with the worse prognosis (TCGA, SNRPD2,
; SNRPD3,
; EIF4A3,
; GSE65904, SNRPD2,
; SNRPD3,
; EIF4A3,
; GSE19234, SNRPD2,
; SNRPD3,
; EIF4A3,
). In the GSE8401, we found that the hub genes were highly expressed in the metastasis compared with the nonmetastasis group (SNRPD2,
vs.
,
; SNRPD3,
vs.
,
; EIF4A3,
vs.
,
). Moreover, the hub genes were identified by the IHC in our data set. The result was similar with the external data set. The hub genes could predict the metastasis and prognosis in the Chinese MM patients. Finally, the GSEA and Pearson analysis demonstrated that the SNRPD2 was associated with the immunotherapy. The three hub genes were identified and validated in MM patients in external and internal data sets. The risk factor model was constructed and verified as a powerful model to predict metastasis and prognosis in MM patients.
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9
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Osadska M, Selicky T, Kretova M, Jurcik J, Sivakova B, Cipakova I, Cipak L. The Interplay of Cohesin and RNA Processing Factors: The Impact of Their Alterations on Genome Stability. Int J Mol Sci 2022; 23:3939. [PMID: 35409298 PMCID: PMC8999970 DOI: 10.3390/ijms23073939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Cohesin, a multi-subunit protein complex, plays important roles in sister chromatid cohesion, DNA replication, chromatin organization, gene expression, transcription regulation, and the recombination or repair of DNA damage. Recently, several studies suggested that the functions of cohesin rely not only on cohesin-related protein-protein interactions, their post-translational modifications or specific DNA modifications, but that some RNA processing factors also play an important role in the regulation of cohesin functions. Therefore, the mutations and changes in the expression of cohesin subunits or alterations in the interactions between cohesin and RNA processing factors have been shown to have an impact on cohesion, the fidelity of chromosome segregation and, ultimately, on genome stability. In this review, we provide an overview of the cohesin complex and its role in chromosome segregation, highlight the causes and consequences of mutations and changes in the expression of cohesin subunits, and discuss the RNA processing factors that participate in the regulation of the processes involved in chromosome segregation. Overall, an understanding of the molecular determinants of the interplay between cohesin and RNA processing factors might help us to better understand the molecular mechanisms ensuring the integrity of the genome.
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Affiliation(s)
- Michaela Osadska
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Tomas Selicky
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Miroslava Kretova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Barbara Sivakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia;
| | - Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
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10
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SF3B14 is involved in the centrosome regulation trough splicing of TUBGCP6 pre-mRNA. Biochem Biophys Res Commun 2021; 588:133-139. [PMID: 34954520 DOI: 10.1016/j.bbrc.2021.12.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022]
Abstract
Splicing precursor messenger RNA (pre-mRNA) is a critical step to produce physiologically functional protein. Splicing failure not only gives rise to dysfunctional proteins but also generates abnormal protein function, which causes several diseases. Several pre-mRNA splicing factors are reported to regulate mitosis directly at mitotic structures and/or indirectly through controlling the pre-mRNA splicing for mitotic proteins. In this study, we described the mitotic functions of SF3B14, a component of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP), which we identified as a candidate involved in mitosis based on the large-scale RNA interference (RNAi) screen of the nucleolar proteome database. We observed that SF3B14 depletion caused prolonged mitosis and several mitotic defects, such as monopolar spindle and chromosome misalignment during metaphase. Although SF3B14 was found in the nucleolar proteome database, our immunofluorescent stainings demonstrated that SF3B14 was predominantly localized in the nucleoplasm and excluded from the nucleolus during interphase. In addition, SF3B14 did not colocalize with specific mitotic structures during mitosis, which is not in line with its direct mitotic function. Notably, we found that the SF3B14 depletion reduced protein levels of TUBGCP6, required for centrosome regulation, and increased the unspliced/spliced ratio of its mRNA. Taken together, we propose that the pre-mRNA of TUBGCP6 is one of the targets for SF3B14 splicing through which SF3B14 controls mitotic chromosome behavior.
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11
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Czarnek M, Sarad K, Karaś A, Kochan J, Bereta J. Non-targeting control for MISSION shRNA library silences SNRPD3 leading to cell death or permanent growth arrest. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:711-731. [PMID: 34703654 PMCID: PMC8517100 DOI: 10.1016/j.omtn.2021.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 09/03/2021] [Indexed: 12/15/2022]
Abstract
In parallel with the expansion of RNA interference (RNAi) techniques, accumulating evidence indicates that RNAi analyses might be seriously biased due to the off-target effects of gene-specific short hairpin RNAs (shRNAs). Our findings indicated that off-target effects of non-targeting shRNA comprise another source of misinterpreted shRNA-based data. We found that SHC016, which is one of two non-targeting shRNA controls for the MISSION (commercialized TRC) library, exerts deleterious effects that lead to elimination of the shRNA-coding cassette from the genomes of cultured murine and human cells. Here, we used a lentiviral vector with inducible SHC016 expression to confirm that this shRNA induces apoptosis in murine cells and senescence or mitotic catastrophe depending on the p53 status in human tumor cells. We identified the core spliceosomal protein, small nuclear ribonucleoprotein Sm D3 (SNRPD3), as a major SHC016 target in several cell lines and confirmed that CRISPRi knockdown of SNRPD3 mimics the effects of SHC016 expression in A549 and U251 cells. The overexpression of SNRPD3 rescued U251 cells from SHC016-induced mitotic catastrophe. Our findings disqualified non-targeting SHC016 shRNA and added a new premise to the discussion about the sources of uncertainty in RNAi results.
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Affiliation(s)
- Maria Czarnek
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Katarzyna Sarad
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Agnieszka Karaś
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Joanna Bereta
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
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12
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Diouf B, Wing C, Panetta JC, Eddins D, Lin W, Yang W, Fan Y, Pei D, Cheng C, Delaney SM, Zhang W, Bonten EJ, Crews KR, Paugh SW, Li L, Freeman BB, Autry RJ, Beard JA, Ferguson DC, Janke LJ, Ness KK, Chen T, Zakharenko SS, Jeha S, Pui CH, Relling MV, Eileen Dolan M, Evans WE. Identification of small molecules that mitigate vincristine-induced neurotoxicity while sensitizing leukemia cells to vincristine. Clin Transl Sci 2021; 14:1490-1504. [PMID: 33742760 PMCID: PMC8301581 DOI: 10.1111/cts.13012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/16/2022] Open
Abstract
Vincristine (VCR) is one of the most widely prescribed medications for treating solid tumors and acute lymphoblastic leukemia (ALL) in children and adults. However, its major dose-limiting toxicity is peripheral neuropathy that can disrupt curative therapy. Peripheral neuropathy can also persist into adulthood, compromising quality of life of childhood cancer survivors. Reducing VCR-induced neurotoxicity without compromising its anticancer effects would be ideal. Here, we show that low expression of NHP2L1 is associated with increased sensitivity of primary leukemia cells to VCR, and that concomitant administration of VCR with inhibitors of NHP2L1 increases VCR cytotoxicity in leukemia cells, prolongs survival of ALL xenograft mice, but decreases VCR effects on human-induced pluripotent stem cell-derived neurons and mitigates neurotoxicity in mice. These findings offer a strategy for increasing VCR's antileukemic effects while reducing peripheral neuropathy in patients treated with this widely prescribed medication.
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Affiliation(s)
- Barthelemy Diouf
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Claudia Wing
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - John C Panetta
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Donnie Eddins
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Wenjian Yang
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shannon M Delaney
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Erik J Bonten
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kristine R Crews
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Steven W Paugh
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lie Li
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Burgess B Freeman
- Preclinical Pharmacokinetics Shared Resource, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Robert J Autry
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jordan A Beard
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Laura J Janke
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kirsten K Ness
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stanislav S Zakharenko
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sima Jeha
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Mary V Relling
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - M Eileen Dolan
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - William E Evans
- Hematological Malignancies Program and Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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13
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Koedoot E, van Steijn E, Vermeer M, González-Prieto R, Vertegaal ACO, Martens JWM, Le Dévédec SE, van de Water B. Splicing factors control triple-negative breast cancer cell mitosis through SUN2 interaction and sororin intron retention. J Exp Clin Cancer Res 2021; 40:82. [PMID: 33648524 PMCID: PMC7919097 DOI: 10.1186/s13046-021-01863-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited therapeutic opportunities. Recently, splicing factors have gained attention as potential targets for cancer treatment. Here we systematically evaluated the role of RNA splicing factors in TNBC cell proliferation. METHODS In this study, we performed an RNAi screen targeting 244 individual splicing factors to systematically evaluate their role in TNBC cell proliferation. For top candidates, mechanistic insight was gained using amongst others western blot, PCR, FACS, molecular imaging and cloning. Pulldown followed by mass spectrometry were used to determine protein-protein interactions and patient-derived RNA sequencing data was used relate splicing factor expression levels to proliferation markers. RESULTS We identified nine splicing factors, including SNRPD2, SNRPD3 and NHP2L1, of which depletion inhibited proliferation in two TNBC cell lines by deregulation of sister chromatid cohesion (SCC) via increased sororin intron 1 retention and down-regulation of SMC1, MAU2 and ESPL1. Protein-protein interaction analysis of SNRPD2, SNRPD3 and NHP2L1 identified that seven out of the nine identified splicing factors belong to the same spliceosome complex including novel component SUN2 that was also critical for efficient sororin splicing. Finally, sororin transcript levels are highly correlated to various proliferation markers in BC patients. CONCLUSION We systematically determined splicing factors that control proliferation of breast cancer cells through a mechanism that involves effective sororin splicing and thereby appropriate sister chromatid cohesion. Moreover, we identified SUN2 as an important new spliceosome complex interacting protein that is critical in this process. We anticipate that deregulating sororin levels through targeting of the relevant splicing factors might be a potential strategy to treat TNBC.
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Affiliation(s)
- Esmee Koedoot
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Eline van Steijn
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marjolein Vermeer
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Román González-Prieto
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - John W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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14
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Abstract
Mutations of the cohesin complex in human cancer were first discovered ~10 years ago. Since then, researchers worldwide have demonstrated that cohesin is among the most commonly mutated protein complexes in cancer. Inactivating mutations in genes encoding cohesin subunits are common in bladder cancers, paediatric sarcomas, leukaemias, brain tumours and other cancer types. Also in those 10 years, the prevailing view of the functions of cohesin in cell biology has undergone a revolutionary transformation. Initially, the predominant view of cohesin was as a ring that encircled and cohered replicated chromosomes until its cleavage triggered the metaphase-to-anaphase transition. As such, early studies focused on the role of tumour-derived cohesin mutations in the fidelity of chromosome segregation and aneuploidy. However, over the past 5 years the cohesin field has shifted dramatically, and research now focuses on the primary role of cohesin in generating, maintaining and regulating the intra-chromosomal DNA looping events that modulate 3D genome organization and gene expression. This Review focuses on recent discoveries in the cohesin field that provide insight into the role of cohesin inactivation in cancer pathogenesis, and opportunities for exploiting these findings for the clinical benefit of patients with cohesin-mutant cancers.
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Affiliation(s)
- Todd Waldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, DC, USA.
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15
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Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability. Cell Rep 2020; 28:1551-1563.e7. [PMID: 31390568 PMCID: PMC6693559 DOI: 10.1016/j.celrep.2019.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 03/18/2019] [Accepted: 07/01/2019] [Indexed: 01/19/2023] Open
Abstract
THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here, we show that human THO interacts with MFAP1 (microfibrillar-associated protein 1), a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent on either transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381 cause similar transcription-independent genome instability, supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses. MFAP1 depletion affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role.
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16
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Park EM, Scott PM, Clutario K, Cassidy KB, Zhan K, Gerber SA, Holland AJ. WBP11 is required for splicing the TUBGCP6 pre-mRNA to promote centriole duplication. J Cell Biol 2020; 219:133543. [PMID: 31874114 PMCID: PMC7039186 DOI: 10.1083/jcb.201904203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/24/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022] Open
Abstract
Centriole duplication occurs once in each cell cycle to maintain centrosome number. A previous genome-wide screen revealed that depletion of 14 RNA splicing factors leads to a specific defect in centriole duplication, but the cause of this deficit remains unknown. Here, we identified an additional pre-mRNA splicing factor, WBP11, as a novel protein required for centriole duplication. Loss of WBP11 results in the retention of ∼200 introns, including multiple introns in TUBGCP6, a central component of the γ-TuRC. WBP11 depletion causes centriole duplication defects, in part by causing a rapid decline in the level of TUBGCP6. Several additional splicing factors that are required for centriole duplication interact with WBP11 and are required for TUBGCP6 expression. These findings provide insight into how the loss of a subset of splicing factors leads to a failure of centriole duplication. This may have clinical implications because mutations in some spliceosome proteins cause microcephaly and/or growth retardation, phenotypes that are strongly linked to centriole defects.
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Affiliation(s)
- Elizabeth M Park
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Phillip M Scott
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kevin Clutario
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Katelyn B Cassidy
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Kevin Zhan
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Scott A Gerber
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH.,Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
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17
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Moonlighting in Mitosis: Analysis of the Mitotic Functions of Transcription and Splicing Factors. Cells 2020; 9:cells9061554. [PMID: 32604778 PMCID: PMC7348712 DOI: 10.3390/cells9061554] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022] Open
Abstract
Moonlighting proteins can perform one or more additional functions besides their primary role. It has been posited that a protein can acquire a moonlighting function through a gradual evolutionary process, which is favored when the primary and secondary functions are exerted in different cellular compartments. Transcription factors (TFs) and splicing factors (SFs) control processes that occur in interphase nuclei and are strongly reduced during cell division, and are therefore in a favorable situation to evolve moonlighting mitotic functions. However, recently published moonlighting protein databases, which comprise almost 400 proteins, do not include TFs and SFs with secondary mitotic functions. We searched the literature and found several TFs and SFs with bona fide moonlighting mitotic functions, namely they localize to specific mitotic structure(s), interact with proteins enriched in the same structure(s), and are required for proper morphology and functioning of the structure(s). In addition, we describe TFs and SFs that localize to mitotic structures but cannot be classified as moonlighting proteins due to insufficient data on their biochemical interactions and mitotic roles. Nevertheless, we hypothesize that most TFs and SFs with specific mitotic localizations have either minor or redundant moonlighting functions, or are evolving towards the acquisition of these functions.
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18
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Jiménez M, Urtasun R, Elizalde M, Azkona M, Latasa MU, Uriarte I, Arechederra M, Alignani D, Bárcena-Varela M, Álvarez-Sola G, Colyn L, Santamaría E, Sangro B, Rodriguez-Ortigosa C, Fernández-Barrena MG, Ávila MA, Berasain C. Splicing events in the control of genome integrity: role of SLU7 and truncated SRSF3 proteins. Nucleic Acids Res 2019; 47:3450-3466. [PMID: 30657957 PMCID: PMC6468163 DOI: 10.1093/nar/gkz014] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/21/2018] [Accepted: 01/08/2019] [Indexed: 12/13/2022] Open
Abstract
Genome instability is related to disease development and carcinogenesis. DNA lesions are caused by genotoxic compounds but also by the dysregulation of fundamental processes like transcription, DNA replication and mitosis. Recent evidence indicates that impaired expression of RNA-binding proteins results in mitotic aberrations and the formation of transcription-associated RNA-DNA hybrids (R-loops), events strongly associated with DNA injury. We identify the splicing regulator SLU7 as a key mediator of genome stability. SLU7 knockdown results in R-loops formation, DNA damage, cell-cycle arrest and severe mitotic derangements with loss of sister chromatid cohesion (SCC). We define a molecular pathway through which SLU7 keeps in check the generation of truncated forms of the splicing factor SRSF3 (SRp20) (SRSF3-TR). Behaving as dominant negative, or by gain-of-function, SRSF3-TR impair the correct splicing and expression of the splicing regulator SRSF1 (ASF/SF2) and the crucial SCC protein sororin. This unique function of SLU7 was found in cancer cells of different tissue origin and also in the normal mouse liver, demonstrating a conserved and fundamental role of SLU7 in the preservation of genome integrity. Therefore, the dowregulation of SLU7 and the alterations of this pathway that we observe in the cirrhotic liver could be involved in the process of hepatocarcinogenesis.
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Affiliation(s)
- Maddalen Jiménez
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Raquel Urtasun
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain
| | - María Elizalde
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - María Azkona
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - M Ujue Latasa
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Iker Uriarte
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - María Arechederra
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Diego Alignani
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,Cytometry Unit, CIMA, University of Navarra, Pamplona 31008, Spain
| | | | - Gloria Álvarez-Sola
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Leticia Colyn
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Eva Santamaría
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Bruno Sangro
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain.,Hepatology Unit, Navarra University Clinic, Pamplona 31008, Spain
| | - Carlos Rodriguez-Ortigosa
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Maite G Fernández-Barrena
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Matías A Ávila
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Carmen Berasain
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
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19
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Zhang H, Cheng G, Yang Z, Wang T, Xu J. Identification of Sugarcane Host Factors Interacting with the 6K2 Protein of the Sugarcane Mosaic Virus. Int J Mol Sci 2019; 20:ijms20163867. [PMID: 31398864 PMCID: PMC6719097 DOI: 10.3390/ijms20163867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022] Open
Abstract
The 6K2 protein of potyviruses plays a key role in the viral infection in plants. In the present study, the coding sequence of 6K2 was cloned from Sugarcane mosaic virus (SCMV) strain FZ1 into pBT3-STE to generate the plasmid pBT3-STE-6K2, which was used as bait to screen a cDNA library prepared from sugarcane plants infected with SCMV based on the DUALmembrane system. One hundred and fifty-seven positive colonies were screened and sequenced, and the corresponding full-length genes were cloned from sugarcane cultivar ROC22. Then, 24 genes with annotations were obtained, and the deduced proteins were classified into three groups, in which eight proteins were involved in the stress response, 12 proteins were involved in transport, and four proteins were involved in photosynthesis based on their biological functions. Of the 24 proteins, 20 proteins were verified to interact with SCMV-6K2 by yeast two-hybrid assays. The possible roles of these proteins in SCMV infection on sugarcane are analyzed and discussed. This is the first report on the interaction of SCMV-6K2 with host factors from sugarcane, and will improve knowledge on the mechanism of SCMV infection in sugarcane.
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Affiliation(s)
- Hai Zhang
- National Engineering Research Center for Sugarcane, Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guangyuan Cheng
- National Engineering Research Center for Sugarcane, Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zongtao Yang
- National Engineering Research Center for Sugarcane, Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tong Wang
- National Engineering Research Center for Sugarcane, Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingsheng Xu
- National Engineering Research Center for Sugarcane, Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China.
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20
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Nishimura K, Cho Y, Tokunaga K, Nakao M, Tani T, Ideue T. DEAH box RNA helicase DHX38 associates with satellite I noncoding RNA involved in chromosome segregation. Genes Cells 2019; 24:585-590. [PMID: 31166646 DOI: 10.1111/gtc.12707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/29/2019] [Accepted: 06/01/2019] [Indexed: 11/29/2022]
Abstract
Noncoding (nc) RNA called satellite I is transcribed from the human centromere region. Depletion of this ncRNA results in abnormal nuclear morphology because of defects in chromosome segregation. Some protein factors interact with this ncRNA and function as a component of a nc ribonucleoprotein (RNP) complex in mitotic regulation. Here, we found that DHX38, a pre-mRNA splicing-related DEAH box RNA helicase, interacts with satellite I ncRNA. Depletion of DHX38 resulted in defective chromosome segregation similar to knockdown of satellite I ncRNA. Interaction between DHX38 and ncRNA was interphase-specific, but DHX38 depletion affected the function of Aurora B, which associated with satellite I ncRNA at mitotic phase. Based on these findings, we suggest that DHX38 has a role in mitotic regulation as a component of the satellite I ncRNP complex at interphase.
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Affiliation(s)
- Kanako Nishimura
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Yukiko Cho
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Kazuaki Tokunaga
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto, Japan
| | - Tokio Tani
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Takashi Ideue
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
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21
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Kim JS, He X, Liu J, Duan Z, Kim T, Gerard J, Kim B, Pillai MM, Lane WS, Noble WS, Budnik B, Waldman T. Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression. J Biol Chem 2019; 294:8760-8772. [PMID: 31010829 PMCID: PMC6552432 DOI: 10.1074/jbc.ra119.007832] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/18/2019] [Indexed: 12/23/2022] Open
Abstract
The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins.
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Affiliation(s)
- Jung-Sik Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Xiaoyuan He
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Jie Liu
- the Department of Genome Sciences
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, and
- Division of Hematology, University of Washington, Seattle, Washington 98195
| | - Taeyeon Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Julia Gerard
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Brian Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Manoj M Pillai
- the Section of Hematology, Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, and
| | - William S Lane
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | | | - Bogdan Budnik
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | - Todd Waldman
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057,
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22
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Tam AS, Stirling PC. Splicing, genome stability and disease: splice like your genome depends on it! Curr Genet 2019; 65:905-912. [PMID: 30953124 DOI: 10.1007/s00294-019-00964-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/21/2022]
Abstract
The spliceosome has been implicated in genome maintenance for decades. Recently, a surge in discoveries in cancer has suggested that the oncogenic mechanism of spliceosomal defects may involve defective genome stability. The action of the core spliceosome prevents R-loop accumulation, and regulates the expression of genome stability factors. At the same time, specific spliceosomal components have non-canonical functions in genome maintenance. Here we review these different models, highlighting their discovery in different model systems, and describing their potential impact on human disease states.
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Affiliation(s)
- Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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23
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Becker H, Greve G, Kataoka K, Mallm JP, Duque-Afonso J, Ma T, Niemöller C, Pantic M, Duyster J, Cleary ML, Schüler J, Rippe K, Ogawa S, Lübbert M. Identification of enhancer of mRNA decapping 4 as a novel fusion partner of MLL in acute myeloid leukemia. Blood Adv 2019; 3:761-765. [PMID: 30833276 PMCID: PMC6418506 DOI: 10.1182/bloodadvances.2018023879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/23/2019] [Indexed: 01/15/2023] Open
Abstract
mRNA decapping gene EDC4 is a novel fusion partner of MLL in AML. Genes functioning in mRNA decapping may compose a distinct group of MLL fusion partners that links MLL function with mRNA decapping in AML.
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Affiliation(s)
- Heiko Becker
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium partner site, Freiburg, Germany
| | - Gabriele Greve
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Jan-Philipp Mallm
- Division of Chromatin Networks and
- Single-cell Open Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - Jesús Duque-Afonso
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Pathology, Stanford University, Stanford, CA; and
| | - Tobias Ma
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Niemöller
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Justus Duyster
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium partner site, Freiburg, Germany
| | | | - Julia Schüler
- Charles River Discovery Research Services Germany GmbH, Freiburg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks and
- Single-cell Open Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - Seishi Ogawa
- German Cancer Consortium partner site, Freiburg, Germany
| | - Michael Lübbert
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium partner site, Freiburg, Germany
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24
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Anufrieva KS, Shender VO, Arapidi GP, Lagarkova MA, Govorun VM. The Diverse Roles of Spliceosomal Proteins in the Regulation of Cell Processes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Pellacani C, Bucciarelli E, Renda F, Hayward D, Palena A, Chen J, Bonaccorsi S, Wakefield JG, Gatti M, Somma MP. Splicing factors Sf3A2 and Prp31 have direct roles in mitotic chromosome segregation. eLife 2018; 7:40325. [PMID: 30475206 PMCID: PMC6287947 DOI: 10.7554/elife.40325] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 11/14/2018] [Indexed: 12/26/2022] Open
Abstract
Several studies have shown that RNAi-mediated depletion of splicing factors (SFs) results in mitotic abnormalities. However, it is currently unclear whether these abnormalities reflect defective splicing of specific pre-mRNAs or a direct role of the SFs in mitosis. Here, we show that two highly conserved SFs, Sf3A2 and Prp31, are required for chromosome segregation in both Drosophila and human cells. Injections of anti-Sf3A2 and anti-Prp31 antibodies into Drosophila embryos disrupt mitotic division within 1 min, arguing strongly against a splicing-related mitotic function of these factors. We demonstrate that both SFs bind spindle microtubules (MTs) and the Ndc80 complex, which in Sf3A2- and Prp31-depleted cells is not tightly associated with the kinetochores; in HeLa cells the Ndc80/HEC1-SF interaction is restricted to the M phase. These results indicate that Sf3A2 and Prp31 directly regulate interactions among kinetochores, spindle microtubules and the Ndc80 complex in both Drosophila and human cells.
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Affiliation(s)
- Claudia Pellacani
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| | - Elisabetta Bucciarelli
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| | - Fioranna Renda
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Daniel Hayward
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Antonella Palena
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| | - Jack Chen
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Silvia Bonaccorsi
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - James G Wakefield
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Maurizio Gatti
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy.,Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Maria Patrizia Somma
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
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26
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Winkler C, Rouget R, Wu D, Beullens M, Van Eynde A, Bollen M. Overexpression of PP1-NIPP1 limits the capacity of cells to repair DNA double-strand breaks. J Cell Sci 2018; 131:jcs.214932. [PMID: 29898919 DOI: 10.1242/jcs.214932] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022] Open
Abstract
The ubiquitously expressed nuclear protein NIPP1 (also known as PPP1R8) recruits phosphoproteins for regulated dephosphorylation by the associated protein phosphatase PP1. To bypass the PP1 titration artifacts seen upon NIPP1 overexpression, we have engineered covalently linked fusions of PP1 and NIPP1, and demonstrate their potential to selectively explore the function of the PP1:NIPP1 holoenzyme. By using inducible stable cell lines, we show that PP1-NIPP1 fusions cause replication stress in a manner that requires both PP1 activity and substrate recruitment via the ForkHead Associated domain of NIPP1. More specifically, PP1-NIPP1 expression resulted in the build up of RNA-DNA hybrids (R-loops), enhanced chromatin compaction and a diminished repair of DNA double-strand breaks (DSBs), culminating in the accumulation of DSBs. These effects were associated with a reduced expression of DNA damage signaling and repair proteins. Our data disclose a key role for dephosphorylation of PP1:NIPP1 substrates in setting the threshold for DNA repair, and indicate that activators of this phosphatase hold therapeutic potential as sensitizers for DNA-damaging agents.
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Affiliation(s)
- Claudia Winkler
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Raphael Rouget
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Dan Wu
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Monique Beullens
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Aleyde Van Eynde
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
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27
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Anufrieva KS, Shender VО, Arapidi GP, Pavlyukov MS, Shakhparonov MI, Shnaider PV, Butenko IO, Lagarkova MA, Govorun VM. Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells. Genome Med 2018; 10:49. [PMID: 29950180 PMCID: PMC6020472 DOI: 10.1186/s13073-018-0557-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/07/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Abnormal pre-mRNA splicing regulation is common in cancer, but the effects of chemotherapy on this process remain unclear. METHODS To evaluate the effect of chemotherapy on slicing regulation, we performed meta-analyses of previously published transcriptomic, proteomic, phosphoproteomic, and secretome datasets. Our findings were verified by LC-MS/MS, western blotting, immunofluorescence, and FACS analyses of multiple cancer cell lines treated with cisplatin and pladienolide B. RESULTS Our results revealed that different types of chemotherapy lead to similar changes in alternative splicing by inducing intron retention in multiple genes. To determine the mechanism underlying this effect, we analyzed gene expression in 101 cell lines affected by ɣ-irradiation, hypoxia, and 10 various chemotherapeutic drugs. Strikingly, оnly genes involved in the cell cycle and pre-mRNA splicing regulation were changed in a similar manner in all 335 tested samples regardless of stress stimuli. We revealed significant downregulation of gene expression levels in these two pathways, which could be explained by the observed decrease in splicing efficiency and global intron retention. We showed that the levels of active spliceosomal proteins might be further post-translationally decreased by phosphorylation and export into the extracellular space. To further explore these bioinformatics findings, we performed proteomic analysis of cisplatin-treated ovarian cancer cells. Finally, we demonstrated that the splicing inhibitor pladienolide B impairs the cellular response to DNA damage and significantly increases the sensitivity of cancer cells to chemotherapy. CONCLUSIONS Decreased splicing efficiency and global intron retention is a novel stress response mechanism that may promote survival of malignant cells following therapy. We found that this mechanism can be inhibited by pladienolide B, which significantly increases the sensitivity of cancer cells to cisplatin which makes it a good candidate drug for improving the efficiency of cancer therapy.
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Affiliation(s)
- Ksenia S Anufrieva
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia.
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
- Systems Biology Lab, Moscow Institute of Physics and Technology (State University), Moscow, Region, 141701, Russia.
| | - Victoria О Shender
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia.
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
| | - Georgij P Arapidi
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
- Systems Biology Lab, Moscow Institute of Physics and Technology (State University), Moscow, Region, 141701, Russia
| | - Marat S Pavlyukov
- Laboratory of Membrane Bioenergetics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Michail I Shakhparonov
- Laboratory of Membrane Bioenergetics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Polina V Shnaider
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Ivan O Butenko
- Laboratory of Proteomic Analysis, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Maria A Lagarkova
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Vadim M Govorun
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Laboratory of Proteomic Analysis, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
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28
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Abdel-Fatah TMA, Rees RC, Pockley AG, Moseley P, Ball GR, Chan SYT, Ellis IO, Miles AK. The localization of pre mRNA splicing factor PRPF38B is a novel prognostic biomarker that may predict survival benefit of trastuzumab in patients with breast cancer overexpressing HER2. Oncotarget 2017; 8:112245-112257. [PMID: 29348822 PMCID: PMC5762507 DOI: 10.18632/oncotarget.22496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/28/2017] [Indexed: 11/25/2022] Open
Abstract
Cancer biomarkers that can define disease status and provide a prognostic insight are essential for the effective management of patients with breast cancer (BC). The prevalence, clinicopathological and prognostic significance of PRPF38B expression in a consecutive series of 1650 patients with primary invasive breast carcinoma were examined using immunohistochemistry. Furthermore, the relationship(s) between clinical outcome and PRPF38B expression was explored in 627 patients with ER-negative (oestrogen receptor) disease, and 322 patients with HER2-overexpressing disease. Membranous expression of PRPF38B was observed in 148/1388 (10.7%) cases and was significantly associated with aggressive clinicopathological features, including high grade, high mitotic index, pleomorphism, invasive ductal carcinoma of no specific type (IDC-NST), ER-negative, HER2-overexpression and p53 mutational status (all p < 0.01). In patients with ER-negative disease receiving chemotherapy, nuclear expression of PRPF38B was significantly associated with a reduced risk of relapse (p = 0.0004), whereas membranous PRPF38B expression was significantly associated with increased risk of relapse (p = 0.004; respectively) at a 5 year follow-up. When patients were stratified according to ER-negative/HER2-positive status, membranous PRPF38B expression was associated with a higher risk of relapse in those patients that did not receive trastuzumab therapy (p = 0.02), whereas in those patients with ER-negative/HER2-positive disease that received trastuzumab adjuvant therapy, membranous PRPF38B expression associated with a lower risk of relapse (p = 0.00018). Nuclear expression of PRPF38B is a good prognostic indicator in both ER-negative patients and ER-negative/HER2-positive BC (breast cancer) patients, whereas membranous localisation of PRPF38B is a poor prognostic biomarker that predicts survival benefit from trastuzumab therapy in patients with ER-negative/HER2-overexpressing BC.
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Affiliation(s)
- Tarek M A Abdel-Fatah
- Department of Clinical Oncology, Nottingham City Hospital, Nottingham University Hospitals NHS Trust, Nottingham, NG5 1PB, UK
| | - Robert C Rees
- The John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - A Graham Pockley
- The John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Paul Moseley
- Department of Clinical Oncology, Nottingham City Hospital, Nottingham University Hospitals NHS Trust, Nottingham, NG5 1PB, UK
| | - Graham R Ball
- The John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Stephen Y T Chan
- Department of Clinical Oncology, Nottingham City Hospital, Nottingham University Hospitals NHS Trust, Nottingham, NG5 1PB, UK
| | - Ian O Ellis
- Department of Histopathology, Nottingham City Hospital, Nottingham University Hospitals NHS Trust, Nottingham, NG5 1PB, UK
| | - Amanda K Miles
- The John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, NG11 8NS, UK
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29
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Kukolj E, Kaufmann T, Dick AE, Zeillinger R, Gerlich DW, Slade D. PARP inhibition causes premature loss of cohesion in cancer cells. Oncotarget 2017; 8:103931-103951. [PMID: 29262611 PMCID: PMC5732777 DOI: 10.18632/oncotarget.21879] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) regulate various aspects of cellular function including mitotic progression. Although PARP inhibitors have been undergoing various clinical trials and the PARP1/2 inhibitor olaparib was approved as monotherapy for BRCA-mutated ovarian cancer, their mode of action in killing tumour cells is not fully understood. We investigated the effect of PARP inhibition on mitosis in cancerous (cervical, ovary, breast and osteosarcoma) and non-cancerous cells by live-cell imaging. The clinically relevant inhibitor olaparib induced strong perturbations in mitosis, including problems with chromosome alignment at the metaphase plate, anaphase delay, and premature loss of cohesion (cohesion fatigue) after a prolonged metaphase arrest, resulting in sister chromatid scattering. PARP1 and PARP2 depletion suppressed the phenotype while PARP2 overexpression enhanced it, suggesting that olaparib-bound PARP1 and PARP2 rather than the lack of catalytic activity causes this phenotype. Olaparib-induced mitotic chromatid scattering was observed in various cancer cell lines with increased protein levels of PARP1 and PARP2, but not in non-cancer or cancer cell lines that expressed lower levels of PARP1 or PARP2. Interestingly, the sister chromatid scattering phenotype occurred only when olaparib was added during the S-phase preceding mitosis, suggesting that PARP1 and PARP2 entrapment at replication forks impairs sister chromatid cohesion. Clinically relevant DNA-damaging agents that impair replication progression such as topoisomerase inhibitors and cisplatin were also found to induce sister chromatid scattering and metaphase plate alignment problems, suggesting that these mitotic phenotypes are a common outcome of replication perturbation.
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Affiliation(s)
- Eva Kukolj
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Tanja Kaufmann
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Amalie E Dick
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Dea Slade
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
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30
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Siebring-van Olst E, Blijlevens M, de Menezes RX, van der Meulen-Muileman IH, Smit EF, van Beusechem VW. A genome-wide siRNA screen for regulators of tumor suppressor p53 activity in human non-small cell lung cancer cells identifies components of the RNA splicing machinery as targets for anticancer treatment. Mol Oncol 2017; 11:534-551. [PMID: 28296343 PMCID: PMC5527466 DOI: 10.1002/1878-0261.12052] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/24/2017] [Accepted: 03/02/2017] [Indexed: 11/11/2022] Open
Abstract
Reinstating wild-type tumor suppressor p53 activity could be a valuable option for the treatment of cancer. To contribute to development of new treatment options for non-small cell lung cancer (NSCLC), we performed genome-wide siRNA screens for determinants of p53 activity in NSCLC cells. We identified many genes not previously known to be involved in regulating p53 activity. Silencing p53 pathway inhibitor genes was associated with loss of cell viability. The largest functional gene cluster influencing p53 activity was mRNA splicing. Prominent p53 activation was observed upon silencing of specific spliceosome components, rather than by general inhibition of the spliceosome. Ten genes were validated as inhibitors of p53 activity in multiple NSCLC cell lines: genes encoding the Ras pathway activator SOS1, the zinc finger protein TSHZ3, the mitochondrial membrane protein COX16, and the spliceosome components SNRPD3, SF3A3, SF3B1, SF3B6, XAB2, CWC22, and HNRNPL. Silencing these genes generally increased p53 levels, with distinct effects on CDKN1A expression, induction of cell cycle arrest and cell death. Silencing spliceosome components was associated with alternative splicing of MDM4 mRNA, which could contribute to activation of p53. In addition, silencing splice factors was particularly effective in killing NSCLC cells, albeit in a p53-independent manner. Interestingly, silencing SNRPD3 and SF3A3 exerted much stronger cytotoxicity to NSCLC cells than to lung fibroblasts, suggesting that these genes could represent useful therapeutic targets.
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Affiliation(s)
| | - Maxime Blijlevens
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Renee X de Menezes
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Egbert F Smit
- Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands.,Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Victor W van Beusechem
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
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31
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Huang CJ, Yuan YF, Wu D, Khan FA, Jiao XF, Huo LJ. The cohesion stabilizer sororin favors DNA repair and chromosome segregation during mouse oocyte meiosis. In Vitro Cell Dev Biol Anim 2017; 53:258-264. [PMID: 27826797 DOI: 10.1007/s11626-016-0107-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/11/2016] [Indexed: 12/11/2022]
Abstract
Maintenance and timely termination of cohesion on chromosomes ensures accurate chromosome segregation to guard against aneuploidy in mammalian oocytes and subsequent chromosomally abnormal pregnancies. Sororin, a cohesion stabilizer whose relevance in antagonizing the anti-cohesive property of Wings-apart like protein (Wapl), has been characterized in mitosis; however, the role of Sororin remains unclear during mammalian oocyte meiosis. Here, we show that Sororin is required for DNA damage repair and cohesion maintenance on chromosomes, and consequently, for mouse oocyte meiotic program. Sororin is constantly expressed throughout meiosis and accumulates on chromatins at germinal vesicle (GV) stage/G2 phase. It localizes onto centromeres from germinal vesicle breakdown (GVBD) to metaphase II stage. Inactivation of Sororin compromises the GVBD and first polar body extrusion (PBE). Furthermore, Sororin inactivation induces DNA damage indicated by positive γH2AX foci in GV oocytes and precocious chromatin segregation in MII oocytes. Finally, our data indicate that PlK1 and MPF dissociate Sororin from chromosome arms without affecting its centromeric localization. Our results define Sororin as a determinant during mouse oocyte meiotic maturation by favoring DNA damage repair and chromosome separation, and thereby, maintaining the genome stability and generating haploid gametes.
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Affiliation(s)
- Chun-Jie Huang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China
| | - Yi-Feng Yuan
- Department of Gynecology and Obstetrics, Peking University Third University, Beijing, China
| | - Di Wu
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China
| | - Faheem Ahmed Khan
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Fei Jiao
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China
| | - Li-Jun Huo
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan, China.
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32
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McKinley KL, Cheeseman IM. Large-Scale Analysis of CRISPR/Cas9 Cell-Cycle Knockouts Reveals the Diversity of p53-Dependent Responses to Cell-Cycle Defects. Dev Cell 2017; 40:405-420.e2. [PMID: 28216383 DOI: 10.1016/j.devcel.2017.01.012] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/23/2016] [Accepted: 01/23/2017] [Indexed: 12/20/2022]
Abstract
Defining the genes that are essential for cellular proliferation is critical for understanding organismal development and identifying high-value targets for disease therapies. However, the requirements for cell-cycle progression in human cells remain incompletely understood. To elucidate the consequences of acute and chronic elimination of cell-cycle proteins, we generated and characterized inducible CRISPR/Cas9 knockout human cell lines targeting 209 genes involved in diverse cell-cycle processes. We performed single-cell microscopic analyses to systematically establish the effects of the knockouts on subcellular architecture. To define variations in cell-cycle requirements between cultured cell lines, we generated knockouts across cell lines of diverse origins. We demonstrate that p53 modulates the phenotype of specific cell-cycle defects through distinct mechanisms, depending on the defect. This work provides a resource to broadly facilitate robust and long-term depletion of cell-cycle proteins and reveals insights into the requirements for cell-cycle progression.
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Affiliation(s)
- Kara L McKinley
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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33
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Zanini IMY, Soneson C, Lorenzi LE, Azzalin CM. Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion. J Cell Sci 2017; 130:767-778. [PMID: 28062851 DOI: 10.1242/jcs.194068] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Cactins constitute a family of eukaryotic proteins broadly conserved from yeast to human and required for fundamental processes such as cell proliferation, genome stability maintenance, organismal development and immune response. Cactin proteins have been found to associate with the spliceosome in several model organisms, nevertheless their molecular functions await elucidation. Here we show that depletion of human cactin leads to premature sister chromatid separation, genome instability and cell proliferation arrest. Moreover, cactin is essential for efficient splicing of thousands of pre-mRNAs, and incomplete splicing of the pre-mRNA of sororin (also known as CDCA5), a cohesin-associated factor, is largely responsible for the aberrant chromatid separation in cactin-depleted cells. Lastly, cactin physically and functionally interacts with the spliceosome-associated factors DHX8 and SRRM2. We propose that cellular complexes comprising cactin, DHX8 and SRRM2 sustain precise chromosome segregation, genome stability and cell proliferation by allowing faithful splicing of specific pre-mRNAs. Our data point to novel pathways of gene expression regulation dependent on cactin, and provide an explanation for the pleiotropic dysfunctions deriving from cactin inactivation in distant eukaryotes.
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Affiliation(s)
- Isabella M Y Zanini
- Institute of Biochemistry (IBC), Department of Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Charlotte Soneson
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland
| | - Luca E Lorenzi
- Institute of Biochemistry (IBC), Department of Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Claus M Azzalin
- Institute of Biochemistry (IBC), Department of Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
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34
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Abramczuk MK, Burkard TR, Rolland V, Steinmann V, Duchek P, Jiang Y, Wissel S, Reichert H, Knoblich JA. The splicing co-factor Barricade/Tat-SF1, is required for cell cycle and lineage progression in Drosophila neural stem cells. Development 2017; 144:3932-3945. [DOI: 10.1242/dev.152199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 09/11/2017] [Indexed: 12/25/2022]
Abstract
Stem cells need to balance self-renewal and differentiation for correct tissue development and homeostasis. Defects in this balance can lead to developmental defects or tumor formation. In recent years, mRNA splicing has emerged as one important mechanism regulating cell fate decisions. Here we address the role of the evolutionary conserved splicing co-factor Barricade (Barc)/Tat-SF1/CUS2 in Drosophila neural stem cell (neuroblast) lineage formation. We show that Barc is required for the generation of neurons during Drosophila brain development by ensuring correct neural progenitor proliferation and differentiation. Barc associates with components of the U2 small nuclear ribonucleic proteins (snRNP), and its depletion causes alternative splicing in form of intron retention in a subset of genes. Using bioinformatics analysis and a cell culture based splicing assay, we found that Barc-dependent introns share three major traits: they are short, GC rich and have weak 3' splice sites. Our results show that Barc, together with the U2snRNP, plays an important role in regulating neural stem cell lineage progression during brain development and facilitates correct splicing of a subset of introns.
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Affiliation(s)
- Monika K. Abramczuk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Thomas R. Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Vivien Rolland
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
- Current address: Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, ACT 2601, Australia
| | - Victoria Steinmann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Yanrui Jiang
- Biozentrum, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
- Current address: D-BSSE ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Sebastian Wissel
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Heinrich Reichert
- Biozentrum, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Juergen A. Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
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35
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Profiling DNA damage response following mitotic perturbations. Nat Commun 2016; 7:13887. [PMID: 27976684 PMCID: PMC5172227 DOI: 10.1038/ncomms13887] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/09/2016] [Indexed: 01/01/2023] Open
Abstract
Genome integrity relies on precise coordination between DNA replication and chromosome segregation. Whereas replication stress attracted much attention, the consequences of mitotic perturbations for genome integrity are less understood. Here, we knockdown 47 validated mitotic regulators to show that a broad spectrum of mitotic errors correlates with increased DNA breakage in daughter cells. Unexpectedly, we find that only a subset of these correlations are functionally linked. We identify the genuine mitosis-born DNA damage events and sub-classify them according to penetrance of the observed phenotypes. To demonstrate the potential of this resource, we show that DNA breakage after cytokinesis failure is preceded by replication stress, which mounts during consecutive cell cycles and coincides with decreased proliferation. Together, our results provide a resource to gauge the magnitude and dynamics of DNA breakage associated with mitotic aberrations and suggest that replication stress might limit propagation of cells with abnormal karyotypes.
DNA damage arising from replication stress is well studied, but the effect of mitotic errors on genome integrity is less understood. Here the authors knock down 47 mitotic regulators and record how they impact on DNA breakage events, providing a resource for future studies on the relation between cell division and genome integrity.
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36
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Mutations of myelodysplastic syndromes (MDS): An update. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 769:47-62. [DOI: 10.1016/j.mrrev.2016.04.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/11/2016] [Indexed: 01/08/2023]
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37
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Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA. Cell Discov 2016; 2:16013. [PMID: 27462460 PMCID: PMC4906801 DOI: 10.1038/celldisc.2016.13] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
The DNA damage response involves coordinated control of gene expression and DNA repair. Using deep sequencing, we found widespread changes of alternative cleavage and polyadenylation site usage on ultraviolet-treatment in mammalian cells. Alternative cleavage and polyadenylation regulation in the 3ʹ untranslated region is substantial, leading to both shortening and lengthening of 3ʹ untranslated regions of genes. Interestingly, a strong activation of intronic alternative cleavage and polyadenylation sites is detected, resulting in widespread expression of truncated transcripts. Intronic alternative cleavage and polyadenylation events are biased to the 5ʹ end of genes and affect gene groups with important functions in DNA damage response and cancer. Moreover, intronic alternative cleavage and polyadenylation site activation during DNA damage response correlates with a decrease in U1 snRNA levels, and is reversible by U1 snRNA overexpression. Importantly, U1 snRNA overexpression mitigates ultraviolet-induced apoptosis. Together, these data reveal a significant gene regulatory scheme in DNA damage response where U1 snRNA impacts gene expression via the U1-alternative cleavage and polyadenylation axis.
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38
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Karamysheva Z, Díaz-Martínez LA, Warrington R, Yu H. Graded requirement for the spliceosome in cell cycle progression. Cell Cycle 2016; 14:1873-83. [PMID: 25892155 DOI: 10.1080/15384101.2015.1039209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Genome stability is ensured by multiple surveillance mechanisms that monitor the duplication, segregation, and integrity of the genome throughout the cell cycle. Depletion of components of the spliceosome, a macromolecular machine essential for mRNA maturation and gene expression, has been associated with increased DNA damage and cell cycle defects. However, the specific role for the spliceosome in these processes has remained elusive, as different cell cycle defects have been reported depending on the specific spliceosome subunit depleted. Through a detailed cell cycle analysis after spliceosome depletion, we demonstrate that the spliceosome is required for progression through multiple phases of the cell cycle. Strikingly, the specific cell cycle phenotype observed after spliceosome depletion correlates with the extent of depletion. Partial depletion of a core spliceosome component results in defects at later stages of the cell cycle (G2 and mitosis), whereas a more complete depletion of the same component elicits an early cell cycle arrest in G1. We propose a quantitative model in which different functional dosages of the spliceosome are required for different cell cycle transitions.
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Affiliation(s)
- Zemfira Karamysheva
- a Department of Physiology; University of Texas Southwestern Medical Center ; Dallas , TX , USA
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39
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Abstract
It is emerging that the pathways that process newly transcribed RNA molecules also regulate the response to DNA damage at multiple levels. Here, we discuss recent insights into how RNA processing pathways participate in DNA damage recognition, signaling, and repair, selectively influence the expression of genome-stabilizing proteins, and resolve deleterious DNA/RNA hybrids (R-loops) formed during transcription and RNA processing. The importance of these pathways for the DNA damage response (DDR) is underscored by the growing appreciation that defects in these regulatory connections may be connected to the genome instability involved in several human diseases, including cancer.
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Affiliation(s)
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
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40
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Daguenet E, Dujardin G, Valcárcel J. The pathogenicity of splicing defects: mechanistic insights into pre-mRNA processing inform novel therapeutic approaches. EMBO Rep 2015; 16:1640-55. [PMID: 26566663 DOI: 10.15252/embr.201541116] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/12/2015] [Indexed: 12/22/2022] Open
Abstract
Removal of introns from pre-mRNA precursors (pre-mRNA splicing) is a necessary step for the expression of most genes in multicellular organisms, and alternative patterns of intron removal diversify and regulate the output of genomic information. Mutation or natural variation in pre-mRNA sequences, as well as in spliceosomal components and regulatory factors, has been implicated in the etiology and progression of numerous pathologies. These range from monogenic to multifactorial genetic diseases, including metabolic syndromes, muscular dystrophies, neurodegenerative and cardiovascular diseases, and cancer. Understanding the molecular mechanisms associated with splicing-related pathologies can provide key insights into the normal function and physiological context of the complex splicing machinery and establish sound basis for novel therapeutic approaches.
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Affiliation(s)
- Elisabeth Daguenet
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu-Fabra, Barcelona, Spain
| | - Gwendal Dujardin
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu-Fabra, Barcelona, Spain
| | - Juan Valcárcel
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu-Fabra, Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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41
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van Maldegem F, Maslen S, Johnson CM, Chandra A, Ganesh K, Skehel M, Rada C. CTNNBL1 facilitates the association of CWC15 with CDC5L and is required to maintain the abundance of the Prp19 spliceosomal complex. Nucleic Acids Res 2015; 43:7058-69. [PMID: 26130721 PMCID: PMC4538830 DOI: 10.1093/nar/gkv643] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 06/09/2015] [Indexed: 12/16/2022] Open
Abstract
In order to catalyse the splicing of messenger RNA, multiple proteins and RNA components associate and dissociate in a dynamic highly choreographed process. The Prp19 complex is a conserved essential part of the splicing machinery thought to facilitate the conformational changes the spliceosome undergoes during catalysis. Dynamic protein interactions often involve highly disordered regions that are difficult to study by structural methods. Using amine crosslinking and hydrogen-deuterium exchange coupled to mass spectrometry, we describe the architecture of the Prp19 sub-complex that contains CTNNBL1. Deficiency in CTNNBL1 leads to delayed initiation of cell division and embryonic lethality. Here we show that in vitro CTNNBL1 enhances the association of CWC15 and CDC5L, both core Prp19 complex proteins and identify an overlap in the region of CDC5L that binds either CTNNBL1 or CWC15 suggesting the two proteins might exchange places in the complex. Furthermore, in vivo, CTNNBL1 is required to maintain normal levels of the Prp19 complex and to facilitate the interaction of CWC15 with CDC5L. Our results identify a chaperone function for CTNNBL1 within the essential Prp19 complex, a function required to maintain the integrity of the complex and to support efficient splicing.
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Affiliation(s)
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Anita Chandra
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Karuna Ganesh
- Department of Medicine and Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Cristina Rada
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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42
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Naro C, Bielli P, Pagliarini V, Sette C. The interplay between DNA damage response and RNA processing: the unexpected role of splicing factors as gatekeepers of genome stability. Front Genet 2015; 6:142. [PMID: 25926848 PMCID: PMC4397863 DOI: 10.3389/fgene.2015.00142] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/25/2015] [Indexed: 12/22/2022] Open
Abstract
Genome integrity is constantly threatened by endogenous and exogenous factors. However, its preservation is ensured by a network of pathways that prevent and/or repair the lesion, which constitute the DNA damage response (DDR). Expression of the key proteins involved in the DDR is controlled by numerous post-transcriptional mechanisms, among which pre-mRNA splicing stands out. Intriguingly, several splicing factors (SFs) have been recently shown to play direct functions in DNA damage prevention and repair, which go beyond their expected splicing activity. At the same time, evidence is emerging that DNA repair proteins (DRPs) can actively sustain the DDR by acting as post-transcriptional regulator of gene expression, in addition to their well-known role in the mechanisms of signaling and repair of the lesion. Herein, we will review these non-canonical functions of both SFs and DRPs, which suggest the existence of a tight interplay between splicing regulation and canonical DNA safeguard mechanisms ensuring genome stability.
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Affiliation(s)
- Chiara Naro
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| | - Vittoria Pagliarini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| | - Claudio Sette
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
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43
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Oka Y, Bekker-Jensen S, Mailand N. Ubiquitin-like protein UBL5 promotes the functional integrity of the Fanconi anemia pathway. EMBO J 2015; 34:1385-98. [PMID: 25862789 DOI: 10.15252/embj.201490376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/19/2015] [Indexed: 11/09/2022] Open
Abstract
Ubiquitin and ubiquitin-like proteins (UBLs) function in a wide array of cellular processes. UBL5 is an atypical UBL that does not form covalent conjugates with cellular proteins and which has a known role in modulating pre-mRNA splicing. Here, we report an unexpected involvement of human UBL5 in promoting the function of the Fanconi anemia (FA) pathway for repair of DNA interstrand crosslinks (ICLs), mediated by a specific interaction with the central FA pathway component FANCI. UBL5-deficient cells display spliceosome-independent reduction of FANCI protein stability, defective FANCI function in response to DNA damage and hypersensitivity to ICLs. By mapping the sequence determinants underlying UBL5-FANCI binding, we generated separation-of-function mutants to demonstrate that key aspects of FA pathway function, including FANCI-FANCD2 heterodimerization, FANCD2 and FANCI monoubiquitylation and maintenance of chromosome stability after ICLs, are compromised when the UBL5-FANCI interaction is selectively inhibited by mutations in either protein. Together, our findings establish UBL5 as a factor that promotes the functionality of the FA DNA repair pathway.
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Affiliation(s)
- Yasuyoshi Oka
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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44
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Pellagatti A, Boultwood J. The molecular pathogenesis of the myelodysplastic syndromes. Eur J Haematol 2015; 95:3-15. [DOI: 10.1111/ejh.12515] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Andrea Pellagatti
- Leukaemia & Lymphoma Research Molecular Haematology Unit; Nuffield Division of Clinical Laboratory Sciences; Radcliffe Department of Medicine; University of Oxford; Oxford UK
| | - Jacqueline Boultwood
- Leukaemia & Lymphoma Research Molecular Haematology Unit; Nuffield Division of Clinical Laboratory Sciences; Radcliffe Department of Medicine; University of Oxford; Oxford UK
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45
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Abstract
Splicing of pre‐mRNAs is a necessary step for expression of the majority of genes in higher eukaryotes, and its regulation through alternative splice site selection shapes their proteomes. Defects in multiple splicing factors result in aberrant mitotic progression, although the molecular basis for this observation has remained elusive. Recent papers in The EMBO Journal and EMBO Reports reveal that expression of sororin, a critical regulator that stabilizes cohesin rings in sister chromatids, is exquisitely sensitive to defects in the splicing machinery, thus explaining the striking link between spliceosome function and chromosome segregation.
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Affiliation(s)
- Juan Valcárcel
- Centre de Regulació Genòmica, Universitat Pompeu Fabra Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Marcos Malumbres
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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van der Lelij P, Stocsits RR, Ladurner R, Petzold G, Kreidl E, Koch B, Schmitz J, Neumann B, Ellenberg J, Peters JM. SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs. EMBO J 2014; 33:2643-58. [PMID: 25257309 DOI: 10.15252/embj.201488202] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Although splicing is essential for the expression of most eukaryotic genes, inactivation of splicing factors causes specific defects in mitosis. The molecular cause of this defect is unknown. Here, we show that the spliceosome subunits SNW1 and PRPF8 are essential for sister chromatid cohesion in human cells. A transcriptome-wide analysis revealed that SNW1 or PRPF8 depletion affects the splicing of specific introns in a subset of pre-mRNAs, including pre-mRNAs encoding the cohesion protein sororin and the APC/C subunit APC2. SNW1 depletion causes cohesion defects predominantly by reducing sororin levels, which causes destabilisation of cohesin on DNA. SNW1 depletion also reduces APC/C activity and contributes to cohesion defects indirectly by delaying mitosis and causing "cohesion fatigue". Simultaneous expression of sororin and APC2 from intron-less cDNAs restores cohesion in SNW1-depleted cells. These results indicate that the spliceosome is required for mitosis because it enables expression of genes essential for cohesion. Our transcriptome-wide identification of retained introns in SNW1- and PRPF8-depleted cells may help to understand the aetiology of diseases associated with splicing defects, such as retinosa pigmentosum and cancer.
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Affiliation(s)
| | | | - Rene Ladurner
- IMP Research Institute of Molecular Pathology, Vienna, Austria
| | - Georg Petzold
- IMP Research Institute of Molecular Pathology, Vienna, Austria
| | - Emanuel Kreidl
- IMP Research Institute of Molecular Pathology, Vienna, Austria
| | - Birgit Koch
- IMP Research Institute of Molecular Pathology, Vienna, Austria EMBL Heidelberg, Heidelberg, Germany
| | - Julia Schmitz
- IMP Research Institute of Molecular Pathology, Vienna, Austria
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