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Liu F, Liu X, Liu X, Li T, Zhu P, Liu Z, Xue H, Wang W, Yang X, Liu J, Han W. Integrated Analyses of Phenotype and Quantitative Proteome of CMTM4 Deficient Mice Reveal Its Association with Male Fertility. Mol Cell Proteomics 2019; 18:1070-1084. [PMID: 30867229 PMCID: PMC6553932 DOI: 10.1074/mcp.ra119.001416] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Indexed: 12/13/2022] Open
Abstract
The chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing family (CMTM) is a gene family that has been implicated in male reproduction. CMTM4 is an evolutionarily conserved member that is highly expressed in the testis. However, its function in male fertility remains unknown. Here, we demonstrate that CMTM4 is associated with spermatogenesis and sperm quality. Using Western blotting and immunohistochemical analyses, we found CMTM4 expression to be decreased in poor-quality human spermatozoa, old human testes, and testicular biopsies with nonobstructive azoospermia. Using CRISPR-Cas9 technology, we knocked out the Cmtm4 gene in mice. These Cmtm4 knockout (KO) mice showed reduced testicular daily sperm production, lower epididymal sperm motility and increased proportion of abnormally backward-curved sperm heads and bent sperm midpieces. These mice also had an evident sub-fertile phenotype, characterized by low pregnancy rates on prolonged breeding with wild type female mice, reduced in vitro fertilization efficiency and a reduced percentage of acrosome reactions. We then performed quantitative proteomic analysis of the testes, where we identified 139 proteins to be downregulated in Cmtm4-KO mice, 100 (71.9%) of which were related to sperm motility and acrosome reaction. The same proteomic analysis was performed on sperm, where we identified 3588 proteins with 409 being differentially regulated in Cmtm4-KO mice. Our enrichment analysis showed that upregulated proteins were enriched with nucleosomal DNA binding functions and the downregulated proteins were enriched with actin binding functions. These findings elucidate the roles of CMTM4 in male fertility and demonstrates its potential as a promising molecular candidate for sperm quality assessment and the diagnosis or treatment of male infertility.
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Affiliation(s)
- FuJun Liu
- From the ‡Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology (Ministry of Health), Peking University Center for Human Disease Genomics, Beijing, 100191, China
| | - XueXia Liu
- §Department of Central Laboratory, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong Province, 264000, China
- ¶Shandong Research Centre for Stem Cell Engineering, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong Province, 264000, China
| | - Xin Liu
- §Department of Central Laboratory, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong Province, 264000, China
- ¶Shandong Research Centre for Stem Cell Engineering, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong Province, 264000, China
| | - Ting Li
- From the ‡Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology (Ministry of Health), Peking University Center for Human Disease Genomics, Beijing, 100191, China
| | - Peng Zhu
- §Department of Central Laboratory, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong Province, 264000, China
- ¶Shandong Research Centre for Stem Cell Engineering, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong Province, 264000, China
| | - ZhengYang Liu
- From the ‡Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology (Ministry of Health), Peking University Center for Human Disease Genomics, Beijing, 100191, China
| | - Hui Xue
- From the ‡Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology (Ministry of Health), Peking University Center for Human Disease Genomics, Beijing, 100191, China
| | - WenJuan Wang
- ‖Reproduction Medical Center, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong, P.R. China
| | - XiuLan Yang
- From the ‡Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology (Ministry of Health), Peking University Center for Human Disease Genomics, Beijing, 100191, China
| | - Juan Liu
- §Department of Central Laboratory, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong Province, 264000, China
- ¶Shandong Research Centre for Stem Cell Engineering, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong Province, 264000, China
| | - WenLing Han
- From the ‡Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology (Ministry of Health), Peking University Center for Human Disease Genomics, Beijing, 100191, China;
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Sinha S, Ray A, Abhilash L, Kumar M, Sreenivasamurthy SK, Keshava Prasad TS, Inamdar MS. Proteomics of Asrij Perturbation in Drosophila Lymph Glands for Identification of New Regulators of Hematopoiesis. Mol Cell Proteomics 2019; 18:1171-1182. [PMID: 30923041 PMCID: PMC6553936 DOI: 10.1074/mcp.ra119.001299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/07/2019] [Indexed: 11/06/2022] Open
Abstract
Hematopoiesis is the process of differentiation of precursor blood cells into mature blood cells that is controlled by a complex set of molecular interactions. Understanding hematopoiesis is important for the study of hematological disorders. However, a comprehensive understanding of how physiological and genetic mechanisms regulate blood cell precursor maintenance and differentiation is lacking. Owing to simplicity and ease of genetic analysis, the Drosophila melanogaster lymph gland (LG) is an excellent model to study hematopoiesis. Here, we quantitatively analyzed the LG proteome under genetic conditions that either maintain precursors or promote their differentiation in vivo, by perturbing expression of Asrij, a conserved endosomal regulator of hematopoiesis. Using iTRAQ-based quantitative proteomics, we determined the relative expression levels of proteins in Asrij-knockout and overexpressing LGs from 1500 larval dissections compared with wild type. Our data showed that at least 6.5% of the Drosophila proteome is expressed in wild type LGs. Of the 2133 proteins identified, 780 and 208 proteins were common to previously reported cardiac tube and hemolymph proteomes, respectively, resulting in the identification of 1238 proteins exclusive to the LG. Perturbation of Asrij levels led to differential expression of 619 proteins, of which 27% have human homologs implicated in various diseases. Proteins regulating metabolism, immune system, signal transduction and vesicle-mediated transport were significantly enriched. Immunostaining of representative candidates from the enriched categories and previous reports confirmed 73% of our results, indicating the validity of our LG proteome. Our study provides, for the first time, an in vivo proteomics resource for identifying novel regulators of hematopoiesis that will also be applicable to understanding vertebrate blood cell development.
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Affiliation(s)
- Saloni Sinha
- From the ‡Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Arindam Ray
- From the ‡Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Lakshman Abhilash
- From the ‡Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Manish Kumar
- §Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- ¶Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sreelakshmi K Sreenivasamurthy
- §Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- ‖NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - T S Keshava Prasad
- §Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- **Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore-575018, India
| | - Maneesha S Inamdar
- From the ‡Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India;
- ‡‡Institute for Stem Cell Biology and Regenerative Medicine, GKVK, Bellary Road, Bangalore 560065, India
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Delcourt V, Brunelle M, Roy AV, Jacques JF, Salzet M, Fournier I, Roucou X. The Protein Coded by a Short Open Reading Frame, Not by the Annotated Coding Sequence, Is the Main Gene Product of the Dual-Coding Gene MIEF1. Mol Cell Proteomics 2018; 17:2402-2411. [PMID: 30181344 PMCID: PMC6283296 DOI: 10.1074/mcp.ra118.000593] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 07/19/2018] [Indexed: 12/18/2022] Open
Abstract
Proteogenomics and ribosome profiling concurrently show that genes may code for both a large and one or more small proteins translated from annotated coding sequences (CDSs) and unannotated alternative open reading frames (named alternative ORFs or altORFs), respectively, but the stoichiometry between large and small proteins translated from a same gene is unknown. MIEF1, a gene recently identified as a dual-coding gene, harbors a CDS and a newly annotated and actively translated altORF located in the 5′UTR. Here, we use absolute quantification with stable isotope-labeled peptides and parallel reaction monitoring to determine levels of both proteins in two human cells lines and in human colon. We report that the main MIEF1 translational product is not the canonical 463 amino acid MiD51 protein but the small 70 amino acid alternative MiD51 protein (altMiD51). These results demonstrate the inadequacy of the single CDS concept and provide a strong argument for incorporating altORFs and small proteins in functional annotations.
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Affiliation(s)
- Vivian Delcourt
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire and Spectrométrie de Masse (PRISM) F-59000 Lille, France; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
| | - Mylène Brunelle
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
| | - Annie V Roy
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
| | - Jean-François Jacques
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
| | - Michel Salzet
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire and Spectrométrie de Masse (PRISM) F-59000 Lille, France
| | - Isabelle Fournier
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire and Spectrométrie de Masse (PRISM) F-59000 Lille, France
| | - Xavier Roucou
- Département de Biochimie, Université de Sherbrooke, Québec, Canada; PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada.
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Beyer T, Bolz S, Junger K, Horn N, Moniruzzaman M, Wissinger Y, Ueffing M, Boldt K. CRISPR/Cas9-mediated Genomic Editing of Cluap1/IFT38 Reveals a New Role in Actin Arrangement. Mol Cell Proteomics 2018; 17:1285-1294. [PMID: 29615496 PMCID: PMC6030719 DOI: 10.1074/mcp.ra117.000487] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/28/2018] [Indexed: 12/24/2022] Open
Abstract
CRISPR/Cas9-mediated gene editing allows manipulation of a gene of interest in its own chromosomal context. When applied to the analysis of protein interactions and in contrast to exogenous expression of a protein, this can be studied maintaining physiological stoichiometry, topology, and context. We have used CRISPR/Cas9-mediated genomic editing to investigate Cluap1/IFT38, a component of the intraflagellar transport complex B (IFT-B). Cluap1 has been implicated in human development as well as in cancer progression. Cluap1 loss of function results in early developmental defects with neural tube closure, sonic hedgehog signaling and left-right defects. Herein, we generated an endogenously tagged Cluap1 for protein complex analysis, which was then correlated to the corresponding interactome determined by ectopic expression. Besides IFT-B complex components, new interacting proteins like Ephrin-B1 and TRIP6, which are known to be involved in cytoskeletal arrangement and protein transport, were identified. With the identification of platelet-derived growth factor A (PDGFA) and coiled-coil domain-containing protein 6 (CCDC6) two new interactions were discovered, which link Cluap1 to ciliogenesis and cancer development. The CRISPR/Cas9-mediated knockout of Cluap1 revealed a new phenotype affecting the actin cytoskeleton. Together, these data provide first evidence for a role of Cluap1 not only for cilia assembly and maintenance but also for cytoskeletal rearrangement and intracellular transport processes.
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Affiliation(s)
- Tina Beyer
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany;
| | - Sylvia Bolz
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Katrin Junger
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Nicola Horn
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Muhammad Moniruzzaman
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Yasmin Wissinger
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
- §Thermo Fisher Scientific, Clinical Diagnostics Systems, Neuendorfstr. 25, 16761 Hennigsdorf, Germany
| | - Marius Ueffing
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany
| | - Karsten Boldt
- From the ‡Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, D-72076 Tübingen, Germany;
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