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Rengarajan S, Derks J, Bellott DW, Slavov N, Page DC. Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602613. [PMID: 39026797 PMCID: PMC11257633 DOI: 10.1101/2024.07.08.602613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The Y-linked gene DDX3Y and its X-linked homolog DDX3X survived the evolution of the human sex chromosomes from ordinary autosomes. DDX3X encodes a multi-functional RNA helicase, with mutations causing developmental disorders and cancers. We find that, among X-linked genes with surviving Y homologs, DDX3X is extraordinarily dosage-sensitive. Studying cells of individuals with sex chromosome aneuploidy, we observe that when the number of Y chromosomes increases, DDX3X transcript levels fall; conversely, when the number of X chromosomes increases, DDX3Y transcript levels fall. In 46,XY cells, CRISPRi knockdown of either DDX3X or DDX3Y causes transcript levels of the homologous gene to rise. In 46,XX cells, chemical inhibition of DDX3X protein activity elicits an increase in DDX3X transcript levels. Thus, perturbation of either DDX3X or DDX3Y expression is buffered - by negative cross-regulation of DDX3X and DDX3Y in 46,XY cells, and by negative auto-regulation of DDX3X in 46,XX cells. DDX3X-DDX3Y cross-regulation is mediated through mRNA destabilization - as shown by metabolic labeling of newly transcribed RNA - and buffers total levels of DDX3X and DDX3Y protein in human cells. We infer that post-transcriptional auto-regulation of the ancestral (autosomal) DDX3 gene transmuted into auto- and cross-regulation of DDX3X and DDX3Y as these sex-linked genes evolved from ordinary alleles of their autosomal precursor.
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Affiliation(s)
- Shruthi Rengarajan
- Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jason Derks
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | | | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
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2
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Cronin SJF, Tejada MA, Song R, Laval K, Cikes D, Ji M, Brai A, Stadlmann J, Novatchikova M, Perlot T, Ali OH, Botta L, Decker T, Lazovic J, Hagelkruys A, Enquist L, Rao S, Koyuncu OO, Penninger JM. Pseudorabies virus hijacks DDX3X, initiating an addictive "mad itch" and immune suppression, to facilitate viral spread. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539956. [PMID: 37214906 PMCID: PMC10197578 DOI: 10.1101/2023.05.09.539956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Infections with defined Herpesviruses, such as Pseudorabies virus (PRV) and Varicella zoster virus (VZV) can cause neuropathic itch, referred to as "mad itch" in multiple species. The underlying mechanisms involved in neuropathic "mad itch" are poorly understood. Here, we show that PRV infections hijack the RNA helicase DDX3X in sensory neurons to facilitate anterograde transport of the virus along axons. PRV induces re-localization of DDX3X from the cell body to the axons which ultimately leads to death of the infected sensory neurons. Inducible genetic ablation of Ddx3x in sensory neurons results in neuronal death and "mad itch" in mice. This neuropathic "mad itch" is propagated through activation of the opioid system making the animals "addicted to itch". Moreover, we show that PRV co-opts and diverts T cell development in the thymus via a sensory neuron-IL-6-hypothalamus-corticosterone stress pathway. Our data reveal how PRV, through regulation of DDX3X in sensory neurons, travels along axons and triggers neuropathic itch and immune deviations to initiate pathophysiological programs which facilitate its spread to enhance infectivity.
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Affiliation(s)
- Shane J F Cronin
- Institute of Molecular Biotechnology Austria (IMBA), Dr. Bohrgasse 3, A-1030 Vienna, Austria
| | - Miguel A Tejada
- Institute of Molecular Biotechnology Austria (IMBA), Dr. Bohrgasse 3, A-1030 Vienna, Austria
| | - Ren Song
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Kathlyn Laval
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Domagoj Cikes
- Institute of Molecular Biotechnology Austria (IMBA), Dr. Bohrgasse 3, A-1030 Vienna, Austria
| | - Ming Ji
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Annalaura Brai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Johannes Stadlmann
- Institute of Molecular Biotechnology Austria (IMBA), Dr. Bohrgasse 3, A-1030 Vienna, Austria
| | - Maria Novatchikova
- Institute of Molecular Biotechnology Austria (IMBA), Dr. Bohrgasse 3, A-1030 Vienna, Austria
| | - Thomas Perlot
- Institute of Molecular Biotechnology Austria (IMBA), Dr. Bohrgasse 3, A-1030 Vienna, Austria
| | - Omar Hasan Ali
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- Institute of Immunobiology, Cantonal Hospital St. Gallen, Rorschacher Strasse 95, 9007 St. Gallen, Switzerland
- Department of Dermatology, University of Zurich, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Lorenzo Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Thomas Decker
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Jelena Lazovic
- Institute of Molecular Biotechnology Austria (IMBA), Dr. Bohrgasse 3, A-1030 Vienna, Austria
| | - Astrid Hagelkruys
- Institute of Molecular Biotechnology Austria (IMBA), Dr. Bohrgasse 3, A-1030 Vienna, Austria
| | - Lynn Enquist
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Shuan Rao
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Orkide O Koyuncu
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA 92697-4025, USA
| | - Josef M Penninger
- Institute of Molecular Biotechnology Austria (IMBA), Dr. Bohrgasse 3, A-1030 Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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Anisimova AS, Kolyupanova NM, Makarova NE, Egorov AA, Kulakovskiy IV, Dmitriev SE. Human Tissues Exhibit Diverse Composition of Translation Machinery. Int J Mol Sci 2023; 24:8361. [PMID: 37176068 PMCID: PMC10179197 DOI: 10.3390/ijms24098361] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
While protein synthesis is vital for the majority of cell types of the human body, diversely differentiated cells require specific translation regulation. This suggests the specialization of translation machinery across tissues and organs. Using transcriptomic data from GTEx, FANTOM, and Gene Atlas, we systematically explored the abundance of transcripts encoding translation factors and aminoacyl-tRNA synthetases (ARSases) in human tissues. We revised a few known and identified several novel translation-related genes exhibiting strict tissue-specific expression. The proteins they encode include eEF1A1, eEF1A2, PABPC1L, PABPC3, eIF1B, eIF4E1B, eIF4ENIF1, and eIF5AL1. Furthermore, our analysis revealed a pervasive tissue-specific relative abundance of translation machinery components (e.g., PABP and eRF3 paralogs, eIF2B and eIF3 subunits, eIF5MPs, and some ARSases), suggesting presumptive variance in the composition of translation initiation, elongation, and termination complexes. These conclusions were largely confirmed by the analysis of proteomic data. Finally, we paid attention to sexual dimorphism in the repertoire of translation factors encoded in sex chromosomes (eIF1A, eIF2γ, and DDX3), and identified the testis and brain as organs with the most diverged expression of translation-associated genes.
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Affiliation(s)
- Aleksandra S. Anisimova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalia M. Kolyupanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nadezhda E. Makarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Artyom A. Egorov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ivan V. Kulakovskiy
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 117971 Moscow, Russia;
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Laboratory of Regulatory Genomics, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Sergey E. Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
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Batdorj E, AlOgayil N, Zhuang QKW, Galvez JH, Bauermeister K, Nagata K, Kimura T, Ward MA, Taketo T, Bourque G, Naumova AK. Genetic variation in the Y chromosome and sex-biased DNA methylation in somatic cells in the mouse. Mamm Genome 2023; 34:44-55. [PMID: 36454369 PMCID: PMC9947081 DOI: 10.1007/s00335-022-09970-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
Several lines of evidence suggest that the presence of the Y chromosome influences DNA methylation of autosomal loci. To better understand the impact of the Y chromosome on autosomal DNA methylation patterns and its contribution to sex bias in methylation, we identified Y chromosome dependent differentially methylated regions (yDMRs) using whole-genome bisulfite sequencing methylation data from livers of mice with different combinations of sex-chromosome complement and gonadal sex. Nearly 90% of the autosomal yDMRs mapped to transposable elements (TEs) and most of them had lower methylation in XY compared to XX or XO mice. Follow-up analyses of four reporter autosomal yDMRs showed that Y-dependent methylation levels were consistent across most somatic tissues but varied in strains with different origins of the Y chromosome, suggesting that genetic variation in the Y chromosome influenced methylation levels of autosomal regions. Mice lacking the q-arm of the Y chromosome (B6.NPYq-2) as well as mice with a loss-of-function mutation in Kdm5d showed no differences in methylation levels compared to wild type mice. In conclusion, the Y-linked modifier of TE methylation is likely to reside on the short arm of Y chromosome and further studies are required to identify this gene.
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Affiliation(s)
- Enkhjin Batdorj
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
| | - Najla AlOgayil
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
| | - Qinwei Kim-Wee Zhuang
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
| | - Jose Hector Galvez
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
| | - Klara Bauermeister
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
| | - Kei Nagata
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Monika A Ward
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii, 1960 East-West Road, HonoluluHonolulu, HIHI, 96822, USA
| | - Teruko Taketo
- The Research Institute of the McGill University Health Centre, Montréal, QC, H4A 3J1, Canada
- Department of Surgery, McGill University, Montréal, QC, H4A 3J1, Canada
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
| | - Anna K Naumova
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada.
- The Research Institute of the McGill University Health Centre, Montréal, QC, H4A 3J1, Canada.
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC, H4A 3J1, Canada.
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Arna AB, Patel H, Singh RS, Vizeacoumar FS, Kusalik A, Freywald A, Vizeacoumar FJ, Wu Y. Synthetic lethal interactions of DEAD/H-box helicases as targets for cancer therapy. Front Oncol 2023; 12:1087989. [PMID: 36761420 PMCID: PMC9905851 DOI: 10.3389/fonc.2022.1087989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
DEAD/H-box helicases are implicated in virtually every aspect of RNA metabolism, including transcription, pre-mRNA splicing, ribosomes biogenesis, nuclear export, translation initiation, RNA degradation, and mRNA editing. Most of these helicases are upregulated in various cancers and mutations in some of them are associated with several malignancies. Lately, synthetic lethality (SL) and synthetic dosage lethality (SDL) approaches, where genetic interactions of cancer-related genes are exploited as therapeutic targets, are emerging as a leading area of cancer research. Several DEAD/H-box helicases, including DDX3, DDX9 (Dbp9), DDX10 (Dbp4), DDX11 (ChlR1), and DDX41 (Sacy-1), have been subjected to SL analyses in humans and different model organisms. It remains to be explored whether SDL can be utilized to identity druggable targets in DEAD/H-box helicase overexpressing cancers. In this review, we analyze gene expression data of a subset of DEAD/H-box helicases in multiple cancer types and discuss how their SL/SDL interactions can be used for therapeutic purposes. We also summarize the latest developments in clinical applications, apart from discussing some of the challenges in drug discovery in the context of targeting DEAD/H-box helicases.
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Affiliation(s)
- Ananna Bhadra Arna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hardikkumar Patel
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Franco J. Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan and Saskatchewan Cancer Agency, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada,*Correspondence: Yuliang Wu, ; Franco J. Vizeacoumar,
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6
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Lacroix M, Beauchemin H, Khandanpour C, Möröy T. The RNA helicase DDX3 and its role in c-MYC driven germinal center-derived B-cell lymphoma. Front Oncol 2023; 13:1148936. [PMID: 37035206 PMCID: PMC10081492 DOI: 10.3389/fonc.2023.1148936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
DDX3X is an RNA helicase with many functions in RNA metabolism such as mRNA translation, alternative pre-mRNA splicing and mRNA stability, but also plays a role as a regulator of transcription as well as in the Wnt/beta-catenin- and Nf-κB signaling pathways. The gene encoding DDX3X is located on the X-chromosome, but escapes X-inactivation. Hence females have two active copies and males only one. However, the Y chromosome contains the gene for the male DDX3 homologue, called DDX3Y, which has a very high sequence similarity and functional redundancy with DDX3X, but shows a more restricted protein expression pattern than DDX3X. High throughput sequencing of germinal center (GC)-derived B-cell malignancies such as Burkitt Lymphoma (BL) and Diffuse large B-cell lymphoma (DLBCL) samples showed a high frequency of loss-of-function (LOF) mutations in the DDX3X gene revealing several features that distinguish this gene from others. First, DDX3X mutations occur with high frequency particularly in those GC-derived B-cell lymphomas that also show translocations of the c-MYC proto-oncogene, which occurs in almost all BL and a subset of DLBCL. Second, DDX3X LOF mutations occur almost exclusively in males and is very rarely found in females. Third, mutations in the male homologue DDX3Y have never been found in any type of malignancy. Studies with human primary GC B cells from male donors showed that a loss of DDX3X function helps the initial process of B-cell lymphomagenesis by buffering the proteotoxic stress induced by c-MYC activation. However, full lymphomagenesis requires DDX3 activity since an upregulation of DDX3Y expression is invariably found in GC derived B-cell lymphoma with DDX3X LOF mutation. Other studies with male transgenic mice that lack Ddx3x, but constitutively express activated c-Myc transgenes in B cells and are therefore prone to develop B-cell malignancies, also showed upregulation of the DDX3Y protein expression during the process of lymphomagenesis. Since DDX3Y is not expressed in normal human cells, these data suggest that DDX3Y may represent a new cancer cell specific target to develop adjuvant therapies for male patients with BL and DLBCL and LOF mutations in the DDX3X gene.
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Affiliation(s)
- Marion Lacroix
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, QC, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Hugues Beauchemin
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, QC, Canada
| | - Cyrus Khandanpour
- Klinik für Hämatologie und Onkologie, University Hospital Schleswig Holstein, University Lübeck, Lübeck, Germany
- *Correspondence: Tarik Möröy, ; Cyrus Khandanpour,
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, QC, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- *Correspondence: Tarik Möröy, ; Cyrus Khandanpour,
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Vogt PH, Rauschendorf MA, Zimmer J, Drummer C, Behr R. AZFa Y gene, DDX3Y, evolved novel testis transcript variants in primates with proximal 3´UTR polyadenylation for germ cell specific translation. Sci Rep 2022; 12:8954. [PMID: 35624115 PMCID: PMC9142519 DOI: 10.1038/s41598-022-12474-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/31/2022] [Indexed: 01/15/2023] Open
Abstract
Translational control is a major level of gene expression regulation in the male germ line. DDX3Y located in the AZFa region of the human Y chromosome encodes a conserved RNA helicase important for translational control at the G1-S phase of the cell cycle. In human, DDX3Y protein is expressed only in premeiotic male germ cells. In primates, DDX3Y evolved a second promoter producing novel testis-specific transcripts. Here, we show primate species-specific use of alternative polyadenylation (APA) sites for these testis-specific DDX3Y transcript variants. They have evolved subsequently in the 3´UTRs of the primates´ DDX3Y transcripts. Whereas a distal APA site (PAS4) is still used for polyadenylation of most DDX3Y testis transcripts in Callithrix jacchus; two proximal APAs (PAS1; PAS2) are used predominantly in Macaca mulatta, in Pan trogloydates and in human. This shift corresponds with a significant increase of DDX3Y protein expression in the macaque testis tissue. In chimpanzee and human, shift to predominant use of the most proximal APA site (PAS1) is associated with translation of these DDX3Y transcripts in only premeiotic male germ cells. We therefore assume evolution of a positive selection process for functional DDX3Y testis transcripts in these primates which increase their stability and translation efficiency to promote its cell cycle balancing function in the human male germ line.
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Affiliation(s)
- P. H. Vogt
- Division of Reproduction Genetics, Department of Gynecological Endocrinology and Fertility Disorders, University Women Hospital, Im Neuenheimer Feld 440, D-69120 Heidelberg, Germany
| | - M-A. Rauschendorf
- Molecular Health GmbH, Kurfürsten-Anlage 21, D-69115 Heidelberg, Germany
| | - J. Zimmer
- Division of Reproduction Genetics, Department of Gynecological Endocrinology and Fertility Disorders, University Women Hospital, Im Neuenheimer Feld 440, D-69120 Heidelberg, Germany
| | - C. Drummer
- grid.418215.b0000 0000 8502 7018Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, D-37077 Göttingen, Germany
| | - R. Behr
- grid.418215.b0000 0000 8502 7018Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, D-37077 Göttingen, Germany
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Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022; 39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.
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Affiliation(s)
- Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Andreas Schlattl
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | | | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Christoph Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
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Suthapot P, Xiao T, Felsenfeld G, Hongeng S, Wongtrakoongate P. The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2. Life Sci 2022; 291:120298. [PMID: 35007564 DOI: 10.1016/j.lfs.2021.120298] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 12/31/2022]
Abstract
AIMS Understanding human neurogenesis is critical toward regenerative medicine for neurodegeneration. However, little is known how neural differentiation is regulated by DEAD box-containing RNA helicases, which comprise a diverse class of RNA remodeling enzymes. MATERIALS AND METHODS ChIP-seq was utilized to identify binding sites of DDX5 and DDX17 in both human pluripotent stem cell (hPSC) line NTERA2 and their retinoic acid-induced neural derivatives. RNA-seq was used to elucidate genes differentially expressed upon depletion of DDX5 and DDX17. Neurosphere assay, flow cytometry, and immunofluorescence staining were performed to test the effect of depletion of the two RNA helicases in neural differentiation. KEY FINDINGS We show here that expression of DDX5 and DDX17 is abundant throughout neural differentiation of NTERA2, and is mostly localized within the nucleus. The two RNA helicases occupy chromatin genome-wide at regions associated with neurogenesis-related genes in both hPSCs and their neural derivatives. Further, both DDX5 and DDX17 are mutually required for controlling transcriptional expression of these genes, but are not important for maintenance of stem cell state of hPSCs. In contrast, they facilitate early neural differentiation of hPSCs, generation of neurospheres from the stem cells, and transcriptional expression of key neurogenic transcription factors such as SOX1 and PAX6 during neural differentiation. Importantly, DDX5 and DDX17 are critical for differentiation of hPSCs toward NESTIN- and TUBB3-positive cells, which represent neural progenitors and mature neurons, respectively. SIGNIFICANCE Collectively, our findings suggest the role of DDX5 and DDX17 in transcriptional regulation of genes involved in neurogenesis, and hence in neural differentiation of hPSCs.
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Affiliation(s)
- Praewa Suthapot
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Tiaojiang Xiao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0540, MD, USA
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0540, MD, USA
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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10
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Yamazaki W, Badescu D, Tan SL, Ragoussis J, Taketo T. Effects of the Sex Chromosome Complement, XX, XO, or XY, on the Transcriptome and Development of Mouse Oocytes During Follicular Growth. Front Genet 2021; 12:792604. [PMID: 34987552 PMCID: PMC8721172 DOI: 10.3389/fgene.2021.792604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/26/2021] [Indexed: 12/26/2022] Open
Abstract
The sex chromosome complement, XX or XY, determines sexual differentiation of the gonadal primordium into a testis or an ovary, which in turn directs differentiation of the germ cells into sperm and oocytes, respectively, in eutherian mammals. When the X monosomy or XY sex reversal occurs, XO and XY females exhibit subfertility and infertility in the mouse on the C57BL/6J genetic background, suggesting that functional germ cell differentiation requires the proper sex chromosome complement. Using these mouse models, we asked how the sex chromosome complement affects gene transcription in the oocytes during follicular growth. An oocyte accumulates cytoplasmic components such as mRNAs and proteins during follicular growth to support subsequent meiotic progression, fertilization, and early embryonic development without de novo transcription. However, how gene transcription is regulated during oocyte growth is not well understood. Our results revealed that XY oocytes became abnormal in chromatin configuration, mitochondria distribution, and de novo transcription compared to XX or XO oocytes near the end of growth phase. Therefore, we compared transcriptomes by RNA-sequencing among the XX, XO, and XY oocytes of 50–60 µm in diameter, which were still morphologically comparable. The results showed that the X chromosome dosage limited the X-linked and autosomal gene transcript levels in XO oocytes whereas many genes were transcribed from the Y chromosome and made the transcriptome in XY oocytes closer to that in XX oocytes. We then compared the transcript levels of 3 X-linked, 3 Y-linked and 2 autosomal genes in the XX, XO, and XY oocytes during the entire growth phase as well as at the end of growth phase using quantitative RT-PCR. The results indicated that the transcript levels of most genes increased with oocyte growth while largely maintaining the X chromosome dosage dependence. Near the end of growth phase, however, transcript levels of some X-linked genes did not increase in XY oocytes as much as XX or XO oocytes, rendering their levels much lower than those in XX oocytes. Thus, XY oocytes established a distinct transcriptome at the end of growth phase, which may be associated with abnormal chromatin configuration and mitochondria distribution.
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Affiliation(s)
- Wataru Yamazaki
- Department of Surgery, McGill University, Montreal, QC, Canada
- Research Institute of McGill University Health Centre, Montreal, QC, Canada
| | - Dunarel Badescu
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Seang Lin Tan
- Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada
- OriginElle Fertility Clinic and Women’s Health Centre, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Teruko Taketo
- Department of Surgery, McGill University, Montreal, QC, Canada
- Research Institute of McGill University Health Centre, Montreal, QC, Canada
- Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada
- Department of Biology, McGill University, Montreal, QC, Canada
- *Correspondence: Teruko Taketo,
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11
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Venkataramanan S, Gadek M, Calviello L, Wilkins K, Floor SN. DDX3X and DDX3Y are redundant in protein synthesis. RNA (NEW YORK, N.Y.) 2021; 27:1577-1588. [PMID: 34535544 PMCID: PMC8594478 DOI: 10.1261/rna.078926.121] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
DDX3 is a DEAD-box RNA helicase that regulates translation and is encoded by the X- and Y-linked paralogs DDX3X and DDX3Y While DDX3X is ubiquitously expressed in human tissues and essential for viability, DDX3Y is male-specific and shows lower and more variable expression than DDX3X in somatic tissues. Heterozygous genetic lesions in DDX3X mediate a class of developmental disorders called DDX3X syndrome, while loss of DDX3Y is implicated in male infertility. One possible explanation for female-bias in DDX3X syndrome is that DDX3Y encodes a polypeptide with different biochemical activity. In this study, we use ribosome profiling and in vitro translation to demonstrate that the X- and Y-linked paralogs of DDX3 play functionally redundant roles in translation. We find that transcripts that are sensitive to DDX3X depletion or mutation are rescued by complementation with DDX3Y. Our data indicate that DDX3X and DDX3Y proteins can functionally complement each other in the context of mRNA translation in human cells. DDX3Y is not expressed in a large fraction of the central nervous system. These findings suggest that expression differences, not differences in paralog-dependent protein synthesis, underlie the sex-bias of DDX3X-associated diseases.
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Affiliation(s)
- Srivats Venkataramanan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Margaret Gadek
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kevin Wilkins
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143, USA
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12
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Abstract
The DEAD-box helicase family member DDX3X (DBX, DDX3) functions in nearly all stages of RNA metabolism and participates in the progression of many diseases, including virus infection, inflammation, intellectual disabilities and cancer. Over two decades, many studies have gradually unveiled the role of DDX3X in tumorigenesis and tumour progression. In fact, DDX3X possesses numerous functions in cancer biology and is closely related to many well-known molecules. In this review, we describe the function of DDX3X in RNA metabolism, cellular stress response, innate immune response, metabolic stress response in pancreatic β cells and embryo development. Then, we focused on the role of DDX3X in cancer biology and systematically demonstrated its functions in various aspects of tumorigenesis and development. To provide a more intuitive understanding of the role of DDX3X in cancer, we summarized its functions and specific mechanisms in various types of cancer and presented its involvement in cancer-related signalling pathways.
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13
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Deschepper CF. Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells. Sci Rep 2020; 10:14900. [PMID: 32913328 PMCID: PMC7484786 DOI: 10.1038/s41598-020-71447-3] [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: 04/10/2020] [Accepted: 08/13/2020] [Indexed: 12/22/2022] Open
Abstract
In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes that include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes. However, no study to date has investigated the functional impact of targeted mutations of any of these genes within adult non-reproductive somatic cells. We thus compared adult male mice carrying a gene trap within their Uty gene (UtyGT) to their wild-type (WT) isogenic controls, and performed deep sequencing of RNA and genome-wide profiling of chromatin features in extracts from either cardiac tissue, cardiomyocyte-specific nuclei or purified cardiomyocytes. The apparent impact of UtyGT on gene transcription concentrated mostly on chrY genes surrounding the locus of insertion, i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs) contained within their introns and Eif2s3y, in addition to possible effects on the autosomal Malat1 lncRNA. Notwithstanding, UtyGT also caused coordinate changes in the abundance of hundreds of mRNA transcripts related to coherent cell functions, including RNA processing and translation. The results altogether indicated that tightly co-regulated chrY genes had nonetheless more widespread effects on the autosomal transcriptome in adult somatic cells, most likely due to mechanisms other than just transcriptional regulation of corresponding protein-coding genes.
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Affiliation(s)
- Christian F Deschepper
- Cardiovascular Biology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM) and Université de Montréal, 100 Pine Ave West, Montréal, QC, H2W 1R7, Canada.
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14
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Cardinal T, Bergeron KF, Soret R, Souchkova O, Faure C, Guillon A, Pilon N. Male-biased aganglionic megacolon in the TashT mouse model of Hirschsprung disease involves upregulation of p53 protein activity and Ddx3y gene expression. PLoS Genet 2020; 16:e1009008. [PMID: 32898154 PMCID: PMC7500598 DOI: 10.1371/journal.pgen.1009008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/18/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Hirschsprung disease (HSCR) is a complex genetic disorder of neural crest development resulting in incomplete formation of the enteric nervous system (ENS). This life-threatening neurocristopathy affects 1/5000 live births, with a currently unexplained male-biased ratio. To address this lack of knowledge, we took advantage of the TashT mutant mouse line, which is the only HSCR model to display a robust male bias. Our prior work revealed that the TashT insertional mutation perturbs a Chr.10 silencer-enriched non-coding region, leading to transcriptional dysregulation of hundreds of genes in neural crest-derived ENS progenitors of both sexes. Here, through sex-stratified transcriptome analyses and targeted overexpression in ENS progenitors, we show that male-biased ENS malformation in TashT embryos is not due to upregulation of Sry-the murine ortholog of a candidate gene for the HSCR male bias in humans-but instead involves upregulation of another Y-linked gene, Ddx3y. This discovery might be clinically relevant since we further found that the DDX3Y protein is also expressed in the ENS of a subset of male HSCR patients. Mechanistically, other data including chromosome conformation captured-based assays and CRISPR/Cas9-mediated deletions suggest that Ddx3y upregulation in male TashT ENS progenitors is due to increased transactivation by p53, which appears especially active in these cells yet without triggering apoptosis. Accordingly, in utero treatment of TashT embryos with the p53 inhibitor pifithrin-α decreased Ddx3y expression and abolished the otherwise more severe ENS defect in TashT males. Our data thus highlight novel pathogenic roles for p53 and DDX3Y during ENS formation in mice, a finding that might help to explain the intriguing male bias of HSCR in humans.
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Affiliation(s)
- Tatiana Cardinal
- Molecular Genetics of Development Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
- Centre d'excellence en recherche sur les maladies orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada
| | - Karl-Frédérik Bergeron
- Centre d'excellence en recherche sur les maladies orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada
- Lipid Metabolism Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
| | - Rodolphe Soret
- Molecular Genetics of Development Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
- Centre d'excellence en recherche sur les maladies orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada
| | - Ouliana Souchkova
- Molecular Genetics of Development Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
- Centre d'excellence en recherche sur les maladies orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada
| | - Christophe Faure
- Centre d'excellence en recherche sur les maladies orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada
- Département de pédiatrie, Université de Montréal, Montréal, Québec, Canada
- Division de gastroentérologie, hépatologie et nutrition pédiatrique, Centre hospitalier universitaire Sainte-Justine, Montréal, Québec, Canada
| | - Amélina Guillon
- Molecular Genetics of Development Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
| | - Nicolas Pilon
- Molecular Genetics of Development Laboratory, Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
- Centre d'excellence en recherche sur les maladies orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, Québec, Canada
- Département de pédiatrie, Université de Montréal, Montréal, Québec, Canada
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15
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Vogt PH, Besikoglu B, Bettendorf M, Frank-Herrmann P, Zimmer J, Bender U, Knauer-Fischer S, Choukair D, Sinn P, Lau YFC, Heidemann PH, Strowitzki T. Gonadoblastoma Y locus genes expressed in germ cells of individuals with dysgenetic gonads and a Y chromosome in their karyotypes include DDX3Y and TSPY. Hum Reprod 2020; 34:770-779. [PMID: 30753444 DOI: 10.1093/humrep/dez004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/17/2018] [Accepted: 01/10/2019] [Indexed: 12/13/2022] Open
Abstract
STUDY QUESTION Which Y genes mapped to the 'Gonadoblastoma Y (GBY)' locus on human Y chromosome are expressed in germ cells of individuals with some Differences of Sexual Development (DSD) and a Y chromosome in their karyotype (DSD-XY groups)? SUMMARY ANSWER The GBY candidate genes DDX3Y and TSPY are expressed in the germ cells of DSD-XY patients from distinct etiologies: patients with mixed gonadal dysgenesis (MGD) and sex chromosome mosaics (45,X0/46,XY; 46,XX/46,XY); patients with complete androgen insensitivity (CAIS), patients with complete gonadal dysgenesis (CGD; e.g. Swyer syndrome). WHAT IS KNOWN ALREADY A GBY locus was proposed to be present on the human Y chromosome because only DSD patients with a Y chromosome in their karyotype have a high-although variable-risk (up to 55%) for germ cell tumour development. GBY was mapped to the proximal part of the short and long Y arm. TSPY located in the proximal part of the short Y arm (Yp11.1) was found to be a strong GBY candidate gene. It is expressed in the germ cells of DSD-XY patients with distinct etiologies but also in foetal and pre-meiotic male spermatogonia. However, the GBY region extends to proximal Yq11 and therefore includes probably more than one candidate gene. STUDY DESIGN, SIZE, DURATION Protein expression of the putative GBY candidate gene in proximal Yq11, DDX3Y, is compared with that of TSPY in serial gonadal tissue sections of 40 DSD-XY individuals from the three DSD patient groups (MGD, Complete Androgen Insensitivity Syndrome [CAIS], CGD) with and without displaying malignancy. Expression of OCT3/4 in the same tissue samples marks the rate of pluripotent germ cells. PARTICIPANTS/MATERIALS, SETTING, METHOD A total of 145 DSD individuals were analysed for the Y chromosome to select the DSD-XY subgroup. PCR multiplex assays with Y gene specific marker set score for putative microdeletions in GBY Locus. Immunohistochemical experiments with specific antisera mark expression of the GBY candidate proteins, DDX3Y, TSPY, in serial sections of the gonadal tissue samples; OCT3/4 expression analyses in parallel reveal the pluripotent germ cell fraction. MAIN RESULTS AND THE ROLE OF CHANCE Similar DDX3Y and TSPY protein expression patterns were found in the germ cells of DSD-XY patients from each subgroup, independent of age. In CAIS patients OCT3/4 expression was often found only in a fraction of these germ cells. This suggest that GBY candidate proteins are also expressed in the non-malignant germ cells of DSD-XY individuals like in male spermatogonia. LIMITATIONS, REASONS FOR CAUTION Variation of the expression profiles of GBY candidate genes in the germ cells of some DSD-XY individuals suggests distinct transcriptional and translational control mechanisms which are functioning during expression of these Y genes in the DSD-XY germ cells. Their proposed GBY tumour susceptibility function to transform these germ cells to pre-malignant GB/Germ Cell Neoplasia in Situ (GB/GCNIS) cells seems therefore to be limited and depending on their state of pluripotency. WIDER IMPLICATIONS OF THE FINDINGS These experimental findings are of general importance for each individual identified in the clinic with DSD and a Y chromosome in the karyotype. To judge their risk of germ cell tumour development, OCT3/4 expression analyses on their gonadal tissue section is mandatory to reveal the fraction of germ cells still being pluripotent. Comparative expression analysis of the GBY candidate genes can be helpful to reveal the fraction of germ cells with genetically still activated Y chromosomes contributing to further development of malignancy if at high expression level. STUDY FUNDING/COMPETING INTEREST(S) This research project was supported by a grant (01GM0627) from the BMBF (Bundesministerium für Bildung und Forschung), Germany to P.H.V. and B.B. The authors have no competing interests.
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Affiliation(s)
- P H Vogt
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Heidelberg, Germany
| | - B Besikoglu
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Heidelberg, Germany.,Novum, Center for Reproductive Medicine, Akazienallee 8, Essen, Germany
| | - M Bettendorf
- Division of Paediatric Endocrinology and Diabetes, Children Hospital, University of Heidelberg, Heidelberg, Germany
| | - P Frank-Herrmann
- Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Heidelberg, Germany
| | - J Zimmer
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Heidelberg, Germany
| | - U Bender
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Heidelberg, Germany
| | - S Knauer-Fischer
- Division of Paediatric Endocrinology and Diabetes, Children Hospital, University of Heidelberg, Heidelberg, Germany
| | - D Choukair
- Division of Paediatric Endocrinology and Diabetes, Children Hospital, University of Heidelberg, Heidelberg, Germany
| | - P Sinn
- Division of Gynaecopathology, Department of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, Heidelberg, Germany
| | - Y-F C Lau
- Division of Cell & Developmental Genetics, Department of Medicine, VAMC 111C5, San Francisco, CA, USA
| | - P H Heidemann
- Children Hospital Augsburg I, Academic Hospital of University of Munich, Stenglinstraβe 2, Augsburg, Germany
| | - T Strowitzki
- Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Heidelberg, Germany
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16
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Godfrey AK, Naqvi S, Chmátal L, Chick JM, Mitchell RN, Gygi SP, Skaletsky H, Page DC. Quantitative analysis of Y-Chromosome gene expression across 36 human tissues. Genome Res 2020; 30:860-873. [PMID: 32461223 PMCID: PMC7370882 DOI: 10.1101/gr.261248.120] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Little is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across 36 human tissues from hundreds of individuals. Although it is often said that Y-Chromosome genes are lowly expressed outside the testis, we report many instances of elevated Y-Chromosome gene expression in a nonreproductive tissue. A notable example is EIF1AY, which encodes eukaryotic translation initiation factor 1A Y-linked, together with its X-linked homolog EIF1AX. Evolutionary loss of a Y-linked microRNA target site enabled up-regulation of EIF1AY, but not of EIF1AX, in the heart. Consequently, this essential translation initiation factor is nearly twice as abundant in male as in female heart tissue at the protein level. Divergence between the X and Y Chromosomes in regulatory sequence can therefore lead to tissue-specific Y-Chromosome-driven sex biases in expression of critical, dosage-sensitive regulatory genes.
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Affiliation(s)
- Alexander K Godfrey
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sahin Naqvi
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Lukáš Chmátal
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Richard N Mitchell
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
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17
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Zhang R, Wang H, Zhu X, Liu S, Wang Z, Lu Q, Shao H, Xiao S, Fang L. Molecular cloning and functional characterization of duck DEAD (Asp-Glu-Ala-Asp) box RNA helicase 3 (DDX3X). Biochem Biophys Res Commun 2020; 527:496-502. [PMID: 32414573 DOI: 10.1016/j.bbrc.2020.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/27/2023]
Abstract
DEAD (Asp-Glu-Ala-Asp) box RNA helicase 3 (DDX3X) is demonstrated to have crucial functions in the antiviral immune response. To our knowledge, little information focuses on the function of duck DDX3X. In this study, duck DDX3X (duDDX3X) was cloned and its role in the type I interferon (IFN) signaling pathway was investigated using duck embryo fibroblast (DEF) cells. Full-length duDDX3X cDNA encodes 652 amino acid residues and contains a DEADc domain and a HELICc domain. According to tissue distribution analysis, duDDX3X mRNA was widely expressed in different tissues, especially the spleen and the liver. Overexpression of duDDX3X in DEF cells induced IFN-β by activating transcription factors IRF1 and NF-κB. Knockdown of duDDX3X in DEF cells with siRNA significantly reduced IFN-β expression induced by poly(I:C), a double-stranded RNA (dsRNA) analog. Our results demonstrated that duck DDX3X was involved in the dsRNA-mediated type I IFN signaling pathway in DEF cells.
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Affiliation(s)
- Rongrong Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430070, China
| | - Honglin Wang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430070, China
| | - Xinyu Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shudan Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zui Wang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430070, China
| | - Qin Lu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430070, China
| | - Huabin Shao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430070, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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18
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Li N, Jiang S, Zhao J, Yang Y, Deng K, Wei L, Cai Y, Li B, Liu S. Molecular identification of duck DDX3X and its potential role in response to Tembusu virus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 106:103599. [PMID: 31899305 DOI: 10.1016/j.dci.2019.103599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 06/10/2023]
Abstract
ATP-dependent DEAD (Asp-Glu-Ala-Asp)-box RNA helicases not only regulate RNA metabolism, but also are involved in host antiviral innate immune responses. It is important to investigate the orthologs of this protein family to broaden our understanding of innate immunity and promote protective strategies against viral infections in ducks. In the current study, duck DDX3X (duDDX3X) was first cloned, which consists of 1959 bp encoding a protein of 652 amino acids. duDDX3X has the typical structure of this family, including nine motifs, DEAD and HELICc domains. The amino acid sequence of duDDX3X shares a high similarity with the DDX3Xs of avian and mammalian. Quantitative real-time PCR indicated that duDDX3X was ubiquitously expressed in nearly all tissues. Overexpression of duDDX3X could activate interferon (IFN)-β and enhance the RIG-I-induced IFN-β yield in duck embryo fibroblast cells. However, duDDX3X had no significant effect on the expression of proinflammatory cytokines such as IL-1β, IL-6, and CXCL-8. Tembusu virus (TMUV) infection significantly downregulated duDDX3X. Overexpression and siRNA interference studies showed that duDDX3X inhibited the replication of TMUV through IFN-β at the early stages of infection. Collectively, our results indicated that duDDX3X could positively modulate type I interferon and play an essential role in response to TMUV infection. This study will contribute to a better understanding of duDDX3X in the innate immune system of ducks and lay a solid foundation for further studies of duDDX3X in antiviral immunity.
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Affiliation(s)
- Ning Li
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Taian City, 271018, Shandong Province, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China
| | - Shengnan Jiang
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Taian City, 271018, Shandong Province, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China
| | - Jun Zhao
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Taian City, 271018, Shandong Province, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China
| | - Yudong Yang
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Taian City, 271018, Shandong Province, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China
| | - Kai Deng
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Taian City, 271018, Shandong Province, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China
| | - Liangmeng Wei
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Taian City, 271018, Shandong Province, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China
| | - Yumei Cai
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Taian City, 271018, Shandong Province, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China
| | - Baoquan Li
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Taian City, 271018, Shandong Province, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China.
| | - Sidang Liu
- College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Road, Taian City, 271018, Shandong Province, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, 271018, Shandong Province, China.
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19
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Cerván-Martín M, Castilla JA, Palomino-Morales RJ, Carmona FD. Genetic Landscape of Nonobstructive Azoospermia and New Perspectives for the Clinic. J Clin Med 2020; 9:jcm9020300. [PMID: 31973052 PMCID: PMC7074441 DOI: 10.3390/jcm9020300] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 02/07/2023] Open
Abstract
Nonobstructive azoospermia (NOA) represents the most severe expression of male infertility, involving around 1% of the male population and 10% of infertile men. This condition is characterised by the inability of the testis to produce sperm cells, and it is considered to have an important genetic component. During the last two decades, different genetic anomalies, including microdeletions of the Y chromosome, karyotype defects, and missense mutations in genes involved in the reproductive function, have been described as the primary cause of NOA in many infertile men. However, these alterations only explain around 25% of azoospermic cases, with the remaining patients showing an idiopathic origin. Recent studies clearly suggest that the so-called idiopathic NOA has a complex aetiology with a polygenic inheritance, which may alter the spermatogenic process. Although we are far from a complete understanding of the molecular mechanisms underlying NOA, the use of the new technologies for genetic analysis has enabled a considerable increase in knowledge during the last years. In this review, we will provide a comprehensive and updated overview of the genetic basis of NOA, with a special focus on the possible application of the recent insights in clinical practice.
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Affiliation(s)
- Miriam Cerván-Martín
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Centro de Investigación Biomédica (CIBM), Parque Tecnológico Ciencias de la Salud, Av. del Conocimiento, s/n, 18016 Granada, Spain;
- Instituto de Investigación Biosanitaria ibs.GRANADA, Av. de Madrid, 15, Pabellón de Consultas Externas 2, 2ª Planta, 18012 Granada, Spain; (J.A.C.); (R.J.P.-M.)
| | - José A. Castilla
- Instituto de Investigación Biosanitaria ibs.GRANADA, Av. de Madrid, 15, Pabellón de Consultas Externas 2, 2ª Planta, 18012 Granada, Spain; (J.A.C.); (R.J.P.-M.)
- Unidad de Reproducción, UGC Obstetricia y Ginecología, HU Virgen de las Nieves, Av. de las Fuerzas Armadas 2, 18014 Granada, Spain
- CEIFER Biobanco—NextClinics, Calle Maestro Bretón 1, 18004 Granada, Spain
| | - Rogelio J. Palomino-Morales
- Instituto de Investigación Biosanitaria ibs.GRANADA, Av. de Madrid, 15, Pabellón de Consultas Externas 2, 2ª Planta, 18012 Granada, Spain; (J.A.C.); (R.J.P.-M.)
- Departamento de Bioquímica y Biología Molecular I, Universidad de Granada, Facultad de Ciencias, Av. de Fuente Nueva s/n, 18071 Granada, Spain
| | - F. David Carmona
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Centro de Investigación Biomédica (CIBM), Parque Tecnológico Ciencias de la Salud, Av. del Conocimiento, s/n, 18016 Granada, Spain;
- Instituto de Investigación Biosanitaria ibs.GRANADA, Av. de Madrid, 15, Pabellón de Consultas Externas 2, 2ª Planta, 18012 Granada, Spain; (J.A.C.); (R.J.P.-M.)
- Correspondence: ; Tel.: +34-958-241-000 (ext 20170)
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20
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Case of Inherited Partial AZFa Deletion without Impact on Male Fertility. Case Rep Genet 2019; 2019:3802613. [PMID: 31781421 PMCID: PMC6874946 DOI: 10.1155/2019/3802613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/27/2019] [Indexed: 11/17/2022] Open
Abstract
Male factor infertility accounts for 40–50% of all infertility cases. Deletions of one or more AZF region parts in chromosome Y are one of the most common genetic causes of male infertility. Usually full or partial AZF deletions, including genes involved in spermatogenesis, are associated with spermatogenic failure. Here we report a case of a Caucasian man with partial AZFa region deletion from a couple with secondary infertility. Partial AZFa deletion, involving part of USP9Y gene appears to be benign, as we proved transmission from father to son. According to our results, it is recommended to revise guidelines on markers selected for testing of AZFa region deletion, to be more selective against DDX3Y gene and exclude probably benign microdeletions involving only USP9Y gene.
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21
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Heaton SM, Atkinson SC, Sweeney MN, Yang SNY, Jans DA, Borg NA. Exportin-1-Dependent Nuclear Export of DEAD-box Helicase DDX3X is Central to its Role in Antiviral Immunity. Cells 2019; 8:E1181. [PMID: 31575075 PMCID: PMC6848931 DOI: 10.3390/cells8101181] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/16/2019] [Accepted: 09/28/2019] [Indexed: 12/14/2022] Open
Abstract
DEAD-box helicase 3, X-linked (DDX3X) regulates the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR)-mediated antiviral response, but can also be a host factor contributing to the replication of viruses of significance to human health, such as human immunodeficiency virus type 1 (HIV-1). These roles are mediated in part through its ability to actively shuttle between the nucleus and the cytoplasm to modulate gene expression, although the trafficking mechanisms, and impact thereof on immune signaling and viral infection, are incompletely defined. We confirm that DDX3X nuclear export is mediated by the nuclear transporter exportin-1/CRM1, dependent on an N-terminal, leucine-rich nuclear export signal (NES) and the monomeric guanine nucleotide binding protein Ran in activated GTP-bound form. Transcriptome profiling and ELISA show that exportin-1-dependent export of DDX3X to the cytoplasm strongly impacts IFN-β production and the upregulation of immune genes in response to infection. That this is key to DDX3X's antiviral role was indicated by enhanced infection by human parainfluenza virus-3 (hPIV-3)/elevated virus production when the DDX3X NES was inactivated. Our results highlight a link between nucleocytoplasmic distribution of DDX3X and its role in antiviral immunity, with strong relevance to hPIV-3, as well as other viruses such as HIV-1.
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Affiliation(s)
- Steven M Heaton
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Sarah C Atkinson
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Melissa N Sweeney
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Sundy N Y Yang
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - David A Jans
- Nuclear Signaling Laboratory, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Natalie A Borg
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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22
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Matsumura T, Endo T, Isotani A, Ogawa M, Ikawa M. An azoospermic factor gene, Ddx3y and its paralog, Ddx3x are dispensable in germ cells for male fertility. J Reprod Dev 2019; 65:121-128. [PMID: 30613052 PMCID: PMC6473106 DOI: 10.1262/jrd.2018-145] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
About 10% of male infertile patients show abnormalities in spermatogenesis. The microdeletion of azoospermia factor a (AZFa) region of the Y chromosome is thought to be a
cause of spermatogenic failure. However, candidate gene responsible for the spermatogenic failure in AZFa deleted patients has not been elucidated yet. Using mice, we
explored the function of Ddx3y, a strong candidate gene in the Azfa region, and Ddx3x, a Ddx3y paralog on the X
chromosome, in spermatogenesis. We first generated Ddx3y KO male mice using CRISPR/Cas9 and found that the Ddx3y KO male mice show normal spermatogenesis,
produce morphologically normal spermatozoa, and sire healthy offspring. Because Ddx3x KO males were embryonic lethal, we next generated chimeric mice, which contain
Ddx3x and Ddx3y double KO (dKO) germ cells, and found that the dKO germ cells can differentiate into spermatozoa and transmit their mutant alleles to
offspring by normal mating. We conclude that Ddx3x and Ddx3y are dispensable for spermatogenesis at least in mice. Unlike human, mice have an additional
Ddx3y paralog D1pas1, that has been reported to be essential for spermatogenesis. These findings suggest that human and mouse DDX3 related proteins have
distinct differences in their functions.
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Affiliation(s)
- Takafumi Matsumura
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Tsutomu Endo
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Ayako Isotani
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Masaki Ogawa
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan.,Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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23
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Szappanos D, Tschismarov R, Perlot T, Westermayer S, Fischer K, Platanitis E, Kallinger F, Novatchkova M, Lassnig C, Müller M, Sexl V, Bennett KL, Foong-Sobis M, Penninger JM, Decker T. The RNA helicase DDX3X is an essential mediator of innate antimicrobial immunity. PLoS Pathog 2018; 14:e1007397. [PMID: 30475900 PMCID: PMC6283616 DOI: 10.1371/journal.ppat.1007397] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 12/06/2018] [Accepted: 10/11/2018] [Indexed: 12/30/2022] Open
Abstract
DExD/H box RNA helicases, such as the RIG-I-like receptors (RLR), are important components of the innate immune system. Here we demonstrate a pivotal and sex-specific role for the heterosomal isoforms of the DEAD box RNA helicase DDX3 in the immune system. Mice lacking DDX3X during hematopoiesis showed an altered leukocyte composition in bone marrow and spleen and a striking inability to combat infection with Listeria monocytogenes. Alterations in innate immune responses resulted from decreased effector cell availability and function as well as a sex-dependent impairment of cytokine synthesis. Thus, our data provide further in vivo evidence for an essential contribution of a non-RLR DExD/H RNA helicase to innate immunity and suggest it may contribute to sex-related differences in resistance to microbes and resilience to inflammatory disease. The establishment of innate immunity to pathogens requires cells to sense microbial molecules and to initiate a de novo transcription-based antimicrobial response. With the identification of Rig I and Mda5, two RNA helicases were shown to serve as pivotal receptors of viral RNA. Subsequently, a considerable number of RNA helicases were proposed to function as sensors or signal transducers for both microbial RNA and DNA. X-chromosome-encoded RNA helicase DDX3X was discovered as an interactor of the S/T kinase TBK1 which regulates the production of type I Interferons (IFN-I). However, the importance of DDX3X for innate immunity in an organismic context remained elusive. Here we describe and analyze mice lacking DDX3X in hematopoietic cells. We show contributions of DDX3X to hematopoiesis and a striking loss in resistance against Listeria monocytogenes. Our data reveal that DDX3X is critically involved in enhancing the expression of numerous antimicrobial genes. Consistently, production of important cytokines such as IL12 or IFNγ is reduced. Furthermore, DDX3X-deficient macrophages show reduced ability to restrict L. monocytogenes growth. Owing to partial redundancy with its close Y-chromosomal homologue, DDX3Y, the observed effects differ between mouse sexes. Thus, DDX3X may contribute to sex differences in immunity to pathogens and inflammatory disease.
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Affiliation(s)
- Daniel Szappanos
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Roland Tschismarov
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Thomas Perlot
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
| | - Sandra Westermayer
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Katrin Fischer
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Ekaterini Platanitis
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Fabian Kallinger
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Caroline Lassnig
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michelle Foong-Sobis
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
| | - Josef M. Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter, Vienna, Austria
- * E-mail: (JMP); (TD)
| | - Thomas Decker
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Vienna, Austria
- * E-mail: (JMP); (TD)
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Abstract
Fundamental differences exist between males and females, encompassing anatomy, physiology, behaviour, and genetics. Such differences undoubtedly play a part in the well documented, yet poorly understood, disparity in disease susceptibility between the sexes. Although traditionally attributed to gonadal sex hormone effects, recent work has begun to shed more light on the contribution of genetics - and in particular the sex chromosomes - to these sexual dimorphisms. Here, we explore the accumulating evidence for a significant genetic component to mammalian sexual dimorphism through the paradigm of sex chromosome evolution. The differences between the extant X and Y chromosomes, at both a sequence and regulatory level, arose across 166 million years. A functional result of these differences is cell autonomous sexual dimorphism. By understanding the process that changed a pair of homologous ancestral autosomes into the extant mammalian X and Y, we believe it easier to consider the mechanisms that may contribute to hormone-independent male-female differences. We highlight key roles for genes with homologues present on both sex chromosomes, where the X-linked copy escapes X chromosome inactivation. Finally, we summarise current experimental paradigms and suggest areas for developments to further increase our understanding of cell autonomous sexual dimorphism in the context of health and disease.
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Affiliation(s)
- Daniel M Snell
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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25
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Brennan R, Haap-Hoff A, Gu L, Gautier V, Long A, Schröder M. Investigating nucleo-cytoplasmic shuttling of the human DEAD-box helicase DDX3. Eur J Cell Biol 2018; 97:501-511. [PMID: 30131165 DOI: 10.1016/j.ejcb.2018.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 01/20/2023] Open
Abstract
The human DEAD-box helicase DDX3 is a multi-functional protein involved in the regulation of gene expression and additional non-conventional roles as signalling adaptor molecule that are independent of its enzymatic RNA remodeling activity. It is a nucleo-cytoplasmic shuttling protein and it has previously been suggested that dysregulation of its subcellular localization could contribute to tumourigenesis. Indeed, both tumour suppressor and oncogenic functions have been attributed to DDX3. In this study, we investigated the regulation of DDX3's nucleocytoplasmic shuttling. We confirmed that an N-terminal conserved Nuclear Export Signal (NES) is required for export of human DDX3 from the nucleus, and identified three regions within DDX3 that can independently facilitate its nuclear import. We also aimed to identify conditions that alter DDX3's subcellular localisation. Viral infection, cytokine treatment and DNA damage only induced minor changes in DDX3's subcellular distribution as determined by High Content Analysis. However, DDX3's nuclear localization increased in early mitotic cells (during prophase) concomitant with an increase in DDX3 expression levels. Our results are likely to have implications for the proposed use of (nuclear) DDX3 as a prognostic biomarker in cancer.
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Affiliation(s)
- Ruth Brennan
- Institute of Immunology, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Antje Haap-Hoff
- School of Medicine, Trinity College Dublin, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Dublin 2, Ireland
| | - Lili Gu
- Institute of Immunology, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Virginie Gautier
- School of Medicine, Centre for Research in Infectious Diseases (CRID), University College Dublin, Belfield, Dublin 4, Ireland
| | - Aideen Long
- School of Medicine, Trinity College Dublin, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Dublin 2, Ireland
| | - Martina Schröder
- Institute of Immunology, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland.
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26
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Wang X, Wang R, Luo M, Li C, Wang HX, Huan CC, Qu YR, Liao Y, Mao X. (DEAD)-box RNA helicase 3 modulates NF-κB signal pathway by controlling the phosphorylation of PP2A-C subunit. Oncotarget 2018; 8:33197-33213. [PMID: 28402257 PMCID: PMC5464861 DOI: 10.18632/oncotarget.16593] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/17/2017] [Indexed: 01/29/2023] Open
Abstract
Asp-Glu-Ala-Asp (DEAD)-box RNA helicase 3 (DDX3), an ATP-dependent RNA helicase, is associated with RNA splicing, mRNA export, transcription, translation, and RNA decay. Recent studies revealed that DDX3 participates in innate immune response during virus infection by interacting with TBK1 and regulating the production of IFN-β. In our studies, we demonstrated that DDX3 regulated NF-κB signal pathway. We found that DDX3 knockdown reduced the phosphorylation of p65 and IKK-β and ultimately attenuated the production of inflammatory cytokines induced by poly(I:C) or TNF-α stimulation. The regulatory effect of DDX3 on NF-κB signal pathway was not affected by the loss of its ATPase or helicase activity. We further identified PP2A C subunit (PP2A-C) as an interaction partner of DDX3 by co-immunoprecipitation and mass spectrum analysis. We confirmed that DDX3 formed the complex with PP2A-C/IKK-β and regulated the interaction between IKK-β and PP2A-C. Furthermore, we demonstrated that DDX3 modulated the activity of PP2A by controlling the phosphorylation of PP2A-C, which might enable PP2A-C to regulate NF-κB signal pathway by dephosphorylating IKK-β. All these findings suggested DDX3 plays multiple roles in modulating innate immune system.
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Affiliation(s)
- Xin Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Rui Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Miao Luo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Chen Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Hua-Xia Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Chang-Chao Huan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yu-Rong Qu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Xiang Mao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China.,Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
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Milani L, Pecci A, Cifaldi C, Maurizii MG. PL10 DEAD-Box Protein is Expressed during Germ Cell Differentiation in the Reptile Podarcis sicula (Family Lacertidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:433-448. [PMID: 28656658 DOI: 10.1002/jez.b.22744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/15/2017] [Accepted: 04/05/2017] [Indexed: 11/09/2022]
Abstract
Among genes involved in the regulation of germ cell differentiation, those of DDX4/Vasa and the Ded1/DDX3 subfamilies encode for DEAD-box ATP-dependent RNA helicases, proteins involved in many mechanisms related to RNA processing. For the first time in reptiles, using specific antibodies at confocal microscopy, we analysed the localization pattern of a Ded1/DDX3 subfamily member in testis and ovary of Podarcis sicula (Ps-PL10) during the reproductive cycle. In testis, Ps-PL10 is expressed in the cytoplasm of spermatocytes and it is not detected in spermatogonia. Differently from Ps-VASA, in round spermatids, Ps-PL10 is not segregated in the chromatoid body but it accumulates in the cytoplasm of residual bodies, and mature spermatozoa are unstained. These observations suggest that in males, Ps-PL10 (1) is involved in spermatogenesis and (2) is then eliminated with residual bodies. In the ovary, Ps-PL10 is present with granules in the cytoplasm of early meiotic cells of the germinal bed (GB), while it is not present in oogonia and somatic cells of the GB stroma. In follicular cells of ovarian follicles, Ps-PL10 expression starts after their fusion with the oocyte. Numerous Ps-PL10 spots are visible in pyriform (nurse-like) cells concomitantly with the protein accumulation in the cytoplasm of differentiating oocyte. In pyriform cells, Ps-PL10 spots are present in the cytoplasm and nuclei, as observed for Ps-VASA, and in the nucleoli, suggesting for Ps-PL10 a role in rRNA processing and in the transport of molecules from the nucleus to cytoplasm and from nurse cells to the oocyte.
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Affiliation(s)
- Liliana Milani
- Department of Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Andrea Pecci
- Department of Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Carmine Cifaldi
- Department of Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Maria Gabriella Maurizii
- Department of Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
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The ATP-Dependent RNA Helicase DDX3X Modulates Herpes Simplex Virus 1 Gene Expression. J Virol 2017; 91:JVI.02411-16. [PMID: 28148788 DOI: 10.1128/jvi.02411-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/25/2017] [Indexed: 01/08/2023] Open
Abstract
The human protein DDX3X is a DEAD box ATP-dependent RNA helicase that regulates transcription, mRNA maturation, and mRNA export and translation. DDX3X concomitantly modulates the replication of several RNA viruses and promotes innate immunity. We previously showed that herpes simplex virus 1 (HSV-1), a human DNA virus, incorporates DDX3X into its mature particles and that DDX3X is required for optimal HSV-1 infectivity. Here, we show that viral gene expression, replication, and propagation depend on optimal DDX3X protein levels. Surprisingly, DDX3X from incoming viral particles was not required for the early stages of the HSV-1 infection, but, rather, the protein controlled the assembly of new viral particles. This was independent of the previously reported ability of DDX3X to stimulate interferon type I production. Instead, both the lack and overexpression of DDX3X disturbed viral gene transcription and thus subsequent genome replication. This suggests that in addition to its effect on RNA viruses, DDX3X impacts DNA viruses such as HSV-1 by an interferon-independent pathway.IMPORTANCE Viruses interact with a variety of cellular proteins to complete their life cycle. Among them is DDX3X, an RNA helicase that participates in most aspects of RNA biology, including transcription, splicing, nuclear export, and translation. Several RNA viruses and a limited number of DNA viruses are known to manipulate DDX3X for their own benefit. In contrast, DDX3X is also known to promote interferon production to limit viral propagation. Here, we show that DDX3X, which we previously identified in mature HSV-1 virions, stimulates HSV-1 gene expression and, consequently, virion assembly by a process that is independent of its ability to promote the interferon pathway.
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29
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Botlagunta M, Kollapalli B, Kakarla L, Gajarla SP, Gade SP, Dadi CL, Penumadu A, Javeed S. In vitro anti-cancer activity of doxorubicin against human RNA helicase, DDX3. Bioinformation 2016; 12:347-353. [PMID: 28246464 PMCID: PMC5311078 DOI: 10.6026/97320630012347] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/09/2016] [Accepted: 10/12/2016] [Indexed: 01/12/2023] Open
Abstract
RNA helicase, DDX3 is a multifunctional enzyme and is known to be associated with several diseases like HIV progression, brain and breast cancer. Some of the ring expanded nucleoside compounds such as REN: NZ51, fused di imidazodiazepine ring (RK33), (Z)-3-(5- (3-bromo benzylidene)-4-oxo-2-thioxothiazolidin-3-yl)-N-(2- hydroxy phenyl) propanamide compound (FE15) have been documented to inhibit DDX3 helicase activity. However, synthesis of these drugs is limited to few research groups. Prevalence of literature study, we found that doxorubicin form strong hydrogen bond interactions with crystallized form of DDX3 using in-silico molecular docking approach. To evaluate the biological inhibitory action of doxorubicin, we performed the ATPase activity assay and anti-cancer activity using H357 cancer cell lines. Results showed that doxorubicin continually declined the inorganic phosphate (Pi) release and inhibited the ATP hydrolysis by directly interacting with DDX3. Anticancer activity was detected by MTT assay. The half maximal inhibitory concentrations of doxorubicin (IC50) for H357 cancer cell line is 50 μM and also doxorubicin significantly down regulated the expression of DDX3. Taken together, our results demonstrate, that inhibition of DDX3 expression by using doxorubicin can be used as an ideal drug candidate to treat DDX3 associated cancer disorder by interacting with unique amino acid residues (Thr 198) and common amino acid residues (Tyr 200 and Thr 201).
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Affiliation(s)
- Mahendran Botlagunta
- Department of Biotechnology, K L University, Guntur, Andhra Pradesh-522502, India
- Sweety Biologicals India Private Limited,Kavali, Andhra Pradesh-524201, India
| | | | - Lavanya Kakarla
- Department of Biotechnology, K L University, Guntur, Andhra Pradesh-522502, India
| | - Siva Priya Gajarla
- Department of Biotechnology, K L University, Guntur, Andhra Pradesh-522502, India
| | - Sai Pujitha Gade
- Department of Biotechnology, K L University, Guntur, Andhra Pradesh-522502, India
| | - Chandra Lekha Dadi
- Department of Biotechnology, K L University, Guntur, Andhra Pradesh-522502, India
| | - Akhila Penumadu
- Department of Biotechnology, K L University, Guntur, Andhra Pradesh-522502, India
| | - Shaik Javeed
- Department of Biotechnology, K L University, Guntur, Andhra Pradesh-522502, India
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30
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Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, Lander ES, Sabatini DM. Identification and characterization of essential genes in the human genome. Science 2015; 350:1096-101. [PMID: 26472758 PMCID: PMC4662922 DOI: 10.1126/science.aac7041] [Citation(s) in RCA: 1112] [Impact Index Per Article: 123.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 10/01/2015] [Indexed: 12/13/2022]
Abstract
Large-scale genetic analysis of lethal phenotypes has elucidated the molecular underpinnings of many biological processes. Using the bacterial clustered regularly interspaced short palindromic repeats (CRISPR) system, we constructed a genome-wide single-guide RNA library to screen for genes required for proliferation and survival in a human cancer cell line. Our screen revealed the set of cell-essential genes, which was validated with an orthogonal gene-trap-based screen and comparison with yeast gene knockouts. This set is enriched for genes that encode components of fundamental pathways, are expressed at high levels, and contain few inactivating polymorphisms in the human population. We also uncovered a large group of uncharacterized genes involved in RNA processing, a number of whose products localize to the nucleolus. Last, screens in additional cell lines showed a high degree of overlap in gene essentiality but also revealed differences specific to each cell line and cancer type that reflect the developmental origin, oncogenic drivers, paralogous gene expression pattern, and chromosomal structure of each line. These results demonstrate the power of CRISPR-based screens and suggest a general strategy for identifying liabilities in cancer cells.
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Affiliation(s)
- Tim Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Kıvanç Birsoy
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Nicholas W Hughes
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Kevin M Krupczak
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Yorick Post
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Jenny J Wei
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Eric S Lander
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - David M Sabatini
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA. Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Abstract
Mammals have the oldest sex chromosome system known: the mammalian X and Y chromosomes evolved from ordinary autosomes beginning at least 180 million years ago. Despite their shared ancestry, mammalian Y chromosomes display enormous variation among species in size, gene content, and structural complexity. Several unique features of the Y chromosome--its lack of a homologous partner for crossing over, its functional specialization for spermatogenesis, and its high degree of sequence amplification--contribute to this extreme variation. However, amid this evolutionary turmoil many commonalities have been revealed that have contributed to our understanding of the selective pressures driving the evolution and biology of the Y chromosome. Two biological themes have defined Y-chromosome research over the past six decades: testis determination and spermatogenesis. A third biological theme begins to emerge from recent insights into the Y chromosome's roles beyond the reproductive tract--a theme that promises to broaden the reach of Y-chromosome research by shedding light on fundamental sex differences in human health and disease.
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Affiliation(s)
- Jennifer F Hughes
- Whitehead Institute, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
| | - David C Page
- Whitehead Institute, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142;
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32
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Snijders Blok L, Madsen E, Juusola J, Gilissen C, Baralle D, Reijnders M, Venselaar H, Helsmoortel C, Cho M, Hoischen A, Vissers LE, Koemans T, Wissink-Lindhout W, Eichler E, Romano C, Van Esch H, Stumpel C, Vreeburg M, Smeets E, Oberndorff K, van Bon B, Shaw M, Gecz J, Haan E, Bienek M, Jensen C, Loeys B, Van Dijck A, Innes A, Racher H, Vermeer S, Di Donato N, Rump A, Tatton-Brown K, Parker M, Henderson A, Lynch S, Fryer A, Ross A, Vasudevan P, Kini U, Newbury-Ecob R, Chandler K, Male A, Dijkstra S, Schieving J, Giltay J, van Gassen K, Schuurs-Hoeijmakers J, Tan P, Pediaditakis I, Haas S, Retterer K, Reed P, Monaghan K, Haverfield E, Natowicz M, Myers A, Kruer M, Stein Q, Strauss K, Brigatti K, Keating K, Burton B, Kim K, Charrow J, Norman J, Foster-Barber A, Kline A, Kimball A, Zackai E, Harr M, Fox J, McLaughlin J, Lindstrom K, Haude K, van Roozendaal K, Brunner H, Chung W, Kooy R, Pfundt R, Kalscheuer V, Mehta S, Katsanis N, Kleefstra T, Kleefstra T. Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling. Am J Hum Genet 2015; 97:343-52. [PMID: 26235985 DOI: 10.1016/j.ajhg.2015.07.004] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/13/2015] [Indexed: 12/22/2022] Open
Abstract
Intellectual disability (ID) affects approximately 1%-3% of humans with a gender bias toward males. Previous studies have identified mutations in more than 100 genes on the X chromosome in males with ID, but there is less evidence for de novo mutations on the X chromosome causing ID in females. In this study we present 35 unique deleterious de novo mutations in DDX3X identified by whole exome sequencing in 38 females with ID and various other features including hypotonia, movement disorders, behavior problems, corpus callosum hypoplasia, and epilepsy. Based on our findings, mutations in DDX3X are one of the more common causes of ID, accounting for 1%-3% of unexplained ID in females. Although no de novo DDX3X mutations were identified in males, we present three families with segregating missense mutations in DDX3X, suggestive of an X-linked recessive inheritance pattern. In these families, all males with the DDX3X variant had ID, whereas carrier females were unaffected. To explore the pathogenic mechanisms accounting for the differences in disease transmission and phenotype between affected females and affected males with DDX3X missense variants, we used canonical Wnt defects in zebrafish as a surrogate measure of DDX3X function in vivo. We demonstrate a consistent loss-of-function effect of all tested de novo mutations on the Wnt pathway, and we further show a differential effect by gender. The differential activity possibly reflects a dose-dependent effect of DDX3X expression in the context of functional mosaic females versus one-copy males, which reflects the complex biological nature of DDX3X mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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33
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Ahmadi Rastegar D, Sharifi Tabar M, Alikhani M, Parsamatin P, Sahraneshin Samani F, Sabbaghian M, Sadighi Gilani MA, Mohammad Ahadi A, Mohseni Meybodi A, Piryaei A, Ansari-Pour N, Gourabi H, Baharvand H, Salekdeh GH. Isoform-Level Gene Expression Profiles of Human Y Chromosome Azoospermia Factor Genes and Their X Chromosome Paralogs in the Testicular Tissue of Non-Obstructive Azoospermia Patients. J Proteome Res 2015; 14:3595-605. [PMID: 26162009 DOI: 10.1021/acs.jproteome.5b00520] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human Y chromosome has an inevitable role in male fertility because it contains many genes critical for spermatogenesis and the development of the male gonads. Any genetic variation or epigenetic modification affecting the expression pattern of Y chromosome genes may thus lead to male infertility. In this study, we performed isoform-level gene expression profiling of Y chromosome genes within the azoospermia factor (AZF) regions, their X chromosome counterparts, and few autosomal paralogues in testicular biopsies of 12 men with preserved spermatogenesis and 68 men with nonobstructive azoospermia (NOA) (40 Sertoli-cell-only syndrome (SCOS) and 28 premiotic maturation arrest (MA)). This was undertaken using quantitative real-time PCR (qPCR) at the transcript level and Western blotting (WB) and immunohistochemistry (IHC) at the protein level. We profiled the expression of 41 alternative transcripts encoded by 14 AZFa, AZFb, and AZFc region genes (USP9Y, DDX3Y, XKRY, HSFY1, CYORF15A, CYORF15B, KDM5D, EIF1AY, RPS4Y2, RBMY1A1, PRY, BPY2, DAZ1, and CDY1) as well as their X chromosome homologue transcripts and a few autosomal homologues. Of the 41 transcripts, 18 were significantly down-regulated in men with NOA when compared with those of men with complete spermatogenesis. In contrast, the expression of five transcripts increased significantly in NOA patients. Furthermore, to confirm the qPCR results at the protein level, we performed immunoblotting and IHC experiments (based on 24 commercial and homemade antibodies) that detected 10 AZF-encoded proteins. In addition, their localization in testis cell types and organelles was determined. Interestingly, the two missing proteins, XKRY and CYORF15A, were detected for the first time. Finally, we focused on the expression patterns of the significantly altered genes in 12 MA patients with successful sperm retrieval compared to those of 12 MA patients with failed sperm retrieval to predict the success of sperm retrieval in azoospermic men. We showed that HSFY1-1, HSFY1-3, BPY2-1, KDM5C2, RBMX2, and DAZL1 transcripts could be used as potential molecular markers to predict the presence of spermatozoa in MA patients. In this study, we have identified isoform level signature that can be used to discriminate effectively between MA, SCOS, and normal testicular tissues and suggests the possibility of diagnosing the presence of mature sperm cell in azoospermic men to prevent additional testicular sperm extraction (TESE) surgery.
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Affiliation(s)
- Diba Ahmadi Rastegar
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran
| | - Mehdi Sharifi Tabar
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran
| | - Mehdi Alikhani
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran
| | - Pouria Parsamatin
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran
| | | | | | | | - Ali Mohammad Ahadi
- Department of Genetics, Faculty of Science, Shahrekord University , Shahrekord, Iran
| | | | - Abbas Piryaei
- Anatomy and Cell Biology Department, School of Medicine, Shahid Beheshti University of Medical Sciences , Tehran, Iran
| | - Naser Ansari-Pour
- Faculty of New Sciences and Technology, University of Tehran , Tehran, Iran
| | | | | | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran.,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran , Karaj, Iran
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34
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Vakilian H, Mirzaei M, Sharifi Tabar M, Pooyan P, Habibi Rezaee L, Parker L, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH. DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation. J Proteome Res 2015; 14:3474-83. [PMID: 26144214 DOI: 10.1021/acs.jproteome.5b00512] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although it is apparent that chromosome complement mediates sexually dimorphic expression patterns of some proteins that lead to functional differences, there has been insufficient evidence following the manipulation of the male-specific region of the Y chromosome (MSY) gene expression during neural development. In this study, we profiled the expression of 23 MSY genes and 15 of their X-linked homologues during neural cell differentiation of NTERA-2 human embryonal carcinoma cell line (NT2) cells in three different developmental stages using qRT-PCR, Western blotting, and immunofluorescence. The expression level of 12 Y-linked genes significantly increased over neural differentiation, including RBMY1, EIF1AY, DDX3Y, HSFY1, BPY2, PCDH11Y, UTY, RPS4Y1, USP9Y, SRY, PRY, and ZFY. We showed that siRNA-mediated knockdown of DDX3Y, a DEAD box RNA helicase enzyme, in neural progenitor cells impaired cell cycle progression and increased apoptosis, consequently interrupting differentiation. Label-free quantitative shotgun proteomics based on a spectral counting approach was then used to characterize the proteomic profile of the cells after DDX3Y knockdown. Among 917 reproducibly identified proteins detected, 71 proteins were differentially expressed following DDX3Y siRNA treatment compared with mock treated cells. Functional grouping indicated that these proteins were involved in cell cycle, RNA splicing, and apoptosis, among other biological functions. Our results suggest that MSY genes may play an important role in neural differentiation and demonstrate that DDX3Y could play a multifunctional role in neural cell development, probably in a sexually dimorphic manner.
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Affiliation(s)
- Haghighat Vakilian
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Mehdi Sharifi Tabar
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Paria Pooyan
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Lida Habibi Rezaee
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Lindsay Parker
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Hamid Gourabi
- Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture , Sharif Esfahani Blvd, Park Street, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran.,Seed and Plant Improvement Institute's Campus, Agricultural Biotechnology Research Institute of Iran , Mahdasht Road, Karaj, Iran
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35
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Li G, Feng T, Pan W, Shi X, Dai J. DEAD-box RNA helicase DDX3X inhibits DENV replication via regulating type one interferon pathway. Biochem Biophys Res Commun 2014; 456:327-32. [PMID: 25437271 DOI: 10.1016/j.bbrc.2014.11.080] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/22/2014] [Indexed: 01/01/2023]
Abstract
Dengue virus (DENV) is a mosquito-borne virus that threatens approximately 2.5 billion people worldwide. Vaccines against DENV are currently unavailable. DEAD-box RNA helicases (DDXs) have been reported to participate in viral replication and host innate immune response. In the present study, we analyzed the role of 40 DDX proteins during DENV replication. Among these proteins, DDX3X showed antiviral effect against DENV infection. Viral replication significantly increased in DDX3X-silenced cells compared with the controls. The interferon (IFN)-β transcription level decreased during the early stage of DENV infection in DDX3X-silenced cells compared with that in the controls. DDX3X could stimulate IFN-β transcription through the IRF3 and the NFκB branches in DENV-infected cells. Our data imply that DDX3X, a member of DEAD-box RNA helicase, is necessary for IFN production and could inhibit DENV replication.
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Affiliation(s)
- Guanghao Li
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou City, Jiangsu Province, People's Republic of China
| | - Tingting Feng
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou City, Jiangsu Province, People's Republic of China.
| | - Wen Pan
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou City, Jiangsu Province, People's Republic of China
| | - Xiaohong Shi
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou City, Jiangsu Province, People's Republic of China
| | - Jianfeng Dai
- Institute of Biology and Medical Sciences, Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou City, Jiangsu Province, People's Republic of China.
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36
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Rauschendorf MA, Zimmer J, Ohnmacht C, Vogt PH. DDX3X, the X homologue of AZFa gene DDX3Y, expresses a complex pattern of transcript variants only in the male germ line. Mol Hum Reprod 2014; 20:1208-22. [PMID: 25208899 DOI: 10.1093/molehr/gau081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
DDX3X, the functional X homologue of the major AZFa gene, DDX3Y, belongs to the highly conserved PL10-subfamily of DEAD-box RNA helicase genes which are functionally conserved from yeast to man. They are mainly involved in cell cycle control and translation initiation control of gene transcripts with long 5'UTR extensions containing complex secondary structures. Interestingly, in humans both gene copies were found to be expressed at different phases of human spermatogenesis. Whereas DDX3Y transcripts are translated only in premeiotic male germ cells, the DDX3X protein is expressed only in postmeiotic spermatids. In this study, we found that the major class of DDX3X transcripts in human testis become activated first after meiosis and at a specific core promoter not active in somatic tissues and not present upstream of the DDX3Y homologue. Two alternative 5'UTR transcript lengths are subsequently produced by an additional testis-specific 5'UTR splicing event. Both transcripts are mainly processed for polyadenylation in their proximal 3'UTR. A minor transcript class starting at the same male germ line-specific core promoter produces primary transcripts with an extremely long 3'UTR (∼ 17 kb), which is subsequently spliced at distinct sites resulting in six short 3'UTR splice variants (I-VI). Comparative analyses of the DDX3X transcripts in mouse and primates revealed that this complex pattern of male germ line-specific transcript variants first evolved in primates. Our data thus suggest complex translational control mechanism(s) for the human DDX3X gene locus functioning only in the male germ line and resulting in expression of its protein only in the postmeiotic spermatids.
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Affiliation(s)
- Marc-Alexander Rauschendorf
- Reproduction Genetics Unit, Department of Gynecological Endocrinology & Reproductive Medicine, University of Heidelberg, Heidelberg, Germany Present address: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Program of Functional Genomics and Cancer, CNRS UDS UMR 7104, INSERM U 964, 67404 Illkirch Cedex, France
| | - Jutta Zimmer
- Reproduction Genetics Unit, Department of Gynecological Endocrinology & Reproductive Medicine, University of Heidelberg, Heidelberg, Germany
| | - Caroline Ohnmacht
- Reproduction Genetics Unit, Department of Gynecological Endocrinology & Reproductive Medicine, University of Heidelberg, Heidelberg, Germany
| | - Peter H Vogt
- Reproduction Genetics Unit, Department of Gynecological Endocrinology & Reproductive Medicine, University of Heidelberg, Heidelberg, Germany
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Senissar M, Le Saux A, Belgareh-Touzé N, Adam C, Banroques J, Tanner NK. The DEAD-box helicase Ded1 from yeast is an mRNP cap-associated protein that shuttles between the cytoplasm and nucleus. Nucleic Acids Res 2014; 42:10005-22. [PMID: 25013175 PMCID: PMC4150762 DOI: 10.1093/nar/gku584] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 06/02/2014] [Accepted: 06/17/2014] [Indexed: 01/13/2023] Open
Abstract
The DEAD-box helicase Ded1 is an essential yeast protein that is closely related to mammalian DDX3 and to other DEAD-box proteins involved in developmental and cell cycle regulation. Ded1 is considered to be a translation-initiation factor that helps the 40S ribosome scan the mRNA from the 5' 7-methylguanosine cap to the AUG start codon. We used IgG pull-down experiments, mass spectrometry analyses, genetic experiments, sucrose gradients, in situ localizations and enzymatic assays to show that Ded1 is a cap-associated protein that actively shuttles between the cytoplasm and the nucleus. NanoLC-MS/MS analyses of purified complexes show that Ded1 is present in both nuclear and cytoplasmic mRNPs. Ded1 physically interacts with purified components of the nuclear CBC and the cytoplasmic eIF4F complexes, and its enzymatic activity is stimulated by these factors. In addition, we show that Ded1 is genetically linked to these factors. Ded1 comigrates with these proteins on sucrose gradients, but treatment with rapamycin does not appreciably alter the distribution of Ded1; thus, most of the Ded1 is in stable mRNP complexes. We conclude that Ded1 is an mRNP cofactor of the cap complex that may function to remodel the different mRNPs and thereby regulate the expression of the mRNAs.
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Affiliation(s)
- Meriem Senissar
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France Université Paris-Sud, Ecole Doctorale 426 GGC, Orsay, France
| | - Agnès Le Saux
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France
| | - Naïma Belgareh-Touzé
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, CNRS UMR8226 (FRE3354), UPMC, Paris 75005, France
| | - Céline Adam
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France
| | - Josette Banroques
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France
| | - N Kyle Tanner
- Expression Génétique Microbienne, CNRS FRE3630 (UPR9073), in association with Université Paris Diderot, Sorbonne Paris Cité, Paris 75005, France
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Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho TJ, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Alföldi J, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 2014; 508:494-9. [PMID: 24759411 PMCID: PMC4139287 DOI: 10.1038/nature13206] [Citation(s) in RCA: 464] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/06/2014] [Indexed: 12/31/2022]
Abstract
The human X and Y chromosomes evolved from an ordinary pair of autosomes, but
millions of years ago genetic decay ravaged the Y chromosome, and only three percent of
its ancestral genes survived. We reconstructed the evolution of the Y chromosome across
eight mammals to identify biases in gene content and the selective pressures that
preserved the surviving ancestral genes. Our findings indicate that survival was
non-random, and in two cases, convergent across placental and marsupial mammals. We
conclude that the Y chromosome's gene content became specialized through selection
to maintain the ancestral dosage of homologous X-Y gene pairs that function as broadly
expressed regulators of transcription, translation and protein stability. We propose that
beyond its roles in testis determination and spermatogenesis, the Y chromosome is
essential for male viability, and plays unappreciated roles in Turner syndrome and in
phenotypic differences between the sexes in health and disease.
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Affiliation(s)
- Daniel W Bellott
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Jennifer F Hughes
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Helen Skaletsky
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Laura G Brown
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Tatyana Pyntikova
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Ting-Jan Cho
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Natalia Koutseva
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Sara Zaghlul
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Susie Rock
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Colin Kremitzki
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Donna Morton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lora Lewis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Qiaoyan Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer Watt
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael Holder
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sandy Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lynne Nazareth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jessica Alföldi
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Steve Rozen
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - David C Page
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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Chen Q, Liu Q, Liu D, Wang D, Chen H, Xiao S, Fang L. Molecular cloning, functional characterization and antiviral activity of porcine DDX3X. Biochem Biophys Res Commun 2013; 443:1169-75. [PMID: 24380861 DOI: 10.1016/j.bbrc.2013.12.098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 12/19/2013] [Indexed: 01/18/2023]
Abstract
Human DDX3X is a newly discovered DEAD-box RNA helicase. In addition to involvement of eukaryotic gene expression regulation, human DDX3X has recently been demonstrated to be a critical molecule in innate immune signaling pathways and to contribute to type I interferon (IFN) induction. In the present study, porcine DDX3X was cloned by RT-PCR from PK-15 cells and its function in regulating IFN-β was characterized. The putative porcine DDX3X ORF encodes 662 amino acids possessing several conserved motifs. Sequence alignments indicated that porcine DDX3X has high identity at the amino acid level to those of horse (96.7%), mouse (97.6%), cattle (98.5%), dog (98.6%) and human (98.9%). Ectopic expression of porcine DDX3X significantly activated IFN-β expression, whereas knockdown of porcine DDX3X inhibited dsRNA- or Sendai virus (SeV)-induced IFN-β. Furthermore, porcine DDX3X co-localized with IPS-1, TBK1 and IKKε, and enhanced IFN-β promoter activation induced by these molecules. We also investigated the role of porcine DDX3X during porcine reproductive and respiratory syndrome virus (PRRSV) infection and found that overexpression of DDX3X significantly inhibited PRRSV replication, indicating that DDX3X is a potential antiviral agent.
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Affiliation(s)
- Quangang Chen
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin Liu
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Dezhi Liu
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Dang Wang
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Huanchun Chen
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaobo Xiao
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Liurong Fang
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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Sekiguchi T, Sasaki H, Kurihara Y, Watanabe S, Moriyama D, Kurose N, Matsuki R, Yamazaki K, Saeki M. New methods for species and sex determination in three sympatric Mustelids, Mustela itatsi, Mustela sibirica and Martes melampus. Mol Ecol Resour 2013; 10:1089-91. [PMID: 21565122 DOI: 10.1111/j.1755-0998.2010.02842.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We developed novel species and sex determination methods for three Japanese mustelid species. We used DDX3Y to determine sex and generated a primer set to amplify both DDX3X and DDX3Y DNA in Mustela itatsi, M. sibirica and Martes melampus. To determine species and sex simultaneously, we generated fluorescence-labelled primers that give different fragment lengths at D-loop, DDX3X and DDX3Y of these three species using a DNA sequencer.
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Affiliation(s)
- T Sekiguchi
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Robert F, Pelletier J. Perturbations of RNA helicases in cancer. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:333-49. [PMID: 23658027 DOI: 10.1002/wrna.1163] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Helicases are implicated in most stages of the gene expression pathway, ranging from DNA replication, RNA transcription, splicing, RNA transport, ribosome biogenesis, mRNA translation, RNA storage and decay. These enzymes utilize energy derived from nucleotide triphosphate hydrolysis to remodel ribonucleoprotein complexes, RNA, or DNA and in this manner affect the information content or output of RNA. Several RNA helicases have been implicated in the oncogenic process--either through altered expression levels, mutations, or due to their role in pathways required for tumor initiation, progression, maintenance, or chemosensitivity. The purpose of this review is to highlight those RNA helicases for which there is significant evidence implicating them in cancer biology.
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Affiliation(s)
- Francis Robert
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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Kasim V, Wu S, Taira K, Miyagishi M. Determination of the role of DDX3 a factor involved in mammalian RNAi pathway using an shRNA-expression library. PLoS One 2013; 8:e59445. [PMID: 23527197 PMCID: PMC3602433 DOI: 10.1371/journal.pone.0059445] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 02/14/2013] [Indexed: 11/18/2022] Open
Abstract
RNA interference (RNAi) is an endogenous RNA-destruction phenomenon induced by certain double-stranded RNAs (dsRNAs). In RNAi, dsRNAs are processed into small interfering RNAs (siRNAs) which in turn trigger the cleavage of the target mRNA. Here, using a short hairpin RNA-expression library, we identified a DEAD-box helicase 3, DDX3, as an essential factor involved in RNAi pathway and revealed that DDX3 is colocalized with Ago2, an essential factor in RNAi pathway that cleaves target mRNA. Results of experiments with a dominant negative mutant of DDX3 further confirmed that this factor affects the RNAi activity. Together, DDX3 functions to assure mammalian RNAi pathway. Together, our results indicate that DDX3 is a new key molecule to understand the molecular mechanism underlying RNAi pathway in mammals.
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Affiliation(s)
- Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kazunari Taira
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
- Tokyo University and Graduate School of Social Welfare, Tokyo, Japan
| | - Makoto Miyagishi
- Molecular Composite Medicine Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- * E-mail:
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Sun M, Zhou T, Jonasch E, Jope RS. DDX3 regulates DNA damage-induced apoptosis and p53 stabilization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1489-97. [PMID: 23470959 DOI: 10.1016/j.bbamcr.2013.02.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 02/04/2013] [Accepted: 02/21/2013] [Indexed: 12/19/2022]
Abstract
The DEAD box protein family member DDX3 was previously identified as an inhibitor of death receptor-mediated extrinsic apoptotic signaling. However, there had been no studies of the role of DDX3 in regulating the other major type of apoptosis, intrinsic apoptotic signaling, which was examined here. Intrinsic apoptosis was induced in MCF-7 cells by treatment with staurosporine, a general kinase inhibitor, thapsigargin, which induces endoplasmic reticulum (ER) stress, and camptothecin, which causes DNA damage. Each of these treatments caused time-dependent activation of caspase-7, the predominant executioner caspase in these cells. Depletion of DDX3 using shRNA did not alter apoptotic responses to staurosporine or thapsigargin. However, caspase-7 activation induced by camptothecin was regulated by DDX3 in a manner dependent on the functional status of p53. Depletion of DDX3 abrogated camptothecin-induced caspase-7 activation in MCF-7 cells expressing functional wild-type p53, but oppositely potentiated camptothecin-mediated caspase activation in cells expressing mutant or non-functional p53, which was accompanied by increased activation of the extrinsic apoptotic signaling initiator caspase-8. In MCF-7 cells, depletion of DDX3 reduced by more than 50% camptothecin-induced p53 accumulation, and this effect was blocked by inhibition of the proteasome with MG132, indicating that DDX3 regulates p53 not at expression level but rather its stabilization after DNA damage. Co-immunoprecipitation experiments demonstrated that DDX3 associates with p53, and overexpression of DDX3 was sufficient to double the accumulation of p53 in the nucleus after DNA damage. Thus, DDX3 associates with p53, increases p53 accumulation, and positively regulates camptothecin-induced apoptotic signaling in cells expressing functional wild-type p53, whereas in cells expressing mutant or non-functional p53 DDX3 inhibits activation of the extrinsic apoptotic pathway to reduce caspase activation. These results demonstrate that DDX3 not only regulates extrinsic apoptotic signaling, as previously reported, but also selectively regulates intrinsic apoptotic signaling following DNA damage.
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Affiliation(s)
- Mianen Sun
- Department of Genitourinary Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
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Card CJ, Anderson EJ, Zamberlan S, Krieger KE, Kaproth M, Sartini BL. Cryopreserved Bovine Spermatozoal Transcript Profile as Revealed by High-Throughput Ribonucleic Acid Sequencing1. Biol Reprod 2013; 88:49. [DOI: 10.1095/biolreprod.112.103788] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Pradhan A, Khalaf H, Ochsner SA, Sreenivasan R, Koskinen J, Karlsson M, Karlsson J, McKenna NJ, Orbán L, Olsson PE. Activation of NF-κB protein prevents the transition from juvenile ovary to testis and promotes ovarian development in zebrafish. J Biol Chem 2012; 287:37926-38. [PMID: 22988238 PMCID: PMC3488064 DOI: 10.1074/jbc.m112.386284] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Testis differentiation in zebrafish involves juvenile ovary to testis transformation initiated by an apoptotic wave. The molecular regulation of this transformation process is not fully understood. NF-κB is activated at an early stage of development and has been shown to interact with steroidogenic factor-1 in mammals, leading to the suppression of anti-Müllerian hormone (Amh) gene expression. Because steroidogenic factor-1 and Amh are important for proper testis development, NF-κB-mediated induction of anti-apoptotic genes could, therefore, also play a role in zebrafish gonad differentiation. The aim of this study was to examine the potential role of NF-κB in zebrafish gonad differentiation. Exposure of juvenile zebrafish to heat-killed Escherichia coli activated the NF-κB pathways and resulted in an increased ratio of females from 30 to 85%. Microarray and quantitative real-time-PCR analysis of gonads showed elevated expression of NF-κB-regulated genes. To confirm the involvement of NF-κB-induced anti-apoptotic effects, zebrafish were treated with sodium deoxycholate, a known inducer of NF-κB or NF-κB activation inhibitor (NAI). Sodium deoxycholate treatment mimicked the effect of heat-killed bacteria and resulted in an increased proportion of females from 25 to 45%, whereas the inhibition of NF-κB using NAI resulted in a decrease in females from 45 to 20%. This study provides proof for an essential role of NF-κB in gonadal differentiation of zebrafish and represents an important step toward the complete understanding of the complicated process of sex differentiation in this species and possibly other cyprinid teleosts as well.
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Affiliation(s)
- Ajay Pradhan
- Department of Biology, Örebro Life Science Center, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
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Navarro-Costa P. Sex, rebellion and decadence: the scandalous evolutionary history of the human Y chromosome. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1851-63. [PMID: 22542510 DOI: 10.1016/j.bbadis.2012.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 03/27/2012] [Accepted: 04/10/2012] [Indexed: 11/19/2022]
Abstract
It can be argued that the Y chromosome brings some of the spirit of rock&roll to our genome. Equal parts degenerate and sex-driven, the Y has boldly rebelled against sexual recombination, one of the sacred pillars of evolution. In evolutionary terms this chromosome also seems to have adopted another of rock&roll's mottos: living fast. Yet, it appears to have refused to die young. In this manuscript the Y chromosome will be analyzed from the intersection between structural, evolutionary and functional biology. Such integrative approach will present the Y as a highly specialized product of a series of remarkable evolutionary processes. These led to the establishment of a sex-specific genomic niche that is maintained by a complex balance between selective pressure and the genetic diversity introduced by intrachromosomal recombination. Central to this equilibrium is the "polish or perish" dilemma faced by the male-specific Y genes: either they are polished by the acquisition of male-related functions or they perish via the accumulation of inactivating mutations. Thus, understanding to what extent the idiosyncrasies of Y recombination may impact this chromosome's role in sex determination and male germline functions should be regarded as essential for added clinical insight into several male infertility phenotypes. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.
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Gueler B, Sonne SB, Zimmer J, Hilscher B, Hilscher W, Græm N, Rajpert-De Meyts E, Vogt PH. AZFa protein DDX3Y is differentially expressed in human male germ cells during development and in testicular tumours: new evidence for phenotypic plasticity of germ cells. Hum Reprod 2012; 27:1547-55. [PMID: 22466863 DOI: 10.1093/humrep/des047] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND DDX3Y (DBY), located within AZoospermia Factor a (AZFa) region of the human Y chromosome (Yq11), encodes a conserved DEAD-box RNA helicase expressed only in germ cells and with a putative function at G1-S phase of the cell cycle. Deletion of AZFa results most often in germ cell aplasia, i.e. Sertoli-cell-only syndrome. To investigate the function of DDX3Y during human spermatogenesis, we examined its expression during development and maturation of the testis and in several types of testicular germ cell tumours (TGCTs), including the pre-invasive carcinoma in situ (CIS) precursor cells which are believed to originate from fetal gonocytes. METHODS DDX3Y protein expression was analysed during development in different tissues by western blotting. The localization of DDX3Y in normal fetal and prepubertal testis tissue of different ages as well as in a series of distinct TGCT tissue samples (CIS, classical seminoma, spermatocytic seminoma, teratoma and embryonal carcinoma) was performed by immunohistochemistry. RESULTS Germ cell-specific expression of DDX3Y protein was revealed in fetal prospermatogonia but not in gonocytes and not before the 17th gestational week. After birth, DDX3Y was expressed at first only in the nuclei of Ap spermatogonia, then also in the cytoplasm similarly to that seen after puberty. In CIS cells, DDX3Y was highly expressed and located predominantly in the nuclei. In invasive TGCT, significant DDX3Y expression was found in seminomas of the classical and spermatocytic type, but not in somatically differentiated non-seminomas, consistent with its germ-cell specific function. CONCLUSIONS The fetal germ cell DDX3Y expression suggests a role in early spermatogonial proliferation and implies that, in men with AZFa deletion, germ cell depletion may begin prenatally. The strong expression of DDX3Y in CIS cells, but not in gonocytes, indicates phenotypic plasticity of CIS cells and suggests partial maturation to spermatogonia, likely due to their postpubertal microenvironment.
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Affiliation(s)
- B Gueler
- Department of Gynaecological Endocrinology and Reproductive Medicine, University of Heidelberg, Heidelberg, Germany
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Schröder PC, Fernández-Irigoyen J, Bigaud E, Serna A, Renández-Alcoceba R, Lu SC, Mato JM, Prieto J, Corrales FJ. Proteomic analysis of human hepatoma cells expressing methionine adenosyltransferase I/III: Characterization of DDX3X as a target of S-adenosylmethionine. J Proteomics 2012; 75:2855-68. [PMID: 22270009 DOI: 10.1016/j.jprot.2012.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/03/2012] [Accepted: 01/05/2012] [Indexed: 02/07/2023]
Abstract
Methionine adenosyltransferase I/III (MATI/III) synthesizes S-adenosylmethionine (SAM) in quiescent hepatocytes. Its activity is compromised in most liver diseases including liver cancer. Since SAM is a driver of hepatocytes fate we have studied the effect of re-expressing MAT1A in hepatoma Huh7 cells using proteomics. MAT1A expression leads to SAM levels close to those found in quiescent hepatocytes and induced apoptosis. Normalization of intracellular SAM induced alteration of 128 proteins identified by 2D-DIGE and gel-free methods, accounting for deregulation of central cellular functions including apoptosis, cell proliferation and survival. Human Dead-box protein 3 (DDX3X), a RNA helicase regulating RNA splicing, export, transcription and translation was down-regulated upon MAT1A expression. Our data support the regulation of DDX3X levels by SAM in a concentration and time dependent manner. Consistently, DDX3X arises as a primary target of SAM and a principal intermediate of its antitumoral effect. Based on the parallelism between SAM and DDX3X along the progression of liver disorders, and the results reported here, it is tempting to suggest that reduced SAM in the liver may lead to DDX3X up-regulation contributing to the pathogenic process and that replenishment of SAM might prove to have beneficial effects, at least in part by reducing DDX3X levels. This article is part of a Special Issue entitled: Proteomics: The clinical link.
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Affiliation(s)
- Paul C Schröder
- Division of Hepatology and Gene Therapy, CIMA, University of Navarra, 31008 Pamplona, Spain
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Liu J, Henao-Mejia J, Liu H, Zhao Y, He JJ. Translational regulation of HIV-1 replication by HIV-1 Rev cellular cofactors Sam68, eIF5A, hRIP, and DDX3. J Neuroimmune Pharmacol 2011; 6:308-21. [PMID: 21360055 DOI: 10.1007/s11481-011-9265-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 02/14/2011] [Indexed: 10/18/2022]
Abstract
Nuclear export and translation of HIV-1 RNA are two important posttranscriptional events for HIV-1 gene expression and replication. HIV-1 Rev functions to export unspliced and incompletely spliced HIV-1 RNA from the nucleus to the cytoplasm; it requires interaction with several cellular cofactors such as Sam68, eIF5A, hRIP, and DDX3. Meanwhile, some studies have also implicated Rev and some of its cofactors such as Sam68 in HIV-1 RNA translation. Thus, in this study, we aimed to characterize the potential function of all these four Rev cofactors in HIV-1 RNA translation. Ectopic expression, siRNA knockdown, and trans-complementation assays confirmed that all these cofactors were very important for HIV-1 gene expression and production through Rev and, accordingly, Rev-dependent reporter gene expression. Importantly, these studies revealed for the first time that each of these cofactors also regulated Rev-independent reporter gene expression. To directly determine the roles of these cofactors in HIV-1 RNA translation, we designed and synthesized a full-length capped HIV-1 RNA in vitro, transfected it into cells to bypass the RNA nuclear export step, and determined HIV-1 Gag expression from the cytoplasmic RNA in the cells that had ectopically expressed or siRNA knocked down cofactors. Gag expression was found to closely correlate with the expression levels of all these cofactors. Furthermore, we took advantage of a HIV-1 internal ribosomal entry site (IRES)-based bicistronic reporter gene assay and determined the effects of these cofactors on cap-independent IRES-mediated HIV-1 translation. The results showed that DDX3, eIF5A, and hRIP enhanced HIV-1 IRES-mediated translation, whereas Sam68 did not. Taken together, these results show that HIV-1 Rev cofactors Sam68, eIF5A, hRIP, and DDX3 also function in the translation of HIV-1 RNA and suggest that the regulatory mechanisms of HIV-1 RNA translation are likely different among these cofactors.
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Affiliation(s)
- Jinfeng Liu
- The First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710061, People's Republic of China
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