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Sahoo B, Gupta MK. Transcriptome Analysis Reveals Spermatogenesis-Related CircRNAs and LncRNAs in Goat Spermatozoa. Biochem Genet 2024; 62:2010-2032. [PMID: 37815627 DOI: 10.1007/s10528-023-10520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/05/2023] [Indexed: 10/11/2023]
Abstract
Mammalian spermatozoa comprises both coding and non-coding RNAs, which are traditionally believed to be a residual of spermatogenesis. The differential expression level of spermatozoal RNAs is also observed between fertile and infertile human, thereby anticipated as potential molecular marker of male fertility. This study investigated the transcriptome profile of goat (Capra hircus) spermatozoa. The sperm transcriptome was analyzed by three different methods viz. RLM-RACE, long-read RNA sequencing (RNAseq) in Nanopore™ platform, and short-read RNAseq in Illumina™ platform. The Illumina™ sequencing discovered 16,604 transcripts with 357 mRNAs having FPKM (fragments per kilobase per million mapped reads) of more than five. The spermatozoal RNA suite included mRNA (94%), rRNA (3%), miscRNA (1%), circRNA (1%), miRNA (1%), etc. This study also predicted circRNAs (127), lncRNAs (655), and imprinted genes (160) that have potential role in male reproduction. The gene ontology analysis revealed the involvement of spermatozoal RNA in regulating male meiosis (TET3, STAT5B), capacitation (ACRBP, CATSPER4), sperm motility (GAS8, TEKT2), spermatogenesis (ADAMTS2, CREB3L4), etc. The spermatozoal RNA were also associated with different biological pathways viz. Wnt signaling pathway, cAMP signaling pathway, AMPK signaling pathway, and MAPK signaling pathways having potential role in spermatogenesis. Overall, this study enlightened the suite of spRNA transcripts in goat and their relevance in male fertility for diagnostic approach.
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Affiliation(s)
- Bijayalaxmi Sahoo
- Gene Manipulation Laboratory, Department of Biotechnology and Medical Engineering, Centre for Bioinformatics and Computational Biology, National Institute of Technology Rourkela, Rourkela, Odisha, 769 008, India
| | - Mukesh Kumar Gupta
- Gene Manipulation Laboratory, Department of Biotechnology and Medical Engineering, Centre for Bioinformatics and Computational Biology, National Institute of Technology Rourkela, Rourkela, Odisha, 769 008, India.
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2
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Klarić ML, Marić T, Žunić L, Trgovec-Greif L, Rokić F, Fiolić A, Šorgić AM, Ježek D, Vugrek O, Jakovčević A, Barbalić M, Belužić R, Katušić Bojanac A. FANCM Gene Variants in a Male Diagnosed with Sertoli Cell-Only Syndrome and Diffuse Astrocytoma. Genes (Basel) 2024; 15:707. [PMID: 38927643 PMCID: PMC11202954 DOI: 10.3390/genes15060707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Azoospermia is a form of male infertility characterized by a complete lack of spermatozoa in the ejaculate. Sertoli cell-only syndrome (SCOS) is the most severe form of azoospermia, where no germ cells are found in the tubules. Recently, FANCM gene variants were reported as novel genetic causes of spermatogenic failure. At the same time, FANCM variants are known to be associated with cancer predisposition. We performed whole-exome sequencing on a male patient diagnosed with SCOS and a healthy father. Two compound heterozygous missense mutations in the FANCM gene were found in the patient, both being inherited from his parents. After the infertility assessment, the patient was diagnosed with diffuse astrocytoma. Immunohistochemical analyses in the testicular and tumor tissues of the patient and adequate controls showed, for the first time, not only the existence of a cytoplasmic and not nuclear pattern of FANCM in astrocytoma but also in non-mitotic neurons. In the testicular tissue of the SCOS patient, cytoplasmic anti-FANCM staining intensity appeared lower than in the control. Our case report raises a novel possibility that the infertile carriers of FANCM gene missense variants could also be prone to cancer development.
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Affiliation(s)
| | - Tihana Marić
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia;
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
| | - Lucija Žunić
- Genom Ltd., Ilica 190, 10000 Zagreb, Croatia; (M.L.K.); (L.Ž.); (A.F.); (M.B.)
| | - Lovro Trgovec-Greif
- Laboratory for Advanced Genomics, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.T.-G.); (F.R.); (O.V.)
| | - Filip Rokić
- Laboratory for Advanced Genomics, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.T.-G.); (F.R.); (O.V.)
| | - Ana Fiolić
- Genom Ltd., Ilica 190, 10000 Zagreb, Croatia; (M.L.K.); (L.Ž.); (A.F.); (M.B.)
| | - Ana Merkler Šorgić
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
| | - Davor Ježek
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
| | - Oliver Vugrek
- Laboratory for Advanced Genomics, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.T.-G.); (F.R.); (O.V.)
| | - Antonia Jakovčević
- Department of Pathology, University Hospital Center Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia
| | - Maja Barbalić
- Genom Ltd., Ilica 190, 10000 Zagreb, Croatia; (M.L.K.); (L.Ž.); (A.F.); (M.B.)
- Faculty of Science, University of Split, Rudjera Bošković 33, 21000 Split, Croatia
| | - Robert Belužić
- Laboratory for Metabolism and Aging, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Ana Katušić Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia;
- Center of Excellence for Reproductive and Regenerative medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (A.M.Š.); (D.J.)
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3
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Xu H, Zhang Y, Wang C, Fu Z, Lv J, Yang Y, Zhang Z, Qi Y, Meng K, Yuan J, Wang X. Research progress on the fanconi anemia signaling pathway in non-obstructive azoospermia. Front Endocrinol (Lausanne) 2024; 15:1393111. [PMID: 38846492 PMCID: PMC11153779 DOI: 10.3389/fendo.2024.1393111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
Non-obstructive azoospermia (NOA) is a disease characterized by spermatogenesis failure and comprises phenotypes such as hypospermatogenesis, mature arrest, and Sertoli cell-only syndrome. Studies have shown that FA cross-linked anemia (FA) pathway is closely related to the occurrence of NOA. There are FA gene mutations in male NOA patients, which cause significant damage to male germ cells. The FA pathway is activated in the presence of DNA interstrand cross-links; the key step in activating this pathway is the mono-ubiquitination of the FANCD2-FANCI complex, and the activation of the FA pathway can repair DNA damage such as DNA double-strand breaks. Therefore, we believe that the FA pathway affects germ cells during DNA damage repair, resulting in minimal or even disappearance of mature sperm in males. This review summarizes the regulatory mechanisms of FA-related genes in male azoospermia, with the aim of providing a theoretical reference for clinical research and exploration of related genes.
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Affiliation(s)
- Haohui Xu
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Yixin Zhang
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Caiqin Wang
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Zhuoyan Fu
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Clinical Medicine, Jining Medical University, Jining, China
| | - Jing Lv
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Clinical Medicine, Jining Medical University, Jining, China
| | - Yufang Yang
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Mental Health, Jining Medical University, Jining, China
| | - Zihan Zhang
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Yuanmin Qi
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
- College of Clinical Medicine, Jining Medical University, Jining, China
| | - Kai Meng
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
| | - Jinxiang Yuan
- Lin He’s Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China
| | - Xiaomei Wang
- College of Basic Medicine, Jining Medical University, Jining, China
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Chi RPA, Xu X, Li JL, Xu X, Hu G, Brown P, Willson C, Kirsanov O, Geyer C, Huang CL, Morgan M, DeMayo F. WNK1 is required during male pachynema to sustain fertility. iScience 2023; 26:107616. [PMID: 37694147 PMCID: PMC10485039 DOI: 10.1016/j.isci.2023.107616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/04/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023] Open
Abstract
WNK1 is an important regulator in many physiological functions, yet its role in male reproduction is unexplored. In the male germline, WNK1 is upregulated in preleptotene spermatocytes indicating possible function(s) in spermatogenic meiosis. Indeed, deletion of Wnk1 in mid-pachytene spermatocytes using the Wnt7a-Cre mouse led to male sterility which resembled non-obstructive azoospermia in humans, where germ cells failed to complete spermatogenesis and produced no sperm. Mechanistically, we found elevated MTOR expression and signaling in the Wnk1-depleted spermatocytes. As MTOR is a central mediator of translation, we speculated that translation may be accelerated in these spermatocytes. Supporting this, we found the acrosome protein, ACRBP to be prematurely expressed in the spermatocytes with Wnk1 deletion. Our study uncovered an MTOR-regulating factor in the male germline with potential implications in translation, and future studies will aim to understand how WNK1 regulates MTOR activity and impact translation on a broader spectrum.
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Affiliation(s)
- Ru-pin Alicia Chi
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Xiaojiang Xu
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Xin Xu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Paula Brown
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Cynthia Willson
- Integrated Laboratory Systems LLC, Research Triangle Park, NC 27709, USA
| | - Oleksandr Kirsanov
- Department of Anatomy & Cell Biology at the Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Christopher Geyer
- Department of Anatomy & Cell Biology at the Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC 27834, USA
| | - Chou-Long Huang
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa, IA 52242, USA
| | - Marcos Morgan
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Francesco DeMayo
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC 27709, USA
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5
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Vanni VS, Campo G, Cioffi R, Papaleo E, Salonia A, Viganò P, Lambertini M, Candiani M, Meirow D, Orvieto R. The neglected members of the family: non-BRCA mutations in the Fanconi anemia/BRCA pathway and reproduction. Hum Reprod Update 2022; 28:296-311. [PMID: 35043201 DOI: 10.1093/humupd/dmab045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND BReast CAncer (BRCA) genes are extensively studied in the context of fertility and reproductive aging. BRCA proteins are part of the DNA repair Fanconi anemia (FA)/BRCA pathway, in which more than 20 proteins are implicated. According to which gene is mutated and which interactions are lost owing to the mutation, carriers and patients with monoallelic or biallelic FA/BRCA mutations exhibit very different phenotypes, from overt FA to cancer predisposition or no pathological implications. The effect of the so far neglected non-BRCA FA mutations on fertility also deserves consideration. OBJECTIVE AND RATIONALE As improved treatments allow a longer life expectancy in patients with biallelic FA mutations and overt FA, infertility is emerging as a predominant feature. We thus reviewed the mechanisms for such a manifestation, as well as whether they also occur in monoallelic carriers of FA non-BRCA mutations. SEARCH METHODS Electronic databases PUBMED, EMBASE and CENTRAL were searched using the following term: 'fanconi' OR 'FANC' OR 'AND' 'fertility' OR 'pregnancy' OR 'ovarian reserve' OR 'spermatogenesis' OR 'hypogonadism'. All pertinent reports in the English-language literature were retrieved until May 2021 and the reference lists were systematically searched in order to identify any potential additional studies. OUTCOMES Biallelic FA mutations causing overt FA disease are associated with premature ovarian insufficiency (POI) occurring in the fourth decade in women and with primary non-obstructive azoospermia (NOA) in men. Hypogonadism in FA patients seems mainly associated with a defect in primordial germ cell proliferation in fetal life. In recent small, exploratory whole-exome sequencing studies, biallelic clinically occult mutations in the FA complementation group A (Fanca) and M (Fancm) genes were found in otherwise healthy patients with isolated NOA or POI, and also monoallelic carrier status for a loss-of-function mutation in Fanca has been implicated as a possible cause for POI. In those patients with known monoallelic FA mutations undergoing pre-implantation genetic testing, poor assisted reproduction outcomes are reported. However, the mechanisms underlying the repeated failures and the high miscarriage rates observed are not fully known. WIDER IMPLICATIONS The so far 'neglected' members of the FA/BRCA family will likely emerge as a relevant focus of investigation in the genetics of reproduction. Several (rather than a single) non-BRCA genes might be implicated. State-of-the-art methods, such as whole-genome/exome sequencing, and further exploratory studies are required to understand the prevalence and mechanisms for occult FA mutations in infertility and recurrent miscarriage.
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Affiliation(s)
- Valeria Stella Vanni
- Università Vita-Salute San Raffaele, Milan, Italy.,Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Raffaella Cioffi
- Università Vita-Salute San Raffaele, Milan, Italy.,Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Enrico Papaleo
- Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Salonia
- Università Vita-Salute San Raffaele, Milan, Italy.,Division of Experimental Oncology/Unit of Urology, URI, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paola Viganò
- Reproductive Sciences Laboratory, Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Lambertini
- Department of Medical Oncology, U.O.C Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy.,Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genova, Italy
| | - Massimo Candiani
- Università Vita-Salute San Raffaele, Milan, Italy.,Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dror Meirow
- Department of Obstetrics and Gynecology, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Raoul Orvieto
- Department of Obstetrics and Gynecology, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
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6
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The birth of piRNAs: how mammalian piRNAs are produced, originated, and evolved. Mamm Genome 2021; 33:293-311. [PMID: 34724117 PMCID: PMC9114089 DOI: 10.1007/s00335-021-09927-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
PIWI-interacting RNAs (piRNAs), small noncoding RNAs 24–35 nucleotides long, are essential for animal fertility. They play critical roles in a range of functions, including transposable element suppression, gene expression regulation, imprinting, and viral defense. In mammals, piRNAs are the most abundant small RNAs in adult testes and the only small RNAs that direct epigenetic modification of chromatin in the nucleus. The production of piRNAs is a complex process from transcription to post-transcription, requiring unique machinery often distinct from the biogenesis of other RNAs. In mice, piRNA biogenesis occurs in specialized subcellular locations, involves dynamic developmental regulation, and displays sexual dimorphism. Furthermore, the genomic loci and sequences of piRNAs evolve much more rapidly than most of the genomic regions. Understanding piRNA biogenesis should reveal novel RNA regulations recognizing and processing piRNA precursors and the forces driving the gain and loss of piRNAs during animal evolution. Such findings may provide the basis for the development of engineered piRNAs capable of modulating epigenetic regulation, thereby offering possible single-dose RNA therapy without changing the genomic DNA. In this review, we focus on the biogenesis of piRNAs in mammalian adult testes that are derived from long non-coding RNAs. Although piRNA biogenesis is believed to be evolutionarily conserved from fruit flies to humans, recent studies argue for the existence of diverse, mammalian-specific RNA-processing pathways that convert precursor RNAs into piRNAs, perhaps associated with the unique features of mammalian piRNAs or germ cell development. We end with the discussion of major questions in the field, including substrate recognition and the birth of new piRNAs.
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Qin F, Cao H, Feng C, Zhu T, Zhu B, Zhang J, Tong J, Pei H. Microarray profiling of LncRNA expression in the testis of pubertal mice following morning and evening exposure to 1800 MHz radiofrequency fields. Chronobiol Int 2021; 38:1745-1760. [PMID: 34369206 DOI: 10.1080/07420528.2021.1962902] [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] [Indexed: 10/20/2022]
Abstract
In this paper, the chronotoxicity of radiofrequency fields (RF) in the pubertal testis development and the involved molecular pathways were investigated by exposing four-week-old mice to RF (1800 MHz, SAR, 0.50 W/kg) in the morning and evening of each day for three weeks. Then, pathological changes and functional indices within the testis were determined. We also used a long non-coding RNA (lncRNA) microarray and GO/KEGG pathway analyses to determine lncRNA expression profiles and predict their potential functions. The cis and trans regulation of lncRNAs were investigated, and an interaction network was constructed using Cytoscape software. RF exposure led to a range of pathological changes in the testes of adolescent mice, as testicular weights and daily sperm productions decreased, and the testosterone secretion reduced. Furthermore, RF induced dysregulation in the expression of testicular lncRNAs. We identified 615 and 183 differentially expressed lncRNAs that were associated with morning and evening exposure to RF, respectively. From 15 differential expression lncRNAs both in morning RF group and evening RF group, we selected 6 lncRNAs to be validated by quantitative reverse transcription PCR (qRT-PCR). The differentially expressed lncRNAs induced by morning RF exposure were highly correlated with many different pathways, including Fanconi syndrome, metabolic processes, cell cycle, DNA damage, and DNA replication. Trans-regulation analyses further showed that differentially expressed lncRNAs were involved in multiple transcription factor-regulated pathways, such as TCFAP4, NFkB, HINFP, TFDP2, FoxN1, and PAX5. These transcription factors have all been shown to be involved in the modulation of testis development, cell cycle progression, and spermatogenesis. These findings suggest that the extent to which 1800 MHz RF induced toxicity in the testes and changed the expression of lncRNAs showed differences between morning exposure and evening exposure. These data indicate that differentially expressed lncRNAs play crucial roles in the RF exposure damage to the developing pubertal testis. Collectively, our findings provide a better understanding of the mechanisms underlying the toxic effects of RF exposure on testicular development.
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Affiliation(s)
- Fenju Qin
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, China.,School of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Honglong Cao
- School of Electronics & Information Engineering, Soochow University, Suzhou, China
| | - Chuhan Feng
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, China
| | - Tianyuan Zhu
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, China
| | - Bingxu Zhu
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou, China
| | - Jie Zhang
- School of Public Health, Soochow University, Suzhou, China
| | - Jian Tong
- School of Public Health, Soochow University, Suzhou, China
| | - Hailong Pei
- School of Radiation Medicine and Protection, Soochow University, Suzhou, China
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8
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Mair B, Tomic J, Masud SN, Tonge P, Weiss A, Usaj M, Tong AHY, Kwan JJ, Brown KR, Titus E, Atkins M, Chan KSK, Munsie L, Habsid A, Han H, Kennedy M, Cohen B, Keller G, Moffat J. Essential Gene Profiles for Human Pluripotent Stem Cells Identify Uncharacterized Genes and Substrate Dependencies. Cell Rep 2020; 27:599-615.e12. [PMID: 30970261 DOI: 10.1016/j.celrep.2019.02.041] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/24/2018] [Accepted: 02/11/2019] [Indexed: 12/20/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) provide an invaluable tool for modeling diseases and hold promise for regenerative medicine. For understanding pluripotency and lineage differentiation mechanisms, a critical first step involves systematically cataloging essential genes (EGs) that are indispensable for hPSC fitness, defined as cell reproduction in this study. To map essential genetic determinants of hPSC fitness, we performed genome-scale loss-of-function screens in an inducible Cas9 H1 hPSC line cultured on feeder cells and laminin to identify EGs. Among these, we found FOXH1 and VENTX, genes that encode transcription factors previously implicated in stem cell biology, as well as an uncharacterized gene, C22orf43/DRICH1. hPSC EGs are substantially different from other human model cell lines, and EGs in hPSCs are highly context dependent with respect to different growth substrates. Our CRISPR screens establish parameters for genome-wide screens in hPSCs, which will facilitate the characterization of unappreciated genetic regulators of hPSC biology.
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Affiliation(s)
- Barbara Mair
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Jelena Tomic
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Sanna N Masud
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter Tonge
- Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada
| | | | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Jamie J Kwan
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Emily Titus
- Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada
| | - Michael Atkins
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | | | - Lise Munsie
- Centre for Commercialization of Regenerative Medicine, Toronto, ON, Canada
| | - Andrea Habsid
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Marion Kennedy
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Brenda Cohen
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Gordon Keller
- McEwen Stem Cell Institute, University Health Network, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Canadian Institute for Advanced Research, Toronto, ON, Canada; Institute for Biomaterials and BioMedical Engineering, University of Toronto, ON, Canada.
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9
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Xiong S, Li Y, Xiang Y, Peng N, Shen C, Cai Y, Song D, Zhang P, Wang X, Zeng X, Zhang X. Dysregulation of lncRNA and circRNA Expression in Mouse Testes after Exposure to Triptolide. Curr Drug Metab 2020; 20:665-673. [PMID: 31362668 PMCID: PMC7062010 DOI: 10.2174/1389200220666190729130020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/05/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Triptolide has been shown to exert various pharmacological effects on systemic autoimmune diseases and cancers. However, its severe toxicity, especially reproductive toxicity, prevents its widespread clinical use for people with fertility needs. Noncoding RNAs including lncRNAs and circRNAs are novel regulatory molecules that mediate a wide variety of physiological activities; they are crucial for spermatogenesis and their dysregulation might cause male infertility. However, whether they are involved in triptolide-induced reproductive toxicity is completely unknown. METHODS After exposure of mice to triptolide, the total RNAs were used to investigate lncRNA/circRNA/mRNA expression profiles by strand-specific RNA sequencing at the transcriptome level to help uncover RNA-related mechanisms in triptolide-induced toxicity. RESULTS Triptolide significantly decreased testicular weight, damaged testis and sperm morphology, and reduced sperm motility and density. Remarkable deformities in sperm head and tail were also found in triptolide-exposed mice. At the transcriptome level, the triptolide-treated mice exhibited aberrant expression profiles of lncRNAs/circRNAs/mRNAs. Gene Ontology and pathway analyses revealed that the functions of the differentially expressed lncRNA targets, circRNA cognate genes, and mRNAs were closely linked to many processes involved in spermatogenesis. In addition, some lncRNAs/circRNAs were greatly upregulated or inducibly expressed, implying their potential value as candidate markers for triptolide-induced male reproductive toxicity. CONCLUSION This study provides a preliminary database of triptolide-induced transcriptome, promotes understanding of the reproductive toxicity of triptolide, and highlights the need for research on increasing the medical efficacy of triptolide and decreasing its toxicity.
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Affiliation(s)
- Suping Xiong
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Yanting Li
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Yang Xiang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Na Peng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Chunmiao Shen
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Yanqiu Cai
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Dandan Song
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Peng Zhang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Xiaolong Wang
- Traditional Chinese Medicine Department, Jilin Women and Children Health Hospital, Changchun, China
| | - Xuihui Zeng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Xiaoning Zhang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China.,Medical School, Institute of Reproductive Medicine, Nantong University, Nantong, China
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10
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Todd EV, Liu H, Lamm MS, Thomas JT, Rutherford K, Thompson KC, Godwin JR, Gemmell NJ. Female Mimicry by Sneaker Males Has a Transcriptomic Signature in Both the Brain and the Gonad in a Sex-Changing Fish. Mol Biol Evol 2019; 35:225-241. [PMID: 29136184 DOI: 10.1093/molbev/msx293] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Phenotypic plasticity represents an elegant adaptive response of individuals to a change in their environment. Bluehead wrasses (Thalassoma bifasciatum) exhibit astonishing sexual plasticity, including female-to-male sex change and discrete male morphs that differ strikingly in behavior, morphology, and gonadal investment. Using RNA-seq transcriptome profiling, we examined the genes and physiological pathways underlying flexible behavioral and gonadal differences among female, dominant (bourgeois) male, and female-mimic (sneaker) male blueheads. For the first time in any organism, we find that female mimicry by sneaker males has a transcriptional signature in both the brain and the gonad. Sneaker males shared striking similarity in neural gene expression with females, supporting the idea that males with alternative reproductive phenotypes have "female-like brains." Sneaker males also overexpressed neuroplasticity genes, suggesting that their opportunistic reproductive strategy requires a heightened capacity for neuroplasticity. Bourgeois males overexpressed genes associated with socio-sexual behaviors (e.g., isotocin), but also neuroprotective genes and biomarkers of oxidative stress and aging, indicating a hitherto unexplored cost to these males of attaining the reproductively privileged position at the top of the social hierarchy. Our novel comparison of testicular transcriptomes in a fish with male sexual polymorphism associates greater gonadal investment by sneaker males with overexpression of genes involved in cell proliferation and sperm quality control. We propose that morphological female-mimicry by sneaker male teleosts entails pervasive downregulation of androgenesis genes, consistent with low androgen production in males lacking well-developed secondary sexual characters.
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Affiliation(s)
- Erica V Todd
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hui Liu
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Melissa S Lamm
- Department of Biological Sciences and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC
| | - Jodi T Thomas
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kelly C Thompson
- Department of Biological Sciences and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC
| | - John R Godwin
- Department of Biological Sciences and WM Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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11
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Kasak L, Punab M, Nagirnaja L, Grigorova M, Minajeva A, Lopes AM, Punab AM, Aston KI, Carvalho F, Laasik E, Smith LB, Conrad DF, Laan M, Laan M. Bi-allelic Recessive Loss-of-Function Variants in FANCM Cause Non-obstructive Azoospermia. Am J Hum Genet 2018; 103:200-212. [PMID: 30075111 DOI: 10.1016/j.ajhg.2018.07.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/02/2018] [Indexed: 01/19/2023] Open
Abstract
Infertility affects around 7% of men worldwide. Idiopathic non-obstructive azoospermia (NOA) is defined as the absence of spermatozoa in the ejaculate due to failed spermatogenesis. There is a high probability that NOA is caused by rare genetic defects. In this study, whole-exome sequencing (WES) was applied to two Estonian brothers diagnosed with NOA and Sertoli cell-only syndrome (SCOS). Compound heterozygous loss-of-function (LoF) variants in FANCM (Fanconi anemia complementation group M) were detected as the most likely cause for their condition. A rare maternally inherited frameshift variant p.Gln498Thrfs∗7 (rs761250416) and a previously undescribed splicing variant (c.4387-10A>G) derived from the father introduce a premature STOP codon leading to a truncated protein. FANCM exhibits enhanced testicular expression. In control subjects, immunohistochemical staining localized FANCM to the Sertoli and spermatogenic cells of seminiferous tubules with increasing intensity through germ cell development. This is consistent with its role in maintaining genomic stability in meiosis and mitosis. In the individual with SCOS carrying bi-allelic FANCM LoF variants, none or only faint expression was detected in the Sertoli cells. As further evidence, we detected two additional NOA-affected case subjects with independent FANCM homozygous nonsense variants, one from Estonia (p.Gln1701∗; rs147021911) and another from Portugal (p.Arg1931∗; rs144567652). The study convincingly demonstrates that bi-allelic recessive LoF variants in FANCM cause azoospermia. FANCM pathogenic variants have also been linked with doubled risk of familial breast and ovarian cancer, providing an example mechanism for the association between infertility and cancer risk, supported by published data on Fancm mutant mouse models.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia.
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12
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Haqshenas G, Wu J, Simpson KJ, Daly RJ, Netter HJ, Baumert TF, Doerig C. Signalome-wide assessment of host cell response to hepatitis C virus. Nat Commun 2017; 8:15158. [PMID: 28480889 PMCID: PMC5424167 DOI: 10.1038/ncomms15158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 03/06/2017] [Indexed: 02/07/2023] Open
Abstract
Host cell signalling during infection with intracellular pathogens remains poorly understood. Here we report on the use of antibody microarray technology to detect variations in the expression levels and phosphorylation status of host cell signalling proteins during hepatitis C virus (HCV) replication. Following transfection with HCV RNA, the JNK and NF-κB pathways are suppressed, while the JAK/STAT5 pathway is activated; furthermore, components of the apoptosis and cell cycle control machineries are affected in the expression and/or phosphorylation status. RNAi-based hit validation identifies components of the JAK/STAT, NF-κB, MAPK and calcium-induced pathways as modulators of HCV replication. Selective chemical inhibition of one of the identified targets, the JNK activator kinase MAP4K2, does impair HCV replication. Thus this study provides a comprehensive picture of host cell pathway mobilization by HCV and uncovers potential therapeutic targets. The strategy of identifying targets for anti-infective intervention within the host cell signalome can be applied to any intracellular pathogen. Development of antiviral strategies depends on an understanding of virus–host interactions. Here, using HCV, Haqshenas et al. show that antibody microarray combined with a targeted siRNA screen can be a powerful tool to identify cellular signalling pathways that are important for virus replication.
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Affiliation(s)
- Gholamreza Haqshenas
- Infection &Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton Victoria 3800, Australia
| | - Jianmin Wu
- Kinghorn Cancer Centre &Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales 2010, Australia.,Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Centre for Cancer Bioinformatics, Peking University Cancer Hospital &Institute, Beijing 100142, China
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, The Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria 3002, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Roger J Daly
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton Victoria 3800, Australia
| | - Hans J Netter
- Infection &Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton Victoria 3800, Australia.,Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute, Melbourne Health, Victoria 3000, Australia
| | - Thomas F Baumert
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67091 Strasbourg, France.,Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Hôpitaux Universitaires de Strasbourg, 67091 Strasbourg, France
| | - Christian Doerig
- Infection &Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton Victoria 3800, Australia
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