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Lin Q, Ge X, Gao L, Chen Y, Su T, Ma M, Wang H, Chen C, Han B, Liu D. Betaine alleviates spermatogenic cells apoptosis of oligoasthenozoospermia rat model by up-regulating methyltransferases and affecting DNA methylation. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 129:155713. [PMID: 38735196 DOI: 10.1016/j.phymed.2024.155713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/27/2024] [Accepted: 05/03/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND Oligoasthenozoospermia is the most common type of semen abnormality in male infertile patients. Betaine (BET) has been proved to have pharmacological effects on improving semen quality. BET also belongs to endogenous physiological active substances in the testis. However, the physiological function of BET in rat testis and its pharmacological mechanism against oligoasthenozoospermia remain unclear. PURPOSE This research aims to prove the therapeutic effect and potential mechanism of BET on oligoasthenozoospermia rat model induced by Tripterygium wilfordii glycosides (TWGs). METHODS The oligoasthenozoospermia rat model was established by a continuous gavage of TWGs (60 mg/kg) for 28 days. Negative control group, oligoasthenozoospermia group, positive drug group (levocarnitine, 300 mg/kg), and 200 mg/kg, 400 mg/kg, and 800 mg/kg BET groups were created for exploring the therapeutic effect of BET on the oligoasthenozoospermia rat model. The therapeutic effect was evaluated by HE and TUNEL staining. Immunofluorescence assay of DNMT3A, PIWIL1, PRMT5, SETDB1, BHMT2, and METTL3, methylation capture sequencing, Pi-RNA sequencing, and molecular docking were used to elucidate potential pharmacological mechanisms. RESULTS It is proved that BET can significantly restore testicular pathological damage induced by TWGs, which also can significantly reverse the apoptosis of spermatogenic cells. The spermatogenic cell protein expression levels of DNMT3A, PIWIL1, PRMT5, SETDB1, BHMT2, and METTL3 significantly decreased in oligoasthenozoospermia group. 400 mg/kg and 800 mg/kg BET groups can significantly increase expression level of the above-mentioned proteins. Methylation capture sequencing showed that BET can significantly increase the 5mC methylation level of Spata, Spag, and Specc spermatogenesis-related genes. Pi-RNA sequencing proved that the above-mentioned genes produce a large number of Pi-RNA under BET intervention. Pi-RNA can form complexes with PIWI proteins to participate in DNA methylation of target genes. Molecular docking indicated that BET may not directly act as substrate for methyltransferase and instead participates in DNA methylation by promoting the methionine cycle and increasing S-adenosylmethionine synthesis. CONCLUSION BET has a significant therapeutic effect on oligoasthenozoospermia rat model induced by TWPs. The mechanism mainly involves that BET can increase the methylation level of Spata, Specc, and Spag target genes through the PIWI/Pi-RNA pathway and up-regulation of methyltransferases (including DNA methyltransferases and histone methyltransferases).
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Affiliation(s)
- Qiyan Lin
- College of Biological and Pharmaceutical Engineering, West Anhui University, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Lu'an, 237012, Anhui, China
| | - Xiyu Ge
- College of Biological and Pharmaceutical Engineering, West Anhui University, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Lu'an, 237012, Anhui, China
| | - Leilei Gao
- College of Biological and Pharmaceutical Engineering, West Anhui University, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Lu'an, 237012, Anhui, China
| | - Yanjun Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Lu'an, 237012, Anhui, China
| | - Ting Su
- College of Biological and Pharmaceutical Engineering, West Anhui University, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Lu'an, 237012, Anhui, China
| | - Menghua Ma
- College of Biological and Pharmaceutical Engineering, West Anhui University, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Lu'an, 237012, Anhui, China
| | - Huijun Wang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Cunwu Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Lu'an, 237012, Anhui, China
| | - Bangxing Han
- College of Biological and Pharmaceutical Engineering, West Anhui University, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Lu'an, 237012, Anhui, China.
| | - Dong Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Generic Technology Research Center for Anhui Traditional Chinese Medicine Industry, Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, Lu'an, 237012, Anhui, China.
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Vrettos N, Oppelt J, Zoch A, Sgourdou P, Yoshida H, Song B, Fink R, O’Carroll D, Mourelatos Z. MIWI N-terminal arginines orchestrate generation of functional pachytene piRNAs and spermiogenesis. Nucleic Acids Res 2024; 52:6558-6570. [PMID: 38520410 PMCID: PMC11194079 DOI: 10.1093/nar/gkae193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
N-terminal arginine (NTR) methylation is a conserved feature of PIWI proteins, which are central components of the PIWI-interacting RNA (piRNA) pathway. The significance and precise function of PIWI NTR methylation in mammals remains unknown. In mice, PIWI NTRs bind Tudor domain containing proteins (TDRDs) that have essential roles in piRNA biogenesis and the formation of the chromatoid body. Using mouse MIWI (PIWIL1) as paradigm, we demonstrate that the NTRs are essential for spermatogenesis through the regulation of transposons and gene expression. The loss of TDRD5 and TDRKH interaction with MIWI results in attenuation of piRNA amplification. We find that piRNA amplification is necessary for transposon control and for sustaining piRNA levels including select, nonconserved, pachytene piRNAs that target specific mRNAs required for spermatogenesis. Our findings support the notion that the vast majority of pachytene piRNAs are dispensable, acting as self-serving genetic elements that rely for propagation on MIWI piRNA amplification. MIWI-NTRs also mediate interactions with TDRD6 that are necessary for chromatoid body compaction. Furthermore, MIWI-NTRs promote stabilization of spermiogenic transcripts that drive nuclear compaction, which is essential for sperm formation. In summary, the NTRs underpin the diversification of MIWI protein function.
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Affiliation(s)
- Nicholas Vrettos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jan Oppelt
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ansgar Zoch
- Centre for Regenerative Medicine, Institute for Stem Cell Research, University of Edinburgh, Edinburgh, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Paraskevi Sgourdou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Haruka Yoshida
- Centre for Regenerative Medicine, Institute for Stem Cell Research, University of Edinburgh, Edinburgh, UK
| | - Brian Song
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryan Fink
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dónal O’Carroll
- Centre for Regenerative Medicine, Institute for Stem Cell Research, University of Edinburgh, Edinburgh, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Dossmann L, Emperle M, Dukatz M, de Mendoza A, Bashtrykov P, Jeltsch A. Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons. Commun Biol 2024; 7:582. [PMID: 38755427 PMCID: PMC11099192 DOI: 10.1038/s42003-024-06252-z] [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: 01/05/2024] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
The DNA methyltransferase DNMT3C appeared as a duplication of the DNMT3B gene in muroids and is required for silencing of young retrotransposons in the male germline. Using specialized assay systems, we investigate the flanking sequence preferences of DNMT3C and observe characteristic preferences for cytosine at the -2 and -1 flank that are unique among DNMT3 enzymes. We identify two amino acids in the catalytic domain of DNMT3C (C543 and V547) that are responsible for the DNMT3C-specific flanking sequence preferences and evolutionary conserved in muroids. Reanalysis of published data shows that DNMT3C flanking preferences are consistent with genome-wide methylation patterns in mouse ES cells only expressing DNMT3C. Strikingly, we show that CpG sites with the preferred flanking sequences of DNMT3C are enriched in murine retrotransposons that were previously identified as DNMT3C targets. Finally, we demonstrate experimentally that DNMT3C has elevated methylation activity on substrates derived from these biological targets. Our data show that DNMT3C flanking sequence preferences match the sequences of young murine retrotransposons which facilitates their methylation. By this, our data provide mechanistic insights into the molecular co-evolution of repeat elements and (epi)genetic defense systems dedicated to maintain genomic stability in mammals.
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Affiliation(s)
- Leonie Dossmann
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Max Emperle
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Dukatz
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Han Q, Ma R, Liu N. Epigenetic reprogramming in the transition from pluripotency to totipotency. J Cell Physiol 2024; 239:e31222. [PMID: 38375873 DOI: 10.1002/jcp.31222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/08/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
Mammalian development commences with the zygote, which can differentiate into both embryonic and extraembryonic tissues, a capability known as totipotency. Only the zygote and embryos around zygotic genome activation (ZGA) (two-cell embryo stage in mice and eight-cell embryo in humans) are totipotent cells. Epigenetic modifications undergo extremely extensive changes during the acquisition of totipotency and subsequent development of differentiation. However, the underlying molecular mechanisms remain elusive. Recently, the discovery of mouse two-cell embryo-like cells, human eight-cell embryo-like cells, extended pluripotent stem cells and totipotent-like stem cells with extra-embryonic developmental potential has greatly expanded our understanding of totipotency. Experiments with these in vitro models have led to insights into epigenetic changes in the reprogramming of pluri-to-totipotency, which have informed the exploration of preimplantation development. In this review, we highlight the recent findings in understanding the mechanisms of epigenetic remodeling during totipotency capture, including RNA splicing, DNA methylation, chromatin configuration, histone modifications, and nuclear organization.
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Affiliation(s)
- Qingsheng Han
- School of Medicine, Nankai University, Tianjin, China
| | - Ru Ma
- School of Medicine, Nankai University, Tianjin, China
| | - Na Liu
- School of Medicine, Nankai University, Tianjin, China
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Wen Y, Zhou S, Gui Y, Li Z, Yin L, Xu W, Feng S, Ma X, Gan S, Xiong M, Dong J, Cheng K, Wang X, Yuan S. hnRNPU is required for spermatogonial stem cell pool establishment in mice. Cell Rep 2024; 43:114113. [PMID: 38625792 DOI: 10.1016/j.celrep.2024.114113] [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: 07/20/2023] [Revised: 01/28/2024] [Accepted: 03/29/2024] [Indexed: 04/18/2024] Open
Abstract
The continuous regeneration of spermatogonial stem cells (SSCs) underpins spermatogenesis and lifelong male fertility, but the developmental origins of the SSC pool remain unclear. Here, we document that hnRNPU is essential for establishing the SSC pool. In male mice, conditional loss of hnRNPU in prospermatogonia (ProSG) arrests spermatogenesis and results in sterility. hnRNPU-deficient ProSG fails to differentiate and migrate to the basement membrane to establish SSC pool in infancy. Moreover, hnRNPU deletion leads to the accumulation of ProSG and disrupts the process of T1-ProSG to T2-ProSG transition. Single-cell transcriptional analyses reveal that germ cells are in a mitotically quiescent state and lose their unique identity upon hnRNPU depletion. We further show that hnRNPU could bind to Vrk1, Slx4, and Dazl transcripts that have been identified to suffer aberrant alternative splicing in hnRNPU-deficient testes. These observations offer important insights into SSC pool establishment and may have translational implications for male fertility.
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Affiliation(s)
- Yujiao Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zeqing Li
- School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning 437100, China
| | - Lisha Yin
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenchao Xu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shenglei Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xixiang Ma
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shiming Gan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengneng Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Juan Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Keren Cheng
- Center for Reproductive Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518057, China.
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6
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Zoch A, Konieczny G, Auchynnikava T, Stallmeyer B, Rotte N, Heep M, Berrens RV, Schito M, Kabayama Y, Schöpp T, Kliesch S, Houston B, Nagirnaja L, O'Bryan MK, Aston KI, Conrad DF, Rappsilber J, Allshire RC, Cook AG, Tüttelmann F, O'Carroll D. C19ORF84 connects piRNA and DNA methylation machineries to defend the mammalian germ line. Mol Cell 2024; 84:1021-1035.e11. [PMID: 38359823 PMCID: PMC10960678 DOI: 10.1016/j.molcel.2024.01.014] [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: 08/01/2023] [Revised: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024]
Abstract
In the male mouse germ line, PIWI-interacting RNAs (piRNAs), bound by the PIWI protein MIWI2 (PIWIL4), guide DNA methylation of young active transposons through SPOCD1. However, the underlying mechanisms of SPOCD1-mediated piRNA-directed transposon methylation and whether this pathway functions to protect the human germ line remain unknown. We identified loss-of-function variants in human SPOCD1 that cause defective transposon silencing and male infertility. Through the analysis of these pathogenic alleles, we discovered that the uncharacterized protein C19ORF84 interacts with SPOCD1. DNMT3C, the DNA methyltransferase responsible for transposon methylation, associates with SPOCD1 and C19ORF84 in fetal gonocytes. Furthermore, C19ORF84 is essential for piRNA-directed DNA methylation and male mouse fertility. Finally, C19ORF84 mediates the in vivo association of SPOCD1 with the de novo methylation machinery. In summary, we have discovered a conserved role for the human piRNA pathway in transposon silencing and C19ORF84, an uncharacterized protein essential for orchestrating piRNA-directed DNA methylation.
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Affiliation(s)
- Ansgar Zoch
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Gabriela Konieczny
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Tania Auchynnikava
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Birgit Stallmeyer
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Nadja Rotte
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Madeleine Heep
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Rebecca V Berrens
- Institute for Developmental and Regenerative Medicine, University of Oxford, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Oxford OX37TY, UK
| | - Martina Schito
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Yuka Kabayama
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Theresa Schöpp
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital Münster, Münster, Germany
| | - Brendan Houston
- School of BioSciences and Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Moira K O'Bryan
- School of BioSciences and Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Kenneth I Aston
- Andrology and In Vitro Fertilization Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA; Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland, OR, USA
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Robin C Allshire
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Atlanta G Cook
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Dónal O'Carroll
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK.
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Garcia-Borja E, Siegl F, Mateu R, Slaby O, Sedo A, Busek P, Sana J. Critical appraisal of the piRNA-PIWI axis in cancer and cancer stem cells. Biomark Res 2024; 12:15. [PMID: 38303021 PMCID: PMC10836005 DOI: 10.1186/s40364-024-00563-3] [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: 11/17/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Small noncoding RNAs play an important role in various disease states, including cancer. PIWI proteins, a subfamily of Argonaute proteins, and PIWI-interacting RNAs (piRNAs) were originally described as germline-specific molecules that inhibit the deleterious activity of transposable elements. However, several studies have suggested a role for the piRNA-PIWI axis in somatic cells, including somatic stem cells. Dysregulated expression of piRNAs and PIWI proteins in human tumors implies that, analogously to their roles in undifferentiated cells under physiological conditions, these molecules may be important for cancer stem cells and thus contribute to cancer progression. We provide an overview of piRNA biogenesis and critically review the evidence for the role of piRNA-PIWI axis in cancer stem cells. In addition, we examine the potential of piRNAs and PIWI proteins to become biomarkers in cancer.
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Affiliation(s)
- Elena Garcia-Borja
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic
| | - Frantisek Siegl
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Rosana Mateu
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Aleksi Sedo
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic
| | - Petr Busek
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic.
| | - Jiri Sana
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic.
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
- Department of Pathology, University Hospital Brno, Brno, Czech Republic.
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Mandal AK. Recent insights into crosstalk between genetic parasites and their host genome. Brief Funct Genomics 2024; 23:15-23. [PMID: 36307128 PMCID: PMC10799329 DOI: 10.1093/bfgp/elac032] [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: 08/04/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2024] Open
Abstract
The bulk of higher order organismal genomes is comprised of transposable element (TE) copies, i.e. genetic parasites. The host-parasite relation is multi-faceted, varying across genomic region (genic versus intergenic), life-cycle stages, tissue-type and of course in health versus pathological state. The reach of functional genomics though, in investigating genotype-to-phenotype relations, has been limited when TEs are involved. The aim of this review is to highlight recent progress made in understanding how TE origin biochemical activity interacts with the central dogma stages of the host genome. Such interaction can also bring about modulation of the immune context and this could have important repercussions in disease state where immunity has a role to play. Thus, the review is to instigate ideas and action points around identifying evolutionary adaptations that the host genome and the genetic parasite have evolved and why they could be relevant.
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Affiliation(s)
- Amit K Mandal
- Corresponding author: A.K. Mandal, Nuffield Department of Surgical Sciences (NDS), University of Oxford, Old Road Campus Research building (ORCRB), Oxford OX3 7DQ, UK. Tel: +44 (0)1865 617123; Fax: +44 (0)1865 768876; E-mail:
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9
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Vrettos N, Oppelt J, Zoch A, Sgourdou P, Yoshida H, Song B, Fink R, O’Carroll D, Mourelatos Z. MIWI arginines orchestrate generation of functional pachytene piRNAs and spermiogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573779. [PMID: 38260298 PMCID: PMC10802271 DOI: 10.1101/2023.12.31.573779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
N-terminal arginine (NTR) methylation is a conserved feature of PIWI proteins, which are central components of the PIWI-interacting RNA (piRNA) pathway. The significance and precise function of PIWI NTR methylation in mammals remains unknown. In mice, PIWI NTRs bind Tudor domain containing proteins (TDRDs) that have essential roles in piRNA biogenesis and the formation of the chromatoid body. Using mouse MIWI (PIWIL1) as paradigm, we demonstrate that the NTRs are essential for spermatogenesis through the regulation of transposons and gene expression. Surprisingly, the loss of TDRD5 and TDRKH interaction with MIWI results in defective piRNA amplification, rather than an expected failure of piRNA biogenesis. We find that piRNA amplification is necessary for both transposon control and for sustaining levels of select, nonconserved, pachytene piRNAs that target specific mRNAs required for spermatogenesis. Our findings support the notion that the vast majority of pachytene piRNAs are dispensable, acting as autonomous genetic elements that rely for propagation on MIWI piRNA amplification. MIWI-NTRs also mediate interactions with TDRD6 that are necessary for chromatoid body compaction. Furthermore, MIWI-NTRs promote stabilization of spermiogenic transcripts that drive nuclear compaction, which is essential for sperm formation. In summary, the NTRs underpin the diversification of MIWI protein function.
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Affiliation(s)
- Nicholas Vrettos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jan Oppelt
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ansgar Zoch
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences
| | - Paraskevi Sgourdou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Haruka Yoshida
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences
| | - Brian Song
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ryan Fink
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dónal O’Carroll
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Wang D, Wei Z, Lin F, Wang Y, Liu X, Li Q, Sun L, Yang S. Protective effects of villi mesenchymal stem cells on human umbilical vein endothelial cells by inducing SPOCD1 expression in cases of gestational diabetes mellitus. Biochem Biophys Res Commun 2023; 686:149177. [PMID: 37953105 DOI: 10.1016/j.bbrc.2023.149177] [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: 08/03/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) is characterized by a lack of response to insulin in pregnancies, and often accompanied by severe complications. GDM is associated with structural and functional alterations, particularly endothelial dysfunction, in various tissues. This study is aimed to investigate the effect of placental mesenchymal stem cells (MSCs) on the endothelial biological function of human umbilical vein endothelial cells (HUVECs) and their molecular mechanisms. METHODS Villi mesenchymal stem cells (VMSCs) were co-cultured with HUVECs, and transcriptomic analysis of differential genes was performed in HUVECs under high-glucose induction. Lentiviral transfection was performed to construct HUVECs with stable knockdown or overexpression of SPOCD1. The immunohistochemical assays were used to detect the expression of SPOCD1 in GDM patients. TUNEL fluorescence staining was applied for detection of the HUVEC apoptosis. β galactosidase staining assay was performed to detect the cell senescence. Electron microscopy was used to detect the cell pyroptosis. qRT-PCR and western blot assays were conducted for identifying the mRNA & protein expressions of genes. RESULTS VMSCs, when co-cultured with HUVECs, could inhibit the apoptosis, pyroptosis and senescence induced by high-glucose condition in HUVECs. Transcriptomic results showed an upregulation of SPOCD1 expression induced by VMSCs in HUVECs. Overexpression of SPOCD1 inhibited high-level glucose-induced apoptosis, pyroptosis and senescence in HUVECs via the β-catenin pathway. CONCLUSION VMSCs induce β-catenin activation by upregulating the expression of SPOCD1 in HUVECs, which ultimately inhibits high-level glucose-induced apoptosis, pyroptosis and senescence in HUVECs. This observation provides potential therapeutic insight for future GDM treatment.
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Affiliation(s)
- Dawei Wang
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhenying Wei
- Department of Obstetrics, The Qingdao Women and Children's Hospital, Qingdao, China
| | - Fangfei Lin
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yiqian Wang
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaogang Liu
- Department of Obstetrics, People's Hospital of Yuxi City, Yuxi, China
| | - Qiuyi Li
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lin Sun
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shengmei Yang
- Department of Obstetrics, The Affiliated Hospital of Qingdao University, Qingdao, China.
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11
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Dabi Y, Suisse S, Marie Y, Delbos L, Poilblanc M, Descamps P, Golfier F, Jornea L, Forlani S, Bouteiller D, Touboul C, Puchar A, Bendifallah S, Daraï E. New class of RNA biomarker for endometriosis diagnosis: The potential of salivary piRNA expression. Eur J Obstet Gynecol Reprod Biol 2023; 291:88-95. [PMID: 37857147 DOI: 10.1016/j.ejogrb.2023.10.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023]
Abstract
OBJECTIVES In contrast to miRNA expression, little attention has been given to piwiRNA (piRNA) expression among endometriosis patients. The aim of the present study was to explore the human piRNAome and to investigate a potential piRNA saliva-based diagnostic signature for endometriosis. METHODS Data from the prospective "ENDOmiRNA" study (ClinicalTrials.gov Identifier: NCT04728152) were used. Saliva samples from 200 patients were analyzed in order to evaluate human piRNA expression using the piRNA bank. Next Generation Sequencing (NGS), barcoding of unique molecular identifiers and both Artificial Intelligence (AI) and machine learning (ML) were used. For each piRNA, sensitivity, specificity, and ROC AUC values were calculated for the diagnosis of endometriosis. RESULTS 201 piRNAs were identified, none had an AUC ≥ 0.70, and only three piRNAs (piR-004153, piR001918, piR-020401) had an AUC between ≥ 0.6 and < 0.70. Seven were differentially expressed: piR-004153, piR-001918, piR-020401, piR-012864, piR-017716, piR-020326 and piR-016904. The respective correlation and accuracy to diagnose endometriosis according to the F1-score, sensitivity, specificity, and AUC ranged from 0 to 0.862 %, 0-0.961 %, 0.085-1, and 0.425-0.618. A correlation was observed between the patients' age (≥35 years) and piR-004153 (p = 0.002) and piR-017716 (p = 0.030). Among the 201 piRNAs, four were differentially expressed in patients with and without hormonal treatment: piR-004153 (p = 0.015), piR-020401 (p = 0.001), piR-012864 (p = 0.036) and piR-017716 (p = 0.009). CONCLUSION Our results support the link between piRNAs and endometriosis physiopathology and establish its utility as a potential diagnostic biomarker using saliva samples. Per se, piRNA expression should be analyzed along with the clinical status of a patient.
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Affiliation(s)
- Yohann Dabi
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France.
| | | | - Yannick Marie
- Department of Obstetrics and Reproductive Medicine - CHU d'Angers, France
| | - Léa Delbos
- Department of Obstetrics and Reproductive Medicine - CHU d'Angers, France; Endometriosis Expert Center - Pays de la Loire, France
| | - Mathieu Poilblanc
- Department of Obstetrics and Reproductive Medicine, Lyon South University Hospital, Lyon Civil Hospices, France; Endometriosis Expert Center - Steering Center of the EndAURA Network, France
| | - Philippe Descamps
- Department of Obstetrics and Reproductive Medicine - CHU d'Angers, France; Endometriosis Expert Center - Pays de la Loire, France
| | - Francois Golfier
- Department of Obstetrics and Reproductive Medicine, Lyon South University Hospital, Lyon Civil Hospices, France; Endometriosis Expert Center - Steering Center of the EndAURA Network, France
| | - Ludmila Jornea
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, AP-HP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Sylvie Forlani
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, AP-HP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Delphine Bouteiller
- Gentoyping and Sequencing Core Facility, iGenSeq, Institut du Cerveau et de la Moelle épinière, ICM, Hôpital Pitié-Salpêtrière, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Cyril Touboul
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France
| | - Anne Puchar
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France
| | - Sofiane Bendifallah
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France
| | - Emile Daraï
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France
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12
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Joshi M, Sethi S, Mehta P, Kumari A, Rajender S. Small RNAs, spermatogenesis, and male infertility: a decade of retrospect. Reprod Biol Endocrinol 2023; 21:106. [PMID: 37924131 PMCID: PMC10625245 DOI: 10.1186/s12958-023-01155-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
Small non-coding RNAs (sncRNAs), being the top regulators of gene expression, have been thoroughly studied in various biological systems, including the testis. Research over the last decade has generated significant evidence in support of the crucial roles of sncRNAs in male reproduction, particularly in the maintenance of primordial germ cells, meiosis, spermiogenesis, sperm fertility, and early post-fertilization development. The most commonly studied small RNAs in spermatogenesis are microRNAs (miRNAs), PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), and transfer RNA-derived small RNAs (ts-RNAs). Small non-coding RNAs are crucial in regulating the dynamic, spatial, and temporal gene expression profiles in developing germ cells. A number of small RNAs, particularly miRNAs and tsRNAs, are loaded on spermatozoa during their epididymal maturation. With regard to their roles in fertility, miRNAs have been studied most often, followed by piRNAs and tsRNAs. Dysregulation of more than 100 miRNAs has been shown to correlate with infertility. piRNA and tsRNA dysregulations in infertility have been studied in only 3-5 studies. Sperm-borne small RNAs hold great potential to act as biomarkers of sperm quality and fertility. In this article, we review the role of small RNAs in spermatogenesis, their association with infertility, and their potential as biomarkers of sperm quality and fertility.
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Affiliation(s)
- Meghali Joshi
- Division of Endocrinology, Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Shruti Sethi
- Division of Endocrinology, Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Poonam Mehta
- Division of Endocrinology, Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Anamika Kumari
- Division of Endocrinology, Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Singh Rajender
- Division of Endocrinology, Central Drug Research Institute, Lucknow, Uttar Pradesh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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13
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Kalmykova AI, Sokolova OA. Retrotransposons and Telomeres. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1739-1753. [PMID: 38105195 DOI: 10.1134/s0006297923110068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/24/2023] [Accepted: 08/12/2023] [Indexed: 12/19/2023]
Abstract
Transposable elements (TEs) comprise a significant part of eukaryotic genomes being a major source of genome instability and mutagenesis. Cellular defense systems suppress the TE expansion at all stages of their life cycle. Piwi proteins and Piwi-interacting RNAs (piRNAs) are key elements of the anti-transposon defense system, which control TE activity in metazoan gonads preventing inheritable transpositions and developmental defects. In this review, we discuss various regulatory mechanisms by which small RNAs combat TE activity. However, active transposons persist, suggesting these powerful anti-transposon defense mechanisms have a limited capacity. A growing body of evidence suggests that increased TE activity coincides with genome reprogramming and telomere lengthening in different species. In the Drosophila fruit fly, whose telomeres consist only of retrotransposons, a piRNA-mediated mechanism is required for telomere maintenance and their length control. Therefore, the efficacy of protective mechanisms must be finely balanced in order not only to suppress the activity of transposons, but also to maintain the proper length and stability of telomeres. Structural and functional relationship between the telomere homeostasis and LINE1 retrotransposon in human cells indicates a close link between selfish TEs and the vital structure of the genome, telomere. This relationship, which permits the retention of active TEs in the genome, is reportedly a legacy of the retrotransposon origin of telomeres. The maintenance of telomeres and the execution of other crucial roles that TEs acquired during the process of their domestication in the genome serve as a type of payment for such a "service."
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Affiliation(s)
- Alla I Kalmykova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Olesya A Sokolova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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14
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Schöpp T, Prigozhin DM, Douse C, Kaji K, Cook AG, O'Carroll D. The DUF3715 domain has a conserved role in RNA-directed transposon silencing. RNA (NEW YORK, N.Y.) 2023; 29:1471-1480. [PMID: 37433650 PMCID: PMC10578480 DOI: 10.1261/rna.079693.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/16/2023] [Indexed: 07/13/2023]
Abstract
RNA-directed transposon silencing operates in the mammalian soma and germline to safeguard genomic integrity. The piRNA pathway and the HUSH complex identify active transposons through recognition of their nascent transcripts, but mechanistic understanding of how these distinct pathways evolved is lacking. TASOR is an essential component of the HUSH complex. TASOR's DUF3715 domain adopts a pseudo-PARP structure and is required for transposon silencing in a manner independent of complex assembly. TEX15, an essential piRNA pathway factor, also contains the DUF3715 domain. Here, we show that TASOR's and TEX15's DUF3715 domain share extensive structural homology. We found that the DUF3715 domain arose in early eukaryotes and that in vertebrates it is restricted to TEX15, TASOR, and TASORB orthologs. While TASOR-like proteins are found throughout metazoa, TEX15 is vertebrate-specific. The branching of TEX15 and the TASOR-like DUF3715 domain likely occurred in early metazoan evolution. Remarkably, despite this vast evolutionary distance, the DUF3715 domain from divergent TEX15 sequences can functionally substitute the DUF3715 domain of TASOR and mediates transposon silencing. We have thus termed this domain of unknown function as the RNA-directed pseudo-PARP transposon silencing (RDTS) domain. In summary, we show an unexpected functional link between these critical transposon silencing pathways.
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Affiliation(s)
- Theresa Schöpp
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Daniil M Prigozhin
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christopher Douse
- Lab of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science and Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Keisuke Kaji
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | - Atlanta G Cook
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Dónal O'Carroll
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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15
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Lawlor MA, Ellison CE. Evolutionary dynamics between transposable elements and their host genomes: mechanisms of suppression and escape. Curr Opin Genet Dev 2023; 82:102092. [PMID: 37517354 PMCID: PMC10530431 DOI: 10.1016/j.gde.2023.102092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/27/2023] [Accepted: 07/02/2023] [Indexed: 08/01/2023]
Abstract
Transposable elements (TEs) are ubiquitous among eukaryotic species. Their evolutionary persistence is likely due to a combination of tolerogenic, evasive/antagonistic, and cooperative interactions with their host genomes. Here, we focus on metazoan species and review recent advances related to the harmful effects of TE insertions, including how epigenetic effects and TE-derived RNAs can damage host cells. We discuss new findings related to host pathways that silence TEs, such as the piRNA pathway and the APOBEC3 and Kruppel-associated box zinc finger gene families. Finally, we summarize novel strategies used by TEs to evade host silencing, including the Y chromosome as a permissive niche for TE mobilization and TE counterdefense strategies to block host silencing factors.
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16
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Gerdes P, Chan D, Lundberg M, Sanchez-Luque FJ, Bodea GO, Ewing AD, Faulkner GJ, Richardson SR. Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development. Genome Res 2023; 33:1465-1481. [PMID: 37798118 PMCID: PMC10620060 DOI: 10.1101/gr.278003.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023]
Abstract
Mice harbor ∼2800 intact copies of the retrotransposon Long Interspersed Element 1 (L1). The in vivo retrotransposition capacity of an L1 copy is defined by both its sequence integrity and epigenetic status, including DNA methylation of the monomeric units constituting young mouse L1 promoters. Locus-specific L1 methylation dynamics during development may therefore elucidate and explain spatiotemporal niches of endogenous retrotransposition but remain unresolved. Here, we interrogate the retrotransposition efficiency and epigenetic fate of source (donor) L1s, identified as mobile in vivo. We show that promoter monomer loss consistently attenuates the relative retrotransposition potential of their offspring (daughter) L1 insertions. We also observe that most donor/daughter L1 pairs are efficiently methylated upon differentiation in vivo and in vitro. We use Oxford Nanopore Technologies (ONT) long-read sequencing to resolve L1 methylation genome-wide and at individual L1 loci, revealing a distinctive "smile" pattern in methylation levels across the L1 promoter region. Using Pacific Biosciences (PacBio) SMRT sequencing of L1 5' RACE products, we then examine DNA methylation dynamics at the mouse L1 promoter in parallel with transcription start site (TSS) distribution at locus-specific resolution. Together, our results offer a novel perspective on the interplay between epigenetic repression, L1 evolution, and genome stability.
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Affiliation(s)
- Patricia Gerdes
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
| | - Dorothy Chan
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
| | - Mischa Lundberg
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland 4102, Australia
- Translational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Sydney, New South Wales 2113, Australia
| | - Francisco J Sanchez-Luque
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
- GENYO. Centre for Genomics and Oncological Research (Pfizer-University of Granada-Andalusian Regional Government), PTS Granada, 18016, Spain
- MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Gabriela O Bodea
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Adam D Ewing
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia;
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sandra R Richardson
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland 4102, Australia;
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Taverna S, Masucci A, Cammarata G. PIWI-RNAs Small Noncoding RNAs with Smart Functions: Potential Theranostic Applications in Cancer. Cancers (Basel) 2023; 15:3912. [PMID: 37568728 PMCID: PMC10417041 DOI: 10.3390/cancers15153912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a new class of small noncoding RNAs (ncRNAs) that bind components of the PIWI protein family. piRNAs are specifically expressed in different human tissues and regulate important signaling pathways. Aberrant expressions of piRNAs and PIWI proteins have been associated with tumorigenesis and cancer progression. Recent studies reported that piRNAs are contained in extracellular vesicles (EVs), nanosized lipid particles, with key roles in cell-cell communication. EVs contain several bioactive molecules, such as proteins, lipids, and nucleic acids, including emerging ncRNAs. EVs are one of the components of liquid biopsy (LB) a non-invasive method for detecting specific molecular biomarkers in liquid samples. LB could become a crucial tool for cancer diagnosis with piRNAs as biomarkers in a precision oncology approach. This review summarizes the current findings on the roles of piRNAs in different cancer types, focusing on potential theranostic applications of piRNAs contained in EVs (EV-piRNAs). Their roles as non-invasive diagnostic and prognostic biomarkers and as new therapeutic options have been also discussed.
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Affiliation(s)
- Simona Taverna
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 90146 Palermo, Italy
| | - Anna Masucci
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Clinical Biochemistry, Clinical Molecular Medicine, Laboratory Medicine, University of Palermo, 90127 Palermo, Italy;
| | - Giuseppe Cammarata
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 90146 Palermo, Italy
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Fu J, Qin T, Li C, Zhu J, Ding Y, Zhou M, Yang Q, Liu X, Zhou J, Chen F. Research progress of LINE-1 in the diagnosis, prognosis, and treatment of gynecologic tumors. Front Oncol 2023; 13:1201568. [PMID: 37546391 PMCID: PMC10399582 DOI: 10.3389/fonc.2023.1201568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
The retrotransposon known as long interspersed nuclear element-1 (LINE-1), which is currently the sole autonomously mobile transposon in the human genome, can result in insertional mutations, chromosomal rearrangements, and genomic instability. In recent years, numerous studies have shown that LINE-1 is involved in the development of various diseases and also plays an important role in the immune regulation of the organism. The expression of LINE-1 in gynecologic tumors suggests that it is expected to be an independent indicator for early diagnosis and prognosis, and also, as a therapeutic target, LINE-1 is closely associated with gynecologic tumor prognosis. This article discusses the function of LINE-1 in the diagnosis, treatment, and prognosis of ovarian, cervical, and endometrial malignancies, as well as other gynecologic malignancies. It offers fresh perspectives on the early detection of tumors and the creation of novel anti-tumor medications.
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Affiliation(s)
- Jiaojiao Fu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Tiansheng Qin
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
- The First Clinical Medical School, Lanzhou University, Lanzhou, Gansu, China
- National Health Commission (NHC) Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Chaoming Li
- The First People’s Hospital of Longnan, Longnan City Hospital, Longnan, Gansu, China
| | - Jiaojiao Zhu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Yaoyao Ding
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Meiying Zhou
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Qing Yang
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Xiaofeng Liu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Juanhong Zhou
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Fan Chen
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
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19
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Tan K, Wilkinson MF. Developmental regulators moonlighting as transposons defense factors. Andrology 2023; 11:891-903. [PMID: 36895139 PMCID: PMC11162177 DOI: 10.1111/andr.13427] [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: 01/11/2023] [Revised: 02/17/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND The germline perpetuates genetic information across generations. To maintain the integrity of the germline, transposable elements in the genome must be silenced, as these mobile elements would otherwise engender widespread mutations passed on to subsequent generations. There are several well-established mechanisms that are dedicated to providing defense against transposable elements, including DNA methylation, RNA interference, and the PIWI-interacting RNA pathway. OBJECTIVES Recently, several studies have provided evidence that transposon defense is not only provided by factors dedicated to this purpose but also factors with other roles, including in germline development. Many of these are transcription factors. Our objective is to summarize what is known about these "bi-functional" transcriptional regulators. MATERIALS AND METHODS Literature search. RESULTS AND CONCLUSION We summarize the evidence that six transcriptional regulators-GLIS3, MYBL1, RB1, RHOX10, SETDB1, and ZBTB16-are both developmental regulators and transposable element-defense factors. These factors act at different stages of germ cell development, including in pro-spermatogonia, spermatogonial stem cells, and spermatocytes. Collectively, the data suggest a model in which specific key transcriptional regulators have acquired multiple functions over evolutionary time to influence developmental decisions and safeguard transgenerational genetic information. It remains to be determined whether their developmental roles were primordial and their transposon defense roles were co-opted, or vice versa.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Miles F. Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
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20
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Zhang M, Sun W, You X, Xu D, Wang L, Yang J, Li E, He S. LINE-1 repression in Epstein-Barr virus-associated gastric cancer through viral-host genome interaction. Nucleic Acids Res 2023; 51:4867-4880. [PMID: 36942479 PMCID: PMC10250212 DOI: 10.1093/nar/gkad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/23/2023] Open
Abstract
Long INterspersed Element 1 (LINE-1 or L1) acts as a major remodeling force in genome regulation and evolution. Accumulating evidence shows that virus infection impacts L1 expression, potentially impacting host antiviral response and diseases. The underlying regulation mechanism is unclear. Epstein-Barr virus (EBV), a double-stranded DNA virus linked to B-cell and epithelial malignancies, is known to have viral-host genome interaction, resulting in transcriptional rewiring in EBV-associated gastric cancer (EBVaGC). By analyzing publicly available datasets from the Gene Expression Omnibus (GEO), we found that EBVaGC has L1 transcriptional repression compared with EBV-negative gastric cancer (EBVnGC). More specifically, retrotransposition-associated young and full-length L1s (FL-L1s) were among the most repressed L1s. Epigenetic alterations, especially increased H3K9me3, were observed on FL-L1s. H3K9me3 deposition was potentially attributed to increased TASOR expression, a key component of the human silencing hub (HUSH) complex for H3K9 trimethylation. The 4C- and HiC-seq data indicated that the viral DNA interacted in the proximity of the TASOR enhancer, strengthening the loop formation between the TASOR enhancer and its promoter. These results indicated that EBV infection is associated with increased H3K9me3 deposition, leading to L1 repression. This study uncovers a regulation mechanism of L1 expression by chromatin topology remodeling associated with viral-host genome interaction in EBVaGC.
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Affiliation(s)
- Mengyu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
- Yancheng Medical Research Center, Medical School, Nanjing University, Yancheng 224000, China
| | - Weikang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Xiaoxin You
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Dongge Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Lingling Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Jingping Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
| | - Erguang Li
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
- Institute of Medical Virology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing 210093, China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China
| | - Susu He
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210093, China
- Yancheng Medical Research Center, Medical School, Nanjing University, Yancheng 224000, China
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21
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Perez MF, Yurieva M, Poddutoori S, Mortensen EM, Crotty Alexander LE, Williams A. Transcriptomic responses in the blood and sputum of cigarette smokers compared to e-cigarette vapers. Respir Res 2023; 24:134. [PMID: 37208747 PMCID: PMC10196320 DOI: 10.1186/s12931-023-02438-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 04/27/2023] [Indexed: 05/21/2023] Open
Abstract
RATIONALE Electronic (e)-cigarettes are popular among youth and cigarette smokers attempting to quit. Studies to date have focused on the utility of e-cigarettes as a smoking cessation tool, but the biological effects are largely unknown. OBJECTIVES To identify transcriptomic differences in the blood and sputum of e-cigarette users compared to conventional cigarettes smokers and healthy controls and describe biological pathways affected by these tobacco products. METHODS Cross-sectional analysis of whole blood and sputum RNA-sequencing data from 8 smokers, 9 e-cigarette users (e-cigs) and 4 controls. Weighted gene co-network analysis (WGCNA) identified gene module associations. Ingenuity Pathway Analysis (IPA) identified canonical pathways associated with tobacco products. MAIN RESULTS In blood, a three-group comparison showed 16 differentially expressed genes (DEGs); pair-wise comparison showed 7 DEGs between e-cigs and controls, 35 DEGs between smokers and controls, and 13 DEGs between smokers and e-cigs. In sputum, 438 DEGs were in the three-group comparison. In pair-wise comparisons, there were 2 DEGs between e-cigs and controls, 270 DEGs between smokers and controls, and 468 DEGs between smokers and e-cigs. Only 2 genes in the smokers vs. control comparison overlapped between blood and sputum. Most gene modules identified through WGCNA associated with tobacco product exposures also were associated with cotinine and exhaled CO levels. IPA showed more canonical pathways altered by conventional cigarette smoking than by e-cigarette use. CONCLUSION Cigarette smoking and e-cigarette use led to transcriptomic changes in both blood and sputum. However, conventional cigarettes induced much stronger transcriptomic responses in both compartments.
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Affiliation(s)
- Mario F Perez
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Connecticut School of Medicine, Farmington, CT, USA.
| | - Marina Yurieva
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Eric M Mortensen
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Laura E Crotty Alexander
- Division of Pulmonary Critical Care, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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22
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Yao Y, Li Y, Zhu X, Zhao C, Yang L, Huang X, Wang L. The emerging role of the piRNA/PIWI complex in respiratory tract diseases. Respir Res 2023; 24:76. [PMID: 36915129 PMCID: PMC10010017 DOI: 10.1186/s12931-023-02367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
PIWI-interacting RNA (piRNA) is a class of recently discovered small non-coding RNA molecules with a length of 18-33 nt that interacts with the PIWI protein to form the piRNA/PIWI complex. The PIWI family is a subfamily of Argonaute (AGO) proteins that also contain the AGO family which bind to microRNA (miRNA). Recently studies indicate that piRNAs are not specific to in the mammalian germline, they are also expressed in a tissue-specific manner in a variety of human tissues and participated in various of diseases, such as cardiovascular, neurological, and urinary tract diseases, and are especially prevalent in malignant tumors in these systems. However, the functions and abnormal expression of piRNAs in respiratory tract diseases and their underlying mechanisms remain incompletely understood. In this review, we discuss current studies summarizing the biogenetic processes, functions, and emerging roles of piRNAs in respiratory tract diseases, providing a reference value for future piRNA research.
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Affiliation(s)
- Yizhu Yao
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yaozhe Li
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Xiayan Zhu
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Chengguang Zhao
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.,School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Lehe Yang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Xiaoying Huang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Liangxing Wang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
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23
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The epigenetic regulatory mechanism of PIWI/piRNAs in human cancers. Mol Cancer 2023; 22:45. [PMID: 36882835 PMCID: PMC9990219 DOI: 10.1186/s12943-023-01749-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
PIWI proteins have a strong correlation with PIWI-interacting RNAs (piRNAs), which are significant in development and reproduction of organisms. Recently, emerging evidences have indicated that apart from the reproductive function, PIWI/piRNAs with abnormal expression, also involve greatly in varieties of human cancers. Moreover, human PIWI proteins are usually expressed only in germ cells and hardly in somatic cells, so the abnormal expression of PIWI proteins in different types of cancer offer a promising opportunity for precision medicine. In this review, we discussed current researches about the biogenesis of piRNA, its epigenetic regulatory mechanisms in human cancers, such as N6-methyladenosine (m6A) methylation, histone modifications, DNA methylation and RNA interference, providing novel insights into the markers for clinical diagnosis, treatment and prognosis in human cancers.
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24
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Appel LM, Benedum J, Engl M, Platzer S, Schleiffer A, Strobl X, Slade D. SPOC domain proteins in health and disease. Genes Dev 2023; 37:140-170. [PMID: 36927757 PMCID: PMC10111866 DOI: 10.1101/gad.350314.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Since it was first described >20 yr ago, the SPOC domain (Spen paralog and ortholog C-terminal domain) has been identified in many proteins all across eukaryotic species. SPOC-containing proteins regulate gene expression on various levels ranging from transcription to RNA processing, modification, export, and stability, as well as X-chromosome inactivation. Their manifold roles in controlling transcriptional output implicate them in a plethora of developmental processes, and their misregulation is often associated with cancer. Here, we provide an overview of the biophysical properties of the SPOC domain and its interaction with phosphorylated binding partners, the phylogenetic origin of SPOC domain proteins, the diverse functions of mammalian SPOC proteins and their homologs, the mechanisms by which they regulate differentiation and development, and their roles in cancer.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
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25
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Spadafora C. The epigenetic basis of evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 178:57-69. [PMID: 36720315 DOI: 10.1016/j.pbiomolbio.2023.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/17/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
An increasing body of data are revealing key roles of epigenetics in evolutionary processes. The scope of this manuscript is to assemble in a coherent frame experimental evidence supporting a role of epigenetic factors and networks, active during embryogenesis, in orchestrating variation-inducing phenomena underlying evolution, seen as a global process. This process unfolds over two crucial levels: i) a flow of RNA-based information - predominantly small regulatory RNAs released from somatic cells exposed to environmental stimuli - taken up by spermatozoa and delivered to oocytes at fertilization and ii) the highly permissive and variation-prone environments offered by zygotes and totipotent early embryos. Totipotent embryos provide a variety of biological tools favouring the emergence of evolutionarily significant phenotypic novelties driven by RNA information. Under this light, neither random genomic mutations, nor the sieving role of natural selection are required, as the sperm-delivered RNA cargo conveys specific information and acts as "phenotypic-inducer" of defined environmentally acquired traits.
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Affiliation(s)
- Corrado Spadafora
- Institute of Translational Pharmacology, National Research Council (CNR), Rome, Italy.
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26
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Stamidis N, Żylicz JJ. RNA-mediated heterochromatin formation at repetitive elements in mammals. EMBO J 2023; 42:e111717. [PMID: 36847618 PMCID: PMC10106986 DOI: 10.15252/embj.2022111717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
The failure to repress transcription of repetitive genomic elements can lead to catastrophic genome instability and is associated with various human diseases. As such, multiple parallel mechanisms cooperate to ensure repression and heterochromatinization of these elements, especially during germline development and early embryogenesis. A vital question in the field is how specificity in establishing heterochromatin at repetitive elements is achieved. Apart from trans-acting protein factors, recent evidence points to a role of different RNA species in targeting repressive histone marks and DNA methylation to these sites in mammals. Here, we review recent discoveries on this topic and predominantly focus on the role of RNA methylation, piRNAs, and other localized satellite RNAs.
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Affiliation(s)
- Nikolaos Stamidis
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Jan Jakub Żylicz
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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27
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Bencurova E, Akash A, Dobson RC, Dandekar T. DNA storage-from natural biology to synthetic biology. Comput Struct Biotechnol J 2023; 21:1227-1235. [PMID: 36817961 PMCID: PMC9932295 DOI: 10.1016/j.csbj.2023.01.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macramé , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades).
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Affiliation(s)
- Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Aman Akash
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany,Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Corresponding author at: Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
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28
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Wang X, Ramat A, Simonelig M, Liu MF. Emerging roles and functional mechanisms of PIWI-interacting RNAs. Nat Rev Mol Cell Biol 2023; 24:123-141. [PMID: 36104626 DOI: 10.1038/s41580-022-00528-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 02/02/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with proteins of the PIWI clade of the Argonaute family. First identified in animal germ line cells, piRNAs have essential roles in germ line development. The first function of PIWI-piRNA complexes to be described was the silencing of transposable elements, which is crucial for maintaining the integrity of the germ line genome. Later studies provided new insights into the functions of PIWI-piRNA complexes by demonstrating that they regulate protein-coding genes. Recent studies of piRNA biology, including in new model organisms such as golden hamsters, have deepened our understanding of both piRNA biogenesis and piRNA function. In this Review, we discuss the most recent advances in our understanding of piRNA biogenesis, the molecular mechanisms of piRNA function and the emerging roles of piRNAs in germ line development mainly in flies and mice, and in infertility, cancer and neurological diseases in humans.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Anne Ramat
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Martine Simonelig
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China. .,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.
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29
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Gan L, Yang C, Zhao L, Wang S, Gao Z, Ye Y. Prognostic Biomarker SPOCD1 and Its Correlation with Immune Infiltrates in Colorectal Cancer. Biomolecules 2023; 13:biom13020209. [PMID: 36830578 PMCID: PMC9953389 DOI: 10.3390/biom13020209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
The biological role of the spen paralogue and orthologue C-terminal domain containing 1 (SPOCD1) has been investigated in human malignancies, but its function in colorectal cancer (CRC) is unclear. This study investigated the association between SPOCD1 expression and clinicopathological features of CRC cases, as well as its prognostic value and biological function based on large-scale databases and clinical samples. The results showed that the expression level of SPOCD1 was elevated in CRC, which was generally associated with shortened survival time and poor clinical indexes, including advanced T, N, and pathologic stages. Multivariate Cox regression analysis showed that elevated SPOCD1 expression was an independent factor for poor prognosis in CRC patients. Functional enrichment analysis of SPOCD1 and its co-expressed genes revealed that SPOCD1 could act as an oncogene by regulating gene expression in essential functions and pathways of tumorigenesis, such as extracellular matrix organization, chemokine signaling pathways, and calcium signaling pathways. In addition, immune cell infiltration results showed that SPOCD1 expression was associated with various immune cells, especially macrophages. Furthermore, our findings suggested a possible function for SPOCD1 in the polarization of macrophages from M1 to M2 in CRC. In conclusion, SPOCD1 is a promising diagnostic and prognostic marker for CRC, opening new avenues for research and treatment.
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Affiliation(s)
- Lin Gan
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Shan Wang
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Zhidong Gao
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
- Correspondence: (Z.G.); (Y.Y.)
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People’s Hospital, Beijing 100044, China
- Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Laboratory of Surgical Oncology, Peking University People’s Hospital, Beijing 100044, China
- Correspondence: (Z.G.); (Y.Y.)
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30
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Appel LM, Franke V, Benedum J, Grishkovskaya I, Strobl X, Polyansky A, Ammann G, Platzer S, Neudolt A, Wunder A, Walch L, Kaiser S, Zagrovic B, Djinovic-Carugo K, Akalin A, Slade D. The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators. Nat Commun 2023; 14:166. [PMID: 36631525 PMCID: PMC9834408 DOI: 10.1038/s41467-023-35853-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The heptad repeats of the C-terminal domain (CTD) of RNA polymerase II (Pol II) are extensively modified throughout the transcription cycle. The CTD coordinates RNA synthesis and processing by recruiting transcription regulators as well as RNA capping, splicing and 3'end processing factors. The SPOC domain of PHF3 was recently identified as a CTD reader domain specifically binding to phosphorylated serine-2 residues in adjacent CTD repeats. Here, we establish the SPOC domains of the human proteins DIDO, SHARP (also known as SPEN) and RBM15 as phosphoserine binding modules that can act as CTD readers but also recognize other phosphorylated binding partners. We report the crystal structure of SHARP SPOC in complex with CTD and identify the molecular determinants for its specific binding to phosphorylated serine-5. PHF3 and DIDO SPOC domains preferentially interact with the Pol II elongation complex, while RBM15 and SHARP SPOC domains engage with writers and readers of m6A, the most abundant RNA modification. RBM15 positively regulates m6A levels and mRNA stability in a SPOC-dependent manner, while SHARP SPOC is essential for its localization to inactive X-chromosomes. Our findings suggest that the SPOC domain is a major interface between the transcription machinery and regulators of transcription and co-transcriptional processes.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Gregor Ammann
- Department of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Andrea Neudolt
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Anna Wunder
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Lena Walch
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Stefanie Kaiser
- Department of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecčna Pot 113, 1000, Ljubljana, Slovenia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
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Saha B, Vannucci L, Saha B, Tenti P, Baral R. Evolvability and emergence of tumor heterogeneity as a space-time function. Cytokine 2023; 161:156061. [PMID: 36252436 DOI: 10.1016/j.cyto.2022.156061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/20/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022]
Abstract
The loss of control of cell proliferation, apoptosis regulation and contact inhibition leads to tumor development. While benign tumors are restricted to their primary space, i.e. where these tumors first originate, the metastatic tumors not only disseminate- facilitated by hypoxia-driven neovascularization- to distant secondary sites but also show substantial changes in metabolism, tissue architectures, gene expression profiles and immune phenotypes. All these alterations result in radio-, chemo- and immune-resistance rendering these metastatic tumor cells refractory to therapy. Since the beginning of the transformation, these factors- which influence each other- are incorporated to the developing and metastasizing tumor. As a result, the complexities in the heterogeneity of tumor progressively increase. This space-time function in the heterogeneity of tumors is generated by various conditions and factors at the genetic as well as microenvironmental levels, for example, endogenous retroviruses, methylation and epigenetic dysregulation that may be etiology-specific, cancer associated inflammation, remodeling of the extracellular matrix and mesenchymal cell shifted functions. On the one hand, these factors may cause de-differentiation of the tumor cells leading to cancer stem cells that contribute to radio-, chemo- and immune-resistance and recurrence of tumors. On the other hand, they may also enhance the heterogeneity under specific microenvironment-driven proliferation. In this editorial, we intend to underline the importance of heterogeneity in cancer progress, its evaluation and its use in correlation with the tumor evolution in a specific patient as a field of research for achieving precise patient-tailored treatments and amelioration of diagnostic (monitoring) tools and prognostic capacity.
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Affiliation(s)
- Bhaskar Saha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Luca Vannucci
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, Praha, Czech Republic.
| | - Baibaswata Saha
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, Praha, Czech Republic
| | - Paolo Tenti
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, Praha, Czech Republic
| | - Rathindranath Baral
- Chittaranjan National Cancer Institute, Shyamaprasad Mukherjee Road, Calcutta 700026, India.
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Zhou D, Zhu F, Huang ZH, Zhang H, Fan LQ, Fan JY. SPOC domain-containing protein 1 regulates the proliferation and apoptosis of human spermatogonial stem cells through adenylate kinase 4. World J Stem Cells 2022; 14:822-838. [PMID: 36619695 PMCID: PMC9813840 DOI: 10.4252/wjsc.v14.i12.822] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/07/2022] [Accepted: 11/30/2022] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Spermatogonial stem cells (SSCs) are the origin of male spermatogenesis, which can reconstruct germ cell lineage in mice. However, the application of SSCs for male fertility restoration is hindered due to the unclear mechanisms of proliferation and self-renewal in humans.
AIM To investigate the role and mechanism of SPOC domain-containing protein 1 (SPOCD1) in human SSC proliferation.
METHODS We analyzed publicly available human testis single-cell RNA sequencing (RNA-seq) data and found that SPOCD1 is predominantly expressed in SSCs in the early developmental stages. Small interfering RNA was applied to suppress SPOCD1 expression to detect the impacts of SPOCD1 inhibition on SSC proliferation and apoptosis. Subsequently, we explored the target genes of SPOCD1 using RNA-seq and confirmed their role by restoring the expression of the target genes. In addition, we examined SPOCD1 expression in some non-obstructive azoospermia (NOA) patients to explore the correlation between SPOCD1 and NOA.
RESULTS The uniform manifold approximation and projection clustering and pseudotime analysis showed that SPOCD1 was highly expressed in the early stages of SSC, and immunohistological results showed that SPOCD1 was mainly localized in glial cell line-derived neurotrophic factor family receptor alpha-1 positive SSCs. SPOCD1 knockdown significantly inhibited cell proliferation and promoted apoptosis. RNA-seq results showed that SPOCD1 knockdown significantly downregulated genes such as adenylate kinase 4 (AK4). Overexpression of AK4 in SPOCD1 knockdown cells partially reversed the phenotypic changes, indicating that AK4 is a functional target gene of SPOCD1. In addition, we found a significant downregulation of SPOCD1 expression in some NOA patients, suggesting that the downregulation of SPOCD1 may be relevant for NOA.
CONCLUSION Our study broadens the understanding of human SSC fate determination and may offer new theories on the etiology of male infertility.
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Affiliation(s)
- Dai Zhou
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, Hunan Province, China
- College of Life Sciences, Hunan Normal University, Changsha 410000, Hunan Province, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, Hunan Province, China
| | - Fang Zhu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
| | - Zeng-Hui Huang
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, Hunan Province, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, Hunan Province, China
| | - Huan Zhang
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, Hunan Province, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, Hunan Province, China
| | - Li-Qing Fan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, Hunan Province, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha 410000, Hunan Province, China
| | - Jing-Yu Fan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medicine Science, Central South University, Changsha 410000, Hunan Province, China
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
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33
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Nagirnaja L, Lopes AM, Charng WL, Miller B, Stakaitis R, Golubickaite I, Stendahl A, Luan T, Friedrich C, Mahyari E, Fadial E, Kasak L, Vigh-Conrad K, Oud MS, Xavier MJ, Cheers SR, James ER, Guo J, Jenkins TG, Riera-Escamilla A, Barros A, Carvalho F, Fernandes S, Gonçalves J, Gurnett CA, Jørgensen N, Jezek D, Jungheim ES, Kliesch S, McLachlan RI, Omurtag KR, Pilatz A, Sandlow JI, Smith J, Eisenberg ML, Hotaling JM, Jarvi KA, Punab M, Rajpert-De Meyts E, Carrell DT, Krausz C, Laan M, O’Bryan MK, Schlegel PN, Tüttelmann F, Veltman JA, Almstrup K, Aston KI, Conrad DF. Diverse monogenic subforms of human spermatogenic failure. Nat Commun 2022; 13:7953. [PMID: 36572685 PMCID: PMC9792524 DOI: 10.1038/s41467-022-35661-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022] Open
Abstract
Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human "knockouts", and, for the most part, have yet to be linked to a Mendelian trait. Integration with single-cell RNA sequencing data shows that azoospermia genes can be grouped into molecular subforms with synchronized expression patterns, and analogs of these subforms exist in mice. This analysis framework identifies groups of genes with known roles in spermatogenesis but also reveals unrecognized subforms, such as a set of genes expressed across mitotic divisions of differentiating spermatogonia. Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may provide a rational basis for disease classification.
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Affiliation(s)
- Liina Nagirnaja
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Alexandra M. Lopes
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Wu-Lin Charng
- grid.4367.60000 0001 2355 7002Department of Neurology, Washington University, St. Louis, MO USA
| | - Brian Miller
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Rytis Stakaitis
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.45083.3a0000 0004 0432 6841Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ieva Golubickaite
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.45083.3a0000 0004 0432 6841Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexandra Stendahl
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Tianpengcheng Luan
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - Corinna Friedrich
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Eisa Mahyari
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Eloise Fadial
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Laura Kasak
- grid.10939.320000 0001 0943 7661Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Katinka Vigh-Conrad
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Manon S. Oud
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Miguel J. Xavier
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Samuel R. Cheers
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - Emma R. James
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Jingtao Guo
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Timothy G. Jenkins
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Antoni Riera-Escamilla
- grid.418813.70000 0004 1767 1951Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia Spain ,grid.7080.f0000 0001 2296 0625Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Catalonia 08025 Spain
| | - Alberto Barros
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Filipa Carvalho
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Susana Fernandes
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - João Gonçalves
- grid.422270.10000 0001 2287 695XDepartamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal ,grid.10772.330000000121511713Centre for Toxicogenomics and Human Health, Nova Medical School, Lisbon, Portugal
| | - Christina A. Gurnett
- grid.4367.60000 0001 2355 7002Department of Neurology, Washington University, St. Louis, MO USA
| | - Niels Jørgensen
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Davor Jezek
- grid.4808.40000 0001 0657 4636Department of Histology and Embryology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Emily S. Jungheim
- grid.16753.360000 0001 2299 3507Department of Obstetrics and Gynecology at Northwestern University, Division of Reproductive Endocrinology, Chicago, IL USA
| | - Sabine Kliesch
- grid.16149.3b0000 0004 0551 4246Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Robert I. McLachlan
- grid.1002.30000 0004 1936 7857Hudson Institute of Medical Research and the Department of Obstetrics and Gynecology, Monash University, Clayton, VIC Australia
| | - Kenan R. Omurtag
- grid.34477.330000000122986657Department of Obstetrics and Gynecology at Washington University, Division of Reproductive Endocrinology, St. Louis, MO USA
| | - Adrian Pilatz
- grid.8664.c0000 0001 2165 8627Clinic for Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
| | - Jay I. Sandlow
- grid.30760.320000 0001 2111 8460Department of Urology, Medical College of Wisconsin, Milwaukee, WI USA
| | - James Smith
- grid.266102.10000 0001 2297 6811Department of Urology, University California San Francisco, San Francisco, CA USA
| | - Michael L. Eisenberg
- grid.168010.e0000000419368956Department of Urology, Stanford University School of Medicine, Stanford, CA USA
| | - James M. Hotaling
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Keith A. Jarvi
- grid.17063.330000 0001 2157 2938Division of Urology, Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, ON Canada
| | - Margus Punab
- grid.412269.a0000 0001 0585 7044Andrology Center, Tartu University Hospital, Tartu, Estonia ,grid.10939.320000 0001 0943 7661Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ewa Rajpert-De Meyts
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Douglas T. Carrell
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Csilla Krausz
- grid.8404.80000 0004 1757 2304Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Maris Laan
- grid.10939.320000 0001 0943 7661Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Moira K. O’Bryan
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia ,grid.1002.30000 0004 1936 7857School of Biological Sciences, Monash University, Clayton, VIC Australia
| | - Peter N. Schlegel
- grid.5386.8000000041936877XDepartment of Urology, Weill Cornell Medicine, New York, NY USA
| | - Frank Tüttelmann
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Joris A. Veltman
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Kristian Almstrup
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Kenneth I. Aston
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Donald F. Conrad
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
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Ramakrishna NB, Battistoni G, Surani MA, Hannon GJ, Miska EA. Mouse primordial germ-cell-like cells lack piRNAs. Dev Cell 2022; 57:2661-2668.e5. [PMID: 36473462 DOI: 10.1016/j.devcel.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/03/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are small RNAs bound by PIWI-clade Argonaute proteins that function to silence transposable elements (TEs). Following mouse primordial germ cell (mPGC) specification around E6.25, fetal piRNAs emerge in male gonocytes from E13.5 onward. The in vitro differentiation of mPGC-like cells (mPGCLCs) has raised the possibility of studying the fetal piRNA pathway in greater depth. However, using single-cell RNA-seq and RT-qPCR along mPGCLC differentiation, we find that piRNA pathway factors are not fully expressed in Day 6 mPGCLCs. Moreover, we do not detect piRNAs across a panel of Day 6 mPGCLC lines using small RNA-seq. Our combined efforts highlight that in vitro differentiated Day 6 mPGCLCs do not yet resemble E13.5 or later mouse gonocytes where the piRNA pathway is active. This Matters Arising paper is in response to von Meyenn et al. (2016), published in Developmental Cell. See also the correction by von Meyenn et al. published in this issue.
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Affiliation(s)
- Navin B Ramakrishna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK
| | - Giorgia Battistoni
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - M Azim Surani
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK; Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Gregory J Hannon
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK.
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
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35
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Liu P, Cuerda-Gil D, Shahid S, Slotkin RK. The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond. Annu Rev Genet 2022; 56:63-87. [DOI: 10.1146/annurev-genet-072920-015534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Within the life cycle of a living organism, another life cycle exists for the selfish genome inhabitants, which are called transposable elements (TEs). These mobile sequences invade, duplicate, amplify, and diversify within a genome, increasing the genome's size and generating new mutations. Cells act to defend their genome, but rather than permanently destroying TEs, they use chromatin-level repression and epigenetic inheritance to silence TE activity. This level of silencing is ephemeral and reversible, leading to a dynamic equilibrium between TE suppression and reactivation within a host genome. The coexistence of the TE and host genome can also lead to the domestication of the TE to serve in host genome evolution and function. In this review, we describe the life cycle of a TE, with emphasis on how epigenetic regulation is harnessed to control TEs for host genome stability and innovation.
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Affiliation(s)
- Peng Liu
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Diego Cuerda-Gil
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
- Graduate Program in the Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Saima Shahid
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
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Mann JM, Wei C, Chen C. How genetic defects in piRNA trimming contribute to male infertility. Andrology 2022. [PMID: 36263612 PMCID: PMC10115909 DOI: 10.1111/andr.13324] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/25/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022]
Abstract
In germ cells, small non-coding PIWI-interacting RNAs (piRNAs) work to silence harmful transposons to maintain genomic stability and regulate gene expression to ensure fertility. However, these piRNAs must undergo a series of steps during biogenesis to be properly loaded onto PIWI proteins and reach the correct nucleotide length. This review is focused on what we are learning about a crucial step in this process, piRNA trimming, in which pre-piRNAs are shortened to final lengths of 21-35 nucleotides. Recently, the 3'-5' exonuclease trimmer has been identified in various models as PNLDC1/PARN-1. Mutations of the piRNA trimmers in vivo lead to increased transposon expression, elevated levels of untrimmed pre-piRNAs, decreased piRNA stability, and male infertility. Here, we will discuss the role of piRNA trimmers in piRNA biogenesis and function, describe consequences of piRNA trimmer mutations using mammalian models and human patients, and examine future avenues of piRNA trimming-related study for clinical advancements for male infertility.
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Affiliation(s)
- Jeffrey M Mann
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chao Wei
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, Michigan, USA
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Wyrwoll MJ, Gaasbeek CM, Golubickaite I, Stakaitis R, Oud MS, Nagirnaja L, Dion C, Sindi EB, Leitch HG, Jayasena CN, Sironen A, Dicke AK, Rotte N, Stallmeyer B, Kliesch S, Grangeiro CHP, Araujo TF, Lasko P, D'Hauwers K, Smits RM, Ramos L, Xavier MJ, Conrad DF, Almstrup K, Veltman JA, Tüttelmann F, van der Heijden GW. The piRNA-pathway factor FKBP6 is essential for spermatogenesis but dispensable for control of meiotic LINE-1 expression in humans. Am J Hum Genet 2022; 109:1850-1866. [PMID: 36150389 PMCID: PMC9606565 DOI: 10.1016/j.ajhg.2022.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/01/2022] [Indexed: 01/25/2023] Open
Abstract
Infertility affects around 7% of the male population and can be due to severe spermatogenic failure (SPGF), resulting in no or very few sperm in the ejaculate. We initially identified a homozygous frameshift variant in FKBP6 in a man with extreme oligozoospermia. Subsequently, we screened a total of 2,699 men with SPGF and detected rare bi-allelic loss-of-function variants in FKBP6 in five additional persons. All six individuals had no or extremely few sperm in the ejaculate, which were not suitable for medically assisted reproduction. Evaluation of testicular tissue revealed an arrest at the stage of round spermatids. Lack of FKBP6 expression in the testis was confirmed by RT-qPCR and immunofluorescence staining. In mice, Fkbp6 is essential for spermatogenesis and has been described as being involved in piRNA biogenesis and formation of the synaptonemal complex (SC). We did not detect FKBP6 as part of the SC in normal human spermatocytes, but small RNA sequencing revealed that loss of FKBP6 severely impacted piRNA levels, supporting a role for FKBP6 in piRNA biogenesis in humans. In contrast to findings in piRNA-pathway mouse models, we did not detect an increase in LINE-1 expression in men with pathogenic FKBP6 variants. Based on our findings, FKBP6 reaches a "strong" level of evidence for being associated with male infertility according to the ClinGen criteria, making it directly applicable for clinical diagnostics. This will improve patient care by providing a causal diagnosis and will help to predict chances for successful surgical sperm retrieval.
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Affiliation(s)
- Margot J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Channah M Gaasbeek
- Department of Human Genetics, Radboudumc, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ieva Golubickaite
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA; Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark; Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rytis Stakaitis
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA; Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark; Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Manon S Oud
- Department of Human Genetics, Radboudumc, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Camille Dion
- MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK
| | - Emad B Sindi
- Section of Investigative Medicine, Imperial College London, London, UK
| | - Harry G Leitch
- MRC London Institute of Medical Sciences, London, UK; Institute of Clinical Sciences, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Channa N Jayasena
- Section of Investigative Medicine, Imperial College London, London, UK
| | - Anu Sironen
- Natural Resources Institute Finland, Production Systems, Jokioinen, Finland; Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ann-Kristin Dicke
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Nadja Rotte
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Birgit Stallmeyer
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology, Department of Clinical and Surgical Andrology, University Hospital of Münster, Münster, Germany
| | | | - Thaís F Araujo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Paul Lasko
- Department of Human Genetics, Radboudumc, Nijmegen, the Netherlands; Department of Biology, McGill University, Montréal, QC, Canada
| | | | - Roos M Smits
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Liliana Ramos
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Miguel J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Don F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Kristian Almstrup
- Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark; Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
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Xiao F, Wang C, Peng J, Zhou X, Ma D, Wang Y, Li Y, Chen X, Wang C. Changes in Small Noncoding RNA Expression during Chondrocyte Senescence. Cartilage 2022; 13:19476035221118165. [PMID: 35993268 PMCID: PMC9403477 DOI: 10.1177/19476035221118165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Osteoarthritis (OA) is characterized by the chronic and progressive deterioration of articular cartilage. Chondrocyte senescence could lead to a shift in the balance between extracellular matrix (ECM) component synthesis and degradation. Small noncoding RNAs (sncRNAs), including microRNAs (miRNAs), P-element-induced wimpy testis-(PIWI-) interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), and repeat-associated siRNAs (rasiRNAs), are a class of important epigenetic molecules. We aimed to gain insights into the changes and roles of sncRNA in chondrocyte senescence. DESIGN Healthy mouse postnatal chondrocytes were isolated, and a replicative aging model was constructed. We used small RNA sequencing (small RNA-seq) to generate extensive small RNA data. We identified differentially expressed sncRNAs and performed tissue-specific analysis using real-time quantitative polymerase chain reaction (qRT-PCR). β-galactosidase staining was used to detect chondrocyte senescence. The results showed that the expression profiles of sncRNA in passage 5 chondrocytes were significantly different from those in passage 0 chondrocytes. The expression of sncRNA was tissue specific. We found that 40 miRNAs were upregulated and 70 miRNAs were downregulated during chondrocyte senescence, and that miR-132-5p expression inhibition prevented chondrocyte senescence. We found that 8 piRNAs were upregulated and 17 piRNAs were downregulated during chondrocyte senescence, and that piRNA piR_025576 overexpression delayed chondrocyte senescence. We found that 24 snoRNAs were upregulated and 28 snoRNAs were downregulated during chondrocyte senescence, and that snoRNA ENSMUSG00000087935 overexpression delayed chondrocyte senescence. We found that 5 snRNAs were upregulated and 6 snRNAs were downregulated during chondrocyte senescence, and that snRNA ENSMUSG00000064682 overexpression delayed chondrocyte senescence. We found that 1 rasiRNA was upregulated and 4 rasiRNAs were downregulated during chondrocyte senescence. CONCLUSIONS These findings might provide novel insights into OA pathogenesis and contribute to the development of candidates for targeted therapeutics in OA.
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Affiliation(s)
- Fei Xiao
- Department of Orthopedic Surgery,
Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine,
Shanghai, China
| | - Chenglong Wang
- Department of Orthopedic Surgery,
Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine,
Shanghai, China
| | - Jianping Peng
- Department of Orthopedic Surgery,
Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine,
Shanghai, China
| | - Xing Zhou
- Guangxi Collaborative Innovation Center
for Biomedicine, Guangxi Medical University, Nanning, China
| | - Ding Ma
- Department of Orthopedic Surgery,
Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine,
Shanghai, China
| | - Yu Wang
- Department of Cardiology, Shidong
Hospital, Shanghai, China
| | - Yanpeng Li
- Department of Spine Surgery, Affiliated
Hospital of Jining Medical University, Jining, China
| | - Xiaodong Chen
- Department of Orthopedic Surgery,
Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine,
Shanghai, China
| | - Chuandong Wang
- Department of Orthopedic Surgery,
Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine,
Shanghai, China,Xiaodong Chen, Department of Orthopedic
Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of
Medicine, 1665 Kongjiang Road, Shanghai 200092, China.
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Di Stefano L. All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing. Cells 2022; 11:cells11162501. [PMID: 36010577 PMCID: PMC9406493 DOI: 10.3390/cells11162501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute a sizeable portion of many eukaryotic genomes. Through their mobility, they represent a major source of genetic variation, and their activation can cause genetic instability and has been linked to aging, cancer and neurodegenerative diseases. Accordingly, tight regulation of TE transcription is necessary for normal development. Chromatin is at the heart of TE regulation; however, we still lack a comprehensive understanding of the precise role of chromatin marks in TE silencing and how chromatin marks are established and maintained at TE loci. In this review, I discuss evidence documenting the contribution of chromatin-associated proteins and histone marks in TE regulation across different species with an emphasis on Drosophila and mammalian systems.
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Affiliation(s)
- Luisa Di Stefano
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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40
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Takamatsu G, Yanagi K, Koganebuchi K, Yoshida F, Lee JS, Toyama K, Hattori K, Katagiri C, Kondo T, Kunugi H, Kimura R, Kaname T, Matsushita M. Haplotype phasing of a bipolar disorder pedigree revealed rare multiple mutations of SPOCD1 gene in the 1p36-35 susceptibility locus. J Affect Disord 2022; 310:96-105. [PMID: 35504398 DOI: 10.1016/j.jad.2022.04.150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND The etiology of bipolar disorder (BD) is poorly understood. Considering the complexity of BD, pedigree-based sequencing studies focusing on haplotypes at specific loci may be practical to discover high-impact risk variants. This study comprehensively examined the haplotype sequence at 1p36-35 BD and recurrent depressive disorder (RDD) susceptibility loci. METHODS We surveyed BD families in Okinawa, Japan. We performed linkage analysis and determined the phased sequence of the affected haplotype using whole genome sequencing. We filtered rare missense variants on the haplotype. For validation, we conducted a case-control genetic association study on approximately 3000 Japanese subjects. RESULTS We identified a three-generation multiplex pedigree with BD and RDD. Strikingly, we identified a significant linkage with mood disorders (logarithm of odds [LOD] = 3.61) at 1p36-35, supported in other ancestry studies. Finally, we determined the entire sequence of the 6.4-Mb haplotype shared by all affected subjects. Moreover, we found a rare triplet of missense variants in the SPOCD1 gene on the haplotype. Notably, despite the rare frequency, one heterozygote with multiple SPOCD1 variants was identified in an independent set of 88 BD type I genotyping samples. LIMITATIONS The 1p36-35 sequence was obtained from only a single pedigree. The replicate sample was small. Short-read sequencing might miss structural variants. A polygenic risk score was not analyzed. CONCLUSION The 1p36-35 haplotype sequence may be valuable for future BD variant studies. In particular, SPOCD1 is a promising candidate gene and should be validated.
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Affiliation(s)
- Gakuya Takamatsu
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan; Department of Neuropsychiatry, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kae Koganebuchi
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Fuyuko Yoshida
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Behavioral Medicine, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Jun-Seok Lee
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan; Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kanako Toyama
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kotaro Hattori
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Bioresources, Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Chiaki Katagiri
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan; Department of Synbiotics, Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Tsuyoshi Kondo
- Department of Neuropsychiatry, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Psychiatry, Teikyo University School of Medicine, Tokyo, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Masayuki Matsushita
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
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Bhat A, Ghatage T, Bhan S, Lahane GP, Dhar A, Kumar R, Pandita RK, Bhat KM, Ramos KS, Pandita TK. Role of Transposable Elements in Genome Stability: Implications for Health and Disease. Int J Mol Sci 2022; 23:ijms23147802. [PMID: 35887150 PMCID: PMC9319628 DOI: 10.3390/ijms23147802] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Most living organisms have in their genome a sizable proportion of DNA sequences capable of mobilization; these sequences are commonly referred to as transposons, transposable elements (TEs), or jumping genes. Although long thought to have no biological significance, advances in DNA sequencing and analytical technologies have enabled precise characterization of TEs and confirmed their ubiquitous presence across all forms of life. These findings have ignited intense debates over their biological significance. The available evidence now supports the notion that TEs exert major influence over many biological aspects of organismal life. Transposable elements contribute significantly to the evolution of the genome by giving rise to genetic variations in both active and passive modes. Due to their intrinsic nature of mobility within the genome, TEs primarily cause gene disruption and large-scale genomic alterations including inversions, deletions, and duplications. Besides genomic instability, growing evidence also points to many physiologically important functions of TEs, such as gene regulation through cis-acting control elements and modulation of the transcriptome through epigenetic control. In this review, we discuss the latest evidence demonstrating the impact of TEs on genome stability and the underling mechanisms, including those developed to mitigate the deleterious impact of TEs on genomic stability and human health. We have also highlighted the potential therapeutic application of TEs.
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Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
- Correspondence: (A.B.); (T.K.P.)
| | - Trupti Ghatage
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Sonali Bhan
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Ganesh P. Lahane
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Arti Dhar
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Rakesh Kumar
- Department of Biotechnology, Shri Mata Vaishnav Devi University, Katra 182320, India;
| | - Raj K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
| | - Tej K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
- Correspondence: (A.B.); (T.K.P.)
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42
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Yu H, Chen M, Hu Y, Ou S, Yu X, Liang S, Li N, Yang M, Kong X, Sun C, Jia S, Zhang Q, Liu L, Hurst LD, Li R, Wang W, Wang J. Dynamic reprogramming of H3K9me3 at hominoid-specific retrotransposons during human preimplantation development. Cell Stem Cell 2022; 29:1031-1050.e12. [PMID: 35803225 DOI: 10.1016/j.stem.2022.06.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Reprogramming of H3K9me3-dependent heterochromatin is required for early development. How H3K9me3 is involved in early human development remains, however, largely unclear. Here, we resolve the temporal landscape of H3K9me3 during human preimplantation development and its regulation for diverse hominoid-specific retrotransposons. At the 8-cell stage, H3K9me3 reprogramming at hominoid-specific retrotransposons termed SINE-VNTR-Alu (SVA) facilitates interaction between certain promoters and SVA-derived enhancers, promoting the zygotic genome activation. In trophectoderm, de novo H3K9me3 domains prevent pluripotent transcription factors from binding to hominoid-specific retrotransposons-derived regulatory elements for inner cell mass (ICM)-specific genes. H3K9me3 re-establishment at SVA elements in the ICM is associated with higher transcription of DNA repair genes, when compared with naive human pluripotent stem cells. Our data demonstrate that species-specific reorganization of H3K9me3-dependent heterochromatin at hominoid-specific retrotransposons plays important roles during early human development, shedding light on how the epigenetic regulation for early development has evolved in mammals.
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Affiliation(s)
- Hanwen Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Manqi Chen
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Yuanlang Hu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Songbang Ou
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiu Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Shiqi Liang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mingzhu Yang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xuhui Kong
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Shiqi Jia
- The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Qingxue Zhang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Ruiqi Li
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Wenjun Wang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Jichang Wang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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43
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Shirane K. The dynamic chromatin landscape and mechanisms of DNA methylation during mouse germ cell development. Gene 2022; 97:3-14. [PMID: 35431282 DOI: 10.1266/ggs.21-00069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Epigenetic marks including DNA methylation (DNAme) play a critical role in the transcriptional regulation of genes and retrotransposons. Defects in DNAme are detected in infertility, imprinting disorders and congenital diseases in humans, highlighting the broad importance of this epigenetic mark in both development and disease. While DNAme in terminally differentiated cells is stably propagated following cell division by the maintenance DNAme machinery, widespread erasure and subsequent de novo establishment of this epigenetic mark occur early in embryonic development as well as in germ cell development. Combined with deep sequencing, low-input methods that have been developed in the past several years have enabled high-resolution and genome-wide mapping of both DNAme and histone post-translational modifications (PTMs) in rare cell populations including developing germ cells. Epigenome studies using these novel methods reveal an unprecedented view of the dynamic chromatin landscape during germ cell development. Furthermore, integrative analysis of chromatin marks in normal germ cells and in those deficient in chromatin-modifying enzymes uncovers a critical interplay between histone PTMs and de novo DNAme in the germline. This review discusses work on mechanisms of the erasure and subsequent de novo DNAme in mouse germ cells as well as the outstanding questions relating to the regulation of the dynamic chromatin landscape in germ cells.
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Affiliation(s)
- Kenjiro Shirane
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University
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Lin Z, Chen L, Wu T, Zhang Y, Huang X, Chen Y, Chen J, Xu Y. Prognostic Value of SPOCD1 in Esophageal Squamous Cell Carcinoma: A Comprehensive Study Based on Bioinformatics and Validation. Front Genet 2022; 13:872026. [PMID: 35646092 PMCID: PMC9130929 DOI: 10.3389/fgene.2022.872026] [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: 02/09/2022] [Accepted: 04/20/2022] [Indexed: 12/24/2022] Open
Abstract
In the study, we aimed to explore and analyze the potential function of SPOC Domain Containing 1 (SPOCD1) in esophageal squamous cell carcinoma (ESCC). We performed a comprehensive analysis of gene expression of SPOCD1 and its corresponding clinicopathological features in ESCC. In particular, the correlation between SPOCD1 and ESCC was evaluated using a wide range of analysis tools and databases, including TCGA, GTEx, GenePattern, CellMiner, GDSC, and STRING datasets. Different bioinformatics analyses, including differential expression analysis, mutation analysis, drug sensitivity analysis, function analysis, pathway analysis, co-expression network analysis, immune cell infiltration analysis, and survival analysis, were carried out to comprehensively explore the potential molecular mechanisms and functional effects of SPOCD1 on the initiation and progression of ESCC. The expression of SPOCD1 was upregulated in ESCC tissues compared to those in normal tissues. In the high SPOCD1 expression group, we found apparent mutations in TP53, TTN, and MUC16 genes, which were 92, 36, and 18%, respectively. GO and KEGG enrichment analysis of SPOCD1 and its co-expressed genes demonstrated that it may serve as an ESCC oncogene by regulating the genes expression in the essential functions and pathways of tumorigenesis, such as glycosaminoglycan binding, Cytokine-cytokine receptor interaction, and Ras signaling pathway. Besides, the immune cell infiltration results revealed that SPOCD1 expression was positively correlated with Macrophages M0 and Mast cells activated cells, and negatively correlated with plasma cells and T cells follicular helper cell infiltration. Finally, ESCC patients with high expression of SPOCD1 indicated poor overall survival. qRT-PCR demonstrated that the SPOCD1 expression in ESCC tissues was significantly higher than adjacent tissues (p < 0.001). Our study indicated that SPOCD1 was increased in ESCC tissues. The current data support the oncogenic role of SPOCD1 in the occurrence and development of ESCC. Most importantly, SPOCD1 might be an independent prognostic factor for ESCC patients.
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Affiliation(s)
- Zhizhong Lin
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Lin Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Tingting Wu
- The School of Nusing, Fujian Medical University, Fuzhou, China.,Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Yiping Zhang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Xinyi Huang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Yuanmei Chen
- Department of Thoracic Surgery, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Junqiang Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Yuanji Xu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
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Wang X, Gou LT, Liu MF. Noncanonical Functions of PIWIL1/piRNAs in animal male germ cells and human diseases. Biol Reprod 2022; 107:101-108. [PMID: 35403682 DOI: 10.1093/biolre/ioac073] [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: 12/23/2021] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
PIWI proteins and PIWI-interacting RNAs (piRNAs) are specifically expressed in animal germlines and play essential roles during gametogenesis in animals. The primary function of PIWI/piRNAs is known to silence transposable elements for protecting genome integrity in animal germlines, while their roles beyond silencing transposons are also documented by us and others. In particular, we show that mouse PIWIL1 (MIWI)/piRNAs play a dual role in regulating protein-coding genes in mouse spermatids through interacting with different protein factors in a developmental stage-dependent manner, including translationally activating a subset of ARE-containing mRNAs in round spermatids and inducing massive mRNA degradation in late spermatids. We further show that MIWI is eliminated through the ubiquitin-26S proteasome pathway during late spermiogenesis. By exploring the biological function of MIWI ubiquitination by APC/C, we identified ubiquitination-deficient mutations in human PIWIL1 of infertile men and further established their causative role in male infertility in mouse model, supporting PIWIL1 as a human male infertility-relevant gene. Additionally, we reported that PIWIL1, aberrantly induced in human tumors, functions as an oncoprotein in a piRNA-independent manner in cancer cells. In the current review, we summarize our latest findings regarding the roles and mechanisms of PIWIL1 and piRNAs in mouse spermatids and human diseases, and discuss the related works in the field.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Lan-Tao Gou
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
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Vandewege MW, Patt RN, Merriman DK, Ray DA, Hoffmann FG. The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements. RNA (NEW YORK, N.Y.) 2022; 28:609-621. [PMID: 35064043 PMCID: PMC8925971 DOI: 10.1261/rna.078862.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs) are genomic parasites that can propagate throughout host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and germline mobilization is a challenge to genome integrity. There are defenses against TE proliferation and the PIWI/piRNA defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The 13-lined ground squirrel provides the opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. To do so, we compared the PIWI/piRNA dynamics in squirrels to observations from the rabbit and mouse. Despite a lack of young insertions in squirrels, TEs were still actively transcribed at higher levels compared to mouse and rabbit. All three Piwi genes were not expressed, prior to P8 in squirrel testis, and there was little TE expression change with the onset of Piwi expression. We also demonstrated there was not a major expression change in the young squirrel LINE families in the transition from juvenile to adult testis in contrast to young mouse and rabbit LINE families. These observations lead us to conclude that PIWI suppression, was weaker for squirrel LINEs and SINEs and did not strongly reduce their transcription. We speculate that, although the PIWI/piRNA system is adaptable to novel TE threats, transcripts from TEs that are no longer threatening receive less attention from PIWI proteins.
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Affiliation(s)
- Michael W Vandewege
- Department of Biology, Eastern New Mexico University, Portales, New Mexico 88130, USA
| | - Roy N Patt
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas 78245-0549, USA
| | - Dana K Merriman
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, Wisconsin 54901, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, USA
- Institute of Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi 39762, USA
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Zhong N, Nong X, Diao J, Yang G. piRNA-6426 increases DNMT3B-mediated SOAT1 methylation and improves heart failure. Aging (Albany NY) 2022; 14:2678-2694. [PMID: 35354120 PMCID: PMC9004576 DOI: 10.18632/aging.203965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/28/2022] [Indexed: 12/02/2022]
Abstract
PURPOSE Previous studies found that piRNAs could participate in disease progression by regulating DNA methylation, but there are few reports on their roles in heart failure (HF). METHODS The level of piRNA-6426 in the venous blood of HF patients and volunteers was detected by RT-qPCR. Hypoxia-induced cardiomyocytes were transfected with lentiviral-mediated piRNA-6426 overexpression vector (LV-piRNA-6426) or together with LV-DNMT3B, and then cell viability and apoptosis, glucose uptake, ROS production, LDH activity and secretion of inflammatory factors were detected. Also, cardiomyocytes were transfected with LV-piRNA-6426, sh-piRNA-6426 or sh-SOAT1, as well as LV-piRNA-6426 or together with LV-DNMT3B or sh-DNMT3B. The interaction between piRNA-6426 and methyltransferase 3B (DNMT3B) was detected with RNA immunoprecipitation (RIP). And the methylation level of sterol o-acyltransferase 1 (SOAT1) and the enrichment of DNMT3B in the SOAT1 promoter were detected with Methylation-specific PCR (MSP) and ChIP assays. Then a HF rat model constructed with coronary artery occlusion method was injected with LV-piRNA-6426, and heart function index and infarcted area of rat heart were detected. RESULTS piRNA-6426 expression was decreased in the blood of HF patients. LV-piRNA-6426 transfection increased the enrichment of DNMT3B in SOAT1 promoter, thereby inhibiting the expression level of SOAT1, and decreased hypoxia-induced oxidative stress and inflammation in cardiomyocytes, while sh-piRNA-6426 transfection had the opposite effect. And LV-DNMT3B transfection enhanced the effect of LV-piRNA-6426 transfection on SOAT1 expression and cardiomyocyte dysfunction. Injection of LV-piRNA-6426 significantly inhibited the heart dysfunction of rats. CONCLUSIONS piRNA-6426 overexpression inhibits hypoxia-induced cardiomyocyte dysfunction and HF by promoting DNMT3B-mediated methylation of SOAT1 promoter.
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Affiliation(s)
- Nier Zhong
- Department of Cardiology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Xiting Nong
- Department of Endocrinology, Xi’an Central Hospital, Xi’an, China
| | - Jiayu Diao
- Department of Cardiology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Guang Yang
- Department of Cardiology, Shaanxi Provincial People’s Hospital, Xi’an, China
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Fukuda K, Makino Y, Kaneko S, Shimura C, Okada Y, Ichiyanagi K, Shinkai Y. Transcriptional states of retroelement-inserted regions and specific KRAB zinc finger protein association are correlated with DNA methylation of retroelements in human male germ cells. eLife 2022; 11:76822. [PMID: 35315771 PMCID: PMC8967385 DOI: 10.7554/elife.76822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/21/2022] [Indexed: 11/14/2022] Open
Abstract
DNA methylation, repressive histone modifications, and PIWI-interacting RNAs are essential for controlling retroelement silencing in mammalian germ lines. Dysregulation of retroelement silencing is associated with male sterility. Although retroelement silencing mechanisms have been extensively studied in mouse germ cells, little progress has been made in humans. Here, we show that the Krüppel-associated box domain zinc finger proteins are associated with DNA methylation of retroelements in human primordial germ cells. Further, we show that the hominoid-specific retroelement SINE-VNTR-Alus (SVA) is subjected to transcription-directed de novo DNA methylation during human spermatogenesis. The degree of de novo DNA methylation in SVAs varies among human individuals, which confers significant inter-individual epigenetic variation in sperm. Collectively, our results highlight potential molecular mechanisms for the regulation of retroelements in human male germ cells.
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Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, RIKEN, Wako, Japan
| | - Yoshinori Makino
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Satoru Kaneko
- Department of Obstetrics and Gynecology, Tokyo Dental College Ichikawa General Hospital, Ichikawa, Japan
| | | | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
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Zhou S, Sakashita A, Yuan S, Namekawa SH. Retrotransposons in the Mammalian Male Germline. Sex Dev 2022:1-19. [PMID: 35231923 DOI: 10.1159/000520683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/25/2021] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are a subset of DNA sequences that constitute a large part of the mammalian genome. They can translocate autonomously or non-autonomously, potentially jeopardizing the heritable germline genome. Retrotransposons coevolved with the host genome, and the germline is the prominent battlefield between retrotransposons and the host genome to maximize their mutual fitness. Host genomes have developed various mechanisms to suppress and control retrotransposons, including DNA methylation, histone modifications, and Piwi-interacting RNA (piRNA), for their own benefit. Thus, rapidly evolved retrotransposons often acquire positive functions, including gene regulation within the germline, conferring reproductive fitness in a species over the course of evolution. The male germline serves as an ideal model to examine the regulation and evolution of retrotransposons, resulting in genomic co-evolution with the host genome. In this review, we summarize and discuss the regulatory mechanisms of retrotransposons, stage-by-stage, during male germ cell development, with a particular focus on mice as an extensively studied mammalian model, highlighting suppression mechanisms and emerging functions of retrotransposons in the male germline.
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Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
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50
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Almeida MV, Vernaz G, Putman AL, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet 2022; 38:529-553. [DOI: 10.1016/j.tig.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022]
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