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Guo C, Wang X, Ren H. Databases and computational methods for the identification of piRNA-related molecules: A survey. Comput Struct Biotechnol J 2024; 23:813-833. [PMID: 38328006 PMCID: PMC10847878 DOI: 10.1016/j.csbj.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/31/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs (ncRNAs) that plays important roles in many biological processes and major cancer diagnosis and treatment, thus becoming a hot research topic. This study aims to provide an in-depth review of computational piRNA-related research, including databases and computational models. Herein, we perform literature analysis and use comparative evaluation methods to summarize and analyze three aspects of computational piRNA-related research: (i) computational models for piRNA-related molecular identification tasks, (ii) computational models for piRNA-disease association prediction tasks, and (iii) computational resources and evaluation metrics for these tasks. This study shows that computational piRNA-related research has significantly progressed, exhibiting promising performance in recent years, whereas they also suffer from the emerging challenges of inconsistent naming systems and the lack of data. Different from other reviews on piRNA-related identification tasks that focus on the organization of datasets and computational methods, we pay more attention to the analysis of computational models, algorithms, and performances that aim to provide valuable references for computational piRNA-related identification tasks. This study will benefit the theoretical development and practical application of piRNAs by better understanding computational models and resources to investigate the biological functions and clinical implications of piRNA.
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Affiliation(s)
- Chang Guo
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Han Ren
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
- Laboratory of Language and Artificial Intelligence, Guangdong University of Foreign Studies, Guangzhou 510420, China
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Uneme Y, Maeda R, Nakayama G, Narita H, Takeda N, Hiramatsu R, Nishihara H, Nakato R, Kanai Y, Araki K, Siomi MC, Yamanaka S. Morc1 reestablishes H3K9me3 heterochromatin on piRNA-targeted transposons in gonocytes. Proc Natl Acad Sci U S A 2024; 121:e2317095121. [PMID: 38502704 PMCID: PMC10990106 DOI: 10.1073/pnas.2317095121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/23/2024] [Indexed: 03/21/2024] Open
Abstract
To maintain fertility, male mice re-repress transposable elements (TEs) that were de-silenced in the early gonocytes before their differentiation into spermatogonia. However, the mechanism of TE silencing re-establishment remains unknown. Here, we found that the DNA-binding protein Morc1, in cooperation with the methyltransferase SetDB1, deposits the repressive histone mark H3K9me3 on a large fraction of activated TEs, leading to heterochromatin. Morc1 also triggers DNA methylation, but TEs targeted by Morc1-driven DNA methylation only slightly overlapped with those repressed by Morc1/SetDB1-dependent heterochromatin formation, suggesting that Morc1 silences TEs in two different manners. In contrast, TEs regulated by Morc1 and Miwi2, the nuclear PIWI-family protein, almost overlapped. Miwi2 binds to PIWI-interacting RNAs (piRNAs) that base-pair with TE mRNAs via sequence complementarity, while Morc1 DNA binding is not sequence specific, suggesting that Miwi2 selects its targets, and then, Morc1 acts to repress them with cofactors. A high-ordered mechanism of TE repression in gonocytes has been identified.
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Affiliation(s)
- Yuta Uneme
- Department of Biophysics and Biochemistry, Faculty of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Ryu Maeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Gen Nakayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Haruka Narita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Naoki Takeda
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto860-0811, Japan
| | - Ryuji Hiramatsu
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo113-8657, Japan
| | - Hidenori Nishihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara631-8505, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo113-0032, Japan
| | - Yoshiakira Kanai
- Department of Veterinary Anatomy, The University of Tokyo, Tokyo113-8657, Japan
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto860-0811, Japan
- Faculty of Life Sciences, Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Honjo, Kumamoto860-8556, Japan
| | - Mikiko C. Siomi
- Department of Biophysics and Biochemistry, Faculty of Science, The University of Tokyo, Tokyo113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo113-0032, Japan
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Hou L, Liu W, Zhang H, Li R, Liu M, Shi H, Wu L. Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes. Genome Biol 2024; 25:80. [PMID: 38532500 DOI: 10.1186/s13059-024-03214-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Small RNAs are essential for germ cell development and fertilization. However, fundamental questions remain, such as the level of conservation in small RNA composition between species and whether small RNAs control transposable elements in mammalian oocytes. RESULTS Here, we use high-throughput sequencing to profile small RNAs and poly(A)-bearing long RNAs in oocytes of 12 representative vertebrate species (including 11 mammals). The results show that miRNAs are generally expressed in the oocytes of each representative species (although at low levels), whereas endo-siRNAs are specific to mice. Notably, piRNAs are predominant in oocytes of all species (except mice) and vary widely in length. We find PIWIL3-associated piRNAs are widespread in mammals and generally lack 3'-2'-O-methylation. Additionally, sequence identity is low between homologous piRNAs in different species, even among those present in syntenic piRNA clusters. Despite the species-specific divergence, piRNAs retain the capacity to silence younger TE subfamilies in oocytes. CONCLUSIONS Collectively, our findings illustrate a high level of diversity in the small RNA populations of mammalian oocytes. Furthermore, we identify sequence features related to conserved roles of small RNAs in silencing TEs, providing a large-scale reference for future in-depth study of small RNA functions in oocytes.
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Affiliation(s)
- Li Hou
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wei Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hongdao Zhang
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ronghong Li
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Miao Liu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200032, China
| | - Huijuan Shi
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200032, China
| | - Ligang Wu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Zhang M, Shi J, Zhu Y, Pan H, Song L, Deng H. Polystyrene nanoplastics induce vascular stenosis via regulation of the PIWI-interacting RNA expression profile. Environ Pollut 2024; 345:123441. [PMID: 38272162 DOI: 10.1016/j.envpol.2024.123441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 01/27/2024]
Abstract
Nanoplastics (NPs) have become common worldwide and attracted increasing attention due to their serious toxic effects. Owing to their higher surface area and volume ratios and ability to easily enter tissues, NPs impose more serious toxic effects than microplastics. However, the effect of NP exposure on vascular stenosis remains unclear. To measure the effects of polystyrene NP (PS-NP) exposure on vascular toxicity, we conducted analyses of blood biochemical parameters, pathological histology, high-throughput sequencing, and bioinformatics. Red fluorescent PS-NPs (100 nm) were effectively uptake by mouse vascular arterial tissue. The uptake of PS-NPs resulted in vascular toxicity, including alterations in lipid metabolism and thickening of the arterial wall. Based on PIWI-interacting RNA (piRNA) sequencing, 1547 and 132 differentially expressed piRNAs (DEpiRNAs) were detected in the PS-NP treatment group after 180 and 30 days, including 787 and 86 upregulated and 760 and 46 downregulated compared with the control group, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that the target genes of DEpiRNAs were mostly involved in cell growth and cell motility-related signaling, such as the MAPK signaling pathway. This is the first study to highlight the alteration in piRNA levels in mouse vascular arterial tissue after PS-NP exposure. This study adds to the knowledge regarding the regulatory mechanism of pathological changes induced by PS-NP exposure.
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Affiliation(s)
- Min Zhang
- Division of Cardiology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 200336, China.
| | - Jun Shi
- Shanghai Institute of Pollution Control and Ecological Security, Key Laboratory of Yangtze River Water Environment Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Yiqian Zhu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Huichao Pan
- Division of Cardiology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 200336, China
| | - Lei Song
- Division of Cardiology, Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 200336, China
| | - Huiping Deng
- Shanghai Institute of Pollution Control and Ecological Security, Key Laboratory of Yangtze River Water Environment Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, China
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Li Z, Liu X, Zhang Y, Li Y, Zhou L, Yuan S. FBXO24 modulates mRNA alternative splicing and MIWI degradation and is required for normal sperm formation and male fertility. eLife 2024; 12:RP91666. [PMID: 38470475 DOI: 10.7554/elife.91666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Spermiogenesis is a critical, post-meiotic phase of male gametogenesis, in which the proper gene expression is essential for sperm maturation. However, the underFlying molecular mechanism that controls mRNA expression in the round spermatids remains elusive. Here, we identify that FBXO24, an orphan F-box protein, is highly expressed in the testis of humans and mice and interacts with the splicing factors (SRSF2, SRSF3, and SRSF9) to modulate the gene alternative splicing in the round spermatids. Genetic mutation of FBXO24 in mice causes many abnormal splicing events in round spermatids, thus affecting a large number of critical genes related to sperm formation that were dysregulated. Further molecular and phenotypical analyses revealed that FBXO24 deficiency results in aberrant histone retention, incomplete axonemes, oversized chromatoid body, and abnormal mitochondrial coiling along sperm flagella, ultimately leading to male sterility. In addition, we discovered that FBXO24 interacts with MIWI and SCF subunits and mediates the degradation of MIWI via K48-linked polyubiquitination. Furthermore, we show that FBXO24 depletion could lead to aberrant piRNA production in testes, which suggests FBXO24 is required for normal piRNA counts. Collectively, these data demonstrate that FBXO24 is essential for sperm formation by regulating mRNA alternative splicing and MIWI degradation during spermiogenesis.
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Affiliation(s)
- Zhiming Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xingping Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liquan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan, China
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Rajeev R, Mishra RK, Khosla S. DNMT3L interacts with Piwi and modulates the expression of piRNAs in transgenic Drosophila. Epigenomics 2024; 16:375-388. [PMID: 38440884 DOI: 10.2217/epi-2023-0405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
Aim: To explore the role of Piwi protein and piRNAs in DNMT3L-mediated epigenetic inheritance. Materials & methods: Transgenic Drosophila were used to examine the effect of ectopically expressed DNMT3L on the profile of piRNAs by sequencing of small RNAs. Results & conclusion: Our previous work showed accumulation and inheritance of epimutations across multiple generations in transgenic DNMT3L Drosophila. Here, we show interaction of DNMT3L with Piwi and a significant alteration in the piRNA profile across multiple generations in transgenic Drosophila. In the light of its interaction with histone H1, we propose that in addition to its role of modulating core histone modifications, DNMT3L allows for inheritance of epigenetic information through its collaboration with Piwi, piRNAs and histone H1.
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Affiliation(s)
- Ramisetti Rajeev
- Centre for DNA Fingerprinting & Diagnostics, Hyderabad, 500 039, India
- Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular & Molecular Biology, Hyderabad, 500 007, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting & Diagnostics, Hyderabad, 500 039, India
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
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Li J, Hong X, Jiang M, Kho AT, Tiwari A, Wang AL, Chase RP, Celedón JC, Weiss ST, McGeachie MJ, Tantisira KG. A novel piwi-interacting RNA associates with type 2-high asthma phenotypes. J Allergy Clin Immunol 2024; 153:695-704. [PMID: 38056635 DOI: 10.1016/j.jaci.2023.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/14/2023] [Accepted: 10/25/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs), comprising the largest noncoding RNA group, regulate transcriptional processes. Whether piRNAs are associated with type 2 (T2)-high asthma is unknown. OBJECTIVE We sought to investigate the association between piRNAs and T2-high asthma in childhood asthma. METHODS We sequenced plasma samples from 462 subjects in the Childhood Asthma Management Program (CAMP) as the discovery cohort and 1165 subjects in the Genetics of Asthma in Costa Rica Study (GACRS) as a replication cohort. Sequencing reads were filtered first, and piRNA reads were annotated and normalized. Linear regression was used for the association analysis of piRNAs and peripheral blood eosinophil count, total serum IgE level, and long-term asthma exacerbation in children with asthma. Mediation analysis was performed to investigate the effect direction. We then ascertained if the circulating piRNAs were present in asthmatic airway epithelial cells in a Gene Expression Omnibus (GEO; www.ncbi.nlm.nih.gov/geo) public data set. RESULTS Fifteen piRNAs were significantly associated with eosinophil count in CAMP (P ≤ .05), and 3 were successfully replicated in GACRS. Eleven piRNAs were associated with total IgE in CAMP, and one of these was replicated in GACRS. All 22 significant piRNAs were identified in epithelial cells in vitro, and 6 of these were differentially expressed between subjects with asthma and healthy controls. Fourteen piRNAs were associated with long-term asthma exacerbation, and effect of piRNAs on long-term asthma exacerbation are mediated through eosinophil count and serum IgE level. CONCLUSION piRNAs are associated with peripheral blood eosinophils and total serum IgE in childhood asthma and may play important roles in T2-high asthma.
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Affiliation(s)
- Jiang Li
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Shenzhen Key Laboratory of Chinese Medicine Active Substance Screening and Translational Research, Shenzhen, China
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Mingye Jiang
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Alvin T Kho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Computational Health Informatics Program, Boston Children's Hospital, Boston, Mass
| | - Anshul Tiwari
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Alberta L Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Juan C Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pa
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Partners Personalized Medicine, Partners Healthcare, Boston, Mass
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Department of Pediatrics, Division of Respiratory Medicine, University of California-San Diego, La Jolla, Calif.
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Pastore B, Hertz HL, Tang W. Pre- piRNA trimming safeguards piRNAs against erroneous targeting by RNA-dependent RNA polymerase. Cell Rep 2024; 43:113692. [PMID: 38244197 PMCID: PMC10949418 DOI: 10.1016/j.celrep.2024.113692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
The Piwi/Piwi-interacting RNA (piRNA) pathway protects genome integrity in animal germ lines. Maturation of piRNAs involves nucleolytic processing at both 5' and 3' ends. The ribonuclease PARN-1 and its orthologs mediate piRNA 3' trimming in worms, insects, and mammals. However, the significance of this evolutionarily conserved processing step is not fully understood. Employing C. elegans as a model, we recently discovered that 3' trimming protects piRNAs against non-templated nucleotide additions and degradation. Here, we find that worms lacking PARN-1 accumulate an uncharacterized RNA species termed anti-piRNAs, which are antisense to piRNAs. Anti-piRNAs associate with Piwi proteins, are 17-19 nucleotides long, and begin with 5' guanine or adenine. Untrimmed pre-piRNAs are misdirected by the terminal nucleotidyltransferase RDE-3 and RNA-dependent RNA polymerase EGO-1, leading to the formation of anti-piRNAs. This work identifies a class of small RNAs in parn-1 mutants and provides insight into the activities of RDE-3, EGO-1, and Piwi proteins.
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Affiliation(s)
- Benjamin Pastore
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Hannah L Hertz
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Wen Tang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
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Gál L, Fóthi Á, Orosz G, Nagy S, Than NG, Orbán TI. Exosomal small RNA profiling in first-trimester maternal blood explores early molecular pathways of preterm preeclampsia. Front Immunol 2024; 15:1321191. [PMID: 38455065 PMCID: PMC10917917 DOI: 10.3389/fimmu.2024.1321191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/25/2024] [Indexed: 03/09/2024] Open
Abstract
Introduction Preeclampsia (PE) is a severe obstetrical syndrome characterized by new-onset hypertension and proteinuria and it is often associated with fetal intrauterine growth restriction (IUGR). PE leads to long-term health complications, so early diagnosis would be crucial for timely prevention. There are multiple etiologies and subtypes of PE, and this heterogeneity has hindered accurate identification in the presymptomatic phase. Recent investigations have pointed to the potential role of small regulatory RNAs in PE, and these species, which travel in extracellular vesicles (EVs) in the circulation, have raised the possibility of non-invasive diagnostics. The aim of this study was to investigate the behavior of exosomal regulatory small RNAs in the most severe subtype of PE with IUGR. Methods We isolated exosomal EVs from first-trimester peripheral blood plasma samples of women who later developed preterm PE with IUGR (n=6) and gestational age-matched healthy controls (n=14). The small RNA content of EVs and their differential expression were determined by next-generation sequencing and further validated by quantitative real-time PCR. We also applied the rigorous exceRpt bioinformatics pipeline for small RNA identification, followed by target verification and Gene Ontology analysis. Results Overall, >2700 small RNAs were identified in all samples and, of interest, the majority belonged to the RNA interference (RNAi) pathways. Among the RNAi species, 16 differentially expressed microRNAs were up-regulated in PE, whereas up-regulated and down-regulated members were equally found among the six identified Piwi-associated RNAs. Gene ontology analysis of the predicted small RNA targets showed enrichment of genes in pathways related to immune processes involved in decidualization, placentation and embryonic development, indicating that dysregulation of the induced small RNAs is connected to the impairment of immune pathways in preeclampsia development. Finally, the subsequent validation experiments revealed that the hsa_piR_016658 piRNA is a promising biomarker candidate for preterm PE associated with IUGR. Discussion Our rigorously designed study in a homogeneous group of patients unraveled small RNAs in circulating maternal exosomes that act on physiological pathways dysregulated in preterm PE with IUGR. Therefore, our small RNA hits are not only suitable biomarker candidates, but the revealed biological pathways may further inform us about the complex pathology of this severe PE subtype.
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Affiliation(s)
- Luca Gál
- Gene Regulation Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ábel Fóthi
- Gene Regulation Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Gergő Orosz
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Sándor Nagy
- Department of Obstetrics and Gynecology, Petz Aladár University Teaching Hospital, Győr, Hungary
- Faculty of Health and Sport Sciences, Széchenyi István University, Győr, Hungary
| | - Nándor Gábor Than
- Systems Biology of Reproduction Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
- Maternity Private Clinic of Obstetrics and Gynecology, Budapest, Hungary
- Genesis Theranostix Group, Budapest, Hungary
| | - Tamás I. Orbán
- Gene Regulation Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
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Zhang Y, Jiao X, Wang T, Yue X, Wang Y, Cai B, Wang C, Lu S. piRNA mmu_piR_037459 suppression alleviated the degeneration of chondrocyte and cartilage. Int Immunopharmacol 2024; 128:111473. [PMID: 38266448 DOI: 10.1016/j.intimp.2023.111473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/13/2023] [Accepted: 12/29/2023] [Indexed: 01/26/2024]
Abstract
OBJECTIVE Osteoarthritis (OA) is a prevalent chronic degenerative joint ailment. Its primary pathological characteristics encompass degeneration of articular cartilage, inflammation of the synovium, and alterations in the subchondral bone proximate to the cartilage. Chondrocytes, as the sole cell type within articular cartilage, assume a crucial role in upholding the dynamic equilibrium between anabolic and catabolic processes within the extracellular matrix of articular cartilage. IL-1β stands as a pivotal inflammatory factor that instigates cartilage degeneration. piRNA, categorized as a subset of brief non-coding RNAs spanning nucleotide lengths of 26-31nt, assumes a significant regulatory role in cellular function. METHODS Small RNA sequencing and quantitative PCR (qPCR) were employed to investigate the impact of the inflammatory factor IL-1β on piRNA expression within chondrocytes. The regulation of mmu_piR_037459 expression in chondrocytes was achieved using piRNA mimics and inhibitors. Additionally, collagen II expression was assessed through both qPCR and Western blot analysis. Chondrocyte apoptosis was evaluated via flow cytometry and clonogenesis assays. To assess the influence of mmu_piR_037459 on osteoarthritis, a mouse model of anterior cruciate ligament transection (ACLT) was established. Furthermore, the regulatory effect of mmu_piR_037459 on USP7 was investigated using bioinformatics and a luciferase reporter gene assay. RESULTS mmu_piR_037459 inhibited the expression of collagen II in chondrocytes, inhibited the proliferation of chondrocytes, and promoted the apoptosis of chondrocytes. mmu_piR_037459 affected the function of chondrocytes by regulating the expression of USP7. Inhibition of mmu_piR_037459 expression could promote chondrocyte proliferation, inhibit chondrocyte apoptosis, and alleviate the degeneration of OA cartilage. CONCLUSIONS This study suggests that mmu_piR_037459 maybe a new therapeutic targets and strategies for the treatment of OA.
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Affiliation(s)
- Yuxin Zhang
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Department of Rehabilitation Medicine, Huangpu Branch, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai 200011, China; Shanghai Key Laboratory of Orthopedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xin Jiao
- Shanghai Key Laboratory of Orthopedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Tianchang Wang
- Shanghai Key Laboratory of Orthopedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xiaokun Yue
- Shanghai Key Laboratory of Orthopedic Implants, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Yijia Wang
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Bin Cai
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Department of Rehabilitation Medicine, Huangpu Branch, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Shenji Lu
- Department of Rehabilitation Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Department of Rehabilitation Medicine, Huangpu Branch, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
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Nagainallur Ravichandran S, Das D, Dayananda EK, Dey A, Banerjee A, Sun-Zhang A, Zhang H, Sun XF, Pathak S. A Review on Emerging Techniques for Diagnosis of Colorectal Cancer. Cancer Invest 2024; 42:119-140. [PMID: 38404236 DOI: 10.1080/07357907.2024.2315443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
Common detection methods in practice for diagnosing colorectal cancer (CRC) are painful and invasive leading to less participation of individuals for CRC diagnosis. Whereas, improved or enhanced imaging systems and other minimally invasive techniques with shorter detection times deliver greater detail and less discomfort in individuals. Thus, this review is a summary of the diagnostic tests, ranging from the simple potential use in developing a flexible CRC treatment to the patient's potential benefits in receiving less invasive procedures and the advanced treatments that might provide a better assessment for the diagnosis of CRC and reduce the mortality related to CRC.
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Affiliation(s)
- Shruthi Nagainallur Ravichandran
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, India
| | - Diptimayee Das
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, India
| | - Erica Katriel Dayananda
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, India
| | - Amit Dey
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, India
| | - Antara Banerjee
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, India
| | - Alexander Sun-Zhang
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Hong Zhang
- Faculty of Medicine and Health, School of Medical Sciences, Orebro University, Örebro, Sweden
| | - Xiao-Feng Sun
- Division of Oncology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Surajit Pathak
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai, India
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Hernández-Contreras KA, Martínez-Díaz JA, Hernández-Aguilar ME, Herrera-Covarrubias D, Rojas-Durán F, Chi-Castañeda LD, García-Hernández LI, Aranda-Abreu GE. Alterations of mRNAs and Non-coding RNAs Associated with Neuroinflammation in Alzheimer's Disease. Mol Neurobiol 2024:10.1007/s12035-023-03908-5. [PMID: 38236345 DOI: 10.1007/s12035-023-03908-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024]
Abstract
Alzheimer's disease is a neurodegenerative pathology whose pathognomonic hallmarks are increased generation of β-amyloid (Aβ) peptide, production of hyperphosphorylated (pTau), and neuroinflammation. The last is an alteration closely related to the progression of AD and although it is present in multiple neurodegenerative diseases, the pathophysiological events that characterize neuroinflammatory processes vary depending on the disease. In this article, we focus on mRNA and non-coding RNA alterations as part of the pathophysiological events characteristic of neuroinflammation in AD and the influence of these alterations on the course of the disease through interaction with multiple RNAs related to the generation of Aβ, pTau, and neuroinflammation itself.
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Affiliation(s)
- Karla Aketzalli Hernández-Contreras
- Doctorado en Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Jorge Antonio Martínez-Díaz
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - María Elena Hernández-Aguilar
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Deissy Herrera-Covarrubias
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Fausto Rojas-Durán
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Lizbeth Donají Chi-Castañeda
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Luis Isauro García-Hernández
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Gonzalo Emiliano Aranda-Abreu
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México.
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Zhang X, Wang X, Yu F, Wang C, Peng J, Wang C, Chen X. PiRNA hsa_piR_019949 promotes chondrocyte anabolic metabolism by inhibiting the expression of lncRNA NEAT1. J Orthop Surg Res 2024; 19:31. [PMID: 38178210 PMCID: PMC10768105 DOI: 10.1186/s13018-023-04511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/25/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Osteoarthritis is a prevalent degenerative joint condition typically found in individuals who are aged 50 years or older. In this study, the focus is on PIWI-interacting RNA (piRNA), which belongs to a category of small non-coding RNAs. These piRNAs play a role in the regulation of gene expression and the preservation of genomic stability. The main objective of this research is to examine the expression of a specific piRNA called hsa_piR_019949 in individuals with osteoarthritis, to understand its impact on chondrocyte metabolism within this condition. METHODS We analyzed piRNA expression in osteoarthritis cartilage using the GEO database. To understand the impact of inflammatory factors on piRNA expression in chondrocytes, we conducted RT-qPCR experiments. We also investigated the effect of piRNA hsa_piR_019949 on chondrocyte proliferation using CCK-8 and clone formation assays. Furthermore, we assessed the influence of piRNA hsa_piR_019949 on chondrocyte apoptosis by conducting flow cytometry analysis. Additionally, we examined the differences in cartilage matrix composition through safranine O staining and explored the downstream regulatory mechanisms of piRNA using transcriptome sequencing. Lentiviral transfection of NEAT1 and NLRP3 was performed to regulate the metabolism of chondrocytes. RESULTS Using RNA sequencing technology, we compared the gene expression profiles of 5 patients with osteoarthritis to 3 normal controls. We found a gene called hsa_piR_019949 that showed differential expression between the two groups. Specifically, hsa_piR_019949 was downregulated in chondrocytes when stimulated by IL-1β, an inflammatory molecule. In further investigations, we discovered that overexpression of hsa_piR_019949 in vitro led to increased proliferation and synthesis of the extracellular matrix in chondrocytes, which are cells responsible for cartilage formation. Conversely, suppressing hsa_piR_019949 expression resulted in increased apoptosis (cell death) and degradation of the extracellular matrix in chondrocytes. Additionally, we found that the NOD-like receptor signaling pathway is linked to the low expression of hsa_piR_019949 in a specific chondrocyte cell line called C28/I2. Furthermore, we observed that hsa_piR_019949 can inhibit the expression of a long non-coding RNA called NEAT1 in chondrocytes. We hypothesize that NEAT1 may serve as a downstream target gene regulated by hsa_piR_019949, potentially influencing chondrocyte metabolism and function in the context of osteoarthritis. CONCLUSIONS PiRNA hsa_piR_019949 has shown potential in promoting the proliferation of chondrocytes and facilitating the synthesis of extracellular matrix in individuals with osteoarthritis. This is achieved by inhibiting the expression of a long non-coding RNA called NEAT1. The implication is that by using hsa_piR_019949 mimics, which are synthetic versions of the piRNA, as a therapeutic approach, it may be possible to effectively treat osteoarthritis.
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Affiliation(s)
- Xinhai Zhang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Xuyi Wang
- Department of Orthopaedics, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Fengbin Yu
- Department of Orthopaedics, The 72, Group Army Hospital of PLA, Huzhou, 313000, Zhejiang, China
| | - Chenglong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Jianping Peng
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China.
| | - Xiaodong Chen
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China.
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Xing X, She Y, Yuan G, Yang G. piR-368 promotes odontoblastic differentiation of dental papilla cells via the Smad1/5 signaling pathway by targeting Smurf1. Connect Tissue Res 2024; 65:53-62. [PMID: 37978579 DOI: 10.1080/03008207.2023.2281319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE The important role of non-coding RNAs in odontoblastic differentiation of dental tissue-derived stem cells has been widely demonstrated; however, whether piRNA (a subclass of non-coding RNA) involved in the course of odontoblastic differentiation is not yet available. This study aimed to investigate the expression profile of piRNA during odontogenic differentiation of mDPCs and the potential molecular mechanism in vitro. MATERIALS AND METHODS The primary mouse dental papilla cells (mDPCs) were isolated from the first molars of 1-day postnatal Kunming mice. Then, they were cultured in odontogenic medium for 9 days. The expression profile of piRNA was detected by Small RNA sequencing. RT-qPCR was used to verify the elevation of piR-368. The mRNA and protein levels of mineralization markers were examined by qRT-PCR and Western blot analysis. Alkaline phosphatase (ALP) activity and alizarin red S staining were conducted to assess the odontoblastic differentiation ability. RESULTS We validated piR-368 was significantly upregulated and interference with piR-368 markedly inhibited the odontogenic differentiation of mDPCs. In addition, the relationship between Smad1/5 signaling pathway and piR-368-induced odontoblastic differentiation has been discovered. Finally, we demonstrated Smurf1 as a target gene of piR-368 using dual-luciferase assays. CONCLUSION This study was the first to illustrate the participation of piRNA in odontoblastic differentiation. We proved that piR-368 promoted odontoblastic differentiation of mouse dental papilla cells via the Smad1/5 signaling pathway by targeting Smurf1.
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Affiliation(s)
- Xinhui Xing
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yawei She
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Guohua Yuan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Guobin Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
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Lea G, Hanna CW. Loss of DNA methylation disrupts syncytiotrophoblast development: Proposed consequences of aberrant germline gene activation. Bioessays 2024; 46:e2300140. [PMID: 37994176 DOI: 10.1002/bies.202300140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/26/2023] [Accepted: 10/24/2023] [Indexed: 11/24/2023]
Abstract
DNA methylation is a repressive epigenetic modification that is essential for development and its disruption is widely implicated in disease. Yet, remarkably, ablation of DNA methylation in transgenic mouse models has limited impact on transcriptional states. Across multiple tissues and developmental contexts, the predominant transcriptional signature upon loss of DNA methylation is the de-repression of a subset of germline genes, normally expressed in gametogenesis. We recently reported loss of de novo DNA methyltransferase DNMT3B resulted in up-regulation of germline genes and impaired syncytiotrophoblast formation in the murine placenta. This defect led to embryonic lethality. We hypothesize that de-repression of germline genes in the Dnmt3b knockout underpins aspects of the placental phenotype by interfering with normal developmental processes. Specifically, we discuss molecular mechanisms by which aberrant expression of the piRNA pathway, meiotic proteins or germline transcriptional regulators may disrupt syncytiotrophoblast development.
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Affiliation(s)
- Georgia Lea
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Courtney W Hanna
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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Yousefi B, Sadoughi F, Asemi Z, Mansournia MA, Hallajzadeh J. Novel Perspectives for the Diagnosis and Treatment of Gynecological Cancers using Dysregulation of PIWI Protein and PiRNAs as Biomarkers. Curr Med Chem 2024; 31:453-463. [PMID: 36786140 DOI: 10.2174/0929867330666230214101837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/23/2022] [Accepted: 12/23/2022] [Indexed: 02/15/2023]
Abstract
The term "gynecological cancer" is used for a group of cancers occurring in the female reproductive system. Some of these cancers are ranked as the leading causes of death in developed and developing countries. The lack of proper diagnostic strategies is one of the most important reasons that make them lethal. PIWI-interacting RNAs or piRNAs are a class of small non-coding RNAs, which contain 24-32 nucleotides. These RNAs take part in some cellular mechanisms, and their role in diverse kinds of cancer is confirmed by accumulative evidence. In this review, we gather some information on the roles of these RNAs and members of the PIWI protein family to provide new insight into accurate diagnostic biomarkers and more effective anti-cancer drugs with fewer side effects.
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Affiliation(s)
- Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Sadoughi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Mohammad Ali Mansournia
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Jamal Hallajzadeh
- Department of Biochemistry and Nutrition, Research Center for Evidence-Based Health Management, Maragheh University of Medical Sciences, Maragheh, Iran
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Miao J, Wang C, Chen W, Wang Y, Kakasani S, Wang Y. GASZ self-interaction clusters mitochondria into the intermitochondrial cement for proper germ cell development. PNAS Nexus 2024; 3:pgad480. [PMID: 38205030 PMCID: PMC10781510 DOI: 10.1093/pnasnexus/pgad480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
Mitochondrial features and activities vary in a cell type- and developmental stage-dependent manner to critically impact cell function and lineage development. Particularly in male germ cells, mitochondria are uniquely clustered into intermitochondrial cement (IMC), an electron-dense granule in the cytoplasm to support proper spermatogenesis. But it remains puzzling how mitochondria assemble into such a stable structure as IMC without limiting membrane during development. Here, we showed that GASZ (germ cell-specific, ankyrin repeat, SAM and basic leucine zipper domain containing protein), a mitochondrion-localized germ cell-specific protein, self-interacted with each other to cluster mitochondria and maintain protein stability for IMC assembling. When the self-interaction of GASZ was disrupted by either deleting its critical interaction motif or using a blocking peptide, the IMC structure was destabilized, which in turn led to impaired spermatogenesis. Notably, the blocked spermatogenesis was reversible once GASZ self-interaction was recovered. Our findings thus reveal a critical mechanism by which mitochondrion-based granules are properly assembled to support germ cell development while providing an alternative strategy for developing nonhormonal male contraceptives by targeting IMC protein interactions.
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Affiliation(s)
- Junru Miao
- Department of Animal Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA
| | - Chuanyun Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wei Chen
- Department of Animal Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA
| | - Yongsheng Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Shalin Kakasani
- Department of Animal Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA
| | - Yuan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
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Ow MC, Hall SE. Inheritance of Stress Responses via Small Non-Coding RNAs in Invertebrates and Mammals. Epigenomes 2023; 8:1. [PMID: 38534792 DOI: 10.3390/epigenomes8010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 03/28/2024] Open
Abstract
While reports on the generational inheritance of a parental response to stress have been widely reported in animals, the molecular mechanisms behind this phenomenon have only recently emerged. The booming interest in epigenetic inheritance has been facilitated in part by the discovery that small non-coding RNAs are one of its principal conduits. Discovered 30 years ago in the Caenorhabditis elegans nematode, these small molecules have since cemented their critical roles in regulating virtually all aspects of eukaryotic development. Here, we provide an overview on the current understanding of epigenetic inheritance in animals, including mice and C. elegans, as it pertains to stresses such as temperature, nutritional, and pathogenic encounters. We focus on C. elegans to address the mechanistic complexity of how small RNAs target their cohort mRNAs to effect gene expression and how they govern the propagation or termination of generational perdurance in epigenetic inheritance. Presently, while a great amount has been learned regarding the heritability of gene expression states, many more questions remain unanswered and warrant further investigation.
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Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Sarah E Hall
- Department of Biology and Program in Neuroscience, Syracuse University, Syracuse, NY 13210, USA
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20
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Elzer D, Bremser M, Zischler H. Human sperm heads harbor modified YsRNA as transgenerationally inherited non-coding RNAs. Front Genet 2023; 14:1294389. [PMID: 38162679 PMCID: PMC10756665 DOI: 10.3389/fgene.2023.1294389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/23/2023] [Indexed: 01/03/2024] Open
Abstract
Most epigenetic information is reprogrammed during gametogenesis and early development. However, some epigenetic information persists and can be inherited, a phenomenon that is common in plants. On the other hand, there are increasing examples of epigenetic inheritance in metazoans, especially for small non-coding RNAs. The presence of regulatory important RNAs in oocytes is undisputed, whereas the corresponding RNA payload in spermatozoa and its regulatory influence in the zygote and early embryogenesis is largely enigmatic. For humans, we herein describe small YRNA fragments (YsRNA) as a paternal contribution to the zygote. First, we trace the biogenesis of these YsRNAs from the source YRNAs with respect to the 5' and 3' modifications. Both the length and modifications make these YsRNAs reminiscent of canonical piRNAs that are not derived from piRNA clusters. Second, from the early stages of spermatogenesis to maturation in the epididymis, we observe distinct YsRNA profile dynamics in the male germline. We detected YsRNAs exclusively in mature sperm heads, the precursor of the male pronucleus in the zygote, suggesting an important role of the epididymis as a site for transmitting and modification of epigenetic information in the form of YsRNA between soma and germline in humans. Since this YsRNA-based epigenetic mechanism is effective across generations, we wondered whether this phenomenon of epigenetic inheritance has an adaptive value. Full-length YRNAs bind to Ro60, an RNA chaperone that additionally binds to non-coding RNAs. We described the profiles of non-coding RNAs bound to Ro60 in the human sperm head and detected specific binding profiles of RNA to Ro60 but no YRNA bound to Ro60. We hypothesize that the sperm head Ro60 system is functional. An adaptive phenotype mediated by the presence of a large amount of YsRNA in the sperm head, and thus as a paternal contribution in the zygote, might be related to an association of YsRNA with YRNA that prevents the adoption of a YRNA secondary structure capable of binding to Ro60. We hypothesize that preventing YRNAs from acting as Ro60-associated gatekeepers for misfolded RNAs in the zygote and early development may enhance RNA chaperoning and, thus, represent the adaptive molecular phenotype.
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Affiliation(s)
- Darja Elzer
- Division of Anthropology, Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Hans Zischler
- Division of Anthropology, Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
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21
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Bronkhorst AW, Lee CY, Möckel MM, Ruegenberg S, de Jesus Domingues AM, Sadouki S, Piccinno R, Sumiyoshi T, Siomi MC, Stelzl L, Luck K, Ketting RF. An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori. EMBO J 2023; 42:e114072. [PMID: 37984437 PMCID: PMC10711660 DOI: 10.15252/embj.2023114072] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) direct PIWI proteins to transposons to silence them, thereby preserving genome integrity and fertility. The piRNA population can be expanded in the ping-pong amplification loop. Within this process, piRNA-associated PIWI proteins (piRISC) enter a membraneless organelle called nuage to cleave their target RNA, which is stimulated by Gtsf proteins. The resulting cleavage product gets loaded into an empty PIWI protein to form a new piRISC complex. However, for piRNA amplification to occur, the new RNA substrates, Gtsf-piRISC, and empty PIWI proteins have to be in physical proximity. In this study, we show that in silkworm cells, the Gtsf1 homolog BmGtsf1L binds to piRNA-loaded BmAgo3 and localizes to granules positive for BmAgo3 and BmVreteno. Biochemical assays further revealed that conserved residues within the unstructured tail of BmGtsf1L directly interact with BmVreteno. Using a combination of AlphaFold modeling, atomistic molecular dynamics simulations, and in vitro assays, we identified a novel binding interface on the BmVreteno-eTudor domain, which is required for BmGtsf1L binding. Our study reveals that a single eTudor domain within BmVreteno provides two binding interfaces and thereby interconnects piRNA-loaded BmAgo3 and BmGtsf1L.
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Affiliation(s)
| | - Chop Y Lee
- International PhD Programme on Gene Regulation, Epigenetics & Genome StabilityMainzGermany
- Integrative Systems Biology GroupInstitute of Molecular BiologyMainzGermany
| | - Martin M Möckel
- Protein Production Core FacilityInstitute of Molecular BiologyMainzGermany
| | - Sabine Ruegenberg
- Protein Production Core FacilityInstitute of Molecular BiologyMainzGermany
| | - Antonio M de Jesus Domingues
- Biology of Non‐coding RNA GroupInstitute of Molecular BiologyMainzGermany
- Present address:
Dewpoint Therapeutics GmbHDresdenGermany
| | - Shéraz Sadouki
- Biology of Non‐coding RNA GroupInstitute of Molecular BiologyMainzGermany
| | - Rossana Piccinno
- Microscopy Core FacilityInstitute of Molecular BiologyMainzGermany
| | - Tetsutaro Sumiyoshi
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
- Present address:
Department of Medical Innovations, Osaka Research Center for Drug DiscoveryOtsuka Pharmaceutical Co., Ltd.OsakaJapan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Lukas Stelzl
- Faculty of BiologyJohannes Gutenberg University MainzMainzGermany
- KOMET 1, Institute of PhysicsJohannes Gutenberg University MainzMainzGermany
| | - Katja Luck
- Integrative Systems Biology GroupInstitute of Molecular BiologyMainzGermany
| | - René F Ketting
- Biology of Non‐coding RNA GroupInstitute of Molecular BiologyMainzGermany
- Institute of Developmental Biology and NeurobiologyJohannes Gutenberg UniversityMainzGermany
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22
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Wu Z, Yu X, Zhang S, He Y, Guo W. Novel roles of PIWI proteins and PIWI-interacting RNAs in human health and diseases. Cell Commun Signal 2023; 21:343. [PMID: 38031146 PMCID: PMC10685540 DOI: 10.1186/s12964-023-01368-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Non-coding RNA has aroused great research interest recently, they play a wide range of biological functions, such as regulating cell cycle, cell proliferation, and intracellular substance metabolism. Piwi-interacting RNAs (piRNAs) are emerging small non-coding RNAs that are 24-31 nucleotides in length. Previous studies on piRNAs were mainly limited to evaluating the binding to the PIWI protein family to play the biological role. However, recent studies have shed more lights on piRNA functions; aberrant piRNAs play unique roles in many human diseases, including diverse lethal cancers. Therefore, understanding the mechanism of piRNAs expression and the specific functional roles of piRNAs in human diseases is crucial for developing its clinical applications. Presently, research on piRNAs mainly focuses on their cancer-specific functions but lacks investigation of their expressions and epigenetic modifications. This review discusses piRNA's biogenesis and functional roles and the recent progress of functions of piRNA/PIWI protein complexes in human diseases. Video Abstract.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
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23
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Wang H, Cai G, Yu F, Li D, Wang C, Ma D, Han X, Chen J, Wang C, He J. Changes in the small noncoding RNA transcriptome in osteosarcoma cells. J Orthop Surg Res 2023; 18:898. [PMID: 38001513 PMCID: PMC10675919 DOI: 10.1186/s13018-023-04362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Osteosarcoma has the highest incidence among bone malignant tumors and mainly occurs in adolescents and the elderly, but the pathological mechanism is still unclear, which makes early diagnosis and treatment very difficult. Bone marrow mesenchymal stem cells (BMSCs) are considered to be one of the sources of osteosarcoma cells. Therefore, a full understanding of the gene expression differences between BMSCs and osteosarcoma cells is very important to explore the pathogenesis of osteosarcoma and facilitate the early diagnosis and treatment of osteosarcoma. Small noncoding RNAs (sncRNAs) are a class of RNAs that do not encode proteins but directly play biological functions at the RNA level. SncRNAs mainly include Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), repeat RNAs and microRNAs (miRNAs). METHODS In this study, we compared the expression of sncRNAs in BMSCs and osteosarcoma cells by high-throughput sequencing and qPCR and looked for differentially expressed sncRNAs. CCK-8, clone formation and transwell assay were used to detect the effect of sncRNA in MG63 cells. RESULTS We found that 66 piRNAs were significantly upregulated and 70 piRNAs were significantly downregulated in MG63 cells. As for snoRNAs, 71 snoRNAs were significantly upregulated and 117 snoRNAs were significantly downregulated in MG63 cells. As for snRNAs, 35 snRNAs were significantly upregulated and 17 snRNAs were significantly downregulated in MG63 cells. As for repeat RNAs, 6 repeat RNAs were significantly upregulated and 7 repeat RNAs were significantly downregulated in MG63 cells. As for miRNAs, 326 miRNAs were significantly upregulated and 281 miRNAs were significantly downregulated in MG63 cells. Overexpression of piRNA DQ596225, snoRNA ENST00000364830.2, snRNA ENST00000410533.1 and miRNA hsa-miR-369-5p inhibited the proliferation and migration of MG63 cells. CONCLUSIONS Our results provide a theoretical basis for the pathogenesis, early diagnosis and treatment of osteosarcoma.
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Affiliation(s)
- Hui Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Guiquan Cai
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Fengbin Yu
- Department of Orthopaedics, The 72nd Group Army Hospital of PLA, Huzhou, 313000, Zhejiang, People's Republic of China
| | - De Li
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Chenglong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Ding Ma
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Xiuguo Han
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Jiajia Chen
- Department of Spine Surgery, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China.
| | - Jiye He
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China.
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24
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Sun M, Fan X, Long Q, Zang H, Zhang Y, Liu X, Feng P, Song Y, Li K, Wu Y, Jiang H, Chen D, Guo R. First Characterization and Regulatory Function of piRNAs in the Apis mellifera Larval Response to Ascosphaera apis Invasion. Int J Mol Sci 2023; 24:16358. [PMID: 38003547 PMCID: PMC10671575 DOI: 10.3390/ijms242216358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
piRNAs are a class of small non-coding RNAs that play essential roles in modulating gene expression and abundant biological processes. To decode the piRNA-regulated larval response of western honeybees (Apis mellifera) to Ascosphaera apis infection, the expression pattern of piRNAs in Apis mellifera ligustica larval guts after A. apis inoculation was analyzed based on previously obtained high-quality small RNA-seq datasets, followed by structural characterization, target prediction, regulatory network investigation, and functional dissection. Here, 504, 657, and 587 piRNAs were respectively identified in the 4-, 5-, and 6-day-old larval guts after inoculation with A. apis, with 411 ones shared. These piRNAs shared a similar length distribution and first base bias with mammal piRNAs. Additionally, 96, 103, and 143 DEpiRNAs were detected in the 4-, 5-, and 6-day-old comparison groups. Targets of the DEpiRNAs were engaged in diverse pathways such as the phosphatidylinositol signaling system, inositol phosphate metabolism, and Wnt signaling pathway. These targets were involved in three energy metabolism-related pathways, eight development-associated signaling pathways, and seven immune-relevant pathways such as the Jak-STAT signaling pathway. The expression trends of five randomly selected DEpiRNAs were verified using a combination of RT-PCR and RT-qPCR. The effective overexpression and knockdown of piR-ame-945760 in A. apis-infected larval guts were achieved by feeding a specific mimic and inhibitor. Furthermore, piR-ame-945760 negatively regulated the expression of two target immune mRNAs, SOCS5 and ARF1, in the larval gut during the A. apis infection. These findings indicated that the overall expression level of piRNAs was increased and the expression pattern of piRNAs in larval guts was altered due to the A. apis infection, DEpiRNAs were putative regulators in the A. apis-response of A. m. ligustica worker larvae. Our data provide not only a platform for the functional investigation of piRNAs in honeybees, especially in bee larvae, but also a foundation for illuminating the piRNA-involved mechanisms underlying the host response to the A. apis infection.
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Affiliation(s)
- Minghui Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Qi Long
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - He Zang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Xiaoyu Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Peilin Feng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Yuxuan Song
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Kunze Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Ying Wu
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (Y.W.); (H.J.)
| | - Haibin Jiang
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (Y.W.); (H.J.)
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Luo Y, He P, Kanrar N, Fejes Toth K, Aravin AA. Maternally inherited siRNAs initiate piRNA cluster formation. Mol Cell 2023; 83:3835-3851.e7. [PMID: 37875112 PMCID: PMC10846595 DOI: 10.1016/j.molcel.2023.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/08/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023]
Abstract
PIWI-interacting RNAs (piRNAs) guide transposable element repression in animal germ lines. In Drosophila, piRNAs are produced from heterochromatic loci, called piRNA clusters, which act as information repositories about genome invaders. piRNA generation by dual-strand clusters depends on the chromatin-bound Rhino-Deadlock-Cutoff (RDC) complex, which is deposited on clusters guided by piRNAs, forming a positive feedback loop in which piRNAs promote their own biogenesis. However, how piRNA clusters are formed before cognate piRNAs are present remains unknown. Here, we report spontaneous de novo piRNA cluster formation from repetitive transgenic sequences. Cluster formation occurs over several generations and requires continuous trans-generational maternal transmission of small RNAs. We discovered that maternally supplied small interfering RNAs (siRNAs) trigger de novo cluster activation in progeny. In contrast, siRNAs are dispensable for cluster function after its establishment. These results reveal an unexpected interplay between the siRNA and piRNA pathways and suggest a mechanism for de novo piRNA cluster formation triggered by siRNAs.
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Affiliation(s)
- Yicheng Luo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peng He
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nivedita Kanrar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Katalin Fejes Toth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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27
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Ding W, Wang D, Cai M, Yan Y, Liu S, Liu X, Luo A, Deng D, Liu X, Jiang H. PIWIL1 gene polymorphism and pediatric acute lymphoblastic leukemia relapse susceptibility among Chinese children: a five-center case-control study. Front Oncol 2023; 13:1203002. [PMID: 38023199 PMCID: PMC10652278 DOI: 10.3389/fonc.2023.1203002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Objective PIWIL1 polymorphisms' role in pediatric acute lymphoblastic leukemia (ALL) relapse susceptibility remains undiscovered. Methods A case-control designed and multiple logistic regression model was performed to evaluate the overall risk of pediatric ALL and five single-nucleotide polymorphisms (SNPs) of PIWIL1 gene (rs35997018 C>T, rs1106042 A>G, rs7957349 C>G, rs10773771 C>T, and rs10848087 A>G) in 785 cases and 1,323 controls, which were genotyped by TaqMan assay. The odds ratio (OR) and its 95% confidence interval (CI) were used to estimate the relationship. Stratified analysis was used to investigate the correlation of rs1106042 and rs10773771 genotypes and pediatric ALL relapse susceptibility in terms of age, sex, number of white blood cells (WBC), immunophenotyping, gene fusion type, karyotype, primitive/naïve lymphocytes, and minimal residual disease (MRD) in bone marrow. Finally, the haplotype analysis was performed to appraise the relationship between inferred haplotypes of PIWIL1 and pediatric ALL risk. Results Among the five analyzed SNPs, rs1106042 A>G was related to increased ALL risk, and rs10773771 C>T was related to decreased ALL risk. Compared to the GG genotype, the rs1106042 GA/AA had a deleterious effect on children of age <120 months, who were female and male, had high or average number of WBC, pro-B ALL, pre-B ALL, T-ALL, low- and middle-risk ALL, E2A-PBX fusion gene, non-gene fusion, abnormal diploid, high hyperdiploid, hypodiploid, and normal diploid. Moreover, rs1106042 A>G harmfully affected primitive/naïve lymphocytes and MRD on days 15-19, day 33, and week 12. On the contrary, rs10773771 TC/CC exhibited a protective effect on ALL children with the TEL-AML fusion gene. Haplotype analysis demonstrated that haplotypes CAGT, TACC, TACT, and TAGT were significantly associated with increased pediatric ALL relapse susceptibility. Conclusion PIWIL1 rs1106042 A>G was related to increased ALL risk, and rs10773771 C>T was linked to decreased ALL risk in eastern Chinese children. Rs1106042 GA/AA may predict poor prognosis.
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Affiliation(s)
- Wenjiao Ding
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Dao Wang
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mansi Cai
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Yaping Yan
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Shanshan Liu
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Xiaodan Liu
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Ailing Luo
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Decheng Deng
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Xiaoping Liu
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Hua Jiang
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Province Clinical Research Center for Child Health, Guangzhou, Guangdong, China
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Tanaka M, Inaba Y, Yariyama A, Nakatani Y, Kunimoto K, Kaminaka C, Yamamoto Y, Makino K, Fukushima S, Jinnin M. Expression of collagen-related piRNA is dysregulated in cultured dermal fibroblasts derived from patients with scleroderma. Intractable Rare Dis Res 2023; 12:241-245. [PMID: 38024581 PMCID: PMC10680164 DOI: 10.5582/irdr.2023.01056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/25/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
PIWI-interacting RNA (piRNA) is a class of recently discovered small non-coding RNAs. piRNAs derive from an initial transcript encompassing a piRNA cluster via a unique biosynthesis process, interact with PIWI proteins, bind to specific targets, and recruit chromatin modifiers to enable transcriptional repression. Abnormal expression of PIWI proteins and piRNAs has been reported in some human cancers, with participation of some PIWI/piRNAs complexes in tumorigenesis and association with cancer prognosis. Their expression in patients with systemic sclerosis (SSc) has not been widely elucidated. PIWI/piRNAs and their role in the pathogenesis of collagen accumulation in SSc was therefore investigated; no difference was found in the PIWIL1-4 levels between normal and cultured SSc dermal fibroblasts. Among piRNAs predicted to target SSc-related molecules, we first found significant piR-32364 up-regulation in SSc dermal fibroblasts, likely due to intrinsic TGF-β signaling. Forced piR-32364 overexpression in normal fibroblasts significantly reduced COL1A1 expression both at mRNA and protein levels, but not COL1A2. Thus, piR-32364 overexpression in SSc fibroblasts may be the negative feedback against collagen up-regulation, which could suggest the potential of piRNAs as a therapeutic target.
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Affiliation(s)
- Minako Tanaka
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Yutaka Inaba
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Azusa Yariyama
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Yumi Nakatani
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Kayo Kunimoto
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Chikako Kaminaka
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Yuki Yamamoto
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Katsunari Makino
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Satoshi Fukushima
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masatoshi Jinnin
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
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Kalmykova AI, Sokolova OA. Retrotransposons and Telomeres. Biochemistry (Mosc) 2023; 88:1739-1753. [PMID: 38105195 DOI: 10.1134/s0006297923110068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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30
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Weigert N, Schweiger AL, Gross J, Matthes M, Corbacioglu S, Sommer G, Heise T. Detection of a 7SL RNA-derived small non-coding RNA using Molecular Beacons in vitro and in cells. Biol Chem 2023; 404:1123-1136. [PMID: 37632732 DOI: 10.1515/hsz-2023-0185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023]
Abstract
Small non-coding RNAs (sncRNA) are involved in many steps of the gene expression cascade and regulate processing and expression of mRNAs by the formation of ribonucleoprotein complexes (RNP) such as the RNA-induced silencing complex (RISC). By analyzing small RNA Seq data sets, we identified a sncRNA annotated as piR-hsa-1254, which is likely derived from the 3'-end of 7SL RNA2 (RN7SL2), herein referred to as snc7SL RNA. The 7SL RNA is an abundant long non-coding RNA polymerase III transcript and serves as structural component of the cytoplasmic signal recognition particle (SRP). To evaluate a potential functional role of snc7SL RNA, we aimed to define its cellular localization by live cell imaging. Therefore, a Molecular Beacon (MB)-based method was established to compare the subcellular localization of snc7SL RNA with its precursor 7SL RNA. We designed and characterized several MBs in vitro and tested those by live cell fluorescence microscopy. Using a multiplex approach, we show that 7SL RNA localizes mainly to the endoplasmic reticulum (ER), as expected for the SRP, whereas snc7SL RNA predominately localizes to the nucleus. This finding suggests a fundamentally different function of 7SL RNA and its derivate snc7SL RNA.
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Affiliation(s)
- Nina Weigert
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Anna-Lena Schweiger
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Jonas Gross
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Marie Matthes
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Selim Corbacioglu
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Gunhild Sommer
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Tilman Heise
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
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Kozlowski P. Thirty Years with ERH: An mRNA Splicing and Mitosis Factor Only or Rather a Novel Genome Integrity Protector? Cells 2023; 12:2449. [PMID: 37887293 PMCID: PMC10605862 DOI: 10.3390/cells12202449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
ERH is a 100 to about 110 aa nuclear protein with unique primary and three-dimensional structures that are very conserved from simple eukaryotes to humans, albeit some species have lost its gene, with most higher fungi being a noteworthy example. Initially, studies on Drosophila melanogaster implied its function in pyrimidine metabolism. Subsequently, research on Xenopus laevis suggested that it acts as a transcriptional repressor. Finally, studies in humans pointed to a role in pre-mRNA splicing and in mitosis but further research, also in Caenorhabditis elegans and Schizosaccharomyces pombe, demonstrated its much broader activity, namely involvement in the biogenesis of mRNA, and miRNA, piRNA and some other ncRNAs, and in repressive heterochromatin formation. ERH interacts with numerous, mostly taxon-specific proteins, like Mmi1 and Mei2 in S. pombe, PID-3/PICS-1, TOST-1 and PID-1 in C. elegans, and DGCR8, CIZ1, PDIP46/SKAR and SAFB1/2 in humans. There are, however, some common themes in this wide range of processes and partners, such as: (a) ERH homodimerizes to form a scaffold for several complexes involved in the metabolism of nucleic acids, (b) all these RNAs are RNA polymerase II transcripts, (c) pre-mRNAs, whose splicing depends on ERH, are enriched in transcripts of DNA damage response and DNA metabolism genes, and (d) heterochromatin is formed to silence unwanted transcription, e.g., from repetitive elements. Thus, it seems that ERH has been adopted for various pathways that serve to maintain genome integrity.
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Affiliation(s)
- Piotr Kozlowski
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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Georgoulis V, Koumpis E, Hatzimichael E. The Role of Non-Coding RNAs in Myelodysplastic Neoplasms. Cancers (Basel) 2023; 15:4810. [PMID: 37835504 PMCID: PMC10571949 DOI: 10.3390/cancers15194810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Myelodysplastic syndromes or neoplasms (MDS) are a heterogeneous group of myeloid clonal disorders characterized by peripheral blood cytopenias, blood and marrow cell dysplasia, and increased risk of evolution to acute myeloid leukemia (AML). Non-coding RNAs, especially microRNAs and long non-coding RNAs, serve as regulators of normal and malignant hematopoiesis and have been implicated in carcinogenesis. This review presents a comprehensive summary of the biology and role of non-coding RNAs, including the less studied circRNA, siRNA, piRNA, and snoRNA as potential prognostic and/or predictive biomarkers or therapeutic targets in MDS.
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Affiliation(s)
- Vasileios Georgoulis
- Department of Haematology, University Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45 500 Ioannina, Greece; (V.G.); (E.K.)
| | - Epameinondas Koumpis
- Department of Haematology, University Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45 500 Ioannina, Greece; (V.G.); (E.K.)
| | - Eleftheria Hatzimichael
- Department of Haematology, University Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45 500 Ioannina, Greece; (V.G.); (E.K.)
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19 107, USA
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Moelling K. Epigenetics and transgenerational inheritance. J Physiol 2023. [PMID: 37772441 DOI: 10.1113/jp284424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Epigenetic modifications can alter the function of genes. The epigenetics changes are caused by environmental effects, which lead to chemical modifications of the DNA or the chromatin. The mechanisms involve the influence of small interfering siRNAs on gene silencing. Epigenetic changes normally last only during the life-time of an individual and are erased in embryos and eggs for a naive progeny. The genomes are reprogrammed and the chemical modifications removed to restart the next generation. However, there are mechanisms that allow the genome to escape from such a clearing effect so that modifications can be transmitted to one or more subsequent generations. In the germline of animal cells small RNAs, including piRNAs, have evolved which guarantee a higher degree of fidelity for transmission of genetic information, guarding especially against the detrimental effect caused by transposon activity. piRNA is essential for transposon silencing for survival of a species and protection of subsequent generations. Inactivation of piRNA results in abundant transposon activity and sperm infertility. The effect in humans has been described but is less distinct. Some stress-induced epigenetic changes are transitory in mice and can be reversed by a change of environment or lifestyle.
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Affiliation(s)
- Karin Moelling
- Institute Medical Microbiology, University Zürich, Zurich, Switzerland
- Max Planck Institute of Molecular Genetics, Berlin, Germany
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Fang C, Zhou P, Li R, Guo J, Qiu H, Zhang J, Li M, Yu C, Meng D, Xu X, Liu X, Guan D, Yan J. Development of a novel forensic age estimation strategy for aged blood samples by combining piRNA and miRNA markers. Int J Legal Med 2023; 137:1327-1335. [PMID: 37264192 DOI: 10.1007/s00414-023-03028-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/22/2023] [Indexed: 06/03/2023]
Abstract
In forensic investigations, age estimation is vital for determining whether a suspect is under or over the legally defined adult age. With breakthroughs in RNA sequencing technology, small noncoding RNAs have provided new ways to solve problems related to the age estimation of trace or aged samples, owing to their small molecular weight and better stability. In our previous study, we had applied miRNAs for the age estimation of bloodstains; however, further improvement of the existing model is needed. PIWI-interacting RNAs (PiRNAs), which are 24-32 nt noncoding small RNA molecules involved in the PIWI-piRNA pathway, play an important role in the aging process. In this study, we explored the possibility of simultaneously analyzing piRNAs and miRNAs for better age estimation purpose. Through massively parallel sequencing, five age-related piRNAs were identified in blood samples that had been stored for eight years. Further real-time PCR analysis revealed that two piRNAs (piR-000753 and piR-020548) showed relatively higher efficiency in age estimation. Additionally, two age-related miRNAs (miR-324-3p and miR-330-5p) were used to build the estimation model. Among all algorithms tested, gradient boosting showed the lowest mean absolute error (MAE) and root mean square error (RMSE) values (3.171 and 4.403 years, respectively) for the validation dataset (n = 110). The errors of the model were less than 5 years and 10 years for 81.82% and 96.36% of the samples, respectively. The results suggest that the combined use of piRNA and miRNA markers may increase the accuracy of age estimation, and our new model has great potential for application in forensic casework.
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Affiliation(s)
- Chen Fang
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China.
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China.
| | - Peng Zhou
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Ran Li
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Jinghan Guo
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Huixian Qiu
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Jingjuan Zhang
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Min Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Chunjiang Yu
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Deping Meng
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Xiaoqun Xu
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Xu Liu
- Institute of Analysis and Testing, Beijing Academy of Science and Technology (Beijing Center for Physical and Chemical Analysis), Beijing, 100094, People's Republic of China
| | - Di Guan
- Institute of Analysis and Testing, Beijing Academy of Science and Technology (Beijing Center for Physical and Chemical Analysis), Beijing, 100094, People's Republic of China
| | - Jiangwei Yan
- Shanxi Medical University, 030001, Taiyuan, People's Republic of China.
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China.
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Samir M. Editorial: Host response to veterinary infectious diseases: role of coding and non-coding RNAs as biomarkers and disease modulators. Front Vet Sci 2023; 10:1275169. [PMID: 37711434 PMCID: PMC10497942 DOI: 10.3389/fvets.2023.1275169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Affiliation(s)
- Mohamed Samir
- The Immunogenetics Group, The Pirbright Institute, Woking, United Kingdom
- Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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van Wolfswinkel JC. Insights in piRNA targeting rules. Wiley Interdiscip Rev RNA 2023; 15:e1811. [PMID: 37632327 PMCID: PMC10895071 DOI: 10.1002/wrna.1811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 08/27/2023]
Abstract
PIWI-interacting RNAs (piRNAs) play an important role in the defense against transposons in the germline and stem cells of animals. To what extent other transcripts are also regulated by piRNAs is an ongoing topic of debate. The amount of sequence complementarity between piRNA and target that is required for effective downregulation of the targeted transcript is guiding in this discussion. Over the years, various methods have been applied to infer targeting requirements from the collections of piRNAs and potential target transcripts, and recent structural studies of the PIWI proteins have provided an additional perspective. In this review, I summarize the findings from these studies and propose a set of requirements that can be used to predict targets to the best of our current abilities. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA-Based Catalysis > RNA-Mediated Cleavage.
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Affiliation(s)
- Josien C van Wolfswinkel
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Center for Stem Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA
- Center for RNA Biology and Medicine, Yale School of Medicine, New Haven, Connecticut, USA
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Olufunmilayo EO, Holsinger RMD. Roles of Non-Coding RNA in Alzheimer's Disease Pathophysiology. Int J Mol Sci 2023; 24:12498. [PMID: 37569871 PMCID: PMC10420049 DOI: 10.3390/ijms241512498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disorder that is accompanied by deficits in memory and cognitive functions. The disease is pathologically characterised by the accumulation and aggregation of an extracellular peptide referred to as amyloid-β (Aβ) in the form of amyloid plaques and the intracellular aggregation of a hyperphosphorelated protein tau in the form of neurofibrillary tangles (NFTs) that cause neuroinflammation, synaptic dysfunction, and oxidative stress. The search for pathomechanisms leading to disease onset and progression has identified many key players that include genetic, epigenetic, behavioural, and environmental factors, which lend support to the fact that this is a multi-faceted disease where failure in various systems contributes to disease onset and progression. Although the vast majority of individuals present with the sporadic (non-genetic) form of the disease, dysfunctions in numerous protein-coding and non-coding genes have been implicated in mechanisms contributing to the disease. Recent studies have provided strong evidence for the association of non-coding RNAs (ncRNAs) with AD. In this review, we highlight the current findings on changes observed in circular RNA (circRNA), microRNA (miRNA), short interfering RNA (siRNA), piwi-interacting RNA (piRNA), and long non-coding RNA (lncRNA) in AD. Variations in these ncRNAs could potentially serve as biomarkers or therapeutic targets for the diagnosis and treatment of Alzheimer's disease. We also discuss the results of studies that have targeted these ncRNAs in cellular and animal models of AD with a view for translating these findings into therapies for Alzheimer's disease.
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Affiliation(s)
- Edward O. Olufunmilayo
- Laboratory of Molecular Neuroscience and Dementia, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Department of Medicine, University College Hospital, Queen Elizabeth Road, Oritamefa, Ibadan 200212, Nigeria
| | - R. M. Damian Holsinger
- Laboratory of Molecular Neuroscience and Dementia, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Neuroscience, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
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Zhang K, Li Y, Huang Y, Sun K. PiRNA in Cardiovascular Disease: Focus on Cardiac Remodeling and Cardiac Protection. J Cardiovasc Transl Res 2023; 16:768-777. [PMID: 37407865 DOI: 10.1007/s12265-023-10353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/08/2023] [Indexed: 07/07/2023]
Abstract
Cardiovascular diseases (CVDs) are common causes of death, which take about 18.6 million lives worldwide every year. Currently, exploring strategies that delay ventricular remodeling, reduce cardiomyocyte death, and promote cardiomyocyte regeneration has been the hotspot and difficulty of the ischemic heart disease (IHD) research field. Previous studies indicate that piwi-interacting RNA (piRNA) plays a vital role in the occurrence and development of cardiac remodeling and may offer novel therapeutic strategies for cardiac repair. The best-known biological function of piRNA is to silence transposons in cells. In the cardiovascular system, piRNA is known to participate in cardiac progenitor cell proliferation, AKT pathway regulation, and cardiac remodeling and decompensation. In this review, we systematically discuss the research progress on piRNA in CVDs, especially the mechanism of cardiac remodeling and the potential functions in cardiac protection, which provides new insights for the progress and treatment of cardiovascular diseases. Piwi-interacting RNA (piRNA) is one of the noncoding RNAs, with the best -known biological function to silence transposons in cells. Now piRNA is found to participate in cardiac progenitor cell proliferation, AKT pathway regulation, cardiac remodeling and decompensation, which implies the potential of piRNA in the diagnosis and treatment of cardiovascular diseases. Over expression of piRNA could promote cardiac apoptosis and cardiac hypertrophy, thus targeted therapy which inhibits expression of associated piRNA may reduce cardiac remodeling and reduce inflammation caused by necrotic cardiomyocytes. PiRNA is also speculated to participate in the proliferation of cardiac progenitor cells, implying the potential to induce cardiac regeneration th erapy, which provides new insights for treatment of cardiovascular diseases. At present, the treatment strategy of cardiac remodeling emphasizes the control of risk factors, prevention of disease progression and individualized treatment. With further studies in mechanism of piRNA, potential therapies above may come true and more therapies in cardiovascular diseases may be found.
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Affiliation(s)
- Kaiyu Zhang
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China
| | - Yafei Li
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China
| | - Ying Huang
- Central Laboratory, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Kangyun Sun
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China.
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Timofeeva AV, Fedorov IS, Asaturova AV, Sannikova MV, Tregubova AV, Mayboroda OA, Khabas GN, Frankevich VE, Sukhikh GT. Blood Plasma Small Non-Coding RNAs as Diagnostic Molecules for the Progesterone-Receptor-Negative Phenotype of Serous Ovarian Tumors. Int J Mol Sci 2023; 24:12214. [PMID: 37569592 PMCID: PMC10419267 DOI: 10.3390/ijms241512214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
The expression level of the progesterone receptor (PGR) plays a crucial role in determining the biological characteristics of serous ovarian carcinoma. Low PGR expression is associated with chemoresistance and a poorer outcome. In this study, our objective was to explore the relationship between tumor progesterone receptor levels and RNA profiles (miRNAs, piwiRNAs, and mRNAs) to understand their biological characteristics and behavior. To achieve this, we employed next-generation sequencing of small non-coding RNAs, quantitative RT-PCR, and immunohistochemistry to analyze both FFPE and frozen tumor samples, as well as blood plasma from patients with benign cystadenoma (BSC), serous borderline tumor (SBT), low-grade serous ovarian carcinoma (LGSOC), and high-grade serous ovarian carcinoma (HGSOC). Our findings revealed significant upregulation of MMP7 and MUC16, along with downregulation of PGR, in LGSOC and HGSOC compared to BSC. We observed significant correlations of PGR expression levels in tumor tissue with the contents of miR-199a-5p, miR-214-3p, miR-424-3p, miR-424-5p, and miR-125b-5p, which potentially target MUC16, MMP7, and MMP9, as well as with the tissue content of miR-16-5p, miR-17-5p, miR-20a-5p, and miR-93-5p, which are associated with the epithelial-mesenchymal transition (EMT) of cells. The levels of EMT-associated miRNAs were significantly correlated with the content of hsa_piR_022437, hsa_piR_009295, hsa_piR_020813, hsa_piR_004307, and hsa_piR_019914 in tumor tissues. We developed two optimal logistic regression models using the quantitation of hsa_piR_020813, miR-16-5p, and hsa_piR_022437 or hsa_piR_004307, hsa_piR_019914, and miR-93-5p in the tumor tissue, which exhibited a significant ability to diagnose the PGR-negative tumor phenotype with 93% sensitivity. Of particular interest, the blood plasma levels of miR-16-5p and hsa_piR_022437 could be used to diagnose the PGR-negative tumor phenotype with 86% sensitivity even before surgery and chemotherapy. This knowledge can help in choosing the most effective treatment strategy for this aggressive type of ovarian cancer, such as neoadjuvant chemotherapy followed by cytoreduction in combination with hyperthermic intraperitoneal chemotherapy and targeted therapy, thus enhancing the treatment's effectiveness and the patient's longevity.
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Affiliation(s)
- Angelika V. Timofeeva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov Ministry of Healthcare of the Russian Federation, Ac. Oparina 4, 117997 Moscow, Russia; (I.S.F.); (A.V.A.); (M.V.S.); (A.V.T.); (G.N.K.); (V.E.F.); (G.T.S.)
| | - Ivan S. Fedorov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov Ministry of Healthcare of the Russian Federation, Ac. Oparina 4, 117997 Moscow, Russia; (I.S.F.); (A.V.A.); (M.V.S.); (A.V.T.); (G.N.K.); (V.E.F.); (G.T.S.)
| | - Aleksandra V. Asaturova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov Ministry of Healthcare of the Russian Federation, Ac. Oparina 4, 117997 Moscow, Russia; (I.S.F.); (A.V.A.); (M.V.S.); (A.V.T.); (G.N.K.); (V.E.F.); (G.T.S.)
| | - Maya V. Sannikova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov Ministry of Healthcare of the Russian Federation, Ac. Oparina 4, 117997 Moscow, Russia; (I.S.F.); (A.V.A.); (M.V.S.); (A.V.T.); (G.N.K.); (V.E.F.); (G.T.S.)
| | - Anna V. Tregubova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov Ministry of Healthcare of the Russian Federation, Ac. Oparina 4, 117997 Moscow, Russia; (I.S.F.); (A.V.A.); (M.V.S.); (A.V.T.); (G.N.K.); (V.E.F.); (G.T.S.)
| | - Oleg A. Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands;
| | - Grigory N. Khabas
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov Ministry of Healthcare of the Russian Federation, Ac. Oparina 4, 117997 Moscow, Russia; (I.S.F.); (A.V.A.); (M.V.S.); (A.V.T.); (G.N.K.); (V.E.F.); (G.T.S.)
| | - Vladimir E. Frankevich
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov Ministry of Healthcare of the Russian Federation, Ac. Oparina 4, 117997 Moscow, Russia; (I.S.F.); (A.V.A.); (M.V.S.); (A.V.T.); (G.N.K.); (V.E.F.); (G.T.S.)
- Laboratory of Translational Medicine, Siberian State Medical University, 634050 Tomsk, Russia
| | - Gennady T. Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov Ministry of Healthcare of the Russian Federation, Ac. Oparina 4, 117997 Moscow, Russia; (I.S.F.); (A.V.A.); (M.V.S.); (A.V.T.); (G.N.K.); (V.E.F.); (G.T.S.)
- Department of Obstetrics, Gynecology, Perinatology and Reproductology, First Moscow State Medical University Named after I.M. Sechenov, 119991 Moscow, Russia
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Kabzinski J, Kucharska-Lusina A, Majsterek I. RNA-Based Liquid Biopsy in Head and Neck Cancer. Cells 2023; 12:1916. [PMID: 37508579 PMCID: PMC10377854 DOI: 10.3390/cells12141916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Early detection and monitoring of HNC are crucial for improving patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, has emerged as a promising tool for cancer detection and monitoring. In this article, we review the application of RNA-based liquid biopsy in HNC. Various types of RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), circular RNA (circRNA) and PIWI-interacting RNA (piRNA), are explored as potential biomarkers in HNC liquid-based diagnostics. The roles of RNAs in HNC diagnosis, metastasis, tumor resistance to radio and chemotherapy, and overall prognosis are discussed. RNA-based liquid biopsy holds great promise for the early detection, prognosis, and personalized treatment of HNC. Further research and validation are necessary to translate these findings into clinical practice and improve patient outcomes.
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Affiliation(s)
- Jacek Kabzinski
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Aleksandra Kucharska-Lusina
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
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Rakhmetullina A, Akimniyazova A, Niyazova T, Pyrkova A, Tauassarova M, Ivashchenko A, Zielenkiewicz P. Interactions of piRNAs with the mRNA of Candidate Genes in Esophageal Squamous Cell Carcinoma. Curr Issues Mol Biol 2023; 45:6140-6153. [PMID: 37504303 PMCID: PMC10378052 DOI: 10.3390/cimb45070387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023] Open
Abstract
Recently, a database of human piRNAs (piwi-interacting RNAs) was created, which allows the study of the binding of many piRNAs to the mRNAs of genes involved in many diseases, including cancer. In the present work, we identified the piRNAs that can interact with candidate esophageal squamous cell carcinoma (ESCC) genes. The binding of 480 thousand piRNAs with the mRNAs of 66 candidate ESCC genes was studied. Bioinformatic studies found that piRNAs bind only to the mRNAs of nine candidate genes: AURKA, BMP7, GCOM1, ERCC1, MTHFR, SASH1, SIX4, SULT1A1, and TP53. It has been shown that piRNAs can bind to mRNA by overlapping nucleotide sequences in limited 3'UTR and 5'UTR regions called clusters of binding sites (BSs). The existence of clusters of piRNA BSs significantly reduces the proportion of the nucleotide sequences of these sites in the mRNA of target genes. Competition between piRNAs occurs for binding to the mRNA of target genes. Individual piRNAs and groups of piRNAs that have separate BSs and clusters of BSs in the mRNAs of two or more candidate genes have been identified in the mRNAs of these genes. This organization of piRNAs BSs indicates the interdependence of the expression of candidate genes through piRNAs. Significant differences in the ability of genes to interact with piRNAs prevent the side effects of piRNAs on genes with a lack of the ability to bind such piRNAs. Individual piRNAs and sets of piRNAs are proposed and recommended for the diagnosis and therapy of ESCC.
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Affiliation(s)
- Aizhan Rakhmetullina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Technology of Production of Livestock Products, A. Baitursynov Kostanay Regional University, Kostanay 110000, Kazakhstan
| | - Aigul Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Togzhan Niyazova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Anna Pyrkova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty 050060, Kazakhstan
| | - Makpal Tauassarova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | | | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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Gao Y, Yan W, Sun L, Zhang X. PiRNA hsa_piR_019914 Promoted Chondrocyte Anabolic Metabolism By Inhibiting LDHA-Dependent ROS Production. Cartilage 2023:19476035231181094. [PMID: 37431854 DOI: 10.1177/19476035231181094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/12/2023] Open
Abstract
OBJECTIVES Osteoarthritis (OA) is the most common joint disease. The occurrence and progression of OA are regulated by epigenetics. A large number of studies have shown the important regulatory role of noncoding RNAs in joint diseases. As the largest class of noncoding small RNAs, the importance of piRNAs in many diseases, especially cancer, has been increasingly recognized. However, few studies have explored the role of piRNAs in OA. Our study showed that hsa_piR_019914 decreased significantly in OA. This study aimed to demonstrate the role of hsa_piR_019914 as a potential biological target of OA in chondrocytes. DESIGN The GEO database and bioinformatics analysis were used for a series of screenings, and the OA model using human articular chondrocytes (C28/I2 cells), SW1353 cells under inflammatory factor stimulation was used to determine that hsa_piR_019914 was significantly downregulated in OA. Overexpression or inhibition of hsa_piR_019914 in C28/I2 cells was achieved by transfecting mimics or inhibitors. The effect of hsa_piR_019914 on the biological function of chondrocytes was verified by qPCR, flow cytometry, and colony formation assays in vitro. The target gene of hsa_piR_019914, lactate dehydrogenase A (LDHA), was screened by small RNA sequencing and quantitative polymerase chain reaction (qPCR), LDHA was knocked out in C28/I2 cells by the transfection of siRNA LDHA, and the relationship between hsa_piR_019914, LDHA, and reactive oxygen species (ROS) production was verified by flow cytometry. RESULTS The piRNA hsa-piR-019914 was significantly downregulated in osteoarthritis (OA). Hsa-piR-019914 reduced inflammation-mediated chondrocyte apoptosis and maintained cell proliferation and clone formation in vitro. Hsa-piR-019914 reduced the production of LDHA-dependent ROS through targeted regulation of LDHA expression, maintained chondrocyte-specific gene expression of ACAN and COL2, and inhibited the gene expression of MMP3 and MMP13. CONCLUSIONS Collectively, this study showed that hsa_piR_019914 was negatively correlated with the expression of LDHA, which mediates ROS production. Under the stimulation of inflammatory factors, overexpression of hsa_piR_019914 had a protective effect on chondrocytes in vitro, and the absence of hsa_piR_019914 exacerbated the negative effect of inflammation on chondrocytes. Studies on piRNAs provide new therapeutic interventions for OA.
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Affiliation(s)
- YuXuan Gao
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan, P.R. China
| | - Wen Yan
- Center of Stomatology, The Second Affiliated Hospital of Soochow University, Soochow, P.R. China
| | - Liangye Sun
- Department of Orthopedic Surgery, Luan Hospital, Anhui Medical University, Luan, China
| | - XiaoLing Zhang
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan, P.R. China
- Department of Orthopedics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
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Isenmann M, Stoddart MJ, Schmelzeisen R, Gross C, Della Bella E, Rothweiler RM. Basic Principles of RNA Interference: Nucleic Acid Types and In Vitro Intracellular Delivery Methods. Micromachines (Basel) 2023; 14:1321. [PMID: 37512632 PMCID: PMC10383872 DOI: 10.3390/mi14071321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Since its discovery in 1989, RNA interference (RNAi) has become a widely used tool for the in vitro downregulation of specific gene expression in molecular biological research. This basically involves a complementary RNA that binds a target sequence to affect its transcription or translation process. Currently, various small RNAs, such as small interfering RNA (siRNA), micro RNA (miRNA), small hairpin RNA (shRNA), and PIWI interacting RNA (piRNA), are available for application on in vitro cell culture, to regulate the cells' gene expression by mimicking the endogenous RNAi-machinery. In addition, several biochemical, physical, and viral methods have been established to deliver these RNAs into the cell or nucleus. Since each RNA and each delivery method entail different off-target effects, limitations, and compatibilities, it is crucial to understand their basic mode of action. This review is intended to provide an overview of different nucleic acids and delivery methods for planning, interpreting, and troubleshooting of RNAi experiments.
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Affiliation(s)
- Marie Isenmann
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Martin James Stoddart
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Rainer Schmelzeisen
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Christian Gross
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Elena Della Bella
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - René Marcel Rothweiler
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
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Saquib M, Agnihotri P, Biswas S. Interrelated grid of non-coding RNA: An important aspect in Rheumatoid Arthritis pathogenesis. Mol Biol Rep 2023:10.1007/s11033-023-08543-w. [PMID: 37294467 DOI: 10.1007/s11033-023-08543-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Inflammation and autoimmunity are the root cause of rheumatoid arthritis, a destructive disease of joints. Multiple biomolecules are involved in the pathogenesis of RA and are related to various events of molecular biology. RNA is a versatile biomolecule, playing numerous roles at structural, functional, and regulatory stages to maintain cellular homeostasis. The involvement of RNA (coding/non-coding) in disease development and progression has left a wide whole to fill with newer approaches. Non-coding RNAs belong to the housekeeping and regulatory categories and both have their specific roles, and their alteration causes specific implications in disease pathogenesis. Housekeeping RNAs, rRNA, tRNA and regulatory RNA, micro-RNA, circular RNA, piRNA and long non-coding RNA were found to be important regulators of inflammation. They work at the pre-and post-transcriptional levels and were found to be more intriguing to study their regulatory impact on disease pathogenesis. The review addresses a question on how the non-coding RNA gets involved in early RA pathogenesis and can be utilized to know their targets to understand the disease better and make way towards the unresolved mystery of RA development.
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Affiliation(s)
- Mohd Saquib
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prachi Agnihotri
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sagarika Biswas
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Integrative and Functional Biology Department CSIR- Institute of Genomics & Integrative Biology, Mall Road, Delhi, 110 007, India.
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DeSouza NR, Quaranto D, Carnazza M, Jarboe T, Tiwari RK, Geliebter J. Interactome of Long Non-Coding RNAs: Transcriptomic Expression Patterns and Shaping Cancer Cell Phenotypes. Int J Mol Sci 2023; 24:9914. [PMID: 37373059 DOI: 10.3390/ijms24129914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
RNA biology has gained extensive recognition in the last two decades due to the identification of novel transcriptomic elements and molecular functions. Cancer arises, in part, due to the accumulation of mutations that greatly contribute to genomic instability. However, the identification of differential gene expression patterns of wild-type loci has exceeded the boundaries of mutational study and has significantly contributed to the identification of molecular mechanisms that drive carcinogenic transformation. Non-coding RNA molecules have provided a novel avenue of exploration, providing additional routes for evaluating genomic and epigenomic regulation. Of particular focus, long non-coding RNA molecule expression has been demonstrated to govern and direct cellular activity, thus evidencing a correlation between aberrant long non-coding RNA expression and the pathological transformation of cells. lncRNA classification, structure, function, and therapeutic utilization have expanded cancer studies and molecular targeting, and understanding the lncRNA interactome aids in defining the unique transcriptomic signatures of cancer cell phenotypes.
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Affiliation(s)
- Nicole R DeSouza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Danielle Quaranto
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Michelle Carnazza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Tara Jarboe
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Raj K Tiwari
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
| | - Jan Geliebter
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
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Hu D, Wang L, Chen X, Lin Y, Zhang S, Fan Z, Peng F. Impact of PIWIL1 Single Nucleotide Polymorphisms on Gastric Cancer Risk in a Chinese Population. Genet Test Mol Biomarkers 2023; 27:185-192. [PMID: 37382906 DOI: 10.1089/gtmb.2022.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Background: PIWI-like proteins contribute to the onset and progression of carcinogenesis. Whether single nucleotide polymorphisms (SNPs) in the PIWI-like 1 (PIWIL1) gene affect the morbidity and mortality of gastric cancer (GC) remains unclear. To investigate the efficacy of PIWIL1 SNPs genotype on the morbidity and mortality of GC and its interaction within PIWIL1 gene SNPs variation and between elevated plasma glucose. Materials and Methods: We conducted a case-control study that contained 216 GC patients and 204 cancer-free controls to compare differential expression of PIWIL1 SNPs. Results: PIWIL1 gene rs1106042 AA and AG genotypes were associated with significantly reduced GC risk (odds ratio [OR]: 0.15 and 0.26, p < 0.001 and p = 0.016), and rs10773771 CT+CC type significantly increased cancer risk (OR: 1.54 p = 0.037). We observed strong associations between rs10773771 and pathological type (p = 0.012), rs11703684, and invasion depth (p = 0.012). We noticed significant gene-gene interaction between rs1106042 and rs10773771 (p = 0.0107). Interaction between the copresence of rs1106042 GG plus hyperglycemia was also significant (relative excess risk due to interaction: 28.78, attributable proportion due to interaction: 68.2%, synergy index: 3.32). Patients with rs1892723 TT and rs1892722 GG+GA type had better survival (p = 0.030 and p = 0.048). Conclusion: rs10773771 CT+CC was associated with GC risk increase, rs1106042 AA and AG function as a protective factor. rs1892723 CT+TT and rs1892722 AA type may portend a poor prognosis. Elevated fasting plasma glucose will significantly increase the risk of PIWIL gene rs1106042 GG carcinogenesis by multiplicative interaction.
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Affiliation(s)
- Dan Hu
- Department of Pathology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Laicheng Wang
- Department of Cardiology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xin Chen
- Department of Cardiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yunchai Lin
- Department of Cardiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Shunpeng Zhang
- Department of Cardiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Zongcheng Fan
- Department of Cardiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Feng Peng
- Department of Cardiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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Ding YH, Ochoa HJ, Ishidate T, Shirayama M, Mello CC. The nuclear Argonaute HRDE-1 directs target gene re-localization and shuttles to nuage to promote small RNA-mediated inherited silencing. Cell Rep 2023; 42:112408. [PMID: 37083324 PMCID: PMC10443184 DOI: 10.1016/j.celrep.2023.112408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/13/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Argonaute/small RNA pathways and heterochromatin work together to propagate transgenerational gene silencing, but the mechanisms behind their interaction are not well understood. Here, we show that induction of heterochromatin silencing in C. elegans by RNAi or by artificially tethering pathway components to target RNA causes co-localization of target alleles in pachytene nuclei. Tethering the nuclear Argonaute WAGO-9/HRDE-1 induces heterochromatin formation and independently induces small RNA amplification. Consistent with this finding, HRDE-1, while predominantly nuclear, also localizes to peri-nuclear nuage domains, where amplification is thought to occur. Tethering a heterochromatin-silencing factor, NRDE-2, induces heterochromatin formation, which subsequently causes de novo synthesis of HRDE-1 guide RNAs. HRDE-1 then acts to further amplify small RNAs that load on downstream Argonautes. These findings suggest that HRDE-1 plays a dual role, acting upstream to initiate heterochromatin silencing and downstream to stimulate a new cycle of small RNA amplification, thus establishing a self-enforcing mechanism that propagates gene silencing to future generations.
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Affiliation(s)
- Yue-He Ding
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Humberto J Ochoa
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Takao Ishidate
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Masaki Shirayama
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Worcester, MA 01605, USA.
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Ren R, Tan H, Huang Z, Wang Y, Yang B. Differential expression and correlation of immunoregulation related piRNA in rheumatoid arthritis. Front Immunol 2023; 14:1175924. [PMID: 37325646 PMCID: PMC10266269 DOI: 10.3389/fimmu.2023.1175924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Background Although PIWI-interacting RNAs (piRNAs) have recently been associated with germline development and many human diseases, their expression pattern and relationship in autoimmune diseases remain indistinct. This study aimed to investigate the presence and correlation of piRNAs in rheumatoid arthritis (RA). Methods We first analyzed the expression profile of piRNAs using small RNA sequencing in peripheral leukocytes of three new-onset untreated RA patients and three healthy controls (HCs). We then selected piRNAs related to immunoregulation by bioinformatics analysis and verified them in 42 new-onset RA patients and 81 HCs by RT-qPCR. Furthermore, a receiver operating characteristic curve was generated to quantify the diagnostic performance of these piRNAs. A correlation analysis was conducted to observe the link between piRNA expression and RA clinical characteristics. Results A total of 15 upregulated and 9 downregulated piRNAs among 1,565 known piRNAs were identified in peripheral leukocytes of RA patients. Dysregulated piRNAs were enriched in numerous pathways related to immunity. After selection and validation, two immunoregulation piRNAs (piR-hsa-27620 and piR-hsa-27124) were significantly elevated in RA patients and have good abilities to distinguish patients from controls, which have the potential to serve as biomarkers. PIWI and other proteins implicated in the piRNA pathway were also associated with RA.
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Affiliation(s)
- Ruyu Ren
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Huiling Tan
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Zhuochun Huang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuanyi Wang
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Bin Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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Tong Y, Guan B, Sun Z, Dong X, Chen Y, Li Y, Jiang Y, Li J. Ratiometric fluorescent detection of exosomal piRNA-823 based on Au NCs/UiO-66-NH 2 and target-triggered rolling circle amplification. Talanta 2023; 257:124307. [PMID: 36764170 DOI: 10.1016/j.talanta.2023.124307] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
piR-823 is a newly discovered colorectal cancer marker with high diagnostic efficacy. However, the current quantification methods have complicated operations and high cost, which restrict its clinical application. Herein, a metal-organic framework (MOF) with a UiO-66 prototype structure which supports gold nanoclusters (Au NCs), Au NCs/UiO-66-NH2, were prepared as a model nanobiosensing platform for ratiometric detection of exosomal piR-823. The rolling circle amplification process provides high sensitivity and the ratiometric detection process ensures good accuracy of the sensor. Such biosensor showed a wide linear range of 0.04-4 pM, and a low detection limit of 10.2 fM towards piR-823. In addition, piR-823 can be used as an effective supplement to carcinoembryonic antigen (CEA) in clinical diagnosis of colorectal cancer. This study not only provides a potentially valuable ratio fluorescence platform involving enzyme catalytic reaction, but also offers a design blueprint for further expansion of nanotechnology in the diverse biological analysis.
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Affiliation(s)
- Yao Tong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Bingxin Guan
- Department of Pathology, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Zhiwei Sun
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Xiangjun Dong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yuqing Chen
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yanru Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yanyan Jiang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China.
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China.
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Chen P, Aravin AA. Genetic control of a sex-specific piRNA program. Curr Biol 2023; 33:1825-1835.e3. [PMID: 37059098 PMCID: PMC10431932 DOI: 10.1016/j.cub.2023.03.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/15/2023] [Accepted: 03/17/2023] [Indexed: 04/16/2023]
Abstract
Sexually dimorphic traits in morphologies are widely studied,1,2,3,4 but those in essential molecular pathways remain largely unexplored. Previous work showed substantial sex differences in Drosophila gonadal piRNAs,5 which guide PIWI proteins to silence selfish genetic elements, thereby safeguarding fertility.6,7,8 However, the genetic control mechanisms of piRNA sexual dimorphism remain unknown. Here, we showed that most sex differences in the piRNA program originate from the germ line rather than the gonadal somatic cells. Building on this, we dissected the contribution of sex chromosomes and cellular sexual identity toward the sex-specific germline piRNA program. We found that the presence of the Y chromosome is sufficient to recapitulate some aspects of the male piRNA program in a female cellular environment. Meanwhile, sexual identity controls the sexually divergent piRNA production from X-linked and autosomal loci, revealing a crucial input from sex determination into piRNA biogenesis. Sexual identity regulates piRNA biogenesis through Sxl, and this effect is mediated, in part, through chromatin proteins Phf7 and Kipferl. Together, our work delineated the genetic control of a sex-specific piRNA program, where sex chromosomes and sexual identity collectively sculpt an essential molecular trait.
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Affiliation(s)
- Peiwei Chen
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA.
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA 91125, USA.
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