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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] [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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Li B, Wang K, Cheng W, Fang B, Li YH, Yang SM, Zhang MH, Wang YH, Wang K. Recent advances of PIWI-interacting RNA in cardiovascular diseases. Clin Transl Med 2024; 14:e1770. [PMID: 39083321 PMCID: PMC11290350 DOI: 10.1002/ctm2.1770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The relationship between noncoding RNAs (ncRNAs) and human diseases has been a hot topic of research, but the study of ncRNAs in cardiovascular diseases (CVDs) is still in its infancy. PIWI-interacting RNA (piRNA), a small ncRNA that binds to the PIWI protein to maintain genome stability by silencing transposons, was widely studied in germ lines and stem cells. In recent years, piRNA has been shown to be involved in key events of multiple CVDs through various epigenetic modifications, revealing the potential value of piRNA as a new biomarker or therapeutic target. CONCLUSION This review explores origin, degradation, function, mechanism and important role of piRNA in CVDs, and the promising therapeutic targets of piRNA were summarized. This review provide a new strategy for the treatment of CVDs and lay a theoretical foundation for future research. KEY POINTS piRNA can be used as a potential therapeutic target and biomaker in CVDs. piRNA influences apoptosis, inflammation and angiogenesis by regulating epigenetic modificaions. Critical knowledge gaps remain in the unifying piRNA nomenclature and PIWI-independent function.
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Affiliation(s)
- Bo Li
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Kai Wang
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Wei Cheng
- Department of Cardiovascular SurgeryBeijing Children's Hospital, Capital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Bo Fang
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Ying Hui Li
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Su Min Yang
- Department of Cardiovascular SurgeryThe Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Mei Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
| | - Yun Hong Wang
- Hypertension CenterBeijing Anzhen HospitalCapital Medical UniversityBeijingChina
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
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3
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Fernandez MV, Liu M, Beric A, Johnson M, Cetin A, Patel M, Budde J, Kohlfeld P, Bergmann K, Lowery J, Flynn A, Brock W, Sanchez Montejo B, Gentsch J, Sykora N, Norton J, Gentsch J, Valdez O, Gorijala P, Sanford J, Sun Y, Wang C, Western D, Timsina J, Mangetti Goncalves T, Do AN, Sung YJ, Zhao G, Morris JC, Moulder K, Holtzman DM, Bateman RJ, Karch C, Hassenstab J, Xiong C, Schindler SE, Balls-Berry JJ, Benzinger TLS, Perrin RJ, Denny A, Snider BJ, Stark SL, Ibanez L, Cruchaga C. Genetic and multi-omic resources for Alzheimer disease and related dementia from the Knight Alzheimer Disease Research Center. Sci Data 2024; 11:768. [PMID: 38997326 PMCID: PMC11245521 DOI: 10.1038/s41597-024-03485-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/06/2024] [Indexed: 07/14/2024] Open
Abstract
The Knight-Alzheimer Disease Research Center (Knight-ADRC) at Washington University in St. Louis has pioneered and led worldwide seminal studies that have expanded our clinical, social, pathological, and molecular understanding of Alzheimer Disease. Over more than 40 years, research volunteers have been recruited to participate in cognitive, neuropsychologic, imaging, fluid biomarkers, genomic and multi-omic studies. Tissue and longitudinal data collected to foster, facilitate, and support research on dementia and aging. The Genetics and high throughput -omics core (GHTO) have collected of more than 26,000 biological samples from 6,625 Knight-ADRC participants. Samples available include longitudinal DNA, RNA, non-fasted plasma, cerebrospinal fluid pellets, and peripheral blood mononuclear cells. The GHTO has performed deep molecular profiling (genomic, transcriptomic, epigenomic, proteomic, and metabolomic) from large number of brain (n = 2,117), CSF (n = 2,012) and blood/plasma (n = 8,265) samples with the goal of identifying novel risk and protective variants, identify novel molecular biomarkers and causal and druggable targets. Overall, the resources available at GHTO support the increase of our understanding of Alzheimer Disease.
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Affiliation(s)
- Maria Victoria Fernandez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Research Center and Memory Clinic, ACE Alzheimer Center, Barcelona, Spain
| | - Menghan Liu
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aleksandra Beric
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Matt Johnson
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Arda Cetin
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Maulik Patel
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joseph Lowery
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Allison Flynn
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - William Brock
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Brenda Sanchez Montejo
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Nicholas Sykora
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jen Gentsch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Olga Valdez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Priyanka Gorijala
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jessie Sanford
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yichen Sun
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ciyang Wang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Anh N Do
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Guoyan Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Pathology and Immunology Department, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John C Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Krista Moulder
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - David M Holtzman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Randall J Bateman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
| | - Celeste Karch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
| | - Jason Hassenstab
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Chengjie Xiong
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
| | - Suzanne E Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Joyce Joy Balls-Berry
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Tammie L S Benzinger
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
- Radiology Department, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Richard J Perrin
- Pathology and Immunology Department, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA
| | - Andrea Denny
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - B Joy Snider
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan L Stark
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Occupational Therapy, Neurology and Social Work, St. Louis, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA.
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.
- Dominantly Inherited Alzheimer Disease Network (DIAN), St. Louis, USA.
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4
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Pan X, Dai W, Wang Z, Li S, Sun T, Miao N. PIWI-Interacting RNAs: A Pivotal Regulator in Neurological Development and Disease. Genes (Basel) 2024; 15:653. [PMID: 38927589 PMCID: PMC11202748 DOI: 10.3390/genes15060653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs), a class of small non-coding RNAs (sncRNAs) with 24-32 nucleotides (nt), were initially identified in the reproductive system. Unlike microRNAs (miRNAs) or small interfering RNAs (siRNAs), piRNAs normally guide P-element-induced wimpy testis protein (PIWI) families to slice extensively complementary transposon transcripts without the seed pairing. Numerous studies have shown that piRNAs are abundantly expressed in the brain, and many of them are aberrantly regulated in central neural system (CNS) disorders. However, the role of piRNAs in the related developmental and pathological processes is unclear. The elucidation of piRNAs/PIWI would greatly improve the understanding of CNS development and ultimately lead to novel strategies to treat neural diseases. In this review, we summarized the relevant structure, properties, and databases of piRNAs and their functional roles in neural development and degenerative disorders. We hope that future studies of these piRNAs will facilitate the development of RNA-based therapeutics for CNS disorders.
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Affiliation(s)
| | | | | | | | | | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen 361021, China; (X.P.); (W.D.); (Z.W.); (S.L.); (T.S.)
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5
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Karpagavalli M, Sivagurunathan S, Panda TS, Srikakulam N, Arora R, Dohadwala L, Tiwary BK, Sadras SR, Arunachalam JP, Pandi G, Chidambaram S. piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress. Mol Omics 2024; 20:248-264. [PMID: 38314503 DOI: 10.1039/d3mo00122a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Long considered active only in the germline, the PIWI/piRNA pathway is now known to play a significant role in somatic cells, especially neurons. In this study, piRNAs were profiled in the human retina and retinal pigment epithelium (RPE). Furthermore, RNA immunoprecipitation with HIWI2 (PIWIL4) in ARPE19 cells yielded 261 piRNAs, and the expression of selective piRNAs in donor eyes was assessed by qRT-PCR. Intriguingly, computational analysis revealed complete and partial seed sequence similarity between piR-hsa-26131 and the sensory organ specific miR-183/96/182 cluster. Furthermore, the expression of retina-enriched piR-hsa-26131 was positively correlated with miR-182 in HIWI2-silenced Y79 cells. In addition, the lnc-ZNF169 sequence matched with two miRNAs of the let-7 family, and piRNAs, piR-hsa-11361 and piR-hsa-11360, which could modulate the regulatory network of retinal differentiation. Interestingly, we annotated four enriched motifs among the piRNAs and found that the piRNAs containing CACAATG and CTCATCAKYG motifs were snoRNA-derived piRNAs, which are significantly associated with developmental functions. However, piRNAs consisting of ACCACTANACCAC and AKCACGYTCSC motifs were mainly tRNA-derived fragments linked to stress response and sensory perception. Additionally, co-expression network analysis revealed cell cycle control, intracellular transport and stress response as the important biological functions regulated by piRNAs in the retina. Moreover, loss of piRNAs in HIWI2 knockdown ARPE19 confirmed altered expression of targets implicated in intracellular transport, circadian clock, and retinal degeneration. Moreover, piRNAs were dysregulated under oxidative stress conditions, indicating their potential role in retinal pathology. Therefore, we postulate that piRNAs, miRNAs, and lncRNAs might have a functional interplay during retinal development and functions to regulate retinal homeostasis.
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Affiliation(s)
| | - Suganya Sivagurunathan
- RS Mehta Jain Department of Biochemistry and Cell Biology, Vision Research Foundation, Chennai, India
| | - T Sayamsmruti Panda
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Nagesh Srikakulam
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Reety Arora
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | | | - Basant K Tiwary
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
| | - Jayamuruga Pandian Arunachalam
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry-607402, India
| | - Gopal Pandi
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Subbulakshmi Chidambaram
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
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6
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Giulietti M, Piva F, Cecati M, Maggio S, Guescini M, Saladino T, Scortichini L, Crocetti S, Caramanti M, Battelli N, Romagnoli E. Effects of Eribulin on the RNA Content of Extracellular Vesicles Released by Metastatic Breast Cancer Cells. Cells 2024; 13:479. [PMID: 38534323 DOI: 10.3390/cells13060479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/23/2024] [Accepted: 03/04/2024] [Indexed: 03/28/2024] Open
Abstract
Extracellular vesicles (EVs) are small lipid particles secreted by almost all human cells into the extracellular space. They perform the essential function of cell-to-cell communication, and their role in promoting breast cancer progression has been well demonstrated. It is known that EVs released by triple-negative and highly aggressive MDA-MB-231 breast cancer cells treated with paclitaxel, a microtubule-targeting agent (MTA), promoted chemoresistance in EV-recipient cells. Here, we studied the RNA content of EVs produced by the same MDA-MB-231 breast cancer cells treated with another MTA, eribulin mesylate. In particular, we analyzed the expression of different RNA species, including mRNAs, lncRNAs, miRNAs, snoRNAs, piRNAs and tRNA fragments by RNA-seq. Then, we performed differential expression analysis, weighted gene co-expression network analysis (WGCNA), functional enrichment analysis, and miRNA-target identification. Our findings demonstrate the possible involvement of EVs from eribulin-treated cells in the spread of chemoresistance, prompting the design of strategies that selectively target tumor EVs.
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Affiliation(s)
- Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Monia Cecati
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Serena Maggio
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Michele Guescini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Tiziana Saladino
- Oncology Unit AST3, Macerata Hospital, Via Santa Lucia 2, 62100 Macerata, Italy
| | - Laura Scortichini
- Oncology Unit AST3, Macerata Hospital, Via Santa Lucia 2, 62100 Macerata, Italy
| | - Sonia Crocetti
- Oncology Unit AST3, Macerata Hospital, Via Santa Lucia 2, 62100 Macerata, Italy
| | - Miriam Caramanti
- Oncology Unit AST3, Macerata Hospital, Via Santa Lucia 2, 62100 Macerata, Italy
| | - Nicola Battelli
- Oncology Unit AST3, Macerata Hospital, Via Santa Lucia 2, 62100 Macerata, Italy
| | - Emanuela Romagnoli
- Oncology Unit AST3, Macerata Hospital, Via Santa Lucia 2, 62100 Macerata, Italy
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7
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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: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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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] [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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9
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Gupta P, Das G, Chattopadhyay T, Ghosh Z, Mallick B. TarpiD, a database of putative and validated targets of piRNAs. Mol Omics 2023; 19:706-713. [PMID: 37427797 DOI: 10.1039/d3mo00098b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are a novel class of 18-36 nts long small non-coding single-stranded RNAs that play crucial roles in a wide array of critical biological activities besides maintaining genome integrity by transposon silencing. piRNAs influence biological processes and pathways by regulating gene expression at transcriptional and post-transcriptional level. Studies have reported that piRNAs silence various endogenous genes post-transcriptionally by binding to respective mRNAs through interaction with the PIWI proteins. Several thousands of piRNAs have been discovered in animals, but their functions remain largely undiscovered owing to a lack of proper guiding principles of piRNA targeting or diversity in targeting patterns amongst piRNAs from the same or different species. Identification of piRNA targets is essential for deciphering their functions. There are a few tools and databases on piRNAs, but there are no systematic and exclusive repositories to obtain information on target genes regulated by piRNAs and other related information. Hence, we developed a user-friendly database named TarpiD (Targets of piRNA Database) that offers comprehensive information on piRNA and its targets, including their expression, methodologies (high-throughput or low-throughput) for target identification/validation, cells/tissue types, diseases, target gene regulation types, target binding regions, and key functions driven by piRNAs through target gene interactions. The contents of TarpiD are curated from the published literature and enable users to search and download the targets of a particular piRNA or the piRNAs that target a specific gene for use in their research. This database harbours 28 682 entries of piRNA-target interactions supported by 15 methodologies reported in hundreds of cell types/tissues from 9 species. TarpiD will be a valuable resource for a better understanding of the functions and gene-regulatory mechanisms mediated by piRNAs. TarpiD is freely accessible for academic use at https://tarpid.nitrkl.ac.in/tarpid_db/.
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Affiliation(s)
- Pooja Gupta
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela-769008, Odisha, India.
| | - Gourab Das
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Trisha Chattopadhyay
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela-769008, Odisha, India.
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela-769008, Odisha, India.
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10
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Huang X, Wang C, Zhang T, Li R, Chen L, Leung KL, Lakso M, Zhou Q, Zhang H, Wong G. PIWI-interacting RNA expression regulates pathogenesis in a Caenorhabditis elegans model of Lewy body disease. Nat Commun 2023; 14:6137. [PMID: 37783675 PMCID: PMC10545829 DOI: 10.1038/s41467-023-41881-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that regulate gene expression, yet their molecular functions in neurobiology are unclear. While investigating neurodegeneration mechanisms using human α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg pan-neuronal overexpressing strains, we unexpectedly observed dysregulation of piRNAs. RNAi screening revealed that knock down of piRNA biogenesis genes improved thrashing behavior; further, a tofu-1 gene deletion ameliorated phenotypic deficits in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg transgenic strains. piRNA expression was extensively downregulated and H3K9me3 marks were decreased after tofu-1 deletion in α-syn(A53T)Tg and AβTg;α-syn(A53T)Tg strains. Dysregulated piRNAs targeted protein degradation genes suggesting that a decrease of piRNA expression leads to an increase of degradation ability in C. elegans. Finally, we interrogated piRNA expression in brain samples from PD patients. piRNAs were observed to be widely overexpressed at late motor stage. In this work, our results provide evidence that piRNAs are mediators in pathogenesis of Lewy body diseases and suggest a molecular mechanism for neurodegeneration in these and related disorders.
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Affiliation(s)
- Xiaobing Huang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, 519000, China
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Changliang Wang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, 510799, China
| | - Tianjiao Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Rongzhen Li
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, 515063, China
| | - Ka Lai Leung
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Merja Lakso
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Qinghua Zhou
- Department of Anesthesiology, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
- Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, 510632, China
| | - Hongjie Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China
| | - Garry Wong
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, 999078, Macau, China.
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Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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12
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Wang X, Lin DH, Yan Y, Wang AH, Liao J, Meng Q, Yang WQ, Zuo H, Hua MM, Zhang F, Zhu H, Zhou H, Huang TY, He R, Li G, Tan YQ, Shi HJ, Gou LT, Li D, Wu L, Zheng Y, Fu XD, Li J, Liu R, Li GH, Liu MF. The PIWI-specific insertion module helps load longer piRNAs for translational activation essential for male fertility. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-023-2390-5. [PMID: 37335463 DOI: 10.1007/s11427-023-2390-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
PIWI-clade proteins harness piRNAs of 24-33 nt in length. Of great puzzles are how PIWI-clade proteins incorporate piRNAs of different sizes and whether the size matters to PIWI/piRNA function. Here we report that a PIWI-Ins module unique in PIWI-clade proteins helps define the length of piRNAs. Deletion of PIWI-Ins in Miwi shifts MIWI to load with shorter piRNAs and causes spermiogenic failure in mice, demonstrating the functional importance of this regulatory module. Mechanistically, we show that longer piRNAs provide additional complementarity to target mRNAs, thereby enhancing the assembly of the MIWI/eIF3f/HuR super-complex for translational activation. Importantly, we identify a c.1108C>T (p.R370W) mutation of HIWI (human PIWIL1) in infertile men and demonstrate in Miwi knock-in mice that this genetic mutation impairs male fertility by altering the property of PIWI-Ins in selecting longer piRNAs. These findings reveal a critical role of PIWI-Ins-ensured longer piRNAs in fine-tuning MIWI/piRNA targeting capacity, proven essential for spermatid development and male fertility.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Di-Hang Lin
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yue Yan
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - An-Hui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiaoyang Liao
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qian Meng
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Heng Zuo
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Min-Min Hua
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, 200032, China
| | - Fengjuan Zhang
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hongwen Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Tian-Yu Huang
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rui He
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China
| | - Guangyong Li
- Department of Urology, General Hospital of Ningxia Medical University, Ningxia Medical University, Yinchuan, 750004, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, College of Basic of Medicine, Central South University, Changsha, 410000, China
| | - Hui-Juan Shi
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, 200032, China
| | - Lan-Tao Gou
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dangsheng Li
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yonggang Zheng
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiang-Dong Fu
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, 310024, China
| | - Jinsong Li
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Rujuan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Guo-Hui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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13
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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] [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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14
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Meng X, Shang J, Ge D, Yang Y, Zhang T, Liu JX. ETGPDA: identification of piRNA-disease associations based on embedding transformation graph convolutional network. BMC Genomics 2023; 24:279. [PMID: 37226081 DOI: 10.1186/s12864-023-09380-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs) have been proven to be closely associated with human diseases. The identification of the potential associations between piRNA and disease is of great significance for complex diseases. Traditional "wet experiment" is time-consuming and high-priced, predicting the piRNA-disease associations by computational methods is of great significance. METHODS In this paper, a method based on the embedding transformation graph convolution network is proposed to predict the piRNA-disease associations, named ETGPDA. Specifically, a heterogeneous network is constructed based on the similarity information of piRNA and disease, as well as the known piRNA-disease associations, which is applied to extract low-dimensional embeddings of piRNA and disease based on graph convolutional network with an attention mechanism. Furthermore, the embedding transformation module is developed for the problem of embedding space inconsistency, which is lightweighter, stronger learning ability and higher accuracy. Finally, the piRNA-disease association score is calculated by the similarity of the piRNA and disease embedding. RESULTS Evaluated by fivefold cross-validation, the AUC of ETGPDA achieves 0.9603, which is better than the other five selected computational models. The case studies based on Head and neck squamous cell carcinoma and Alzheimer's disease further prove the superior performance of ETGPDA. CONCLUSIONS Hence, the ETGPDA is an effective method for predicting the hidden piRNA-disease associations.
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Affiliation(s)
- Xianghan Meng
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Junliang Shang
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China.
| | - Daohui Ge
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China.
| | - Yi Yang
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Tongdui Zhang
- Science and Technology Innovation Service Institution of Rizhao, Rizhao, 276826, China
| | - Jin-Xing Liu
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
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15
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Pathania AS. Crosstalk between Noncoding RNAs and the Epigenetics Machinery in Pediatric Tumors and Their Microenvironment. Cancers (Basel) 2023; 15:2833. [PMID: 37345170 DOI: 10.3390/cancers15102833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
According to the World Health Organization, every year, an estimated 400,000+ new cancer cases affect children under the age of 20 worldwide. Unlike adult cancers, pediatric cancers develop very early in life due to alterations in signaling pathways that regulate embryonic development, and environmental factors do not contribute much to cancer development. The highly organized complex microenvironment controlled by synchronized gene expression patterns plays an essential role in the embryonic stages of development. Dysregulated development can lead to tumor initiation and growth. The low mutational burden in pediatric tumors suggests the predominant role of epigenetic changes in driving the cancer phenotype. However, one more upstream layer of regulation driven by ncRNAs regulates gene expression and signaling pathways involved in the development. Deregulation of ncRNAs can alter the epigenetic machinery of a cell, affecting the transcription and translation profiles of gene regulatory networks required for cellular proliferation and differentiation during embryonic development. Therefore, it is essential to understand the role of ncRNAs in pediatric tumor development to accelerate translational research to discover new treatments for childhood cancers. This review focuses on the role of ncRNA in regulating the epigenetics of pediatric tumors and their tumor microenvironment, the impact of their deregulation on driving pediatric tumor progress, and their potential as effective therapeutic targets.
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Affiliation(s)
- Anup S Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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16
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Wajnberg G, Allain EP, Roy JW, Srivastava S, Saucier D, Morin P, Marrero A, O’Connell C, Ghosh A, Lewis SM, Ouellette RJ, Crapoulet N. Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy. FRONTIERS IN BIOINFORMATICS 2023; 3:1127661. [PMID: 37252342 PMCID: PMC10213969 DOI: 10.3389/fbinf.2023.1127661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
RNA sequencing analysis is an important field in the study of extracellular vesicles (EVs), as these particles contain a variety of RNA species that may have diagnostic, prognostic and predictive value. Many of the bioinformatics tools currently used to analyze EV cargo rely on third-party annotations. Recently, analysis of unannotated expressed RNAs has become of interest, since these may provide complementary information to traditional annotated biomarkers or may help refine biological signatures used in machine learning by including unknown regions. Here we perform a comparative analysis of annotation-free and classical read-summarization tools for the analysis of RNA sequencing data generated for EVs isolated from persons with amyotrophic lateral sclerosis (ALS) and healthy donors. Differential expression analysis and digital-droplet PCR validation of unannotated RNAs also confirmed their existence and demonstrates the usefulness of including such potential biomarkers in transcriptome analysis. We show that find-then-annotate methods perform similarly to standard tools for the analysis of known features, and can also identify unannotated expressed RNAs, two of which were validated as overexpressed in ALS samples. We demonstrate that these tools can therefore be used for a stand-alone analysis or easily integrated into current workflows and may be useful for re-analysis as annotations can be integrated post hoc.
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Affiliation(s)
| | - Eric P. Allain
- Atlantic Cancer Research Institute, Moncton, NB, Canada
- Department of Clinical Genetics, Vitalité Health Network, Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Jeremy W. Roy
- Atlantic Cancer Research Institute, Moncton, NB, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | | | - Daniel Saucier
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Pier Morin
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Alier Marrero
- Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada
| | | | - Anirban Ghosh
- Atlantic Cancer Research Institute, Moncton, NB, Canada
| | - Stephen M. Lewis
- Atlantic Cancer Research Institute, Moncton, NB, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Rodney J. Ouellette
- Atlantic Cancer Research Institute, Moncton, NB, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
- Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada
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17
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Wang X, Huang P, Lei M, Ma Y, Chen H, Sun J, Hu Y, Shi J. Global expression and functional analysis of human piRNAs during HSV-1 infection. Virus Res 2023; 328:199087. [PMID: 36894069 DOI: 10.1016/j.virusres.2023.199087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/18/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs that play a key role in spermatogenesis. However, little is known about their expression characterization and role in somatic cells infected with herpes simplex virus type 1 (HSV-1). In this study, we systematically investigated the cellular piRNA expression profiles of HSV-1-infected human lung fibroblasts. Compared with the control group, 69 differentially expressed piRNAs were identified in the infection group, among which 52 were up-regulated and 17 were down-regulated. The changes in the expression of 8 piRNAs were further verified by RT-qPCR with a similar expression trend. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the target genes of piRNAs were mainly involved in antiviral immunity and various human disease-related signaling pathways. Furthermore, we tested the effects of four up-regulated piRNAs on viral replication by transfecting piRNA mimics. The results showed that the virus titers of the group transfected with piRNA-hsa-28,382 (alias piR-36,233) mimic decreased significantly, and that of the group transfected piRNA-hsa-28,190 (alias piR-36,041) mimic significantly increased. Overall, our results revealed the expression characteristics of piRNAs in HSV-1-infected cells. We also screened two piRNAs that potentially regulate HSV-1 replication. These results may promote a better understanding of the regulatory mechanism of pathophysiological changes induced by HSV-1 infection.
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Affiliation(s)
- Xu Wang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Pu Huang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Mengyue Lei
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Ying Ma
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Hongli Chen
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China; Kunming Medical University, Kunming, Yunnan, China
| | - Jing Sun
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
| | - Yunzhang Hu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
| | - Jiandong Shi
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
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18
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Rakhmetullina A, Akimniyazova A, Niyazova T, Pyrkova A, Kamenova S, Kondybayeva A, Ryskulova AG, Ivashchenko A, Zielenkiewicz P. Endogenous piRNAs Can Interact with the Omicron Variant of the SARS-CoV-2 Genome. Curr Issues Mol Biol 2023; 45:2950-2964. [PMID: 37185717 PMCID: PMC10136802 DOI: 10.3390/cimb45040193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the COVID-19 pandemic, can still infect populations in many countries around the globe. The Omicron strain is the most mutated variant of SARS-CoV-2. The high transmissibility of the strain and its ability to evade immunity necessitate a priority study of its properties in order to quickly create effective means of preventing its spread. The current research aimed to examine the in silico interaction between PIWI-interacting RNAs (piRNAs) and the SARS-CoV-2 genome (gRNA) to identify endogenous piRNAs and propose synthetic piRNAs with strong antiviral activity for drug development. This study used validated bioinformatic approaches regarding the interaction of more than eight million piRNAs with the SARS-CoV-2 genome. The piRNAs’ binding sites (BSs) in the 5′UTR were located with overlapping nucleotide sequences termed clusters of BSs. Several BSs clusters have been found in the nsp3, nsp7, RNA-dependent RNA polymerase, endoRNAse, S surface glycoprotein, ORF7a, and nucleocapsid. Sixteen synthetic piRNAs that interact with gRNA have been proposed with free binding energy ranging from −170 kJ/mol to −175 kJ/mol, which can be used to create drugs that suppress the reproduction of SARS-CoV-2.
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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
| | - Saltanat Kamenova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Aida Kondybayeva
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Alma-Gul Ryskulova
- Department of Population Health and Social Sciences, Kazakhstan’s Medical University “KSPH”, Almaty 050060, Kazakhstan
| | | | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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19
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Wang J, Li S, Wang T, Xu S, Wang X, Kong X, Lu X, Zhang H, Li L, Feng M, Ning S, Wang L. RNA2Immune: A Database of Experimentally Supported Data Linking Non-coding RNA Regulation to The Immune System. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:283-291. [PMID: 35595213 PMCID: PMC10626051 DOI: 10.1016/j.gpb.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/30/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have emerged as important regulators of the immune system and are involved in the control of immune cell biology, disease pathogenesis, as well as vaccine responses. A repository of ncRNA-immune associations will facilitate our understanding of ncRNA-dependent mechanisms in the immune system and advance the development of therapeutics and prevention for immune disorders. Here, we describe a comprehensive database, RNA2Immune, which aims to provide a high-quality resource of experimentally supported database linking ncRNA regulatory mechanisms to immune cell function, immune disease, cancer immunology, and vaccines. The current version of RNA2Immune documents 50,433 immune-ncRNA associations in 42 host species, including (1) 6690 ncRNA associations with immune functions involving 31 immune cell types; (2) 38,672 ncRNA associations with 348 immune diseases; (3) 4833 ncRNA associations with cancer immunology; and (4) 238 ncRNA associations with vaccine responses involving 26 vaccine types targeting 22 diseases. RNA2Immune provides a user-friendly interface for browsing, searching, and downloading ncRNA-immune system associations. Collectively, RNA2Immune provides important information about how ncRNAs influence immune cell function, how dysregulation of these ncRNAs leads to pathological consequences (immune diseases and cancers), and how ncRNAs affect immune responses to vaccines. RNA2Immune is available at http://bio-bigdata.hrbmu.edu.cn/rna2immune/home.jsp.
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Affiliation(s)
- Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Shuang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Si Xu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xu Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Lifang Li
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Meng Feng
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China.
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20
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Giannella A, Castelblanco E, Zambon CF, Basso D, Hernandez M, Ortega E, Alonso N, Mauricio D, Avogaro A, Ceolotto G, Vigili de Kreutzenberg S. Circulating Small Noncoding RNA Profiling as a Potential Biomarker of Atherosclerotic Plaque Composition in Type 1 Diabetes. Diabetes Care 2023; 46:551-560. [PMID: 36577032 PMCID: PMC10020028 DOI: 10.2337/dc22-1441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 12/05/2022] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Cardiovascular disease (CVD) accounts for most deaths in patients with type 1 diabetes (T1D); however, the determinants of plaque composition are unknown. miRNAs regulate gene expression, participate in the development of atherosclerosis, and represent promising CVD biomarkers. This study analyzed the circulating miRNA expression profile in T1D with either carotid calcified (CCP) or fibrous plaque (CFP). RESEARCH DESIGN AND METHODS Circulating small noncoding RNAs were sequenced and quantified using next-generation sequencing and bioinformatic analysis in an exploratory set of 26 subjects with T1D with CCP and in 25 with CFP. Then, in a validation set of 40 subjects with CCP, 40 with CFP, and 24 control subjects with T1D, selected miRNA expression was measured by digital droplet PCR. Putative gene targets enriched for pathways implicated in atherosclerosis/vascular calcification/diabetes were analyzed. The patients' main clinical characteristics were also recorded. RESULTS miR-503-5p, let-7d-5p, miR-106b-3p, and miR-93-5p were significantly upregulated, while miR-10a-5p was downregulated in patients with CCP compared with CFP (all fold change >±1.5; P < 0.05). All candidate miRNAs showed a significant correlation with LDL-cholesterol, direct for the upregulated and inverse for the downregulated miRNA, in CCP. Many target genes of upregulated miRNAs in CCP participate in osteogenic differentiation, apoptosis, inflammation, cholesterol metabolism, and extracellular matrix organization. CONCLUSIONS These findings characterize miRNAs and their signature in the regulatory network of carotid plaque phenotype in T1D, providing new insights into plaque pathophysiology and possibly novel biomarkers of plaque composition.
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Affiliation(s)
| | - Esmeralda Castelblanco
- Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO
- Unitat de Suport a la Recerca Barcelona, Institut Universitari d’Investigació en Atenció Primària Jordi Gol i Gurina, Barcelona, Spain
| | | | - Daniela Basso
- Department of Medicine, University of Padova, Padova, Italy
| | - Marta Hernandez
- Department of Endocrinology & Nutrition, Hospital Arnau de Vilanova and Institut d’Investigació Biomédica de Lleida, Lleida, Spain
| | - Emilio Ortega
- Department of Endocrinology & Nutrition, Diabetes Unit, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Center for Biomedical Research on Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
| | - Nuria Alonso
- Department of Endocrinology and Nutrition, Health Sciences Research Institute and University Hospital Germans Trias i Pujol, Badalona, Spain
- CIBERDEM, Barcelona, Spain
| | - Didac Mauricio
- Unitat de Suport a la Recerca Barcelona, Institut Universitari d’Investigació en Atenció Primària Jordi Gol i Gurina, Barcelona, Spain
- CIBERDEM, Barcelona, Spain
- Department of Endocrinology and Nutrition, Hospital de la Santa Creu i Sant Pau and Sant Pau Biomedical Research Institute, Barcelona, Spain
- Faculty of Medicine, University of Vic–Central University of Catalonia, Vic, Spain
| | - Angelo Avogaro
- Department of Medicine, University of Padova, Padova, Italy
- Corresponding authors: Saula Vigili de Kreutzenberg, , and Angelo Avogaro,
| | | | - Saula Vigili de Kreutzenberg
- Department of Medicine, University of Padova, Padova, Italy
- Corresponding authors: Saula Vigili de Kreutzenberg, , and Angelo Avogaro,
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21
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Ramesh R, Skog S, Örkenby L, Kugelberg U, Nätt D, Öst A. Dietary Sugar Shifts Mitochondrial Metabolism and Small RNA Biogenesis in Sperm. Antioxid Redox Signal 2023; 38:1167-1183. [PMID: 36509450 DOI: 10.1089/ars.2022.0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aims: Increasing concentrations of dietary sugar results in a linear accumulation of triglycerides in male Drosophila, while inducing a U-shaped obesity response in their offspring. Here, using a combination of proteomics and small RNA (sRNA) sequencing, we aimed at understanding the molecular underpinning in sperm for such plasticity. Results: Proteomic analysis of seminal vesicles revealed that increasing concentrations of dietary sugar resulted in a bell-shaped induction of proteins involved in metabolic/redox regulation. Using stains and in vivo redox reporter flies, this pattern could be explained by changes in sperm production of reactive oxygen species (ROS), more exactly mitochondria-derived H2O2. By quenching ROS with the antioxidant N-acetyl cysteine and performing sRNA-seq on sperm, we found that sperm miRNA is increased in response to ROS. Moreover, we found sperm mitosRNA to be increased in high-sugar diet conditions (independent of ROS). Reanalyzing our previously published data revealed a similar global upregulation of human sperm mitosRNA in response to a high-sugar diet, suggesting evolutionary conserved mechanisms. Innovation: This work highlights a fast response to dietary sugar in mitochondria-produced H2O2 in Drosophila sperm and identifies redox-sensitive miRNA downstream of this event. Conclusions: Our data support a model where changes in the sperm mitochondria in response to dietary sugar are the primary event, and changes in redox homoeostasis are secondary to mitochondrial ROS production. These data provide multiple candidates for paternal intergenerational metabolic responses as well as potential biomarkers for human male fertility.
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Affiliation(s)
- Rashmi Ramesh
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Signe Skog
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lovisa Örkenby
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Unn Kugelberg
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Daniel Nätt
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anita Öst
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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22
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Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24044163. [PMID: 36835575 PMCID: PMC9959880 DOI: 10.3390/ijms24044163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The human genome encodes a multitude of different noncoding transcripts that have been traditionally separated on the basis of their lengths into long (>200 nt) or small (<200 nt) noncoding RNAs. The functions, mechanisms of action, and biological relevance of the vast majority of both long and short noncoding transcripts remain unknown. However, according to the functional understanding of the known classes of long and small noncoding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Nevertheless, direct evidence of functionality is lacking for most noncoding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we developed a high-throughput assay to test the functionality of sncRNAs by overexpressing them in human cells. Surprisingly, we found that a significant fraction (>40%) of unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small noncoding transcriptome can harbor multiple functional transcripts that warrant future studies.
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23
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Sex-Inclined Piwi-Interacting RNAs in Serum Exosomes for Sex Determination in the Greater Amberjack ( Seriola dumerili). Int J Mol Sci 2023; 24:ijms24043438. [PMID: 36834847 PMCID: PMC9962539 DOI: 10.3390/ijms24043438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
The greater amberjack (Seriola dumerili) is a gonochoristic fish with no sexual dimorphism in appearance, making sex identification difficult. Piwi-interacting RNAs (piRNAs) function in transposon silencing and gametogenesis and are involved in various physiological processes, including sex development and differentiation. Exosomal piRNAs can be indicators for the determination of sex and physiological status. In this study, four piRNAs were differentially expressed in both serum exosomes and gonads between male and female greater amberjack. Three piRNAs (piR-dre-32793, piR-dre-5797, and piR-dre-73318) were significantly up-regulated and piR-dre-332 was significantly down-regulated in serum exosomes and gonads of male fish, compared to female fish, consistent with the serum exosomal results. According to the relative expression of four marker piRNAs derived from the serum exosomes of greater amberjack, the highest relative expression of piR-dre-32793, piR-dre-5797, and piR-dre-73318 in seven female fish and that of piR-dre-332 in seven male fish can be used as the standard for sex determination. The method of sex identification can ascertain the sex of greater amberjack by blood collection from the living body, without sacrificing fish. The four piRNAs did not show sex-inclined expression in the hypothalamus, pituitary, heart, liver, intestine, and muscle tissue. A piRNA-target interaction network involving 32 piRNA-mRNA pairs was generated. Sex-related target genes were enriched in sex-related pathways, including oocyte meiosis, transforming growth factor-beta signaling pathway, progesterone-mediated oocyte maturation, and gonadotropin releasing hormone signaling pathway. These results provide a basis for sex determination in greater amberjack and improve our understanding of the mechanisms underlying sex development and differentiation in the species.
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24
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Bajo-Santos C, Brokāne A, Zayakin P, Endzeliņš E, Soboļevska K, Belovs A, Jansons J, Sperga M, Llorente A, Radoviča-Spalviņa I, Lietuvietis V, Linē A. Plasma and urinary extracellular vesicles as a source of RNA biomarkers for prostate cancer in liquid biopsies. Front Mol Biosci 2023; 10:980433. [PMID: 36818049 PMCID: PMC9935579 DOI: 10.3389/fmolb.2023.980433] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction: Extracellular vesicles (EVs) have emerged as a very attractive source of cancer- derived RNA biomarkers for the early detection, prognosis and monitoring of various cancers, including prostate cancer (PC). However, biofluids contain a mixture of EVs released from a variety of tissues and the fraction of total EVs that are derived from PC tissue is not known. Moreover, the optimal biofluid-plasma or urine-that is more suitable for the detection of EV- enclosed RNA biomarkers is not yet clear. Methodology: In the current study, we performed RNA sequencing analysis of plasma and urinary EVs collected before and after radical prostatectomy, and matched tumor and normal prostate tissues of 10 patients with prostate cancer. Results and Discussion: The most abundant RNA biotypes in EVs were miRNA, piRNA, tRNA, lncRNA, rRNA and mRNA. To identify putative cancer-derived RNA biomarkers, we searched for RNAs that were overexpressed in tumor as compared to normal tissues, present in the pre-operation EVs and decreased in the post-operation EVs in each RNA biotype. The levels of 63 mRNAs, 3 lncRNAs, 2 miRNAs and 1 piRNA were significantly increased in the tumors and decreased in the post-operation urinary EVs, thus suggesting that these RNAs mainly originate from PC tissue. No such RNA biomarkers were identified in plasma EVs. This suggests that the fraction of PC-derived EVs in urine is larger than in plasma and allows the detection and tracking of PC-derived RNAs.
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Affiliation(s)
| | - Agnese Brokāne
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | | | | | - Alicia Llorente
- Department Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway,Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, Oslo, Norway
| | | | | | - Aija Linē
- Latvian Biomedical Research and Study Centre, Riga, Latvia,*Correspondence: Aija Linē,
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25
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Koffler-Brill T, Noy Y, Avraham KB. The long and short: Non-coding RNAs in the mammalian inner ear. Hear Res 2023; 428:108666. [PMID: 36566643 PMCID: PMC9883734 DOI: 10.1016/j.heares.2022.108666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 10/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Non-coding RNAs (ncRNAs) play a critical role in the entire body, and their mis-regulation is often associated with disease. In parallel with the advances in high-throughput sequencing technologies, there is a great deal of focus on this broad class of RNAs. Although these molecules are not translated into proteins, they are now well established as significant regulatory components in many biological pathways and pathological conditions. ncRNAs can be roughly divided into two main sub-groups based on the length of the transcript, with both the small and long non-coding RNAs having diverse regulatory functions. The smaller length group includes ribosomal RNAs (rRNA), transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), microRNAs (miRNA), small interfering RNAs (siRNA), and PIWI-associated RNAs (piRNA). The longer length group includes linear long non-coding RNAs (lncRNA) and circular RNAs (circRNA). This review is designed to present the different classes of small and long ncRNA molecules and describe some of their known roles in physiological and pathological conditions, as well as methods used to assess the validity and function of miRNAs and lncRNAs, with a focus on their role and functions in the inner ear, hearing and deafness.
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Affiliation(s)
- Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Noy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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26
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Zheng K, Zhang XL, Wang L, You ZH, Ji BY, Liang X, Li ZW. SPRDA: a link prediction approach based on the structural perturbation to infer disease-associated Piwi-interacting RNAs. Brief Bioinform 2023; 24:6850564. [PMID: 36445194 DOI: 10.1093/bib/bbac498] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
piRNA and PIWI proteins have been confirmed for disease diagnosis and treatment as novel biomarkers due to its abnormal expression in various cancers. However, the current research is not strong enough to further clarify the functions of piRNA in cancer and its underlying mechanism. Therefore, how to provide large-scale and serious piRNA candidates for biological research has grown up to be a pressing issue. In this study, a novel computational model based on the structural perturbation method is proposed to predict potential disease-associated piRNAs, called SPRDA. Notably, SPRDA belongs to positive-unlabeled learning, which is unaffected by negative examples in contrast to previous approaches. In the 5-fold cross-validation, SPRDA shows high performance on the benchmark dataset piRDisease, with an AUC of 0.9529. Furthermore, the predictive performance of SPRDA for 10 diseases shows the robustness of the proposed method. Overall, the proposed approach can provide unique insights into the pathogenesis of the disease and will advance the field of oncology diagnosis and treatment.
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Affiliation(s)
- Kai Zheng
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China.,College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China
| | - Xin-Lu Zhang
- Civil Product General Research Institute, The 36th Research Institute of China Electronics Technology Group Corporation, Jiaxing, 314000, China
| | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Zhu-Hong You
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Bo-Ya Ji
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410006, China
| | - Xiao Liang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Zheng-Wei Li
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
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27
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Zhang P, Sun W, Wei D, Li G, Xu J, You Z, Zhao B, Li L. PDA-PRGCN: identification of Piwi-interacting RNA-disease associations through subgraph projection and residual scaling-based feature augmentation. BMC Bioinformatics 2023; 24:18. [PMID: 36650439 PMCID: PMC9843905 DOI: 10.1186/s12859-022-05073-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/10/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Emerging evidences show that Piwi-interacting RNAs (piRNAs) play a pivotal role in numerous complex human diseases. Identifying potential piRNA-disease associations (PDAs) is crucial for understanding disease pathogenesis at molecular level. Compared to the biological wet experiments, the computational methods provide a cost-effective strategy. However, few computational methods have been developed so far. RESULTS Here, we proposed an end-to-end model, referred to as PDA-PRGCN (PDA prediction using subgraph Projection and Residual scaling-based feature augmentation through Graph Convolutional Network). Specifically, starting with the known piRNA-disease associations represented as a graph, we applied subgraph projection to construct piRNA-piRNA and disease-disease subgraphs for the first time, followed by a residual scaling-based feature augmentation algorithm for node initial representation. Then, we adopted graph convolutional network (GCN) to learn and identify potential PDAs as a link prediction task on the constructed heterogeneous graph. Comprehensive experiments, including the performance comparison of individual components in PDA-PRGCN, indicated the significant improvement of integrating subgraph projection, node feature augmentation and dual-loss mechanism into GCN for PDA prediction. Compared with state-of-the-art approaches, PDA-PRGCN gave more accurate and robust predictions. Finally, the case studies further corroborated that PDA-PRGCN can reliably detect PDAs. CONCLUSION PDA-PRGCN provides a powerful method for PDA prediction, which can also serve as a screening tool for studies of complex diseases.
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Affiliation(s)
- Ping Zhang
- grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weicheng Sun
- grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dengguo Wei
- grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China ,grid.35155.370000 0004 1790 4137Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000 China ,grid.488316.00000 0004 4912 1102Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000 China
| | - Guodong Li
- grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsheng Xu
- grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuhong You
- grid.440588.50000 0001 0307 1240School of Computer Science, Northwestern Polytechnical University, Xi’an, 710129 China
| | - Bowei Zhao
- grid.9227.e0000000119573309The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011 China
| | - Li Li
- grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China ,grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, People’s Republic of China
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28
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Kumar D, Sahoo SS, Chauss D, Kazemian M, Afzali B. Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations. J Autoimmun 2023; 134:102982. [PMID: 36592512 PMCID: PMC9908861 DOI: 10.1016/j.jaut.2022.102982] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/02/2023]
Abstract
Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.
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Affiliation(s)
- Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Subhransu Sekhar Sahoo
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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29
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Ray SK, Mukherjee S. Piwi-interacting RNAs (piRNAs) and Colorectal Carcinoma: Emerging Non-invasive diagnostic Biomarkers with Potential Therapeutic Target Based Clinical Implications. Curr Mol Med 2023; 23:300-311. [PMID: 35068393 DOI: 10.2174/1566524022666220124102616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/22/2022]
Abstract
PIWI-interacting RNAs (piRNAs) constitute new small non-coding RNA molecules of around 24-31 nucleotides in length, mostly performing regulatory roles for the piwi protein family members. In recent times, developing evidence proposes that piRNAs are expressed in a tissue-specific way in various human tissues and act as moderate vital signalling pathways at the transcriptional or post-transcriptional level in addition to mammalian germline. Recent findings, however, show that the unusual expression of piRNAs is an exclusive and discrete feature in several diseases, including many human cancers. Recently, considerable evidence indicates that piRNAs could be dysregulated thus playing critical roles in tumorigenesis. The function and underlying mechanisms of piRNAs in cancer, particularly in colorectal carcinoma, are not fully understood to date. Abnormal expression of piRNAs is emerging as a critical player in cancer cell proliferation, apoptosis, invasion, and migration in vitro and in vivo. Functionally, piRNAs preserve genomic integrity and regulate the expression of downstream target genes through transcriptional or post-transcriptional mechanisms by repressing transposable elements' mobilization. However, little research has been done to check Piwi and piRNAs' potential role in cancer and preserve genome integrity by epigenetically silencing transposons via DNA methylation, especially in germline cancer stem cells. This review reveals emerging insights into piRNA functions in colorectal carcinoma, revealing novel findings behind various piRNA-mediated gene regulation mechanisms, biogenetic piRNA processes, and possible applications of piRNAs and piwi proteins in cancer diagnosis and their potential clinical significance in the treatment of colorectal carcinoma patients.
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Affiliation(s)
| | - Sukhes Mukherjee
- Associate Professor, Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
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30
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Ng L, Navarro A, Law WL. Editorial: Evolving roles of piRNAs in solid tumors. Front Oncol 2023; 13:1178634. [PMID: 37124490 PMCID: PMC10140357 DOI: 10.3389/fonc.2023.1178634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Affiliation(s)
- Lui Ng
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- *Correspondence: Lui Ng, ; Alfons Navarro,
| | - Alfons Navarro
- Faculty of Medicine, University of Barcelona, Barcelona, Spain
- *Correspondence: Lui Ng, ; Alfons Navarro,
| | - Wai-Lun Law
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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31
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Kamenova S, Sharapkhanova A, Akimniyazova A, Kuzhybayeva K, Kondybayeva A, Rakhmetullina A, Pyrkova A, Ivashchenko A. piRNA and miRNA Can Suppress the Expression of Multiple Sclerosis Candidate Genes. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 13:nano13010022. [PMID: 36615932 PMCID: PMC9823834 DOI: 10.3390/nano13010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/02/2022] [Accepted: 12/17/2022] [Indexed: 05/14/2023]
Abstract
Multiple sclerosis (MS) is a common inflammatory demyelinating disease with a high mortality rate. MS is caused by many candidate genes whose specific involvement has yet to be established. The aim of our study was to identify endogenous miRNAs and piRNAs involved in the regulation of MS candidate gene expression using bioinformatic methods. A program was used to quantify the interaction of miRNA and piRNA nucleotides with mRNA of the target genes. We used 7310 miRNAs from three databases and 40,000 piRNAs. The mRNAs of the candidate genes revealed miRNA binding sites (BSs), which were located separately or formed clusters of BSs with overlapping nucleotide sequences. The miRNAs from the studied databases were generally bound to mRNAs in different combinations, but miRNAs from only one database were bound to the mRNAs of some genes. For the first time, a direct interaction between the complete sequence of piRNA nucleotides and the nucleotides of their mRNA BSs of target genes was shown. One to several clusters of BSs of miRNA and piRNA were identified in the mRNA of ADAM17, AHI1, CD226, EOMES, EVI5, IL12B, IL2RA, KIF21B, MGAT5, MLANA, SOX8, TNFRSF1A, and ZBTB46 MS candidate genes. These piRNAs form the expression regulation system of the MS candidate genes to coordinate the synthesis of their proteins. Based on these findings, associations of miRNAs, piRNAs, and candidate genes for MS diagnosis are recommended.
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Affiliation(s)
- Saltanat Kamenova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Aksholpan Sharapkhanova
- Department of Nervous Diseases, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Aigul Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Karlygash Kuzhybayeva
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Aida Kondybayeva
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Aizhan Rakhmetullina
- Department of Technology of Production of Livestock Products, A. Baitursynov Kostanay Regional University, Kostanay 110000, Kazakhstan
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Anna Pyrkova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty 050060, Kazakhstan
| | - Anatoliy Ivashchenko
- Center for Bioinformatics and Nanomedicine, Almaty 050060, Kazakhstan
- Correspondence:
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Yang X, Chen D, Zheng S, Yi M, Liu Z, Liu Y, Yang D, Liu Y, Tang L, Zhu C, Huang Y. BmHen1 is essential for eupyrene sperm development in Bombyx mori but PIWI proteins are not. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 151:103874. [PMID: 36375757 DOI: 10.1016/j.ibmb.2022.103874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
In lepidopteran insects, sperm dimorphism is a remarkable feature, in which males exhibit two different types of sperms. Both sperm morphs are essential for fertilization: Eupyrene sperm carry DNA and fertilize eggs, whereas apyrene sperm, which do not have nuclei, are necessary for transport of eupyrene sperm into eggs. In this study, we showed that the gene BmHen1, which encodes a methyltransferase that modifies piRNAs, is necessary for eupyrene sperm development in the lepidopteran model insect, Bombyx mori. Loss-of-function mutants of BmHen1 of both sexes were sterile. BmHen1 female mutants laid fewer eggs than wild-type females, and the eggs laid had morphological defects. Immunofluorescence analysis of BmHen1 male mutants revealed that nuclei formation in the eupyrene sperm was defective, whereas apyrene sperm were normal. In mice, worms, and flies, the components in piRNA biogenesis pathway play an important role in gonad development; therefore, we constructed mutations in genes encoding core elements in the piRNA biogenesis pathway, Siwi, and BmAgo3. To our surprise, no obvious phenotypes were observed in the male reproduction system in the Siwi and BmAgo3 mutants, which demonstrated that sperm development in B. mori does not depend on piRNAs. As the sperm development phenotype in BmHen1 mutants mimics the phenotype of the BmPnldc1 mutants, we then performed RNA sequencing analysis of sperm bundles from both mutants. We found that the defects in eupyrene sperm resulted from dysregulation of the expression of genes involved in energy metabolism. Taken together, our findings demonstrate the crucial functions of BmHen1 in the development of eupyrene sperm and provide evidence that spermatogenesis in B. mori is PIWI-independent. Our results suggest potential targets for lepidopteran pest control and broaden our knowledge of the reproduction in this order of insects.
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Affiliation(s)
- Xu Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dongbin Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Shirui Zheng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Meiyan Yi
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Zulian Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongjian Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dehong Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yujia Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Linmeng Tang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chenxu Zhu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Akimniyazova AN, Niyazova TK, Yurikova OY, Pyrkova AY, Zhanuzakov MA, Ivashchenko AT. piRNAs may regulate expression of candidate genes of esophageal adenocarcinoma. Front Genet 2022; 13:1069637. [PMID: 36531220 PMCID: PMC9747755 DOI: 10.3389/fgene.2022.1069637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/18/2022] [Indexed: 07/29/2023] Open
Abstract
Elucidation of ways to regulate the expression of candidate cancer genes will contribute to the development of methods for cancer diagnosis and therapy. The aim of the present study was to show the role of piRNAs as efficient regulators of mRNA translation of esophageal adenocarcinoma (EAC) candidate genes. We used bioinformatic methods to study the interaction characteristics of up to 200 thousand piRNAs with mRNAs of 38 candidate EAC genes. The piRNAs capable of binding to mRNA of AR, BTG3, CD55, ERBB3, FKBP5, FOXP1, LEP, SEPP1, SMAD4, and TP53 genes with high free energy by the formation of hydrogen bonds between canonical (G-C, A-U) and noncanonical (G-U, A-C) piRNA and mRNA nucleotide pairs were revealed. The organization of piRNA binding sites (BSs) in the mRNA of candidate genes was found to overlap nucleotide sequences to form clusters. Clusters of piRNA BSs were detected in the 5'-untranslated region, coding domain sequence, and 3'-untranslated region of mRNA. Due to the formation of piRNA binding site clusters, compaction of BSs occurs and competition between piRNAs for binding to mRNA of candidate EAC genes occurs. Associations of piRNA and candidate genes were selected for use as markers for the diagnosis of EAC.
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Affiliation(s)
- A. N. Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - T. K. Niyazova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - O. Yu. Yurikova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - A. Yu. Pyrkova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty, Kazakhstan
| | - M. A. Zhanuzakov
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Singh D, Roy J. A large-scale benchmark study of tools for the classification of protein-coding and non-coding RNAs. Nucleic Acids Res 2022; 50:12094-12111. [PMID: 36420898 PMCID: PMC9757047 DOI: 10.1093/nar/gkac1092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 10/22/2022] [Accepted: 10/28/2022] [Indexed: 11/27/2022] Open
Abstract
Identification of protein-coding and non-coding transcripts is paramount for understanding their biological roles. Computational approaches have been addressing this task for over a decade; however, generalized and high-performance models are still unreliable. This benchmark study assessed the performance of 24 tools producing >55 models on the datasets covering a wide range of species. We have collected 135 small and large transcriptomic datasets from existing studies for comparison and identified the potential bottlenecks hampering the performance of current tools. The key insights of this study include lack of standardized training sets, reliance on homogeneous training data, gradual changes in annotated data, lack of augmentation with homology searches, the presence of false positives and negatives in datasets and the lower performance of end-to-end deep learning models. We also derived a new dataset, RNAChallenge, from the benchmark considering hard instances that may include potential false alarms. The best and least well performing models under- and overfit the dataset, respectively, thereby serving a dual purpose. For computational approaches, it will be valuable to develop accurate and unbiased models. The identification of false alarms will be of interest for genome annotators, and experimental study of hard RNAs will help to untangle the complexity of the RNA world.
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Affiliation(s)
- Dalwinder Singh
- To whom correspondence should be addressed. Tel: +91 172 5221206;
| | - Joy Roy
- Correspondence may also be addressed to Joy Roy.
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Dindhoria K, Monga I, Thind AS. Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq. Funct Integr Genomics 2022; 22:1105-1112. [DOI: 10.1007/s10142-022-00915-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022]
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Zheng K, Zhang XL, Wang L, You ZH, Zhan ZH, Li HY. Line graph attention networks for predicting disease-associated Piwi-interacting RNAs. Brief Bioinform 2022; 23:6748487. [PMID: 36198846 DOI: 10.1093/bib/bbac393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022] Open
Abstract
PIWI proteins and Piwi-Interacting RNAs (piRNAs) are commonly detected in human cancers, especially in germline and somatic tissues, and correlate with poorer clinical outcomes, suggesting that they play a functional role in cancer. As the problem of combinatorial explosions between ncRNA and disease exposes gradually, new bioinformatics methods for large-scale identification and prioritization of potential associations are therefore of interest. However, in the real world, the network of interactions between molecules is enormously intricate and noisy, which poses a problem for efficient graph mining. Line graphs can extend many heterogeneous networks to replace dichotomous networks. In this study, we present a new graph neural network framework, line graph attention networks (LGAT). And we apply it to predict PiRNA disease association (GAPDA). In the experiment, GAPDA performs excellently in 5-fold cross-validation with an AUC of 0.9038. Not only that, it still has superior performance compared with methods based on collaborative filtering and attribute features. The experimental results show that GAPDA ensures the prospect of the graph neural network on such problems and can be an excellent supplement for future biomedical research.
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Affiliation(s)
- Kai Zheng
- College of Information Science and Engineering, Zaozhuang University, Shandong 277100, China.,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | | | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Shandong 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Zhu-Hong You
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Zhao-Hui Zhan
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Hao-Yuan Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
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Moreira FC, Sarquis DP, de Souza JES, Avelar DDS, Araújo TMT, Khayat AS, dos Santos SEB, de Assumpção PP. Treasures from trash in cancer research. Oncotarget 2022; 13:1246-1257. [PMID: 36395362 PMCID: PMC9671455 DOI: 10.18632/oncotarget.28308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Cancer research has significantly improved in recent years, primarily due to next-generation sequencing (NGS) technology. Consequently, an enormous amount of genomic and transcriptomic data has been generated. In most cases, the data needed for research goals are used, and unwanted reads are discarded. However, these eliminated data contain relevant information. Aiming to test this hypothesis, genomic and transcriptomic data were acquired from public datasets. MATERIALS AND METHODS Metagenomic tools were used to explore genomic cancer data; additional annotations were used to explore differentially expressed ncRNAs from miRNA experiments, and variants in adjacent to tumor samples from RNA-seq experiments were also investigated. RESULTS In all analyses, new data were obtained: from DNA-seq data, microbiome taxonomies were characterized with a similar performance of dedicated metagenomic research; from miRNA-seq data, additional differentially expressed sncRNAs were found; and in tumor and adjacent to tumor tissue data, somatic variants were found. CONCLUSIONS These findings indicate that unexplored data from NGS experiments could help elucidate carcinogenesis and discover putative biomarkers with clinical applications. Further investigations should be considered for experimental design, providing opportunities to optimize data, saving time and resources while granting access to multiple genomic perspectives from the same sample and experimental run.
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Affiliation(s)
- Fabiano Cordeiro Moreira
- 1Núcleo de Pesquisas em Oncologia/Universidade Federal do Pará, Belém, Pará, Brazil,*Co-first authors
| | - Dionison Pereira Sarquis
- 1Núcleo de Pesquisas em Oncologia/Universidade Federal do Pará, Belém, Pará, Brazil,*Co-first authors
| | | | | | | | - André Salim Khayat
- 1Núcleo de Pesquisas em Oncologia/Universidade Federal do Pará, Belém, Pará, Brazil
| | - Sidney Emanuel Batista dos Santos
- 1Núcleo de Pesquisas em Oncologia/Universidade Federal do Pará, Belém, Pará, Brazil,3Instituto de Ciências Biológicas/Universidade Federal do Pará, Belém, Pará, Brazil
| | - Paulo Pimentel de Assumpção
- 1Núcleo de Pesquisas em Oncologia/Universidade Federal do Pará, Belém, Pará, Brazil,Correspondence to:Paulo Pimentel de Assumpção, email:
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Identification and Characterization of Piwi-Interacting RNAs for Early Testicular Development in Yak. Int J Mol Sci 2022; 23:ijms232012320. [PMID: 36293174 PMCID: PMC9603861 DOI: 10.3390/ijms232012320] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Normal testicular development plays a crucial role in male reproduction and is the precondition for spermatogenesis. PIWI-interacting RNAs (piRNAs) are novel noncoding RNAs expressed in animal germ cells that form complexes with PIWI family proteins and are involved in germ cell development, differentiation, and spermatogenesis. However, changes in piRNA expression profiles during early testicular development in yak have not been investigated. In this study, we used small RNA sequencing to evaluate the differences and potential functions of piRNA expression profiles in 6-, 18-, and 30-month-old yak testis tissues. Differential expression analysis found 109, 293, and 336 differentially expressed piRNAs in M30 vs. M18, M18 vs. M6, and M30 vs. M6, respectively, and found 30 common differentially expressed piRNAs in the three groups of M6, M18, and M30. In addition, the functional enrichment analysis of differentially expressed piRNAs target genes indicated that they were related to testicular development and spermatogenesis. Finally, we detected the expression of the PIWI protein family in the yak testis at different developmental stages and found that PIWIL1, PIWIL2, PIWIL3, and PIWIL4 were highly expressed in 18- and 30-month-old yak testis and almost not expressed in 6-month-old yak testis. In conclusion, this study summarizes the changes of piRNA expression patterns during the early development of yak testis and provides new clues for the regulatory role of piRNA in yak testis.
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Chen J, Lin J, Hu Y, Ye M, Yao L, Wu L, Zhang W, Wang M, Deng T, Guo F, Huang Y, Zhu B, Wang D. RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction. Nucleic Acids Res 2022; 51:D1397-D1404. [PMID: 36134718 PMCID: PMC9825423 DOI: 10.1093/nar/gkac814] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 02/06/2023] Open
Abstract
Numerous studies have shown that RNA plays an important role in the occurrence and development of diseases, and RNA-disease associations are not limited to noncoding RNAs in mammals but also exist for protein-coding RNAs. Furthermore, RNA-associated diseases are found across species including plants and nonmammals. To better analyze diseases at the RNA level and facilitate researchers in exploring the pathogenic mechanism of diseases, we decided to update and change MNDR v3.0 to RNADisease v4.0, a repository for RNA-disease association (http://www.rnadisease.org/ or http://www.rna-society.org/mndr/). Compared to the previous version, new features include: (i) expanded data sources and categories of species, RNA types, and diseases; (ii) the addition of a comprehensive analysis of RNAs from thousands of high-throughput sequencing data of cancer samples and normal samples; (iii) the addition of an RNA-disease enrichment tool and (iv) the addition of four RNA-disease prediction tools. In summary, RNADisease v4.0 provides a comprehensive and concise data resource of RNA-disease associations which contains a total of 3 428 058 RNA-disease entries covering 18 RNA types, 117 species and 4090 diseases to meet the needs of biological research and lay the foundation for future therapeutic applications of diseases.
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Affiliation(s)
| | | | | | | | | | - Le Wu
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wenhai Zhang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Meiyi Wang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tingting Deng
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Feng Guo
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yan Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bofeng Zhu
- Correspondence may also be addressed to Bofeng Zhu. Tel: +86 20 61648787; Fax: +86 20 61648787;
| | - Dong Wang
- To whom correspondence should be addressed. Tel: +86 20 61648279; Fax: +86 20 61648279;
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Oliveira JIN, Cardoso AL, Wolf IR, de Oliveira RA, Martins C. First characterization of PIWI-interacting RNA clusters in a cichlid fish with a B chromosome. BMC Biol 2022; 20:204. [PMID: 36127679 PMCID: PMC9490952 DOI: 10.1186/s12915-022-01403-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND B chromosomes are extra elements found in several eukaryote species. Usually, they do not express a phenotype in the host. However, advances in bioinformatics over the last decades have allowed us to describe several genes and molecular functions related to B chromosomes. These advances enable investigations of the relationship between the B chromosome and the host to understand how this element has been preserved in genomes. However, considering that transposable elements (TEs) are highly abundant in this supernumerary chromosome, there is a lack of knowledge concerning the dynamics of TE control in B-carrying cells. Thus, the present study characterized PIWI-interacting RNA (piRNA) clusters and pathways responsible for silencing the mobilization of TEs in gonads of the cichlid fish Astatotilapia latifasciata carrying the B chromosome. RESULTS Through small RNA-seq and genome assembly, we predicted and annotated piRNA clusters in the A. latifasciata genome for the first time. We observed that these clusters had biased expression related to sex and the presence of the B chromosome. Furthermore, three piRNA clusters, named curupira, were identified in the B chromosome. Two of them were expressed exclusively in gonads of samples with the B chromosome. The composition of these curupira sequences was derived from LTR, LINE, and DNA elements, representing old and recent transposition events in the A. latifasciata genome and the B chromosome. The presence of the B chromosome also affected the expression of piRNA pathway genes. The mitochondrial cardiolipin hydrolase-like (pld6) gene is present in the B chromosome, as previously reported, and an increase in its expression was detected in gonads with the B chromosome. CONCLUSIONS Due to the high abundance of TEs in the B chromosome, it was possible to investigate the origin of piRNA from these jumping genes. We hypothesize that the B chromosome has evolved its own genomic guardians to prevent uncontrolled TE mobilization. Furthermore, we also detected an expression bias in the presence of the B chromosome over A. latifasciata piRNA clusters and pathway genes.
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Affiliation(s)
- Jordana Inácio Nascimento Oliveira
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Ivan Rodrigo Wolf
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Rogério Antônio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
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Corsello T, Kudlicki AS, Liu T, Casola A. Respiratory syncytial virus infection changes the piwi-interacting RNA content of airway epithelial cells. Front Mol Biosci 2022; 9:931354. [PMID: 36158569 PMCID: PMC9493205 DOI: 10.3389/fmolb.2022.931354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are small non-coding RNAs (sncRNAs) of about 26–32 nucleotides in length and represent the largest class of sncRNA molecules expressed in animal cells. piRNAs have been shown to play a crucial role to safeguard the genome, maintaining genome complexity and integrity, as they suppress the insertional mutations caused by transposable elements. However, there is growing evidence for the role of piRNAs in controlling gene expression in somatic cells as well. Little is known about changes in piRNA expression and possible function occurring in response to viral infections. In this study, we investigated the piRNA expression profile, using a human piRNA microarray, in human small airway epithelial (SAE) cells infected with respiratory syncytial virus (RSV), a leading cause of acute respiratory tract infections in children. We found a time-dependent increase in piRNAs differentially expressed in RSV-infected SAE cells. We validated the top piRNAs upregulated and downregulated at 24 h post-infection by RT-qPCR and identified potential targets. We then used Gene Ontology (GO) tool to predict the biological processes of the predicted targets of the most represented piRNAs in infected cells over the time course of RSV infection. We found that the most significant groups of targets of regulated piRNAs are related to cytoskeletal or Golgi organization and nucleic acid/nucleotide binding at 15 and 24 h p.i. To identify common patterns of time-dependent responses to infection, we clustered the significantly regulated expression profiles. Each of the clusters of temporal profiles have a distinct set of potential targets of the piRNAs in the cluster Understanding changes in piRNA expression in RSV-infected airway epithelial cells will increase our knowledge of the piRNA role in viral infection and might identify novel therapeutic targets for viral lung-mediated diseases.
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Affiliation(s)
- Tiziana Corsello
- Department of Pediatrics, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
| | - Andrzej S Kudlicki
- Institute for Translational Sciences, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
| | - Tianshuang Liu
- Department of Pediatrics, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
| | - Antonella Casola
- Department of Pediatrics, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
- Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston (UTMB), Galveston, TX, United States
- *Correspondence: Antonella Casola,
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Akimniyazova A, Yurikova O, Pyrkova A, Rakhmetullina A, Niyazova T, Ryskulova AG, Ivashchenko A. In Silico Study of piRNA Interactions with the SARS-CoV-2 Genome. Int J Mol Sci 2022; 23:9919. [PMID: 36077317 PMCID: PMC9456458 DOI: 10.3390/ijms23179919] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/27/2022] [Accepted: 08/28/2022] [Indexed: 11/25/2022] Open
Abstract
A prolonged pandemic with numerous human casualties requires a rapid search for means to control the various strains of SARS-CoV-2. Since only part of the human population is affected by coronaviruses, there are probably endogenous compounds preventing the spread of these viral pathogens. It has been shown that piRNA (PIWI-interacting RNAs) interact with the mRNA of human genes and can block protein synthesis at the stage of translation. Estimated the effects of piRNA on SARS-CoV-2 genomic RNA (gRNA) in silico. A cluster of 13 piRNA binding sites (BS) in the SARS-CoV-2 gRNA region encoding the oligopeptide was identified. The second cluster of BSs 39 piRNAs also encodes the oligopeptide. The third cluster of 24 piRNA BS encodes the oligopeptide. Twelve piRNAs were identified that strongly interact with the gRNA. Based on the identified functionally important endogenous piRNAs, synthetic piRNAs (spiRNAs) are proposed that will suppress the multiplication of the coronavirus even more strongly. These spiRNAs and selected endogenous piRNAs have little effect on human 17494 protein-coding genes, indicating a low probability of side effects. The piRNA and spiRNA selection methodology created for the control of SARS-CoV-2 (NC_045512.2) can be used to control all strains of SARS-CoV-2.
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Affiliation(s)
- Aigul Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Oxana Yurikova
- 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
| | - Aizhan Rakhmetullina
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Togzhan Niyazova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Alma-Gul Ryskulova
- Department of Population Health and Social Sciences, Kazakhstan’s Medical University “KSPH”, Almaty 050060, Kazakhstan
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iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank. PLoS Comput Biol 2022; 18:e1010404. [PMID: 35969645 PMCID: PMC9410559 DOI: 10.1371/journal.pcbi.1010404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 08/25/2022] [Accepted: 07/18/2022] [Indexed: 12/01/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are regarded as drug targets and biomarkers for the diagnosis and therapy of diseases. However, biological experiments cost substantial time and resources, and the existing computational methods only focus on identifying missing associations between known piRNAs and diseases. With the fast development of biological experiments, more and more piRNAs are detected. Therefore, the identification of piRNA-disease associations of newly detected piRNAs has significant theoretical value and practical significance on pathogenesis of diseases. In this study, the iPiDA-LTR predictor is proposed to identify associations between piRNAs and diseases based on Learning to Rank. The iPiDA-LTR predictor not only identifies the missing associations between known piRNAs and diseases, but also detects diseases associated with newly detected piRNAs. Experimental results demonstrate that iPiDA-LTR effectively predicts piRNA-disease associations outperforming the other related methods. Accumulating evidences have indicated that dysfunction and abnormal expression of piRNAs are closely associated with the emergence and development of diseases. Currently, identifying piRNA-disease associations mainly focuses on biological experimental methods and computational methods. However, biological experimental methods take substantial time and resources. Computational methods mainly focused on identifying diseases associated known piRNAs. With the development of biological technology, more and more newly detected piRNAs were detected. Therefore, identifying diseases associated with newly detected piRNAs is more important compared with identifying diseases associated with known piRNAs. Information retrieval (IR)’s goal is to rank documents based on the relevance to certain topics. This task is particularly similar with identification of piRNA-disease associations. Specifically, ranking documents related to previous topics corresponds to identify diseases associated with known piRNAs, and ranking documents related to novel topics is similar to identify diseases associated with newly detected piRNAs. Therefore, we propose a new predictor called iPiDA-LTR to predict associations between piRNAs and diseases based on information retrieval technology. Experimental results indicated that iPiDA-LTR is promising in identifying diseases associated with known piRNAs and newly detected piRNAs.
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Zheng K, Liang Y, Liu YY, Yasir M, Wang P. A decision support system based on multi-sources information to predict piRNA–disease associations using stacked autoencoder. Soft comput 2022. [DOI: 10.1007/s00500-022-07396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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He X, Wu H, Ye Y, Gong X, Bao B. Transcriptome analysis revealed gene expression feminization of testis after exogenous tetrodotoxin administration in pufferfish Takifugu flavidus. BMC Genomics 2022; 23:553. [PMID: 35922761 PMCID: PMC9347094 DOI: 10.1186/s12864-022-08787-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 07/22/2022] [Indexed: 11/29/2022] Open
Abstract
Tetrodotoxin (TTX) is a deadly neurotoxin and usually accumulates in large amounts in the ovaries but is non-toxic or low toxic in the testis of pufferfish. The molecular mechanism underlying sexual dimorphism accumulation of TTX in ovary and testis, and the relationship between TTX accumulation with sex related genes expression remain largely unknown. The present study investigated the effects of exogenous TTX treatment on Takifugu flavidus. The results demonstrated that exogenous TTX administration significantly incresed level of TTX concentration in kidney, cholecyst, skin, liver, heart, muscle, ovary and testis of the treatment group (TG) than that of the control group (CG). Transcriptome sequencing and analysis were performed to study differential expression profiles of mRNA and piRNA after TTX administration of the ovary and testis. The results showed that compared with female control group (FCG) and male control group (MCG), TTX administration resulted in 80 and 23 piRNAs, 126 and 223 genes up and down regulated expression in female TTX-treated group (FTG), meanwhile, 286 and 223 piRNAs, 2 and 443 genes up and down regulated expression in male TTX-treated group (MTG). The female dominant genes cyp19a1, gdf9 and foxl2 were found to be up-regulated in MTG. The cyp19a1, whose corresponding target piRNA uniq_554482 was identified as down-regulated in the MTG, indicating the gene expression feminization in testis after exogenous TTX administration. The KEGG enrichment analysis revealed that differentially expressed genes (DEGs) and piRNAs (DEpiRNAs) in MTG vs MCG group were more enriched in metabolism pathways, indicating that the testis produced more metabolic pathways in response to exogenous TTX, which might be a reason for the sexual dimorphism of TTX distribution in gonads. In addition, TdT-mediated dUTP-biotin nick end labeling staining showed that significant apoptosis was detected in the MTG testis, and the role of the cell apoptotic pathways was further confirmed. Overall, our research revealed that the response of the ovary and testis to TTX administration was largely different, the ovary is more tolerant whereas the testis is more sensitive to TTX. These data will deepen our understanding on the accumulation of TTX sexual dimorphism in Takifugu.
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Affiliation(s)
- Xue He
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hexing Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yaping Ye
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaolin Gong
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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Liu Z, Wang T, Yang X, Zhou Q, Zhu S, Zeng J, Chen H, Sun J, Li L, Xu J, Geng C, Xu X, Wang J, Yang H, Zhu S, Chen F, Wang WJ. Polyadenylation ligation-mediated sequencing (PALM-Seq) characterizes cell-free coding and non-coding RNAs in human biofluids. Clin Transl Med 2022; 12:e987. [PMID: 35858042 PMCID: PMC9299576 DOI: 10.1002/ctm2.987] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/16/2022] [Accepted: 07/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background Cell‐free messenger RNA (cf‐mRNA) and long non‐coding RNA (cf‐lncRNA) are becoming increasingly important in liquid biopsy by providing biomarkers for disease prediction, diagnosis and prognosis, but the simultaneous characterization of coding and non‐coding RNAs in human biofluids remains challenging. Methods Here, we developed polyadenylation ligation‐mediated sequencing (PALM‐Seq), an RNA sequencing strategy employing treatment of RNA with T4 polynucleotide kinase to generate cell‐free RNA (cfRNA) fragments with 5′ phosphate and 3′ hydroxyl and RNase H to deplete abundant RNAs, achieving simultaneous quantification and characterization of cfRNAs. Results Using PALM‐Seq, we successfully identified well‐known differentially abundant mRNA, lncRNA and microRNA in the blood plasma of pregnant women. We further characterized cfRNAs in blood plasma, saliva, urine, seminal plasma and amniotic fluid and found that the detected numbers of different RNA biotypes varied with body fluids. The profiles of cf‐mRNA reflected the function of originated tissues, and immune cells significantly contributed RNA to blood plasma and saliva. Short fragments (<50 nt) of mRNA and lncRNA were major in biofluids, whereas seminal plasma and amniotic fluid tended to retain long RNA. Body fluids showed distinct preferences of pyrimidine at the 3′ end and adenine at the 5′ end of cf‐mRNA and cf‐lncRNA, which were correlated with the proportions of short fragments. Conclusion Together, PALM‐Seq enables a simultaneous characterization of cf‐mRNA and cf‐lncRNA, contributing to elucidating the biology and promoting the application of cfRNAs.
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Affiliation(s)
| | | | - Xi Yang
- BGI-Shenzhen, Shenzhen, China
| | | | - Sujun Zhu
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Juan Zeng
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | | | - Jinghua Sun
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
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47
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Unraveling mitochondrial piRNAs in mouse embryonic gonadal cells. Sci Rep 2022; 12:10730. [PMID: 35750721 PMCID: PMC9232517 DOI: 10.1038/s41598-022-14414-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Although mitochondria are widely studied organelles, the recent interest in the role of mitochondrial small noncoding RNAs (sncRNAs), miRNAs, and more recently, piRNAs, is providing new functional perspectives in germ cell development and differentiation. piRNAs (PIWI-interacting RNAs) are single-stranded sncRNAs of mostly about 20-35 nucleotides, generated from the processing of pre-piRNAs. We leverage next-generation sequencing data obtained from mouse primordial germ cells and somatic cells purified from early-differentiating embryonic ovaries and testis from 11.5 to 13.5 days postcoitum. Using bioinformatic tools, we elucidate (i) the origins of piRNAs as transcribed from mitochondrial DNA fragments inserted in the nucleus or from the mitochondrial genome; (ii) their levels of expression; and (iii) their potential roles, as well as their association with genomic regions encoding other sncRNAs (such as tRNAs and rRNAs) and the mitochondrial regulatory region (D-loop). Finally, our results suggest how nucleo-mitochondrial communication, both anterograde and retrograde signaling, may be mediated by mitochondria-associated piRNAs.
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48
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Gong J, Wang P, Liu JC, Li J, Zeng QX, Yang C, Li Y, Yu D, Cao D, Duan YG. Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis. Front Immunol 2022; 13:883803. [PMID: 35634321 PMCID: PMC9130659 DOI: 10.3389/fimmu.2022.883803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Chronic epididymitis (CE) refers to a long-lasting inflammatory condition of the epididymis, which is considered the most common site of intrascrotal inflammation and an important aetiological factor of male infertility. Recent studies demonstrate that small RNAs secreted from epididymal epithelium modulate embryo development and offspring phenotypes via sperm transmission, and the resulting modifications may lead to transgenerational inheritance. However, to date, the genome-wide analysis of small RNA together with the transcriptomic expression profiles of human epididymis and CE is still lacking. In this study, we facilitated next-generation sequencing and bioinformatics to comprehensively analyze the small RNA and mRNA in an integrative way and identified signatures associated with CE. Both of the small RNA and mRNA expression data demonstrated relatively larger molecular differences among the segmental region of the epididymides, including caput, corpus, and cauda, than that of the inflammatory conditions. By comparing the inflamed caputs to the controls, a total of 1727 genes (1220 upregulated and 507 downregulated; 42 most significant genes, adjusted P <0.05) and 34 miRNAs (23 upregulated and 11 downregulated) were identified as differentially expressed. In silico functional enrichment analysis showed their roles in regulating different biological activities, including leukocyte chemotaxis, extracellular milieu reconstruction, ion channel and transporter-related processes, and nervous system development. Integrative analysis of miRNA and mRNA identified a regulatory network consisting of 22 miRNAs and 31 genes (miRNA-mRNA) which are strong candidates for CE. In addition, analysis about other species of small RNA, including (miRNA), piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA), Y RNA, and rsRNA identified the distinct expression pattern of tsRNA in CE. In summary, our study performed small RNA and miRNA profiling and integrative analysis in human CE. The findings will help to understand the role of miRNA-mRNA in the pathogenesis of CE and provide molecular candidates for the development of potential biomarkers for human CE.
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Affiliation(s)
- Jialei Gong
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China.,The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Peng Wang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, China
| | - Jin-Chuan Liu
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China.,Department of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jianlin Li
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China.,Department of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Qun-Xiong Zeng
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China.,Department of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Chen Yang
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Yanfeng Li
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, China
| | - Di Yu
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Dandan Cao
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Yong-Gang Duan
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
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Riffo-Campos AL, Perez-Hernandez J, Martinez-Arroyo O, Ortega A, Flores-Chova A, Redon J, Cortes R. Biofluid Specificity of Long Non-Coding RNA Profile in Hypertension: Relevance of Exosomal Fraction. Int J Mol Sci 2022; 23:ijms23095199. [PMID: 35563588 PMCID: PMC9101961 DOI: 10.3390/ijms23095199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNA (ncRNA)-mediated targeting of various genes regulates the molecular mechanisms of the pathogenesis of hypertension (HTN). However, very few circulating long ncRNAs (lncRNAs) have been reported to be altered in essential HTN. The aim of our study was to identify a lncRNA profile in plasma and plasma exosomes associated with urinary albumin excretion in HTN by next-generation sequencing and to assess biological functions enriched in response to albuminuria using GO and KEGG analysis. Plasma exosomes showed higher diversity and fold change of lncRNAs than plasma, and low transcript overlapping was found between the two biofluids. Enrichment analysis identified different biological pathways regulated in plasma or exosome fraction, which were implicated in fatty acid metabolism, extracellular matrix, and mechanisms of sorting ncRNAs into exosomes, while plasma pathways were implicated in genome reorganization, interference with RNA polymerase, and as scaffolds for assembling transcriptional regulators. Our study found a biofluid specific lncRNA profile associated with albuminuria, with higher diversity in exosomal fraction, which identifies several potential targets that may be utilized to study mechanisms of albuminuria and cardiovascular damage.
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Affiliation(s)
- Angela L. Riffo-Campos
- Millennium Nucleus on Sociomedicine (SocioMed) and Vicerrectoría Académica, Universidad de La Frontera, Temuco 4780000, Chile;
- Department of Computer Science, ETSE, University of Valencia, 46010 Valencia, Spain
| | - Javier Perez-Hernandez
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
- Department of Nutrition and Health, Valencian International University (VIU), 46002 Valencia, Spain
- T-Cell Tolerance, Biomarkers and Therapies in Type 1 Diabetes Team, Institut Cochin CNRS, INSERM, Université de Paris Cité, F-75014 Paris, France
| | - Olga Martinez-Arroyo
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Ana Ortega
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
- Correspondence: (A.O.); (R.C.); Tel.: +34-961973517 (R.C.)
| | - Ana Flores-Chova
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Josep Redon
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
- Internal Medicine Unit, Hospital Clinico Universitario, 46010 Valencia, Spain
- CIBER of Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, Minister of Health, 28029 Madrid, Spain
| | - Raquel Cortes
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
- Correspondence: (A.O.); (R.C.); Tel.: +34-961973517 (R.C.)
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50
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van Riet J, Saha C, Strepis N, Brouwer RWW, Martens-Uzunova ES, van de Geer WS, Swagemakers SMA, Stubbs A, Halimi Y, Voogd S, Tanmoy AM, Komor MA, Hoogstrate Y, Janssen B, Fijneman RJA, Niknafs YS, Chinnaiyan AM, van IJcken WFJ, van der Spek PJ, Jenster G, Louwen R. CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue. Commun Biol 2022; 5:338. [PMID: 35396392 PMCID: PMC8993844 DOI: 10.1038/s42003-022-03249-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) have been identified in bacteria, archaea and mitochondria of plants, but not in eukaryotes. Here, we report the discovery of 12,572 putative CRISPRs randomly distributed across the human chromosomes, which we termed hCRISPRs. By using available transcriptome datasets, we demonstrate that hCRISPRs are distinctively expressed as small non-coding RNAs (sncRNAs) in cell lines and human tissues. Moreover, expression patterns thereof enabled us to distinguish normal from malignant tissues. In prostate cancer, we confirmed the differential hCRISPR expression between normal adjacent and malignant primary prostate tissue by RT-qPCR and demonstrate that the SHERLOCK and DETECTR dipstick tools are suitable to detect these sncRNAs. We anticipate that the discovery of CRISPRs in the human genome can be further exploited for diagnostic purposes in cancer and other medical conditions, which certainly will lead to the development of point-of-care tests based on the differential expression of the hCRISPRs. CRISPR elements in the human genome are expressed in both healthy tissues and tumors but with distinct patterns, representing a potential biomarker for cancer.
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Affiliation(s)
- Job van Riet
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands.,Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Chinmoy Saha
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nikolaos Strepis
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wesley S van de Geer
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sigrid M A Swagemakers
- Clinical Bioinformatics, Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Andrew Stubbs
- Clinical Bioinformatics, Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Yassir Halimi
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sanne Voogd
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Arif Mohammad Tanmoy
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.,Child Health Research Foundation, 23/2 SEL Huq Skypark, Block-B, Khilji Rd, Dhaka, 1207, Bangladesh
| | - Malgorzata A Komor
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands.,Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, Netherlands
| | - Youri Hoogstrate
- Department of Neurology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | | | - Remond J A Fijneman
- Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Yashar S Niknafs
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Peter J van der Spek
- Clinical Bioinformatics, Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rogier Louwen
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.
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