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Shen LP, Zhang WC, Deng JR, Qi ZH, Lin ZW, Wang ZD. Advances in the mechanism of small nucleolar RNA and its role in DNA damage response. Mil Med Res 2024; 11:53. [PMID: 39118131 PMCID: PMC11308251 DOI: 10.1186/s40779-024-00553-4] [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: 10/24/2023] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) were previously regarded as a class of functionally conserved housekeeping genes, primarily involved in the regulation of ribosome biogenesis by ribosomal RNA (rRNA) modification. However, some of them are involved in several biological processes via complex molecular mechanisms. DNA damage response (DDR) is a conserved mechanism for maintaining genomic stability to prevent the occurrence of various human diseases. It has recently been revealed that snoRNAs are involved in DDR at multiple levels, indicating their relevant theoretical and clinical significance in this field. The present review systematically addresses four main points, including the biosynthesis and classification of snoRNAs, the mechanisms through which snoRNAs regulate target molecules, snoRNAs in the process of DDR, and the significance of snoRNA in disease diagnosis and treatment. It focuses on the potential functions of snoRNAs in DDR to help in the discovery of the roles of snoRNAs in maintaining genome stability and pathological processes.
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Affiliation(s)
- Li-Ping Shen
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Wen-Cheng Zhang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Jia-Rong Deng
- Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Zhen-Hua Qi
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Zhong-Wu Lin
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Zhi-Dong Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
- Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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James JP, Riis LB, Søkilde R, Malham M, Høgdall E, Langholz E, Nielsen BS. Short noncoding RNAs as predictive biomarkers for the development from inflammatory bowel disease unclassified to Crohn's disease or ulcerative colitis. PLoS One 2024; 19:e0297353. [PMID: 38408066 PMCID: PMC10896517 DOI: 10.1371/journal.pone.0297353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/22/2023] [Indexed: 02/28/2024] Open
Abstract
Numerous pathogenic processes are mediated by short noncoding RNAs (sncRNA). Twenty percent of inflammatory bowel disease (IBD) patients are labelled as IBD unclassified (IBDU) at disease onset. Most IBDU patients are reclassified as Crohn's disease (CD) or ulcerative colitis (UC) within few years. Since the therapeutic methods for CD and UC differ, biomarkers that can forecast the categorization of IBDU into CD or UC are highly desired. Here, we investigated whether sncRNAs can predict CD or UC among IBDU patients. 35 IBDU patients who were initially diagnosed with IBDU were included in this retrospective investigation; of them, 12, 15, and 8 were reclassified into CD (IBDU-CD), UC (IBDU-UC), or remained as IBDU (IBDU-IBDU), respectively. Eight IBD patients, were included as references. SncRNA profiling on RNA from mucosal biopsies were performed using Affymetrix miRNA 4.0 array. Selected probe sets were validated using RT-qPCR. Among all patients and only adults, 306 and 499 probe sets respectively were differentially expressed between IBDU-CD and IBDU-UC. Six of the probe sets were evaluated by RT-qPCR, of which miR-182-5p, miR-451a and ENSG00000239080 (snoU13) together with age and sex resulted in an AUC of 78.6% (95% CI: 60-97) in discriminating IBDU-CD from IBDU-UC. Based on the three sncRNAs profile it is possible to predict if IBDU patients within 3 years will be reclassified as CD or UC. We showed that the expression profile of IBDU patients differ from that of definite CD or UC, suggesting that a subgroup of IBDU patients may compose a third unique IBD subtype.
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Affiliation(s)
- Jaslin P. James
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
| | - Lene Buhl Riis
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rolf Søkilde
- Bioneer A/S, Hørsholm, Kogle Allé 2, Hørsholm, Denmark
| | - Mikkel Malham
- The Pediatric Department, Copenhagen University Hospital—Amager and Hvidovre, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ebbe Langholz
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Gastroenheden, Herlev University Hospital, Herlev, Denmark
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Zhang L, Guo H, Zhang X, Wang L, Wei F, Zhao Y, Wang B, Meng Y, Li Y. Small nucleolar RNA Snora73 promotes psoriasis progression by sponging miR-3074-5p and regulating PBX1 expression. Funct Integr Genomics 2024; 24:15. [PMID: 38240925 PMCID: PMC10799104 DOI: 10.1007/s10142-024-01300-7] [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: 11/07/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/22/2024]
Abstract
Chronic psoriasis is a kind of immune-mediated skin illness and the underlying molecular mechanisms of pathogenesis remain incompletely understood. Here, we used small RNA microarray assays to scan the differential expressed RNAs in psoriasis patient samples. The downstream miRNAs and its targets were predicted using bioinformatics analysis from online bases and confirmed using fluorescence in situ hybridization and dual‑luciferase report gene assay. Cell ability of proliferation and migration were detected using CCK-8 and transwell assays. The results showed that a new snoRNA Snora73 was upregulated in psoriasis patient samples. Overexpression of Snora73 significantly increased psoriasis cells viability and migration, while knockdown of Snora73 got the opposite results. Mechanistically, our results showed that Snora73 acted as a sponge for miR-3074-5p and PBX1 is a direct target of miR-3074-5p in psoriasis cells. Furthermore, miR-3074-5p suppressed psoriasis cell proliferation and migration, while PBX1 promoted cell proliferation and migration in psoriasis. Collectively, these findings reveal a crucial role of Snora73 in progression of psoriasis through miR-3074-5p/PBX1 signaling pathway and suggest a potential therapeutic strategy.
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Affiliation(s)
- Lihua Zhang
- Department of Dermatology, Clinical Medical Research Center of Dermatology and Venereal Disease in Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Construction Unit of the Sub-Center of the National Center for Clinical Medical Research On Skin and Immunological Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Hui Guo
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoguang Zhang
- Department of Dermatology, Clinical Medical Research Center of Dermatology and Venereal Disease in Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Construction Unit of the Sub-Center of the National Center for Clinical Medical Research On Skin and Immunological Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Ling Wang
- Department of Dermatology, Clinical Medical Research Center of Dermatology and Venereal Disease in Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Construction Unit of the Sub-Center of the National Center for Clinical Medical Research On Skin and Immunological Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Feng Wei
- Department of Dermatology, Clinical Medical Research Center of Dermatology and Venereal Disease in Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Construction Unit of the Sub-Center of the National Center for Clinical Medical Research On Skin and Immunological Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Yike Zhao
- Department of Dermatology, Clinical Medical Research Center of Dermatology and Venereal Disease in Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Construction Unit of the Sub-Center of the National Center for Clinical Medical Research On Skin and Immunological Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Bo Wang
- Department of Dermatology, Clinical Medical Research Center of Dermatology and Venereal Disease in Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Construction Unit of the Sub-Center of the National Center for Clinical Medical Research On Skin and Immunological Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Yibo Meng
- Department of Dermatology, Clinical Medical Research Center of Dermatology and Venereal Disease in Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Construction Unit of the Sub-Center of the National Center for Clinical Medical Research On Skin and Immunological Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Yanling Li
- Department of Dermatology, Clinical Medical Research Center of Dermatology and Venereal Disease in Hebei Province, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China.
- Construction Unit of the Sub-Center of the National Center for Clinical Medical Research On Skin and Immunological Diseases, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China.
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Dubey G, Singh M, Singh H, Agarwal M, Chandel SS, Mishra A, Singh RP, Kukreti N. Emerging roles of SnoRNAs in the pathogenesis and treatment of autoimmune disorders. Pathol Res Pract 2024; 253:154952. [PMID: 38000202 DOI: 10.1016/j.prp.2023.154952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
SnoRNAs (small non-coding RNAs) have recently gained prominence in autoimmune diseases, revealing their crucial role in modulating the immune response and contributing to disease pathogenesis. Initially known for their involvement in ribosomal RNA processing and modification, molecular biology and genomics advancements have uncovered their broader impact on cellular function, especially in autoimmune disorders. Autoimmune diseases represent conditions characterized by the immune system's erroneous attacks on self-tissues, encompassing disorders like systemic lupus erythematosus, rheumatoid arthritis, and multiple sclerosis. The complex etiology of these conditions involves a delicate interplay of genetic and environmental factors. Emerging evidence suggests that snoRNAs initially recognized for their housekeeping roles, extend their influence on immune regulation through diverse mechanisms. SnoRNAs have been implicated in epigenetic modification, directly affecting the gene expression profiles of immune cells. Their ability to guide site-specific changes on ribosomal RNAs and other non-coding RNAs can significantly influence the translation of proteins involved in immune response pathways. Moreover, snoRNAs interact with key immune-related proteins, modulating their functions and subsequently impacting immune cell development, activation, and tolerance. Dysregulation of snoRNA expression has been observed in various autoimmune diseases, underscoring their potential as biomarkers for disease diagnosis, prognosis, and therapeutic targets. Manipulating snoRNA expression or activity is a promising therapeutic intervention avenue, offering the potential for personalized treatment strategies in autoimmune diseases. However, there remains a need for comprehensive research efforts to elucidate the precise molecular mechanisms underlying snoRNA-mediated immune modulation. Further investigations in this domain are essential to unravel the potential of snoRNAs in autoimmune disorders.
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Affiliation(s)
- Gaurav Dubey
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, India
| | - Mithilesh Singh
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, India.
| | - Himmat Singh
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, India
| | - Mohit Agarwal
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, India
| | | | - Anurag Mishra
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, India
| | - Ravindra Pal Singh
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, Rajasthan, India
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
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