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Stasevich EM, Simonova AV, Bogomolova EA, Murashko MM, Uvarova AN, Zheremyan EA, Korneev KV, Schwartz AM, Kuprash DV, Demin DE. Cut from the same cloth: RNAs transcribed from regulatory elements. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195049. [PMID: 38964653 DOI: 10.1016/j.bbagrm.2024.195049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
A certain degree of chromatin openness is necessary for the activity of transcription-regulating regions within the genome, facilitating accessibility to RNA polymerases and subsequent synthesis of regulatory element RNAs (regRNAs) from these regions. The rapidly increasing number of studies underscores the significance of regRNAs across diverse cellular processes and diseases, challenging the paradigm that these transcripts are non-functional transcriptional noise. This review explores the multifaceted roles of regRNAs in human cells, encompassing rather well-studied entities such as promoter RNAs and enhancer RNAs (eRNAs), while also providing insights into overshadowed silencer RNAs and insulator RNAs. Furthermore, we assess notable examples of shorter regRNAs, like miRNAs, snRNAs, and snoRNAs, playing important roles. Expanding our discourse, we deliberate on the potential usage of regRNAs as biomarkers and novel targets for cancer and other human diseases.
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Affiliation(s)
- E M Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A V Simonova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Bogomolova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - M M Murashko
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - A N Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - K V Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A M Schwartz
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - D V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D E Demin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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2
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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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3
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Liu X, Zhang H, Fan Y, Cai D, Lei R, Wang Q, Li Y, Shen L, Gu Y, Zhang Q, Qi Z, Wang Z. SNORA28 Promotes Proliferation and Radioresistance in Colorectal Cancer Cells through the STAT3 Pathway by Increasing H3K9 Acetylation in the LIFR Promoter. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2405332. [PMID: 38924373 PMCID: PMC11347989 DOI: 10.1002/advs.202405332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Radiotherapy is essential for treating colorectal cancer (CRC), especially in advanced rectal cancer. However, the low radiosensitivity of CRC cells greatly limits radiotherapy efficacy. Small nucleolar RNAs (snoRNAs) are a class of noncoding RNA that primarily direct post-transcriptional modifications of ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs), and other cellular RNAs. While snoRNAs are involved in tumor progression and chemoresistance, their association with radiosensitivity remains largely unknown. Herein, SNORA28 is shown highly expressed in CRC and is positively associated with poor prognosis. Furthermore, SNORA28 overexpression enhances the growth and radioresistance of CRC cells in vitro and in vivo. Mechanistically, SNORA28 acts as a molecular decoy that recruits bromodomain-containing protein 4 (BRD4), which increases the level of H3K9 acetylation at the LIFR promoter region. This stimulates LIFR transcription, which in turn triggers the JAK1/STAT3 pathway, enhancing the proliferation and radioresistance of CRC cells. Overall, these results highlight the ability of snoRNAs to regulate radiosensitivity in tumor cells and affect histone acetylation modification in the promoter region of target genes, thus broadening the current knowledge of snoRNA biological functions and the mechanism underlying target gene regulation.
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Affiliation(s)
- Xin Liu
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Hong Zhang
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Ying Fan
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Dan Cai
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
- Graduate Collaborative Training Base of Academy of Military SciencesHengyang Medical SchoolUniversity of South ChinaHengyangHunan421001China
| | - Ridan Lei
- Department of Epidemiology and Health StatisticsXiangya School of Public HealthCentral South UniversityChangshaHunan410078China
| | - Qi Wang
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Yaqiong Li
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Liping Shen
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Yongqing Gu
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Qingtong Zhang
- Department of Colorectal SurgeryLiaoning Cancer Hospital & InstituteCancer Hospital of China Medical UniversityCancer Hospital of Dalian University of TechnologyShenyang110042China
| | - Zhenhua Qi
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
| | - Zhidong Wang
- Department of RadiobiologyBeijing Key Laboratory for RadiobiologyBeijing Institute of Radiation MedicineBeijing100850China
- Graduate Collaborative Training Base of Academy of Military SciencesHengyang Medical SchoolUniversity of South ChinaHengyangHunan421001China
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4
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Li S, Jin Z, Song X, Ma J, Peng Z, Yu H, Song J, Zhang Y, Sun X, He M, Yu X, Jin F, Zheng A. The small nucleolar RNA SNORA51 enhances breast cancer stem cell-like properties via the RPL3/NPM1/c-MYC pathway. Mol Carcinog 2024; 63:1117-1132. [PMID: 38421204 DOI: 10.1002/mc.23713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 02/02/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
Breast cancer stem cells (BCSCs) are key players in carcinogenesis and development. Small nucleolar RNAs (snoRNAs) seem to have a crucial influence on regulating stem cell-like properties in various cancers, but the underlying mechanism in breast cancer has not been determined. In this study, we first found that the expression of SNORA51 might be strongly and positively related to BCSCs-like properties. SNORA51 expression was assessed in breast cancer tissues (n = 158 patients) by in situ hybridization. Colony formation, cell counting kit-8, and sphere formation assays were used to detect cell proliferation and self-renewal, respectively. Wound healing and transwell assays were used to detect cell migration. Coimmunoprecipitation and molecular docking were used to determine the underlying mechanism through which SNORA51 regulates BCSCs-like properties. High SNORA51 expression was associated with a worse prognosis, overall survival, and disease-free survival, in 158 breast cancer patients and was also closely related to lymph node status, ER status, the Ki-67 index, histological grade, and TNM stage. Further analysis proved that SNORA51 could enhance and maintain stem cell-like properties, including cell proliferation, self-renewal, and migration, in breast cancer. Moreover, high SNORA51 expression could reduce nucleolar RPL3 expression, induce changes in the expression of NPM1 in the nucleolus and nucleoplasm, and ultimately increase c-MYC expression. Taken together, our findings demonstrated that SNORA51 could enhance BCSCs-like properties via the RPL3/NPM1/c-MYC pathway both in vitro and in vivo. Therefore, SNORA51 might be a significant biomarker and potential therapeutic target and might even provide a new viewpoint on the regulatory mechanism of snoRNAs in breast cancer or other malignant tumors.
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Affiliation(s)
- Shan Li
- Department of Breast Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zining Jin
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xinyue Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Jinfei Ma
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ziqi Peng
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hao Yu
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jian Song
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yiqi Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Xiaoyu Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Xinmiao Yu
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Feng Jin
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ang Zheng
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
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5
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Chabronova A, Holmes TL, Hoang DM, Denning C, James V, Smith JGW, Peffers MJ. SnoRNAs in cardiovascular development, function, and disease. Trends Mol Med 2024; 30:562-578. [PMID: 38523014 DOI: 10.1016/j.molmed.2024.03.004] [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: 12/15/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
Small nucleolar RNAs (snoRNAs) are emerging as important regulators of cardiovascular (patho)biology. Several roles of snoRNAs have recently been identified in heart development and congenital heart diseases, as well as their dynamic regulation in hypertrophic and dilated cardiomyopathies, coronary heart disease (CHD), myocardial infarction (MI), cardiac fibrosis, and heart failure. Furthermore, reports of changes in vesicular snoRNA expression and altered levels of circulating snoRNAs in response to cardiac stress suggest that snoRNAs also function in cardiac signaling and intercellular communication. In this review, we summarize and discuss key findings and outline the clinical potential of snoRNAs considering current challenges and gaps in the field of cardiovascular diseases (CVDs).
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Affiliation(s)
- Alzbeta Chabronova
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK.
| | - Terri L Holmes
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Duc M Hoang
- Department of Stem Cell Biology, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Chris Denning
- Department of Stem Cell Biology, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Victoria James
- School of Veterinary Medicine and Science, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - James G W Smith
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Mandy J Peffers
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK
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6
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Arefnezhad R, Ashna S, Rezaei-Tazangi F, Arfazadeh SM, Seyedsalehie SS, Yeganeafrouz S, Aghaei M, Sanandaji M, Davoodi R, Abadi SRK, Vosough M. Noncoding RNAs and programmed cell death in hepatocellular carcinoma: Significant role of epigenetic modifications in prognosis, chemoresistance, and tumor recurrence rate. Cell Biol Int 2024; 48:556-576. [PMID: 38411312 DOI: 10.1002/cbin.12145] [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: 05/30/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/28/2024]
Abstract
Hepatocellular carcinoma (HCC) is the most common type of liver cancer with a high death rate in the world. The molecular mechanisms related to the pathogenesis of HCC have not been precisely defined so far. Hence, this review aimed to address the potential cross-talk between noncoding RNAs (ncRNAs) and programmed cell death in HCC. All related papers in the English language up to June 2023 were collected and screened. The searched keywords in scientific databases, including Scopus, PubMed, and Google Scholar, were HCC, ncRNAs, Epigenetic, Programmed cell death, Autophagy, Apoptosis, Ferroptosis, Chemoresistance, Tumor recurrence, Prognosis, and Prediction. According to the reports, ncRNAs, comprising long ncRNAs, microRNAs, circular RNAs, and small nucleolar RNAs can affect cell proliferation, migration, invasion, and metastasis, as well as cell death-related processes, such as autophagy, ferroptosis, necroptosis, and apoptosis in HCC by regulating cancer-associated genes and signaling pathways, for example, phosphoinositide 3-kinase/Akt, extracellular signal-regulated kinase/MAPK, and Wnt/β-catenin signaling pathways. It seems that ncRNAs, as epigenetic regulators, can be utilized as biomarkers in diagnosis, prognosis, survival and recurrence rates prediction, chemoresistance, and evaluation of therapeutic response in HCC patients. However, more scientific evidence is suggested to be accomplished to confirm these results.
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Affiliation(s)
- Reza Arefnezhad
- Coenzyme R Research Institute, Tehran, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Ashna
- Student Research Committee, Islamic Azad University Science and Research Branch, Tehran, Iran
| | - Fatemeh Rezaei-Tazangi
- Department of Anatomy, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Seyede Shabnam Seyedsalehie
- Department of Pediatrics, Faculty of Medicine, Ahvaz Jundishapur, University of Medical Sciences, Ahvaz, Iran
| | - Shaghayegh Yeganeafrouz
- Department of Medical Science, Faculty of Medicine, Islamic Azad University, Medical branch, Tehran, Iran
| | - Melika Aghaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mandana Sanandaji
- Department of Physical Education and Sport Sciences, Tehran University, Tehran, Iran
| | | | | | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Institution for Laboratory Medicine, Karolinska Institutet, Experimental Cancer Medicine, Huddinge, Sweden
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7
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Gao L, Fan J, He J, Che X, Wang X, Han C. Small Nucleolar RNAs as Diagnostic and Prognostic Biomarkers in Cancer: A Systematic Review and Meta-Analysis. Technol Cancer Res Treat 2024; 23:15330338241245939. [PMID: 38752263 PMCID: PMC11102679 DOI: 10.1177/15330338241245939] [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: 09/16/2023] [Revised: 01/14/2024] [Accepted: 02/12/2024] [Indexed: 05/21/2024] Open
Abstract
OBJECTIVES Small nucleolar RNAs (snoRNAs) form clusters within the genome, representing a mysterious category of small non-coding RNAs. Research has demonstrated that aberrant snoRNAs can contribute to the development of various types of cancers. Recent studies have identified snoRNAs as potentially valuable biomarkers for the diagnosis or/and prognosis of cancers. However, there has been a lack of comprehensive reviews on prognostic and diagnostic snoRNAs across different types of cancers. METHODS We conducted a systematic search of various databases including Google Scholar, Medline, Cochrane, Scopus, PubMed, Embase, ScienceDirect, Ovid-Medline, Chinese National Knowledge Infrastructure, WanFang, and SinoMed with a time frame reception to December 30, 2022. A total of 49 relevant articles were included in our analysis, consisting of 21 articles focusing on diagnostic aspects and 41 articles focusing on prognostic aspects. Pooled odds ratio, 95% confidence intervals (CIs), and hazard ratio (HR) were utilized to evaluate clinical parameters and overall survival (OS), respectively. RESULT The findings indicated that area under the curve, sensitivity, and specificity were 0.85, 75%, and 80% in cancer, respectively. There was a possibility that snoRNAs had a positive impact on the diagnosis (risk ratio, RR = 2.95, 95% CI: 2.75-3.16, P = 0.000) and OS (HR = 1) in cancer. Additionally, abnormally expressed snoRNAs were associated with a positive impact on OS time for chronic lymphocytic leukemia (HR: 0.88, 95%Cl: 0.69-1.11, P < 0.00001), colon adenocarcinoma (HR: 0.97, 95%Cl: 0.91-1.03, P < 0.0001), and ovarian cancer (HR: 0.98, 95%Cl: 0.98-0.99, P < 0.00001). However, dysregulated snoRNAs of colon cancer and colorectal cancer had a negative impact on OS time (HR = 3.01 and 1.01 respectively, P < 0.0001). CONCLUSION The results strongly suggested that snoRNAs could serve as potential novel indicators for prognosis and diagnosis in cancers. This systematic review followed the guidelines of the Transparent Reporting of Systematic Review and Meta-Analyses (PROSPERO register: CRD42020209096).
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Affiliation(s)
- Liyun Gao
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
- Jiangxi Provincial Key Laboratory of Cell Precision Therapy, School of Basic Medical Sciences, Jiujiang University, China
| | - Junfei Fan
- School of Humanities, Shangluo University, Shangluo, China
| | - Jiayin He
- School of Literature and Journalism, South-central Minzu University, Wuhan, China
| | - Xiangxin Che
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Xin Wang
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Chunhua Han
- Internal Medicine, Jiujiang First People's Hospital, Jiujiang, China
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8
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Shen L, Lin C, Lu W, He J, Wang Q, Huang Y, Zheng X, Wang Z. Involvement of the oncogenic small nucleolar RNA SNORA24 in regulation of p53 stability in colorectal cancer. Cell Biol Toxicol 2023; 39:1377-1394. [PMID: 36087186 DOI: 10.1007/s10565-022-09765-7] [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: 01/25/2022] [Accepted: 08/26/2022] [Indexed: 11/02/2022]
Abstract
Colorectal cancer (CRC) is a common malignant cancer worldwide. Although the molecular mechanism of CRC carcinogenesis has been studied extensively, the details remain unclear. Small nucleolar RNAs (snoRNAs) have recently been reported to have essential functions in carcinogenesis, although their roles in CRC pathogenesis are largely unknown. In this study, we found that the H/ACA snoRNA SNORA24 was upregulated in various cancers, including CRC. SNORA24 expression was significantly associated with age and history of colon polyps in CRC patient cohorts, with high expression associated with a decreased 5-year overall survival. Our results indicated that the oncogenic function of SNORA24 is mediated by promoting G1/S phase transformation, cell proliferation, colony formation, and growth of xenograft tumors. Furthermore, SNORA24 knockdown induced massive apoptosis. RNA-sequencing and gene ontology (GO) enrichment analyses were performed to explore its downstream targets. Finally, we confirmed that SNORA24 regulates p53 protein stability in a proteasomal degradation pathway. Our study clarifies the oncogenic role of SNORA24 in CRC and advance the current model of the role of the p53 pathway in this process.
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Affiliation(s)
- Liping Shen
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Chuxian Lin
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Wenqing Lu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
- College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Junyan He
- The First Affiliated Hospital, Department of Radiation Oncology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Qi Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yujv Huang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xiaofei Zheng
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Zhidong Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
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9
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Zhu J, Mao S, Zhen N, Zhu G, Bian Z, Xie Y, Tang X, Ding M, Wu H, Ma J, Zhu Y, Sun F, Pan Q. SNORA14A inhibits hepatoblastoma cell proliferation by regulating SDHB-mediated succinate metabolism. Cell Death Dis 2023; 9:36. [PMID: 36717552 PMCID: PMC9886955 DOI: 10.1038/s41420-023-01325-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/31/2023]
Abstract
Hepatoblastoma (HB) is the most common paediatric liver malignancy. Dysregulation of small nucleolar RNAs (snoRNAs) is a critical inducer of tumour initiation and progression. However, the association between snoRNAs and HB remains unknown. Here, we conducted snoRNA expression profiling in HB by snoRNA sequencing and identified a decreased level of SNORA14A, a box H/ACA snoRNA, in HB tissues. Low expression of SNORA14A was correlated with PRETEXT stage and metastasis in patients. Functionally, overexpression of SNORA14A suppressed HB cell proliferation and triggered cell apoptosis and G2/M phase arrest. Mechanistically, SNORA14A overexpression promoted the processing and maturation of the 18 S ribosomal RNA (rRNA) precursor to increase succinate dehydrogenase subunit B (SDHB) protein levels. In accordance with SNORA14A downregulation, SDHB protein expression was significantly reduced in HB tissues and cells, accompanied by abnormal accumulation of succinate. Overexpression of SDHB showed antiproliferative and proapoptotic effects and the capacity to induce G2/M phase arrest, while succinate dose-dependently stimulated HB cell growth. Furthermore, the inhibition of SNORA14A in HB malignant phenotypes was mediated by SDHB upregulation-induced reduction of cellular succinate levels. Therefore, the SNORA14A/18 S rRNA/SDHB axis suppresses HB progression by preventing cellular accumulation of the oncometabolite succinate and provides promising prognostic biomarkers and novel therapeutic targets for HB.
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Affiliation(s)
- Jiabei Zhu
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China ,Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127 China
| | - Siwei Mao
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China ,Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127 China
| | - Ni Zhen
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Guoqing Zhu
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhixuan Bian
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Yi Xie
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Xiaochen Tang
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Miao Ding
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Han Wu
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Ji Ma
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Yizhun Zhu
- grid.259384.10000 0000 8945 4455State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau, 999078 China
| | - Fenyong Sun
- grid.412538.90000 0004 0527 0050Department of Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai, 200072 China
| | - Qiuhui Pan
- grid.16821.3c0000 0004 0368 8293Department of Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China ,Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127 China ,grid.415626.20000 0004 4903 1529Sanya Women and Children’s Hospital Managed by Shanghai Children’s Medical Center, Sanya, 572000 China
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10
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Zhang W, Liu B. iSnoDi-LSGT: identifying snoRNA-disease associations based on local similarity constraints and global topological constraints. RNA (NEW YORK, N.Y.) 2022; 28:1558-1567. [PMID: 36192132 PMCID: PMC9670808 DOI: 10.1261/rna.079325.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Growing evidence proves that small nucleolar RNAs (snoRNAs) have important functions in various biological processes, the malfunction of which leads to the emergence and development of complex diseases. However, identifying snoRNA-disease associations is an ongoing challenging task due to the considerable time- and money-consuming biological experiments. Therefore, it is urgent to design efficient and economical methods for the identification of snoRNA-disease associations. In this regard, we propose a computational method named iSnoDi-LSGT, which utilizes snoRNA sequence similarity and disease similarity as local similarity constraints. The iSnoDi-LSGT predictor further employs network embedding technology to extract topological features of snoRNAs and diseases, based on which snoRNA topological similarity and disease topological similarity are calculated as global topological constraints. To the best of our knowledge, the iSnoDi-LSGT is the first computational method for snoRNA-disease association identification. The experimental results indicate that the iSnoDi-LSGT predictor can effectively predict unknown snoRNA-disease associations. The web server of the iSnoDi-LSGT predictor is freely available at http://bliulab.net/iSnoDi-LSGT.
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Affiliation(s)
- Wenxiang Zhang
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
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11
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Xie Q, Zhang D, Ye H, Wu Z, Sun Y, Shen H. Identification of key snoRNAs serves as biomarkers for hepatocellular carcinoma by bioinformatics methods. Medicine (Baltimore) 2022; 101:e30813. [PMID: 36181013 PMCID: PMC9524901 DOI: 10.1097/md.0000000000030813] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common malignancy with high mortality and poor prognosis due to a lack of predictive markers. However, research on small nuclear RNAs (snoRNAs) in HCC were very little. This study aimed to identify a potential diagnostic and prognostic snoRNA signature for HCC. METHODS HCC datasets from the cancer genome atlas (TCGA) and international cancer genome consortium (ICGC) cohorts were used. Differentially expressed snoRNA (DEs) were identified using the limma package. Based on the DEs, diagnostic and prognostic models were established by the least absolute shrinkage and selection operator (LASSO) regression and COX analysis, and Kaplan-Meier (K-M) survival analysis and receiver operating characteristic (ROC) curve analysis were conducted to evaluate the efficiency of signatures. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to analyze the risk score and further explore the potential correlation between the risk groups and tumor immune status in TCGA. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to determine the functions of key snoRNAs. RESULTS We constructed a 6-snoRNAs signature which could classify patients into high- or low-risk groups and found that patients in the high-risk group had a worse prognosis than those in the low-risk group and were significantly involved in p53 processes. Tumor immune status analysis revealed that CTLA4 and PDCD1 (PD1) were highly expressed in the high-risk group, which responded to PD1 inhibitor therapy. Additionally, a 25-snoRNAs diagnostic signature was constructed with an area under the curve (AUC) of 0.933 for distinguishing HCCs from normal controls. Finally, 3 key snoRNAs (SNORA11, SNORD124, and SNORD46) were identified with both diagnostic and prognostic efficacy, some of which were closely related to the spliceosome and Notch signaling pathways. CONCLUSIONS Our study identified 6 snoRNAs that may serve as novel prognostic models and 3 key snoRNAs with both diagnostic and prognostic efficacy for HCC.
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Affiliation(s)
- Qingqing Xie
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangxi University of Chinese Medicine, Liuzhou, Guangxi, China
| | - Di Zhang
- Department of Clinical Laboratory, The Third Xiangya Hospital of Central South University, Hunan, China
| | - Huifeng Ye
- Department of Clinical Laboratory, Eighth Affiliated Hospital of Guangxi Medical University, Guigang City People’s Hospital, Guigang, Guangxi, China
| | - Zhitong Wu
- Department of Clinical Laboratory, Eighth Affiliated Hospital of Guangxi Medical University, Guigang City People’s Hospital, Guigang, Guangxi, China
| | - Yifan Sun
- Department of Clinical Laboratory, Eighth Affiliated Hospital of Guangxi Medical University, Guigang City People’s Hospital, Guigang, Guangxi, China
| | - Haoming Shen
- Department of Clinical Laboratory, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan, China
- *Correspondence: Haoming Shen, Department of Clinical Laboratory, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Xianjia Lake Street 410031, Changsha, Hunan, China (e-mail: )
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12
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Non-Coding RNAs in Hepatocellular Carcinoma. LIVERS 2022. [DOI: 10.3390/livers2030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Liver cancer ranks as the fourth leading cause of cancer-related deaths. Despite extensive research efforts aiming to evaluate the biological mechanisms underlying hepatocellular carcinoma (HCC) development, little has been translated towards new diagnostic and treatment options for HCC patients. Historically, the focus has been centered on coding RNAs and their respective proteins. However, significant advances in sequencing and RNA detection technologies have shifted the research focus towards non-coding RNAs (ncRNA), as well as their impact on HCC development and progression. A number of studies reported complex post-transcriptional interactions between various ncRNA and coding RNA molecules. These interactions offer insights into the role of ncRNAs in both the known pathways leading to oncogenesis, such as dysregulation of p53, and lesser-known mechanisms, such as small nucleolar RNA methylation. Studies investigating these mechanisms have identified prevalent ncRNA changes in microRNAs, snoRNAs, and long non-coding RNAs that can both pre- and post-translationally regulate key factors in HCC progression. In this review, we present relevant publications describing ncRNAs to summarize the impact of different ncRNA species on liver cancer development and progression and to evaluate recent attempts at clinical translation.
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13
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Small Nucleolar RNAs and Their Comprehensive Biological Functions in Hepatocellular Carcinoma. Cells 2022; 11:cells11172654. [PMID: 36078062 PMCID: PMC9454744 DOI: 10.3390/cells11172654] [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: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a class of highly conserved, stable non-coding RNAs involved in both post-transcriptional modification of RNA and in ribosome biogenesis. Recent research shows that the dysfunction of snoRNAs plays a pivotal role in hepatocellular carcinoma (HCC) and related etiologies, such as hepatitis B virus (HBV), hepatitis C virus (HCV), and non-alcoholic fatty liver disease (NAFLD). Growing evidence suggests that snoRNAs act as oncogenes or tumor suppressors in hepatocellular carcinoma (HCC) through multiple mechanisms. Furthermore, snoRNAs are characterized by their stability in body fluids and their clinical relevance and represent promising tools as diagnostic and prognostic biomarkers. SnoRNAs represent an emerging area of cancer research. In this review, we summarize the classification, biogenesis, activity, and functions of snoRNAs, as well as highlight the mechanism and roles of snoRNAs in HCC and related diseases. Our findings will aid in the understanding of complex processes of tumor occurrence and development, as well as suggest potential diagnostic markers and treatment targets. Furthermore, we discuss several limitations and suggest future research and application directions.
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14
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snoRNAs: functions and mechanisms in biological processes, and roles in tumor pathophysiology. Cell Death Dis 2022; 8:259. [PMID: 35552378 PMCID: PMC9098889 DOI: 10.1038/s41420-022-01056-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Small nucleolar RNAs (snoRNAs), a type of non-coding RNA, are widely present in the nucleoli of eukaryotic cells and play an important role in rRNA modification. With the recent increase in research on snoRNAs, new evidence has emerged indicating that snoRNAs also participate in tRNA and mRNA modification. Studies suggest that numerous snoRNAs, including tumor-promoting and tumor-suppressing snoRNAs, are not only dysregulated in tumors but also show associations with clinical prognosis. In this review, we summarize the reported functions of snoRNAs and the possible mechanisms underlying their role in tumorigenesis and cancer development to guide the snoRNA-based clinical diagnosis and treatment of cancer in the future.
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15
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SNORD1C maintains stemness and 5-FU resistance by activation of Wnt signaling pathway in colorectal cancer. Cell Death Dis 2022; 8:200. [PMID: 35422067 PMCID: PMC9010412 DOI: 10.1038/s41420-022-00996-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/05/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that play indispensable roles in cancers, including colorectal cancer (CRC). However, the role of SNORD1C in CRC is unclear. In the current study, SNORD1C expression was measured in CRC tissues using quantitative real-time PCR. A series of in vivo and in vitro experiments were performed to examine the functional role of SNORD1C in CRC. Quantitative real-time PCR, western blotting, sphere formation assay, and chemotherapy resistance analysis were conducted to illustrate the SNORD1C molecular mechanism. SNORD1C was upregulated in CRC and that high SNORD1C expression was related to poor prognosis. After knocking down SNORD1C in CRC cell lines, cell proliferation, colony formation, cell migration, and invasion were alleviated, while apoptosis was increased. Transcriptional RNA-sequencing analysis revealed that following SNORD1C knockdown, β-catenin was downregulated, as was the transcription factor TCF7, which inhibited the Wnt/β-catenin pathway. Meanwhile, levels of the stem cell-related factors were reduced, diminishing cell stemness and tumorigenesis. Our findings suggest that SNORD1C functions via the Wnt/β-catenin pathway to enhance cancer cell stemness in CRC and could be a predictive biomarker for the prognosis ad aggressiveness of this malignancy. Additionally, targeting SNORD1C may be a novel therapeutic strategy for CRC.
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16
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Wu F, Zhang L, Wu P, Wu Y, Zhang T, Zhang D, Tian J. The Potential Role of Small Nucleolar RNAs in Cancers – An Evidence Map. Int J Gen Med 2022; 15:3851-3864. [PMID: 35431571 PMCID: PMC9005336 DOI: 10.2147/ijgm.s352333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/29/2022] [Indexed: 12/11/2022] Open
Abstract
Purpose Cancer seriously endangers human health in every country of the world. New evidence shows that small nucleolar RNAs play important roles in tumorigenesis. Herein, we created this evidence map to systematically assess the impact of dysregulated snoRNAs on cancers. Methods We searched four databases to February 2022 using the keywords, “carcinoma”, “neoplasms”, “tumor”, “cancer”, “snoRNA”, and “small nucleolar rna”. The research data were independently screened by two reviewers. Bubble plot, mind map, heatmap were used to depict the relationship between snoRNAs and cancers. Results In total, 102 studies met the inclusion criteria and were analyzed in this evidence map. In this study, we found that dysregulated snoRNAs were statistically associated with the clinicopathological characteristics of cancer patients, and affected tumor cell phenotypes. Abnormally expressed snoRNAs were associated with poor survival in cancer patients. Current research confirmed that snoRNAs have good diagnostic efficiency for cancers. snoRNAs could modulate biological processes and signaling pathways of different cancer cells by altering rRNA, regulating mRNA, and recruiting protein factors. Conclusion Taken all together, ectopic snoRNAs may serve as new biomarkers for clinical assessment, diagnostic, prognostic prediction of cancer patients, and provide a potential therapeutic strategy for cancer treatment. This article provided a visual analysis of existing evidence on snoRNAs and cancers, which can offer useful information for different researchers interested in snoRNAs.
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Affiliation(s)
- Fanqi Wu
- Department of Respiratory, Lanzhou University Second Hospital, Lanzhou, Gansu Province, People’s Republic of China
| | - Longguo Zhang
- The Second Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, People’s Republic of China
| | - Pingfan Wu
- Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People’s Liberation Army, Lanzhou, Gansu Province, People’s Republic of China
| | - Yi Wu
- The Second Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, People’s Republic of China
| | - Tao Zhang
- Department of Endocrinology and Metabolism, Lanzhou University Second Hospital, Lanzhou, Gansu Province, People’s Republic of China
| | - Dekui Zhang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, Gansu Province, People’s Republic of China
- Correspondence: Dekui Zhang; Jinhui Tian, Tel +86 139 1978 8616; +86 136 1934 2312, Email ;
| | - Jinhui Tian
- Evidence-Based Medicine Center, Lanzhou University, Lanzhou, Gansu Province, People’s Republic of China
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Braghini MR, Lo Re O, Romito I, Fernandez-Barrena MG, Barbaro B, Pomella S, Rota R, Vinciguerra M, Avila MA, Alisi A. Epigenetic remodelling in human hepatocellular carcinoma. J Exp Clin Cancer Res 2022; 41:107. [PMID: 35331312 PMCID: PMC8943959 DOI: 10.1186/s13046-022-02297-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/19/2022] [Indexed: 04/13/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most frequent primary liver cancer, being the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related death. As other heterogeneous solid tumours, HCC results from a unique synergistic combination of genetic alterations mixed with epigenetic modifications.In HCC the patterns and frequencies of somatic variations change depending on the nearby chromatin. On the other hand, epigenetic alterations often induce genomic instability prone to mutations. Epigenetics refers to heritable states of gene expression without alteration to the DNA sequence itself and, unlike genetic changes, the epigenetic modifications are reversible and affect gene expression more extensively than genetic changes. Thus, studies of epigenetic regulation and the involved molecular machinery are greatly contributing to the understanding of the mechanisms that underline HCC onset and heterogeneity. Moreover, this knowledge may help to identify biomarkers for HCC diagnosis and prognosis, as well as future new targets for more efficacious therapeutic approaches.In this comprehensive review we will discuss the state-of-the-art knowledge about the epigenetic landscape in hepatocarcinogenesis, including evidence on the diagnostic and prognostic role of non-coding RNAs, modifications occurring at the chromatin level, and their role in the era of precision medicine.Apart from other better-known risk factors that predispose to the development of HCC, characterization of the epigenetic remodelling that occurs during hepatocarcinogenesis could open the way to the identification of personalized biomarkers. It may also enable a more accurate diagnosis and stratification of patients, and the discovery of new targets for more efficient therapeutic approaches.
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Affiliation(s)
- Maria Rita Braghini
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Oriana Lo Re
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Ilaria Romito
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Maite G Fernandez-Barrena
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Barbara Barbaro
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Silvia Pomella
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Rota
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manlio Vinciguerra
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Matias A Avila
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Anna Alisi
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy.
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18
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Barros-Silva D, Klavert J, Jenster G, Jerónimo C, Lafontaine DLJ, Martens-Uzunova ES. The role of OncoSnoRNAs and Ribosomal RNA 2'-O-methylation in Cancer. RNA Biol 2021; 18:61-74. [PMID: 34775914 PMCID: PMC8677010 DOI: 10.1080/15476286.2021.1991167] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ribosomes are essential nanomachines responsible for all protein production in cells. Ribosome biogenesis and function are energy costly processes, they are tightly regulated to match cellular needs. In cancer, major pathways that control ribosome biogenesis and function are often deregulated to ensure cell survival and to accommodate the continuous proliferation of tumour cells. Ribosomal RNAs (rRNAs) are abundantly modified with 2'-O-methylation (Nm, ribomethylation) being one of the most common modifications. In eukaryotic ribosomes, ribomethylation is performed by the methyltransferase Fibrillarin guided by box C/D small nucleolar RNAs (snoRNAs). Accumulating evidences indicate that snoRNA expression and ribosome methylation profiles are altered in cancer. Here we review our current knowledge on differential snoRNA expression and rRNA 2ʹ-O methylation in the context of human malignancies, and discuss the consequences and opportunities for cancer diagnostics, prognostics, and therapeutics.
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Affiliation(s)
- Daniela Barros-Silva
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Jonathan Klavert
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (Icbas-up), Porto, Portugal
| | - Denis L J Lafontaine
- Rna Molecular Biology, Fonds De La Recherche Scientifique (F.r.s./fnrs), Université Libre De Bruxelles (Ulb), BioPark Campus, Gosselies, Belgium
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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Chen X, Zhang Q, Yang Z, Yu H, Qu Y, Tan R, Gao Y, He Y, Li L. An SNP reducing SNORD105 and PPAN expression decreases the risk of hepatocellular carcinoma in a Chinese population. J Clin Lab Anal 2021; 35:e24095. [PMID: 34741342 PMCID: PMC8649375 DOI: 10.1002/jcla.24095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/12/2021] [Accepted: 10/25/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND With hepatocellular carcinoma (HCC) becoming a heavy disease burden in China, it is particular to reveal its pathological mechanism. Recent researches have indicated that small nucleolar RNAs (snoRNAs) may be involved in various cancers including HCC. Polymorphisms within snoRNAs may affect its function or expression level, and even its host gene, then produce series of effects related to itself or its host gene. METHODS The association of the single nucleotide polymorphism (SNP) rs2305789 in SNORD105 with HCC susceptibility was evaluated in two independent case-control sets (712 HCC and 801 controls). The contribution of rs2305789 to HCC risk was investigated using case-control, genotype-phenotype correlation analysis, and functional assays. RESULTS The SNP rs2305789 was significantly associated with a decreased risk of HCC in both case-control sets (OR = 0.80, 95% CI: 0.69-0.93, p = 0.003). Compared with the AA genotype, the GG genotype was significantly correlated with lower expression of both SNORD105 and PPAN (p < 0.01). Furthermore, the overexpressed SNORD105 up-regulated PPAN expression level (p < 0.05). Finally, the in vivo experiment showed that the overexpressed SNORD105 increased cell viability and motility in both HepG2 and Huh7 cell lines (p < 0.05). CONCLUSIONS To sum up, our results suggested that rs2305789 decreased the risk of HCC by reducing the expression of both SNORD105 and PPAN, which reduced HCC cell viability and motility.
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Affiliation(s)
- Xuekun Chen
- Department of Forensic Medicine, Soochow University Medical College, Suzhou, China
| | - Qing Zhang
- Department of Forensic Medicine, Soochow University Medical College, Suzhou, China
| | - Zhenzhen Yang
- Department of Forensic Medicine, Soochow University Medical College, Suzhou, China
| | - Huan Yu
- Department of Forensic Medicine, Soochow University Medical College, Suzhou, China
| | - Yiling Qu
- Department of Forensic Medicine, Soochow University Medical College, Suzhou, China
| | - Rui Tan
- Department of Forensic Medicine, Soochow University Medical College, Suzhou, China
| | - Yuzhen Gao
- Department of Forensic Medicine, Soochow University Medical College, Suzhou, China
| | - Yan He
- Department of Epidemiology, Soochow University Medical College, Suzhou, China
| | - Lijuan Li
- Department of Forensic Medicine, Soochow University Medical College, Suzhou, China
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20
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Baptista B, Riscado M, Queiroz J, Pichon C, Sousa F. Non-coding RNAs: Emerging from the discovery to therapeutic applications. Biochem Pharmacol 2021. [DOI: 10.1016/j.bcp.2021.114469 order by 22025--] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
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21
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Baptista B, Riscado M, Queiroz JA, Pichon C, Sousa F. Non-coding RNAs: Emerging from the discovery to therapeutic applications. Biochem Pharmacol 2021; 189:114469. [PMID: 33577888 DOI: 10.1016/j.bcp.2021.114469] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023]
Abstract
The knowledge about non-coding RNAs (ncRNAs) is rapidly increasing with new data continuously emerging, regarding their diverse types, applications, and roles. Particular attention has been given to ncRNA with regulatory functions, which may have a critical role both in biological and pathological conditions. As a result of the diversity of ncRNAs and their ubiquitous involvement in several biologic processes, ncRNA started to be considered in the biomedical field, with immense potential to be exploited either as biomarkers or as therapeutic agents in certain pathologies. Indeed, ncRNA-based therapeutics have been proposed in many disorders and some even reached clinical trials. However, to prepare an RNA product suitable for pharmacological applications, certain criteria must be fulfilled, and it has to be guaranteed RNA purity, stability, and bioactivity. So, in this review, the different types of ncRNAs are identified and characterized, by describing their biogenesis, functions, and applications. A perspective on the main challenges and innovative approaches for the future and broad therapeutic application of RNA is also presented.
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Affiliation(s)
- B Baptista
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - M Riscado
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - J A Queiroz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - C Pichon
- Centre de Biophysique Moléculaire (CBM), UPR 4301 CNRS & University of Orléans Orléans, France
| | - F Sousa
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Avenida Infante D. Henrique, 6200-506 Covilhã, Portugal.
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22
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Xu A, Huang MF, Zhu D, Gingold JA, Bazer DA, Chang B, Wang D, Lai CC, Lemischka IR, Zhao R, Lee DF. LncRNA H19 Suppresses Osteosarcomagenesis by Regulating snoRNAs and DNA Repair Protein Complexes. Front Genet 2021; 11:611823. [PMID: 33519915 PMCID: PMC7844330 DOI: 10.3389/fgene.2020.611823] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022] Open
Abstract
Osteosarcoma is one of the most frequent common primary malignant tumors in childhood and adolescence. Long non-coding RNAs (lncRNAs) have been reported to regulate the initiation and progression of tumors. However, the exact molecular mechanisms involving lncRNA in osteosarcomagenesis remain largely unknown. Li-Fraumeni syndrome (LFS) is a familial cancer syndrome caused by germline p53 mutation. We investigated the tumor suppressor function of lncRNA H19 in LFS-associated osteosarcoma. Analyzing H19-induced transcriptome alterations in LFS induced pluripotent stem cell (iPSC)-derived osteoblasts, we unexpectedly discovered a large group of snoRNAs whose expression was significantly affected by H19. We identified SNORA7A among the H19-suppressed snoRNAs. SNORA7A restoration impairs H19-mediated osteogenesis and tumor suppression, indicating an oncogenic role of SNORA7A. TCGA analysis indicated that SNORA7A expression is associated with activation of oncogenic signaling and poor survival in cancer patients. Using an optimized streptavidin-binding RNA aptamer designed from H19 lncRNA, we revealed that H19-tethered protein complexes include proteins critical for DNA damage response and repair, confirming H19's tumor suppressor role. In summary, our findings demonstrate a critical role of H19-modulated SNORA7A expression in LFS-associated osteosarcomas.
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Affiliation(s)
- An Xu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Mo-Fan Huang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Dandan Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Julian A Gingold
- Department of Obstetrics and Gynecology and Women's Health, Einstein/Montefiore Medical Center, Bronx, NY, United States
| | - Danielle A Bazer
- Department of Neurology, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, United States
| | - Betty Chang
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Donghui Wang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Graduate Institute of Chinese Medical Science, China Medical University, Taichung, Taiwan
| | - Ihor R Lemischka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ruiying Zhao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States.,Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Precision Health, School of Biomedical Informatics and School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
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23
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Cao P, Jin Q, Feng L, Li H, Qin G, Zhou G. Emerging roles and potential clinical applications of noncoding RNAs in hepatocellular carcinoma. Semin Cancer Biol 2020; 75:136-152. [PMID: 32931952 DOI: 10.1016/j.semcancer.2020.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma(HCC) is one of the most common forms of cancer, and accounts for a high proportion of cancer-associated deaths. Growing evidences have demonstrated that non- protein-coding regions of the genome could give rise to transcripts, termed noncoding RNA (ncRNA), that form novel functional layers of the cellular activity. ncRNAs are implicated in different molecular mechanisms and functions at transcriptional, translational and post-translational levels. An increasing number of studies have demonstrated a complex array of molecular and cellular functions of ncRNAs in different stages of the HCC tumorigenesis, either in an oncogenic or tumor-suppressive manner. As a result, several pre-clinical studies have highlighted the great potentials of ncRNAs as novel biomarkers for cancer diagnosis or therapeutics in targeting HCC progression. In this review, we briefly described the characteristics of several representative ncRNAs and summarized the latest findings of their roles and mechanisms in the development of HCC, in order to better understand the cancer biology and their potential clinical applications in this malignancy.
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Affiliation(s)
- Pengbo Cao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qian Jin
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Lan Feng
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Haibei Li
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, Tianjin City, China
| | - Geng Qin
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun City, China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China; Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, China; Medical College, Guizhou University, Guiyang City, China.
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24
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Non-Coding RNAs: Regulating Disease Progression and Therapy Resistance in Hepatocellular Carcinoma. Cancers (Basel) 2020; 12:cancers12051243. [PMID: 32429062 PMCID: PMC7281199 DOI: 10.3390/cancers12051243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the primary liver cancer arising from hepatocytes, is a universal health problem and one of the most common malignant tumors. Surgery followed by chemotherapy as well as tyrosine kinase inhibitors (TKIs), such as sorafenib, are primary treatment procedures for HCC, but recurrence of disease because of therapy resistance results in high mortality. It is necessary to identify novel regulators of HCC for developing effective targeted therapies that can significantly interfere with progression of the disease process. Non-coding RNAs (ncRNAs) are an abundant group of versatile RNA transcripts that do not translate into proteins, rather serve as potentially functional RNAs. The role of ncRNAs in regulating diverse aspects of the carcinogenesis process are gradually being elucidated. Recent advances in RNA sequencing technology have identified a plethora of ncRNAs regulating all aspects of hepatocarcinogenesis process and serving as potential prognostic or diagnostic biomarkers. The present review provides a comprehensive description of the biological roles of ncRNAs in disease process and therapy resistance, and potential clinical application of these ncRNAs in HCC.
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25
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He JY, Liu X, Qi ZH, Wang Q, Lu WQ, Zhang QT, He SY, Wang ZD. Small Nucleolar RNA, C/D Box 16 (SNORD16) Acts as a Potential Prognostic Biomarker in Colon Cancer. Dose Response 2020; 18:1559325820917829. [PMID: 32704240 PMCID: PMC7359415 DOI: 10.1177/1559325820917829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/01/2020] [Accepted: 03/07/2020] [Indexed: 12/15/2022] Open
Abstract
Colon cancer (CC) is considered one of the most common and lethal malignancies occurring both in male and female. Its widespread prevalence demonstrates the need for novel diagnostic and prognostic biomarkers for CC. Emerging evidence has shown that small nucleolar RNAs play critical roles in tumor development. In this study, we investigated the expression profile and functions of SNORD16 in CC. Our data showed that SNORD16, rather than its host gene (RPL4), was upregulated in CC cell lines. Compared to matched adjacent normal tissues, CC tissues showed higher SNORD16 expression levels, and no correlation was found between SNORD16 and RPL4. Patients with high SNORD16 expression levels had a worse prognosis, and multivariate analysis showed the high SNORD16 expression was an independent prognostic factor for CC. In vitro gain- and loss-of-function studies revealed that SNORD16 can promote cell growth, proliferation, migration, and invasion of CC cells by inhibiting apoptosis. These results suggested that SNORD16 has an oncogenic role in CC and might be a novel diagnostic and prognostic biomarker for CC.
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Affiliation(s)
- Jun-Yan He
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, China.,Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xin Liu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Zhen-Hua Qi
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qi Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Wen-Qing Lu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qing-Tong Zhang
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Shu-Ya He
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, China
| | - Zhi-Dong Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.,School of Public Health, University of South China, Hengyang, China
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26
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Li J, Kho AT, Chase RP, Pantano L, Farnam L, Amr SS, Tantisira KG. COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis. Sci Rep 2020; 10:4552. [PMID: 32165660 PMCID: PMC7067867 DOI: 10.1038/s41598-020-61495-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/20/2020] [Indexed: 11/09/2022] Open
Abstract
Small RNA-Seq is a common means to interrogate the small RNA’ome or the full spectrum of small RNAs (<200 nucleotide length) of a biological system. A pivotal problem in NGS based small RNA analysis is identifying and quantifying the small RNA’ome constituent components. For example, small RNAs in the circulatory system (circulating RNAs) are potential disease biomarkers and their function is being actively investigated. Most existing NGS data analysis tools focus on the microRNA component and a few other small RNA types like piRNA, snRNA and snoRNA. A comprehensive platform is needed to interrogate the full small RNA’ome, a prerequisite for down-stream data analysis. We present COMPSRA, a comprehensive modular stand-alone platform for identifying and quantifying small RNAs from small RNA sequencing data. COMPSRA contains prebuilt customizable standard RNA databases and sequence processing tools to enable turnkey basic small RNA analysis. We evaluated COMPSRA against comparable existing tools on small RNA sequencing data set from serum samples of 12 healthy human controls, and COMPSRA identified a greater diversity and abundance of small RNA molecules. COMPSRA is modular, stand-alone and integrates multiple customizable RNA databases and sequence processing tool and is distributed under the GNU General Public License free to non-commercial registered users at https://github.com/cougarlj/COMPSRA.
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Affiliation(s)
- Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | | | - Robert P Chase
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorena Pantano
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Leanna Farnam
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sami S Amr
- Partners Personalized Medicine, Boston, MA, USA
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
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27
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Shuwen H, Xi Y, Quan Q, Yin J, Miao D. Can small nucleolar RNA be a novel molecular target for hepatocellular carcinoma? Gene 2020; 733:144384. [PMID: 31978508 DOI: 10.1016/j.gene.2020.144384] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Globally, hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death. Recently, many studies have demonstrated that small nucleolar RNA (snoRNA) was closely related to HCC. OBJECTIVE To explore whether snoRNA can be used as a molecular target for HCC. METHODS The PubMed, Embase, and Cochrane databases were searched for the published literatures related to snoRNA and HCC until August 12, 2019. After identification, screening, and verification, this study finally included 26 studies correlating small nucleolar RNA host gene (SNHG) and HCC, and 8 studies correlating snoRNA and HCC. Based on the collation of the relevant literature, the correlation network diagram between snoRNAs and HCC was constructed. RESULTS The SNHGs, such as SNHG1, SNHG6, SNHG16, and SNHG20 can play varied roles in HCC through different regulatory mechanisms. These SNHGs can promote and inhibit tumorigenesis. SNORD76 can promote the proliferation of tumor tissues and cells in vitro through different pathways. SnoU2_19 and SNORD76 can function through the same pathway. SNHG3, SNHG20, SNHG6, SNORD76, and snoRA47 can modulate epithelial-mesenchymal transition (EMT) to regulate the development of HCC cell or tissue. SNHG16, SNORD76, and SnoU2_19 can regulate the development of HCC through Wnt/β-catenin signaling pathway. CONCLUSION snoRNA can regulate the occurrence of HCC by modulating multiple molecular signaling pathways. Hence, snoRNA can be a potential molecular target for HCC.
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Affiliation(s)
- Han Shuwen
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops HuZhou University, 198 Hongqi Rd, Huzhou, Zhejiang, PR China
| | - Yang Xi
- Department of Intervention and Radiotherapy, Huzhou Central Hospital, No. 198 Hongqi Road, Huzhou, Zhejiang Province 313000, PR China
| | - Qi Quan
- Department of Oncology, Huzhou Central Hospital, No. 198 Hongqi Road, Huzhou, Zhejiang Province 313000, PR China
| | - Jin Yin
- Department of Clinical Laboratory, Huzhou Central Hospital, No. 198 Hongqi Road, Huzhou, Zhejiang Province 313000, PR China
| | - Da Miao
- Department of Nursing, Huzhou Third Municipal Hospital, Huzhou, Zhejiang Province, PR China.
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28
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Gougelet A, Desbois-Mouthon C. Non-coding RNAs open a new chapter in liver cancer treatment. Clin Res Hepatol Gastroenterol 2019; 43:630-637. [PMID: 31401041 DOI: 10.1016/j.clinre.2019.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 02/08/2023]
Abstract
Despite the intensive efforts to identify the molecular events responsible for the emergence of liver cancer, hepatocellular carcinoma (HCC) remains a major health problem in the world. Thus, the identification of new therapeutic opportunities is a short-term necessity. These last few decades, non-coding RNAs appeared as interesting therapeutic strategies with their pleiotropic inhibitory action in the cell itself but also in recipient cells via their secretion into extracellular vesicles. This short review recapitulates recent advancements concerning non-coding RNAs and their deregulations in liver cancer.
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Affiliation(s)
- Angélique Gougelet
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Team "Oncogenic functions of beta-catenin signaling in the liver", 75006 Paris, France.
| | - Christèle Desbois-Mouthon
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Team "Oncogenic functions of beta-catenin signaling in the liver", 75006 Paris, France
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29
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Liang J, Wen J, Huang Z, Chen XP, Zhang BX, Chu L. Small Nucleolar RNAs: Insight Into Their Function in Cancer. Front Oncol 2019; 9:587. [PMID: 31338327 PMCID: PMC6629867 DOI: 10.3389/fonc.2019.00587] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/17/2019] [Indexed: 02/04/2023] Open
Abstract
Small nucleolar RNAs (SnoRNAs) are a class of non-coding RNAs divided into two classes: C/D box snoRNAs and H/ACA box snoRNAs. The canonical function of C/D box and H/ACA box snoRNAs are 2'-O-ribose methylation and pseudouridylation of ribosomal RNAs (rRNAs), respectively. Emerging evidence has demonstrated that snoRNAs are involved in various physiological and pathological cellular processes. Mutations and aberrant expression of snoRNAs have been reported in cell transformation, tumorigenesis, and metastasis, indicating that snoRNAs may serve as biomarkers and/or therapeutic targets of cancer. Hence, further study of the functions and underlying mechanism of snoRNAs is valuable. In this review, we summarize the biogenesis and functions of snoRNAs, as well as the association of snoRNAs in different types of cancers and their potential roles in cancer diagnosis and therapy.
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Affiliation(s)
- Junnan Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingyuan Wen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhao Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Ping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bi-Xiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Chu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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30
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Guide snoRNAs: Drivers or Passengers in Human Disease? BIOLOGY 2018; 8:biology8010001. [PMID: 30577491 PMCID: PMC6466398 DOI: 10.3390/biology8010001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 01/17/2023]
Abstract
In every domain of life, RNA-protein interactions play a significant role in co- and post-transcriptional modifications and mRNA translation. RNA performs diverse roles inside the cell, and therefore any aberrancy in their function can cause various diseases. During maturation from its primary transcript, RNA undergoes several functionally important post-transcriptional modifications including pseudouridylation and ribose 2′-O-methylation. These modifications play a critical role in the stability of the RNA. In the last few decades, small nucleolar RNAs (snoRNAs) were revealed to be one of the main components to guide these modifications. Due to their active links to the nucleoside modification, deregulation in the snoRNA expressions can cause multiple disorders in humans. Additionally, host genes carrying snoRNA-encoding sequences in their introns also show differential expression in disease. Although few reports support a causal link between snoRNA expression and disease manifestation, this emerging field will have an impact on the way we think about biomarkers or identify novel targets for therapy. This review focuses on the intriguing aspect of snoRNAs that function as a guide in post-transcriptional RNA modification, and regulation of their host genes in human disease.
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31
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Prospects of Noncoding RNAs in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6579436. [PMID: 30148169 PMCID: PMC6083484 DOI: 10.1155/2018/6579436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/16/2018] [Accepted: 06/06/2018] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is a global health problem and one of the most common malignant tumors. Recent studies have shown that noncoding RNAs (ncRNAs) contribute to the pathogenesis of hepatocellular carcinoma (HCC). These RNAs may be involved in a variety of pathological processes such as cell proliferation, apoptosis, angiogenesis, invasion, and metastasis. In addition, abnormal expression of ncRNAs in HCC may provide potential prognostic or diagnostic biomarkers. This review provides an overview of the role and potential applications of ncRNAs, miRNAs, lncRNAs, circRNAs, and snoRNAs in liver cancer.
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32
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Baral D, Wu L, Katwal G, Yan X, Wang Y, Ye Q. Clinical significance and biological roles of small nucleolar RNAs in hepatocellular carcinoma. Biomed Rep 2018. [PMID: 29541452 PMCID: PMC5838311 DOI: 10.3892/br.2018.1063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is among the most common and fatal cancers. It is a multistage and multifactorial carcinoma, in which a number of factors serve roles in its initiation and progression. Small nucleolar RNAs (snoRNAs), considered to serve a role in various cancers, have recently been identified to have significant contributions to HCC tumorigenesis. Recent studies suggest that snoRNAs have a critical role in the pathogenesis of HCC. Moreover, detailed studies have demonstrated that various snoRNAs are involved in a range of biological processes associated with HCC, including initiation, proliferation, tumor growth, the cell cycle, apoptosis and metastasis. In the present review, an overview of recent studies to date has been provided, focusing on the association of snoRNAs with HCC. Based on the findings, further studies focusing on the association of snoRNAs with HCC are required to verify the diagnostic and therapeutic capacities of snoRNAs in HCC.
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Affiliation(s)
- Dilip Baral
- Wuhan University, Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| | - Long Wu
- Wuhan University, Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| | - Gaurav Katwal
- Wuhan University, Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| | - Xiong Yan
- Wuhan University, Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| | - Yanfeng Wang
- Wuhan University, Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China
| | - Qifa Ye
- Wuhan University, Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan, Hubei 430071, P.R. China.,The Third Xiangya Hospital of Central South University, Research Center of National Health Ministry on Transplantation Medicine Engineering and Technology, Changsha, Hunan 410013, P.R. China
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