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Rostami S, Rounge TB, Pestarino L, Lyle R, Fortner RT, Haaland ØA, Lie RT, Wiklund F, Bjørge T, Langseth H. Differential levels of circulating RNAs prior to endometrial cancer diagnosis. Int J Cancer 2024; 155:946-956. [PMID: 38733362 DOI: 10.1002/ijc.34951] [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: 12/01/2023] [Revised: 03/01/2024] [Accepted: 03/15/2024] [Indexed: 05/13/2024]
Abstract
Endometrial cancer (EC) is one of the most common female cancers and there is currently no routine screening strategy for early detection. An altered abundance of circulating microRNAs (miRNAs) and other RNA classes have the potential as early cancer biomarkers. We analyzed circulating RNA levels using small RNA sequencing, targeting RNAs in the size range of 17-47 nucleotides, in EC patients with samples collected prior to diagnosis compared to cancer-free controls. The analysis included 316 cases with samples collected 1-11 years prior to EC diagnosis, and 316 matched controls, both from the Janus Serum Bank cohort in Norway. We identified differentially abundant (DA) miRNAs, isomiRs, and small nuclear RNAs between EC cases and controls. The top EC DA miRNAs were miR-155-5p, miR-200b-3p, miR-589-5p, miR-151a-5p, miR-543, miR-485-5p, miR-625-p, and miR-671-3p. miR-200b-3p was previously reported to be among one of the top miRNAs with higher abundance in EC cases. We observed 47, 41, and 32 DA miRNAs for EC interacting with BMI, smoking status, and physical activity, respectively, including two miRNAs (miR-223-3p and miR-29b-3p) interacting with all three factors. The circulating RNAs are altered and show temporal dynamics prior to EC diagnosis. Notably, DA miRNAs for EC had the lowest q-value 4.39-6.66 years before diagnosis. Enrichment analysis of miRNAs showed that signaling pathways Fc epsilon RI, prolactin, toll-like receptor, and VEGF had the strongest associations.
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Affiliation(s)
- Sina Rostami
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
- Center for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Luca Pestarino
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
- Department of Gynecological Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Renée Turzanski Fortner
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Rolv T Lie
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tone Bjørge
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Section for Cervical Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Hilde Langseth
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
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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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't Hart LM, de Klerk JA, Bouland GA, Peerlings JHD, Blom MT, Cramer SJ, Bijkerk R, Beulens JWJ, Slieker RC. Small RNA sequencing reveals snoRNAs and piRNA-019825 as novel players in diabetic kidney disease. Endocrine 2024:10.1007/s12020-024-03884-3. [PMID: 38801599 DOI: 10.1007/s12020-024-03884-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024]
Abstract
INTRODUCTION Micro- and macrovascular complications are common among persons with type 2 diabetes. Recently there has been growing interest to investigate the potential of circulating small non-coding RNAs (sncRNAs) as contributors to the development of diabetic complications. In this study we investigate to what extent circulating sncRNAs levels associate with prevalent diabetic kidney disease (DKD) in persons with type 2 diabetes. METHODS Plasma sncRNAs levels were determined using small RNA-seq, allowing detection of miRNAs, snoRNAs, piRNAs, tRNA fragments, and various other sncRNA classes. We tested for differentially expressed sncRNAs in persons with type 2 diabetes, with DKD (n = 69) or without DKD (n = 405). In secondary analyses, we also tested the association with eGFR, albuminuria (UACR), and the plasma proteome. RESULTS In total seven sncRNAs were negatively associated with prevalent DKD (all PFDR ≤ 0.05). Including one microRNA (miR-143-5p), five snoRNAs (U8, SNORD118, SNORD24, SNORD107, SNORD87) and a piRNA (piR-019825 | DQ597218). Proteomic analyses showed that the seven sncRNAs, and especially the piRNA piR-019825, were associated with plasma levels of 24 proteins of which several have known associations with kidney function including TNF sR-I (TNFRFS1A), DAN (NBL1) and cystatin C (CST3). CONCLUSION We have identified novel small non-coding RNAs, primarily from classes other than microRNAs, that are associated with diabetic kidney disease. Our results show that the involvement of small non-coding RNAs in DKD goes beyond the already known microRNAs and also involves other classes of sncRNA, in particular snoRNAs and the piRNA piR-019825, that have never been studied before in relation to kidney function.
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Affiliation(s)
- L M 't Hart
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Epidemiology and Data Sciences, Amsterdam University Medical Center, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Health Behaviors & Chronic Diseases Research Program & Personalised Medicine Research Program, Amsterdam Public Health, Amsterdam, The Netherlands.
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - J A de Klerk
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - G A Bouland
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - J H D Peerlings
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - M T Blom
- Health Behaviors & Chronic Diseases Research Program & Personalised Medicine Research Program, Amsterdam Public Health, Amsterdam, The Netherlands
- Department of General Practice, Amsterdam University Medical Center, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - S J Cramer
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - R Bijkerk
- Department of Internal Medicine, Division of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - J W J Beulens
- Department of Epidemiology and Data Sciences, Amsterdam University Medical Center, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Health Behaviors & Chronic Diseases Research Program & Personalised Medicine Research Program, Amsterdam Public Health, Amsterdam, The Netherlands
| | - R C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
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Saeinasab M, Atlasi Y, M Matin M. Functional role of lncRNAs in gastrointestinal malignancies: the peculiar case of small nucleolar RNA host gene family. FEBS J 2024; 291:1353-1385. [PMID: 36282516 DOI: 10.1111/febs.16668] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/18/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in normal physiology and are often de-regulated in disease states such as cancer. Recently, a class of lncRNAs referred to as the small nucleolar RNA host gene (SNHG) family have emerged as important players in tumourigenesis. Here, we discuss new findings describing the role of SNHGs in gastrointestinal tumours and summarize the three main functions by which these lncRNAs promote carcinogenesis, namely: competing with endogenous RNAs, modulating protein function, and regulating epigenetic marking. Furthermore, we discuss how SNHGs participate in different hallmarks of cancer, and how this class of lncRNAs may serve as potential biomarkers in cancer diagnosis and therapy.
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Affiliation(s)
- Morvarid Saeinasab
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Iran
| | - Yaser Atlasi
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Iran
- Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Iran
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5
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Gómez-Matas J, Duran-Sanchon S, Lozano JJ, Ferrero G, Tarallo S, Pardini B, Naccarati A, Castells A, Gironella M. SnoRNA profiling in colorectal cancer and assessment of non-invasive biomarker capacity by ddPCR in fecal samples. iScience 2024; 27:109283. [PMID: 38450150 PMCID: PMC10915595 DOI: 10.1016/j.isci.2024.109283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/26/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) have been identified dysregulated in several pathologies, and these alterations can be detected in tissues and in circulation. The main aim of this study was to analyze the whole snoRNome in advanced colorectal neoplasms and to identify new potential non-invasive snoRNA-based biomarkers in fecal samples by different analytical approaches. SNORA51, SNORD15B, SNORA54, SNORD12B, SNORD12C, SNORD72, SNORD89, and several members of SNORD115 and SNORD116 clusters were consistently deregulated in both tissue sets. After technical validation, SNORA51 and SNORD15B were detected in FIT+ samples. SNORA51 was significantly upregulated in FIT+ samples from CRC patients compared to healthy controls. This upregulation, together with the fecal hemoglobin concentration, was sufficient to identify, among FIT+ individuals, patients with CRC (AUC = 0.86) and individuals with advanced adenomas (AUC = 0.68). These findings portray snoRNAs as an alternative source of candidates for further studies and SNORA51 appears as a potential non-invasive biomarker for CRC detection.
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Affiliation(s)
- Javier Gómez-Matas
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
| | - Saray Duran-Sanchon
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
| | | | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Antoni Castells
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
| | - Meritxell Gironella
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona-Spanish National Research Council (IIBB-CSIC), Barcelona, Spain
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6
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Lan YZ, Wu Z, Chen WJ, Fang ZX, Yu XN, Wu HT, Liu J. Small nucleolar RNA and its potential role in the oncogenesis and development of colorectal cancer. World J Gastroenterol 2024; 30:115-127. [PMID: 38312115 PMCID: PMC10835520 DOI: 10.3748/wjg.v30.i2.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) represent a class of non-coding RNAs that play pivotal roles in post-transcriptional RNA processing and modification, thereby contributing significantly to the maintenance of cellular functions related to protein synthesis. SnoRNAs have been discovered to possess the ability to influence cell fate and alter disease progression, holding immense potential in controlling human diseases. It is suggested that the dysregulation of snoRNAs in cancer exhibits differential expression across various cancer types, stages, metastasis, treatment response and/or prognosis in patients. On the other hand, colorectal cancer (CRC), a prevalent malignancy of the digestive system, is characterized by high incidence and mortality rates, ranking as the third most common cancer type. Recent research indicates that snoRNA dysregulation is associated with CRC, as snoRNA expression significantly differs between normal and cancerous conditions. Consequently, assessing snoRNA expression level and function holds promise for the prognosis and diagnosis of CRC. Nevertheless, current comprehension of the potential roles of snoRNAs in CRC remains limited. This review offers a comprehensive survey of the aberrant regulation of snoRNAs in CRC, providing valuable insights into the discovery of novel biomarkers, therapeutic targets, and potential tools for the diagnosis and treatment of CRC and furnishing critical cues for advancing research into CRC and the judicious selection of therapeutic targets.
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Affiliation(s)
- Yang-Zheng Lan
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Zheng Wu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Wen-Jia Chen
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Ze-Xuan Fang
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Xin-Ning Yu
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Hua-Tao Wu
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Jing Liu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
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Ow MC, Hall SE. Inheritance of Stress Responses via Small Non-Coding RNAs in Invertebrates and Mammals. EPIGENOMES 2023; 8:1. [PMID: 38534792 DOI: 10.3390/epigenomes8010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 03/28/2024] Open
Abstract
While reports on the generational inheritance of a parental response to stress have been widely reported in animals, the molecular mechanisms behind this phenomenon have only recently emerged. The booming interest in epigenetic inheritance has been facilitated in part by the discovery that small non-coding RNAs are one of its principal conduits. Discovered 30 years ago in the Caenorhabditis elegans nematode, these small molecules have since cemented their critical roles in regulating virtually all aspects of eukaryotic development. Here, we provide an overview on the current understanding of epigenetic inheritance in animals, including mice and C. elegans, as it pertains to stresses such as temperature, nutritional, and pathogenic encounters. We focus on C. elegans to address the mechanistic complexity of how small RNAs target their cohort mRNAs to effect gene expression and how they govern the propagation or termination of generational perdurance in epigenetic inheritance. Presently, while a great amount has been learned regarding the heritability of gene expression states, many more questions remain unanswered and warrant further investigation.
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Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Sarah E Hall
- Department of Biology and Program in Neuroscience, Syracuse University, Syracuse, NY 13210, USA
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8
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Zhang L, Chen M, Hu X, Deng L. Graph Convolutional Network and Contrastive Learning Small Nucleolar RNA (snoRNA) Disease Associations (GCLSDA): Predicting snoRNA-Disease Associations via Graph Convolutional Network and Contrastive Learning. Int J Mol Sci 2023; 24:14429. [PMID: 37833876 PMCID: PMC10572952 DOI: 10.3390/ijms241914429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) constitute a prevalent class of noncoding RNAs localized within the nucleoli of eukaryotic cells. Their involvement in diverse diseases underscores the significance of forecasting associations between snoRNAs and diseases. However, conventional experimental techniques for such predictions suffer limitations in scalability, protracted timelines, and suboptimal success rates. Consequently, efficient computational methodologies are imperative to realize the accurate predictions of snoRNA-disease associations. Herein, we introduce GCLSDA-graph Convolutional Network and contrastive learning predict snoRNA disease associations. GCLSDA is an innovative framework that combines graph convolution networks and self-supervised learning for snoRNA-disease association prediction. Leveraging the repository of MNDR v4.0 and ncRPheno databases, we construct a robust snoRNA-disease association dataset, which serves as the foundation to create bipartite graphs. The computational prowess of the light graph convolutional network (LightGCN) is harnessed to acquire nuanced embedded representations of both snoRNAs and diseases. With careful consideration, GCLSDA intelligently incorporates contrast learning to address the challenging issues of sparsity and over-smoothing inside correlation matrices. This combination not only ensures the precision of predictions but also amplifies the model's robustness. Moreover, we introduce the augmentation technique of random noise to refine the embedded snoRNA representations, consequently enhancing the precision of predictions. Within the domain of contrast learning, we unite the tasks of contrast and recommendation. This harmonization streamlines the cross-layer contrast process, simplifying the information propagation and concurrently curtailing computational complexity. In the area of snoRNA-disease associations, GCLSDA constantly shows its promising capacity for prediction through extensive research. This success not only contributes valuable insights into the functional roles of snoRNAs in disease etiology, but also plays an instrumental role in identifying potential drug targets and catalyzing innovative treatment modalities.
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Affiliation(s)
| | | | | | - Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha 410083, China; (L.Z.); (M.C.); (X.H.)
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9
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Hassanzadeh A, Yegdaneh A, Rabbani M. Effects of hydroalcoholic, methanolic, and hexane extracts of brown algae Sargassum angustifolium on scopolamine-induced memory impairment and learning deficit in rodents. Res Pharm Sci 2023; 18:292-302. [PMID: 37593166 PMCID: PMC10427794 DOI: 10.4103/1735-5362.371585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/08/2022] [Accepted: 02/28/2023] [Indexed: 08/19/2023] Open
Abstract
Background and purpose Properties of Alzheimer's disease, can be caused by several reasons and there is no definite treatment for it. We aimed to study the effect of the hydroalcoholic extract, methanolic and n-hexane fractions of brown algae Sargassum angustifolium on memory impairment in mice and rats. Experimental approach Hydroalcoholic extract (25, 50, 100, 200 mg/kg), methanolic (20 and 40 mg/kg) and n-hexane (40 and 60 mg/kg) fractions of S. angustifolium were administered for 21 days intraperitoneally before scopolamine injection (2 mg/kg) on day 21. Rivastigmine was administered for 3 weeks intraperitoneally as well. Then, cognitive function was evaluated by three behavioral tests: passive avoidance, object recognition, and the Morris Water Maze test. Findings/Results Scopolamine induced memory impairment and rivastigmine significantly reversed the memory dysfunction in all three tests. Hydroalcoholic extract and methanolic fraction significantly reversed scopolamine-induced memory impairment in passive avoidance by 64% and 55% and enhanced the recognition index in the object recognition test. In the Morris water maze test probe trial and training session, on days 3 and 4, the hydroalcoholic extract showed a significant decrease in time spent in the target quadrant and path length, respectively. Also, hydroalcoholic extract and methanolic fraction decreased escape latency time in training sessions on days 3 and 4, by 50% and 31% in comparison to scopolamine. N-hexane fractions had no significant effect on scopolamine-induced cognitive impairment. Conclusion and implications Although the n-hexane fraction wasn't effective, the administration of hydroalcoholic extract and the methanolic fraction of S. angustifolium enhanced scopolamine-induced memory impairment.
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Affiliation(s)
- Azin Hassanzadeh
- Department of Pharmacology and Toxicology and Isfahan Pharmaceutical Research Centre, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Afsaneh Yegdaneh
- Department of Pharmacognosy, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Mohammad Rabbani
- Department of Pharmacology and Toxicology and Isfahan Pharmaceutical Research Centre, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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10
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Andrades E, Toll A, Deza G, Segura S, Gimeno R, Espadas G, Sabidó E, Haro N, Pozo ÓJ, Bódalo M, Torres P, Pujol RM, Hernández-Muñoz I. Loss of dyskerin facilitates the acquisition of metastatic traits by altering the mevalonate pathway. Life Sci Alliance 2023; 6:e202201692. [PMID: 36732018 PMCID: PMC9899484 DOI: 10.26508/lsa.202201692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 02/04/2023] Open
Abstract
The initial dissemination of cancer cells from many primary tumors implies intravasation to lymphatic nodes or blood vessels. To investigate the mechanisms involved, we analyzed the expression of small non-coding RNAs in cutaneous squamous cell carcinoma (cSCC), a prevalent tumor that mainly spreads to lymph nodes. We report the reduced expression of small nucleolar RNAs in primary cSCCs that metastasized when compared to non-metastasizing cSCCs, and the progressive loss of DKC1 (dyskerin, which stabilizes the small nucleolar RNAs) along the metastasis. DKC1 depletion in cSCC cells triggered lipid metabolism by altering the mevalonate pathway and the acquisition of metastatic traits. Treatment of DKC1-depleted cells with simvastatin, an inhibitor of the mevalonate pathway, blocked the expression of proteins involved in the epithelial-to-mesenchymal transition. Consistently, the expression of the enzyme 3-hydroxy-3-methylglutaryl-CoA synthase 1 was associated with pathological features of high metastatic risk in cSCC patients. Our data underpin the relevance of the mevalonate metabolism in metastatic dissemination and pave the possible incorporation of therapeutic approaches among the antineoplastic drugs used in routine patient care.
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Affiliation(s)
- Evelyn Andrades
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Agustí Toll
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, University of Barcelona and Institut d'Investigacions Biomèdiques August Pi i Sunyer; Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Gustavo Deza
- Department of Dermatology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Sonia Segura
- Department of Dermatology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Ramón Gimeno
- Laboratory of Immunology, Department of Pathology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Guadalupe Espadas
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Noemí Haro
- Applied Metabolomics Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Óscar J Pozo
- Applied Metabolomics Research Group, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Marta Bódalo
- MARGenomics, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Paloma Torres
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Ramon M Pujol
- Department of Dermatology, Hospital del Mar, Parc de Salut Mar, Barcelona, Spain
| | - Inmaculada Hernández-Muñoz
- Group of Inflammatory and Neoplastic Dermatological Diseases, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
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11
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Nir R, Hoernes TP, Muramatsu H, Faserl K, Karikó K, Erlacher MD, Sas-Chen A, Schwartz S. A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA. Nucleic Acids Res 2022; 50:4900-4916. [PMID: 35536311 PMCID: PMC9122591 DOI: 10.1093/nar/gkac347] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 04/18/2022] [Accepted: 04/24/2022] [Indexed: 12/25/2022] Open
Abstract
RNA can be extensively modified post-transcriptionally with >170 covalent modifications, expanding its functional and structural repertoire. Pseudouridine (Ψ), the most abundant modified nucleoside in rRNA and tRNA, has recently been found within mRNA molecules. It remains unclear whether pseudouridylation of mRNA can be snoRNA-guided, bearing important implications for understanding the physiological target spectrum of snoRNAs and for their potential therapeutic exploitation in genetic diseases. Here, using a massively parallel reporter based strategy we simultaneously interrogate Ψ levels across hundreds of synthetic constructs with predesigned complementarity against endogenous snoRNAs. Our results demonstrate that snoRNA-mediated pseudouridylation can occur on mRNA targets. However, this is typically achieved at relatively low efficiencies, and is constrained by mRNA localization, snoRNA expression levels and the length of the snoRNA:mRNA complementarity stretches. We exploited these insights for the design of snoRNAs targeting pseudouridylation at premature termination codons, which was previously shown to suppress translational termination. However, in this and follow-up experiments in human cells we observe no evidence for significant levels of readthrough of pseudouridylated stop codons. Our study enhances our understanding of the scope, 'design rules', constraints and consequences of snoRNA-mediated pseudouridylation.
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Affiliation(s)
- Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Thomas Philipp Hoernes
- Institute of Genomics and RNomics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Hiromi Muramatsu
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Klaus Faserl
- Institute of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Katalin Karikó
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA.,BioNTech RNA Pharmaceuticals, Mainz, Germany
| | | | - Aldema Sas-Chen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.,The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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12
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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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13
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Talross GJS, Deryusheva S, Gall JG. Stable lariats bearing a snoRNA (slb-snoRNA) in eukaryotic cells: A level of regulation for guide RNAs. Proc Natl Acad Sci U S A 2021; 118:e2114156118. [PMID: 34725166 PMCID: PMC8609340 DOI: 10.1073/pnas.2114156118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2021] [Indexed: 12/31/2022] Open
Abstract
Small nucleolar (sno)RNAs guide posttranscriptional modifications essential for the biogenesis and function of their target. The majority of snoRNAs in higher eukaryotes are encoded within introns. They are first released from nascent transcripts in the form of a lariat and rapidly targeted by the debranching enzyme and nuclear exonucleases for linearization and further trimming. In this study, we report that some snoRNAs are encoded within unusually stable intronic RNAs. These intronic sequences can escape the debranching enzyme and accumulate as lariats. Stable lariats bearing a snoRNA, or slb-snoRNA, are associated with snoRNA binding proteins but do not guide posttranscriptional modification. While most slb-snoRNAs accumulate in the nucleus, some can be exported to the cytoplasm. We find that this export competes with snoRNA maturation. Slb-snoRNAs provide a previously unknown layer of regulation to snoRNA and snoRNA binding proteins.
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Affiliation(s)
- Gaëlle J S Talross
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
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14
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Fitz NF, Wang J, Kamboh MI, Koldamova R, Lefterov I. Small nucleolar RNAs in plasma extracellular vesicles and their discriminatory power as diagnostic biomarkers of Alzheimer's disease. Neurobiol Dis 2021; 159:105481. [PMID: 34411703 PMCID: PMC9382696 DOI: 10.1016/j.nbd.2021.105481] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
The clinical diagnosis of Alzheimer's disease, at its early stage, remains a difficult task. Advanced imaging technologies and laboratory assays to detect Aβ peptides Aβ42 and Aβ40, total and phosphorylated tau in CSF provide a set of biomarkers of developing AD brain pathology and facilitate the diagnostic process. The search for biofluid biomarkers, other than in CSF, and the development of biomarker assays have accelerated significantly and now represent the fastest-growing field in AD research. The goal of this study was to determine the differential enrichment of noncoding RNAs (ncRNAs) in plasma-derived extracellular vesicles (EV) of AD patients and Cognitively Normal controls (NC). Using RNA-seq, we profiled four significant classes of ncRNAs: miRNAs, snoRNAs, tRNAs, and piRNAs. We report a significant enrichment of SNORDs - a group of snoRNAs, in AD samples compared to NC. To verify the differential enrichment of two clusters of SNORDs - SNORD115 and SNORD116, localized on human chromosome 15q11-q13, we used plasma samples of an independent group of AD patients and NC. We applied ddPCR technique and identified SNORD115 and SNORD116 with a high discriminatory power to differentiate AD samples from NC. The results of our study present evidence that AD is associated with changes in the enrichment of SNORDs, transcribed from imprinted genomic loci, in plasma EV and provide a rationale to further explore the validity of those SNORDs as plasma biomarkers of AD.
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Affiliation(s)
- Nicholas F Fitz
- Department of Environmental & Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
| | - Jiebiao Wang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
| | - M Ilyas Kamboh
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
| | - Radosveta Koldamova
- Department of Environmental & Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America.
| | - Iliya Lefterov
- Department of Environmental & Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States of America.
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15
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Kumari K, Groza P, Aguilo F. Regulatory roles of RNA modifications in breast cancer. NAR Cancer 2021; 3:zcab036. [PMID: 34541538 PMCID: PMC8445368 DOI: 10.1093/narcan/zcab036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Collectively referred to as the epitranscriptome, RNA modifications play important roles in gene expression control regulating relevant cellular processes. In the last few decades, growing numbers of RNA modifications have been identified not only in abundant ribosomal (rRNA) and transfer RNA (tRNA) but also in messenger RNA (mRNA). In addition, many writers, erasers and readers that dynamically regulate the chemical marks have also been characterized. Correct deposition of RNA modifications is prerequisite for cellular homeostasis, and its alteration results in aberrant transcriptional programs that dictate human disease, including breast cancer, the most frequent female malignancy, and the leading cause of cancer-related death in women. In this review, we emphasize the major RNA modifications that are present in tRNA, rRNA and mRNA. We have categorized breast cancer-associated chemical marks and summarize their contribution to breast tumorigenesis. In addition, we describe less abundant tRNA modifications with related pathways implicated in breast cancer. Finally, we discuss current limitations and perspectives on epitranscriptomics for use in therapeutic strategies against breast and other cancers.
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Affiliation(s)
- Kanchan Kumari
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Paula Groza
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden
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16
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Kovalenko TF, Larionova TD, Antipova NV, Shakhparonov MI, Pavlyukov MS. The Role of Non-coding RNAs in the Pathogenesis of Glial Tumors. Acta Naturae 2021; 13:38-51. [PMID: 34707896 PMCID: PMC8526181 DOI: 10.32607/actanaturae.11270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 11/25/2022] Open
Abstract
Among the many malignant neoplasms, glioblastoma (GBM) leads to one of the worst prognosis for patients and has an almost 100% recurrence rate. The only chemotherapeutic drug that is widely used for treating glioblastoma is temozolomide, a DNA alkylating agent. Its impact, however, is only minor; it increases patients' survival just by 12 to 14 months. Multiple highly selective compounds that affect specific proteins and have performed well in other types of cancer have proved ineffective against glioblastoma. Hence, there is an urgent need for novel methods that could help achieve the long-awaited progress in glioblastoma treatment. One of the potentially promising approaches is the targeting of non-coding RNAs (ncRNAs). These molecules are characterized by extremely high multifunctionality and often act as integrators by coordinating multiple key signaling pathways within the cell. Thus, the impact on ncRNAs has the potential to lead to a broader and stronger impact on cells, as opposed to the more focused action of inhibitors targeting specific proteins. In this review, we summarize the functions of long noncoding RNAs, circular RNAs, as well as microRNAs, PIWI-interacting RNAs, small nuclear and small nucleolar RNAs. We provide a classification of these transcripts and describe their role in various signaling pathways and physiological processes. We also provide examples of oncogenic and tumor suppressor ncRNAs belonging to each of these classes in the context of their involvement in the pathogenesis of gliomas and glioblastomas. In conclusion, we considered the potential use of ncRNAs as diagnostic markers and therapeutic targets for the treatment of glioblastoma.
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Affiliation(s)
- T. F. Kovalenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
| | - T. D. Larionova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
| | - N. V. Antipova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
| | - M. I. Shakhparonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
| | - M. S. Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, 117997 Russia
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17
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Kitamura K, Nimura K. Regulation of RNA Splicing: Aberrant Splicing Regulation and Therapeutic Targets in Cancer. Cells 2021; 10:923. [PMID: 33923658 PMCID: PMC8073995 DOI: 10.3390/cells10040923] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/16/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023] Open
Abstract
RNA splicing is a critical step in the maturation of precursor mRNA (pre-mRNA) by removing introns and exons. The combination of inclusion and exclusion of introns and exons in pre-mRNA can generate vast diversity in mature mRNA from a limited number of genes. Cancer cells acquire cancer-specific mechanisms through aberrant splicing regulation to acquire resistance to treatment and to promote malignancy. Splicing regulation involves many factors, such as proteins, non-coding RNAs, and DNA sequences at many steps. Thus, the dysregulation of splicing is caused by many factors, including mutations in RNA splicing factors, aberrant expression levels of RNA splicing factors, small nuclear ribonucleoproteins biogenesis, mutations in snRNA, or genomic sequences that are involved in the regulation of splicing, such as 5' and 3' splice sites, branch point site, splicing enhancer/silencer, and changes in the chromatin status that affect the splicing profile. This review focuses on the dysregulation of RNA splicing related to cancer and the associated therapeutic methods.
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Affiliation(s)
- Koji Kitamura
- Division of Gene Therapy Science, Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan;
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Keisuke Nimura
- Division of Gene Therapy Science, Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan;
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18
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Breuer R, Gomes-Filho JV, Randau L. Conservation of Archaeal C/D Box sRNA-Guided RNA Modifications. Front Microbiol 2021; 12:654029. [PMID: 33776983 PMCID: PMC7994747 DOI: 10.3389/fmicb.2021.654029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/19/2021] [Indexed: 12/18/2022] Open
Abstract
Post-transcriptional modifications fulfill many important roles during ribosomal RNA maturation in all three domains of life. Ribose 2'-O-methylations constitute the most abundant chemical rRNA modification and are, for example, involved in RNA folding and stabilization. In archaea, these modification sites are determined by variable sets of C/D box sRNAs that guide the activity of the rRNA 2'-O-methyltransferase fibrillarin. Each C/D box sRNA contains two guide sequences that can act in coordination to bridge rRNA sequences. Here, we will review the landscape of archaeal C/D box sRNA genes and their target sites. One focus is placed on the apparent accelerated evolution of guide sequences and the varied pairing of the two individual guides, which results in different rRNA modification patterns and RNA chaperone activities.
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Affiliation(s)
| | | | - Lennart Randau
- Prokaryotic RNA Biology, Philipps-Universität Marburg, Marburg, Germany
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19
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Tallo CA, Duncan LH, Yamamoto AH, Slaydon JD, Arya GH, Turlapati L, Mackay TFC, Carbone MA. Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy. G3 (BETHESDA, MD.) 2021; 11:jkaa014. [PMID: 33561224 PMCID: PMC7849908 DOI: 10.1093/g3journal/jkaa014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/16/2020] [Indexed: 11/13/2022]
Abstract
In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.
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Affiliation(s)
- Christian A Tallo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Laura H Duncan
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Akihiko H Yamamoto
- The Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Joshua D Slaydon
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Gunjan H Arya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- The Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
| | - Mary A Carbone
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- The Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695-7244, USA
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20
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Tallo CA, Duncan LH, Yamamoto AH, Slaydon JD, Arya GH, Turlapati L, Mackay TFC, Carbone MA. Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy. G3 (BETHESDA, MD.) 2021. [PMID: 33561224 DOI: 10.1093/g3journal/jkaa014.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans.
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Affiliation(s)
- Christian A Tallo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Laura H Duncan
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Akihiko H Yamamoto
- The Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Joshua D Slaydon
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Gunjan H Arya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Lavanya Turlapati
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Trudy F C Mackay
- The Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC 29646, USA
| | - Mary A Carbone
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA.,The Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695-7244, USA
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21
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Alghamdi MA, AL-Eitan LN, Tarkhan AH, Al-Qarqaz FA. Global gene methylation profiling of common warts caused by human papillomaviruses infection. Saudi J Biol Sci 2021; 28:612-622. [PMID: 33424347 PMCID: PMC7783806 DOI: 10.1016/j.sjbs.2020.10.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022] Open
Abstract
Infection with the human papillomaviruses (HPV) often involves the epigenetic modification of the host genome. Despite its prevalence among the population, host genome methylation in HPV-induced warts is not clearly understood. In this study, genome-wide methylation profiling was carried out on paired healthy skin and wart samples in order to investigate the effects that benign HPV infection has on gene methylation status. To overcome this gap in knowledge, paired wart (n = 12) and normal skin (n = 12) samples were obtained from Arab males in order to perform DNA extraction and subsequent genome-wide methylation profiling on the Infinium Methylation EPIC Bead Chip microarray. Analysis of differential methylation revealed a clear pattern of discrimination between the wart and normal skin samples. In warts, the most differentially methylated (DM) genes included long non-coding RNAs (AC005884, AL049646.2, AC126121.2, AP001790.1, and AC107959.3), microRNAs (MIR374B, MIR596, MIR1255B1, MIR26B, and MIR196A2),snoRNAs (SNORD114-22, SNORD70, and SNORD114-31), pseudogenes (AC069366.1, RNU4ATAC11P, AC120057.1, NANOGP3, AC106038.2, TPT1P2, SDC4P, PKMP3, and VN2R3P), and protein-coding genes (AREG, GJB2, C12orf71, AC020909.2, S100A8, ZBED2, FABP7, and CYSLTR1). In addition, pathway analysis revealed that, among the most differentially methylated genes, STAT5A, RARA, MEF2D, MAP3K8, and THRA were the common regulators. It can be observed that HPV-induced warts involve a clear and unique epigenetic alteration to the host genome.
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Affiliation(s)
- Mansour A. Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
- Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
| | - Laith N. AL-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Amneh H. Tarkhan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Firas A. Al-Qarqaz
- Department of Internal Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
- Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital Jordan University of Science and Technology, Irbid 22110, Jordan
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22
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Aznaourova M, Schmerer N, Schmeck B, Schulte LN. Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci. Front Genet 2020; 11:527484. [PMID: 33329688 PMCID: PMC7735109 DOI: 10.3389/fgene.2020.527484] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.
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Affiliation(s)
- Marina Aznaourova
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Nils Schmerer
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany
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23
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Peffers MJ, Chabronova A, Balaskas P, Fang Y, Dyer P, Cremers A, Emans PJ, Feczko PZ, Caron MM, Welting TJM. SnoRNA signatures in cartilage ageing and osteoarthritis. Sci Rep 2020; 10:10641. [PMID: 32606371 PMCID: PMC7326970 DOI: 10.1038/s41598-020-67446-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/08/2020] [Indexed: 01/23/2023] Open
Abstract
Osteoarthritis presents as a change in the chondrocyte phenotype and an imbalance between anabolic and catabolic processes. Age affects its onset and progression. Small nucleolar RNAs (SnoRNAs) direct chemical modification of RNA substrates to fine-tune spliceosomal and rRNA function, accommodating changing requirements for splicing and protein synthesis during health and disease. Articular cartilage from young, old and OA knees was used in a microarray study to identify alterations in snoRNA expression. Changes in snoRNAs in osteoarthritis-like conditions were studied in chondrocytes using interleukin-1 and osteoarthritic synovial fluid. SNORD26 and SNORD96A knockdown and overexpression were undertaken using antisense oligonucleotides and overexpression plasmids. We identified panels of snoRNAs differentially expressed due to ageing (including SNORD96A, SNORD44) and osteoarthritis (including SNORD26 and SNORD116). In vitro experiments using osteoarthritis-like conditions affected snoRNA expression. Knockdown or overexpression of SNORD26 or SNORD96A resulted in changes in chondrogenic, hypertrophic, rRNA and osteoarthritis related gene expression. We demonstrate that snoRNA expression changes in cartilage ageing, and osteoarthritis and in osteoarthritis-like conditions, and when the expression of these snoRNAs is altered this affects chondrogenic and hypertrophic gene expression. Thus, we propose an additional dimension in the molecular mechanisms underlying cartilage ageing and osteoarthritis through the dysregulation of snoRNAs.
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Affiliation(s)
- Mandy J Peffers
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - Alzbeta Chabronova
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, 6202 AZ, Maastricht, The Netherlands
| | - Panagiotis Balaskas
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Philip Dyer
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Andy Cremers
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, 6202 AZ, Maastricht, The Netherlands
| | - Pieter J Emans
- Department of Orthopaedic Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Peter Z Feczko
- Department of Orthopaedic Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marjolein M Caron
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, 6202 AZ, Maastricht, The Netherlands
| | - Tim J M Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Centre, 6202 AZ, Maastricht, The Netherlands.,Department of Orthopaedic Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
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24
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Godel M, Morena D, Ananthanarayanan P, Buondonno I, Ferrero G, Hattinger CM, Di Nicolantonio F, Serra M, Taulli R, Cordero F, Riganti C, Kopecka J. Small Nucleolar RNAs Determine Resistance to Doxorubicin in Human Osteosarcoma. Int J Mol Sci 2020; 21:ijms21124500. [PMID: 32599901 PMCID: PMC7349977 DOI: 10.3390/ijms21124500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 02/07/2023] Open
Abstract
Doxorubicin (Dox) is one of the most important first-line drugs used in osteosarcoma therapy. Multiple and not fully clarified mechanisms, however, determine resistance to Dox. With the aim of identifying new markers associated with Dox-resistance, we found a global up-regulation of small nucleolar RNAs (snoRNAs) in human Dox-resistant osteosarcoma cells. We investigated if and how snoRNAs are linked to resistance. After RT-PCR validation of snoRNAs up-regulated in osteosarcoma cells with different degrees of resistance to Dox, we overexpressed them in Dox-sensitive cells. We then evaluated Dox cytotoxicity and changes in genes relevant for osteosarcoma pathogenesis by PCR arrays. SNORD3A, SNORA13 and SNORA28 reduced Dox-cytotoxicity when over-expressed in Dox-sensitive cells. In these cells, GADD45A and MYC were up-regulated, TOP2A was down-regulated. The same profile was detected in cells with acquired resistance to Dox. GADD45A/MYC-silencing and TOP2A-over-expression counteracted the resistance to Dox induced by snoRNAs. We reported for the first time that snoRNAs induce resistance to Dox in human osteosarcoma, by modulating the expression of genes involved in DNA damaging sensing, DNA repair, ribosome biogenesis, and proliferation. Targeting snoRNAs or down-stream genes may open new treatment perspectives in chemoresistant osteosarcomas.
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Affiliation(s)
- Martina Godel
- Department of Oncology, University of Torino, 1026 Torino, Italy; (M.G.); (D.M.); (P.A.); (I.B.); (F.D.N.); (R.T.)
| | - Deborah Morena
- Department of Oncology, University of Torino, 1026 Torino, Italy; (M.G.); (D.M.); (P.A.); (I.B.); (F.D.N.); (R.T.)
| | - Preeta Ananthanarayanan
- Department of Oncology, University of Torino, 1026 Torino, Italy; (M.G.); (D.M.); (P.A.); (I.B.); (F.D.N.); (R.T.)
| | - Ilaria Buondonno
- Department of Oncology, University of Torino, 1026 Torino, Italy; (M.G.); (D.M.); (P.A.); (I.B.); (F.D.N.); (R.T.)
| | - Giulio Ferrero
- Department of Computer Science, University of Torino, 10149 Torino, Italy; (G.F.); (F.C.)
- Department of Clinical and Biological Sciences, University of Torino, 10043 Orbassano, Italy
| | - Claudia M. Hattinger
- Laboratory of Experimental Oncology, Pharmacogenomics and Pharmacogenetics Research Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (C.M.H.); (M.S.)
| | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, 1026 Torino, Italy; (M.G.); (D.M.); (P.A.); (I.B.); (F.D.N.); (R.T.)
- Candiolo Cancer Institute, FPO–IRCCS, 10060 Candiolo, Italy
| | - Massimo Serra
- Laboratory of Experimental Oncology, Pharmacogenomics and Pharmacogenetics Research Unit, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy; (C.M.H.); (M.S.)
| | - Riccardo Taulli
- Department of Oncology, University of Torino, 1026 Torino, Italy; (M.G.); (D.M.); (P.A.); (I.B.); (F.D.N.); (R.T.)
| | - Francesca Cordero
- Department of Computer Science, University of Torino, 10149 Torino, Italy; (G.F.); (F.C.)
| | - Chiara Riganti
- Department of Oncology, University of Torino, 1026 Torino, Italy; (M.G.); (D.M.); (P.A.); (I.B.); (F.D.N.); (R.T.)
- Correspondence: (C.R.); (J.K.); Tel.: +39-0116705857 (C.R.); +39-0116705849 (J.K.)
| | - Joanna Kopecka
- Department of Oncology, University of Torino, 1026 Torino, Italy; (M.G.); (D.M.); (P.A.); (I.B.); (F.D.N.); (R.T.)
- Correspondence: (C.R.); (J.K.); Tel.: +39-0116705857 (C.R.); +39-0116705849 (J.K.)
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25
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Kakihara Y, Kiguchi T, Ohazama A, Saeki M. R2TP/PAQosome as a promising chemotherapeutic target in cancer. JAPANESE DENTAL SCIENCE REVIEW 2020; 56:38-42. [PMID: 31890057 PMCID: PMC6926247 DOI: 10.1016/j.jdsr.2019.08.001] [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: 06/27/2019] [Revised: 07/27/2019] [Accepted: 08/21/2019] [Indexed: 11/30/2022] Open
Abstract
R2TP/PAQosome (particle for arrangement of quaternary structure) is a novel multisubunit chaperone specialized in the assembly/maturation of protein complexes that are involved in essential cellular processes such as PIKKs (phosphatidylinositol 3-kinase-like kinases) signaling, snoRNP (small nucleolar ribonucleoprotein) biogenesis, and RNAP II (RNA polymerase II) complex formation. In this review article, we describe the current understanding of R2TP/PAQosome functions and characteristics as well as how the chaperone complex is involved in oncogenesis, highlighting DNA damage response, mTOR (mammalian target of rapamycin) pathway as well as snoRNP biogenesis. Also, we discuss its possible involvement in HNSCC (head and neck squamous cell carcinoma) including OSCC (oral squamous cell carcinoma). Finally, we provide an overview of current anti-cancer drug development efforts targeting R2TP/PAQosome.
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Affiliation(s)
- Yoshito Kakihara
- Division of Dental Pharmacology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tetsuo Kiguchi
- Division of Dental Pharmacology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Atsushi Ohazama
- Division of Oral Anatomy, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Makio Saeki
- Division of Dental Pharmacology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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26
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Lefterov I, Wolfe CM, Fitz NF, Nam KN, Letronne F, Biedrzycki RJ, Kofler J, Han X, Wang J, Schug J, Koldamova R. APOE2 orchestrated differences in transcriptomic and lipidomic profiles of postmortem AD brain. Alzheimers Res Ther 2019; 11:113. [PMID: 31888770 PMCID: PMC6937981 DOI: 10.1186/s13195-019-0558-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND The application of advanced sequencing technologies and improved mass-spectrometry platforms revealed significant changes in gene expression and lipids in Alzheimer's disease (AD) brain. The results so far have prompted further research using "multi-omics" approaches. These approaches become particularly relevant, considering the inheritance of APOEε4 allele as a major genetic risk factor of AD, disease protective effect of APOEε2 allele, and a major role of APOE in brain lipid metabolism. METHODS Postmortem brain samples from inferior parietal lobule genotyped as APOEε2/c (APOEε2/carriers), APOEε3/3, and APOEε4/c (APOEε4/carriers), age- and gender-matched, were used to reveal APOE allele-associated changes in transcriptomes and lipidomes. Differential gene expression and co-expression network analyses were applied to identify up- and downregulated Gene Ontology (GO) terms and pathways for correlation to lipidomics data. RESULTS Significantly affected GO terms and pathways were determined based on the comparisons of APOEε2/c datasets to those of APOEε3/3 and APOEε4/c brain samples. The analysis of lists of genes in highly correlated network modules and of those differentially expressed demonstrated significant enrichment in GO terms associated with genes involved in intracellular proteasomal and lysosomal degradation of proteins, protein aggregates and organelles, ER stress, and response to unfolded protein, as well as mitochondrial function, electron transport, and ATP synthesis. Small nucleolar RNA coding units important for posttranscriptional modification of mRNA and therefore translation and protein synthesis were upregulated in APOEε2/c brain samples compared to both APOEε3/3 and APOEε4/c. The analysis of lipidomics datasets revealed significant changes in ten major lipid classes (exclusively a decrease in APOEε4/c samples), most notably non-bilayer-forming phosphatidylethanolamine and phosphatidic acid, as well as mitochondrial membrane-forming lipids. CONCLUSIONS The results of this study, despite the advanced stage of AD, point to the significant differences in postmortem brain transcriptomes and lipidomes, suggesting APOE allele associated differences in pathogenic mechanisms. Correlations within and between lipidomes and transcriptomes indicate coordinated effects of changes in the proteasomal system and autophagy-canonical and selective, facilitating intracellular degradation, protein entry into ER, response to ER stress, nucleolar modifications of mRNA, and likely myelination in APOEε2/c brains. Additional research and a better knowledge of the molecular mechanisms of proteostasis in the early stages of AD are required to develop more effective diagnostic approaches and eventually efficient therapeutic strategies.
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Affiliation(s)
- Iliya Lefterov
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA.
| | - Cody M Wolfe
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Nicholas F Fitz
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Kyong Nyon Nam
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Florent Letronne
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Richard J Biedrzycki
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Xianlin Han
- Department of Medicine & Biochemistry, Barshop Institute for Longevity and Aging Studies, UT Health-San Antonio, San Antonio, TX, 78229, USA
| | - Jianing Wang
- Department of Medicine & Biochemistry, Barshop Institute for Longevity and Aging Studies, UT Health-San Antonio, San Antonio, TX, 78229, USA
| | - Jonathan Schug
- Department of Genetics, Functional Genomics Core, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Radosveta Koldamova
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA.
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27
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Rahman MM, Lai YC, Husna AA, Chen HW, Tanaka Y, Kawaguchi H, Hatai H, Miyoshi N, Nakagawa T, Fukushima R, Miura N. Aberrantly expressed snoRNA, snRNA, piRNA and tRFs in canine melanoma. Vet Comp Oncol 2019; 18:353-361. [PMID: 31769925 DOI: 10.1111/vco.12558] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
Among small non-coding RNAs (sncRNAs/sRNAs), the functional regulation of microRNAs (miRNAs) has been studied in canine oral melanoma (COM). However, the expression level of other sncRNAs, like small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), transfer RNA-derived fragments (tRFs) and PIWI-interacting RNAs (piRNAs), in COM is unknown. The aim of this study was to investigate sncRNAs other than miRNAs in COM from our small RNA sequencing project (PRJNA516252). We found that several snRNAs and piRNAs were upregulated, whereas tRFs and snoRNAs were downregulated in COM. Upregulation of U1 snRNA and piR-972, and downregulation of tRNA-ser (1) and snoRA24 was confirmed in dog melanoma tissue and cell lines by quantitative reverse transcription PCR. Consistently, the expression of tRNA-ser (1) and snoRA24 in plasma of COM cases was also decreased. Finally, we found a similar expression trend of U1 and snoRA24 in the human cutaneous melanoma cell line, MEWO, compared with human epidermal melanocyte cells (HEMa-Lp). In our study, snRNA, snoRNA, tRFs and piRNA were dysregulated during melanoma progression. Moreover, the melanoma-associated expression of U1 and snoRA24 was similar in human and dog melanoma.
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Affiliation(s)
- Md Mahfuzur Rahman
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Yu-Chang Lai
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Al Asmaul Husna
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Hui-Wen Chen
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Yuiko Tanaka
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Kawaguchi
- Hygiene and Health Promotion Medicine, Kagoshima University Graduate School of Medicine and Dental Science, Kagoshima, Japan
| | - Hitoshi Hatai
- Department of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Noriaki Miyoshi
- Department of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Takayuki Nakagawa
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryuji Fukushima
- Animal Medical Centre, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Naoki Miura
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan.,Joint Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
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28
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Abel Y, Rederstorff M. SnoRNAs and the emerging class of sdRNAs: Multifaceted players in oncogenesis. Biochimie 2019; 164:17-21. [DOI: 10.1016/j.biochi.2019.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023]
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