1
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Zacchini F, Barozzi C, Venturi G, Montanaro L. How snoRNAs can contribute to cancer at multiple levels. NAR Cancer 2024; 6:zcae005. [PMID: 38406265 PMCID: PMC10894041 DOI: 10.1093/narcan/zcae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
snoRNAs are a class of non-coding RNAs known to guide site specifically RNA modifications such as 2'-O-methylation and pseudouridylation. Recent results regarding snoRNA alterations in cancer has been made available and suggest their potential evaluation as diagnostic and prognostic biomarkers. A large part of these data, however, was not consistently confirmed and failed to provide mechanistic insights on the contribution of altered snoRNA expression to the neoplastic process. Here, we aim to critically review the available literature on snoRNA in cancer focusing on the studies elucidating the functional consequences of their deregulation. Beyond the canonical guide function in RNA processing and modification we also considered additional roles in which snoRNA, in various forms and through different modalities, are involved and that have been recently reported.
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Affiliation(s)
- Federico Zacchini
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Chiara Barozzi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
| | - Giulia Venturi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Lorenzo Montanaro
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
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2
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Dong J, Wang H, Zhang Z, Yang L, Qian X, Qian W, Han Y, Huang H, Qian P. Small but strong: Pivotal roles and potential applications of snoRNAs in hematopoietic malignancies. Front Oncol 2022; 12:939465. [PMID: 36033520 PMCID: PMC9413531 DOI: 10.3389/fonc.2022.939465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) belong to a family of noncoding RNAs that are 60-300 nucleotides in length, and they are classified into two classes according to their structure and function: C/D box snoRNAs, playing an essential role in 2’-O-methylation modification on ribosomal RNA; H/ACA box snoRNAs, involved in the pseudouridylation of rRNA. SnoRNAs with unclear functions, no predictable targets, and unusual subcellular locations are called orphan snoRNAs. Recent studies have revealed abnormal expression and demonstrated the pivotal roles of snoRNAs and their host genes in various types of hematological malignancies. This review discusses recent discoveries concerning snoRNAs in a variety of hematological malignancies, including multiple myeloma, lymphoma and leukemia, and sheds light on the application of snoRNAs as diagnostic and prognostic markers as well as therapeutic targets of hematological malignancies in the future.
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Affiliation(s)
- Jian Dong
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Hui Wang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Zhaoru Zhang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Lin Yang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Xinyue Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Wenchang Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Yingli Han
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - He Huang
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Pengxu Qian, ; He Huang,
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
- *Correspondence: Pengxu Qian, ; He Huang,
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3
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Bortolin-Cavaillé ML, Quillien A, Thalalla Gamage S, Thomas J, Sas-Chen A, Sharma S, Plisson-Chastang C, Vandel L, Blader P, Lafontaine DLJ, Schwartz S, Meier J, Cavaillé J. Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution. Nucleic Acids Res 2022; 50:6284-6299. [PMID: 35648437 PMCID: PMC9226516 DOI: 10.1093/nar/gkac404] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/28/2022] [Accepted: 05/31/2022] [Indexed: 01/06/2023] Open
Abstract
NAT10 is an essential enzyme that catalyzes N4-acetylcytidine (ac4C) in eukaryotic transfer RNA and 18S ribosomal RNA. Recent studies suggested that rRNA acetylation is dependent on SNORD13, a box C/D small nucleolar RNA predicted to base-pair with 18S rRNA via two antisense elements. However, the selectivity of SNORD13-dependent cytidine acetylation and its relationship to NAT10's essential function remain to be defined. Here, we demonstrate that SNORD13 is required for acetylation of a single cytidine of human and zebrafish 18S rRNA. In-depth characterization revealed that SNORD13-dependent ac4C is dispensable for human cell growth, ribosome biogenesis, translation and development. This loss of function analysis inspired a cross-evolutionary survey of the eukaryotic rRNA acetylation 'machinery' that led to the characterization of many novel metazoan SNORD13 genes. This includes an atypical SNORD13-like RNA in Drosophila melanogaster which guides ac4C to 18S rRNA helix 45 despite lacking one of the two rRNA antisense elements. Finally, we discover that Caenorhabditis elegans 18S rRNA is not acetylated despite the presence of an essential NAT10 homolog. Our findings shed light on the molecular mechanisms underlying SNORD13-mediated rRNA acetylation across eukaryotic evolution and raise new questions regarding the biological and evolutionary relevance of this highly conserved rRNA modification.
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Affiliation(s)
- Marie-Line Bortolin-Cavaillé
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | | | | | - Justin M Thomas
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Aldema Sas-Chen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sunny Sharma
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041 Gosselies, Belgium
| | - Célia Plisson-Chastang
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Laurence Vandel
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Patrick Blader
- Molecular, Cellular and Developmental Biology (MCD), UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041 Gosselies, Belgium
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Jérôme Cavaillé
- To whom correspondence should be addressed. Tel: +33 561335927; Fax: +33 561335886;
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4
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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: 14] [Impact Index Per Article: 4.7] [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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5
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Calvo Sánchez J, Köhn M. Small but Mighty-The Emerging Role of snoRNAs in Hematological Malignancies. Noncoding RNA 2021; 7:68. [PMID: 34842767 PMCID: PMC8629011 DOI: 10.3390/ncrna7040068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Over recent years, the long known class of small nucleolar RNAs (snoRNAs) have gained interest among the scientific community, especially in the clinical context. The main molecular role of this interesting family of non-coding RNAs is to serve as scaffolding RNAs to mediate site-specific RNA modification of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). With the development of new sequencing techniques and sophisticated analysis pipelines, new members of the snoRNA family were identified and global expression patterns in disease backgrounds could be determined. We will herein shed light on the current research progress in snoRNA biology and their clinical role by influencing disease outcome in hematological diseases. Astonishingly, in recent studies snoRNAs emerged as potent biomarkers in a variety of these clinical setups, which is also highlighted by the frequent deregulation of snoRNA levels in the hema-oncological context. However, research is only starting to reveal how snoRNAs might influence cellular functions and the connected disease hallmarks in hematological malignancies.
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Affiliation(s)
| | - Marcel Köhn
- Junior Research Group ‘RBPs and ncRNAs in Human Diseases’, Medical Faculty, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Saale, Germany;
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6
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Separated Siamese Twins: Intronic Small Nucleolar RNAs and Matched Host Genes May be Altered in Conjunction or Separately in Multiple Cancer Types. Cells 2020; 9:cells9020387. [PMID: 32046192 PMCID: PMC7072173 DOI: 10.3390/cells9020387] [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: 01/10/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/15/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are non-coding RNAs involved in RNA modification and processing. Approximately half of the so far identified snoRNA genes map within the intronic regions of host genes, and their expression, as well as the expression of their host genes, is dependent on transcript splicing and maturation. Growing evidence indicates that mutations and/or deregulations that affect snoRNAs, as well as host genes, play a significant role in oncogenesis. Among the possible factors underlying snoRNA/host gene expression deregulation is copy number alteration (CNA). We analyzed the data available in The Cancer Genome Atlas database, relative to CNA and expression of 295 snoRNA/host gene couples in 10 cancer types, to understand whether the genetic or expression alteration of snoRNAs and their matched host genes would have overlapping trends. Our results show that, counterintuitively, copy number and expression alterations of snoRNAs and matched host genes are not necessarily coupled. In addition, some snoRNA/host genes are mutated and overexpressed recurrently in multiple cancer types. Our findings suggest that the differential contribution to cancer development of both snoRNAs and host genes should always be considered, and that snoRNAs and their host genes may contribute to cancer development in conjunction or independently.
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7
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lncRNA SNHG5 Modulates Endometrial Cancer Progression via the miR-25-3p/BTG2 Axis. JOURNAL OF ONCOLOGY 2019; 2019:7024675. [PMID: 31885582 PMCID: PMC6925730 DOI: 10.1155/2019/7024675] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/01/2019] [Accepted: 07/18/2019] [Indexed: 01/11/2023]
Abstract
Endometrial carcinoma (EC) is one of the most common malignancies of the female genital tract, although the mechanisms of EC initiation and development remain incompletely understood. In this study, we demonstrated that the noncoding RNA SNHG5 can inhibit the proliferation, migration, and invasion of EC cells by suppressing the expression of its putative target miR-25-3p. Overexpression of miR-25-3p significantly promoted the proliferation, migration, and invasion of EC cells. In addition, we showed that miR-25-3p represses the expression of BTG2 by directly binding to the 3′-UTR of BTG2 mRNA. Furthermore, increased miR-25-3p expression and decreased SNHG5 and BTG2 expression were observed in EC tissues, and the expression of SNHG5 was negatively correlated to that of miR-25-3p but positively correlated to that of BTG2. In summary, for the first time, we report that the SNHG5/miR-25-3p/BTG2 axis plays an important role in EC progression and is of great potential clinical significance for EC diagnosis and therapy.
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8
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Liu X, Wang M, Cui Y. LncRNA TP73-AS1 interacted with miR-141-3p to promote the proliferation of non-small cell lung cancer. Arch Med Sci 2019; 15:1547-1554. [PMID: 31749884 PMCID: PMC6855159 DOI: 10.5114/aoms.2019.86820] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 07/25/2017] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION Recent studies have shown that long non-coding RNAs (lncRNAs) are involved in a variety of biological processes and diseases in humans, including cancer. However, the exact effects and molecular mechanisms of TP73-AS1 in non-small cell lung cancer (NSCLC) progression are still unknown. The present study is aimed to reveal the detailed functions and the mechanism of TP73-AS1 in the regulation of NSCLC cell proliferation. MATERIAL AND METHODS TP73-AS1 expression in NSCLC tissues and cell lines was determined using real-time PCR assays. The functions of TP73-AS1 in the regulation of NSCLC cell proliferation was evaluated using BrdU assays. The interaction between TP73-AS1 and miR-141-3p was confirmed using luciferase report gene assays. RESULTS TP73-AS1 was upregulated in NSCLC tissues and cell lines. However, when knockdown of TP73-AS1 inhibited the NSCLC proliferation. By using online tools, we screened out miR-141-3p may combined with TP73-AS1. With use of luciferase assays, we confirmed that miR-141-3p could directly bind to TP73-AS1. In NSCLC tissues, miR-141-3p was down-regulated; TP73-AS1 was inversely correlated with miR-141-3p. CONCLUSIONS Our data suggest that TP73-AS1 might be an oncogenic lncRNA that promotes proliferation of NSCLC and might be regarded as a therapeutic target in NSCLC.
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Affiliation(s)
- Xinfa Liu
- Department of Respiration, Hebei Provincial Hospital of Traditional Chinese Medicine, Shi Jiazhuang, China
| | - Mingming Wang
- Department of Clinical Laboratory, Qingdao Woman and Children’s Hospital, Qingdao, China
| | - Yanzhi Cui
- Tumour Institute, Fourth Hospital of Hebei Medical University, Shi Jiazhuang, China
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9
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Huang C, Shi J, Guo Y, Huang W, Huang S, Ming S, Wu X, Zhang R, Ding J, Zhao W, Jia J, Huang X, Xiang AP, Shi Y, Yao C. A snoRNA modulates mRNA 3' end processing and regulates the expression of a subset of mRNAs. Nucleic Acids Res 2017; 45:8647-8660. [PMID: 28911119 PMCID: PMC5587809 DOI: 10.1093/nar/gkx651] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/15/2017] [Indexed: 01/08/2023] Open
Abstract
mRNA 3′ end processing is an essential step in gene expression. It is well established that canonical eukaryotic pre-mRNA 3′ processing is carried out within a macromolecular machinery consisting of dozens of trans-acting proteins. However, it is unknown whether RNAs play any role in this process. Unexpectedly, we found that a subset of small nucleolar RNAs (snoRNAs) are associated with the mammalian mRNA 3′ processing complex. These snoRNAs primarily interact with Fip1, a component of cleavage and polyadenylation specificity factor (CPSF). We have functionally characterized one of these snoRNAs and our results demonstrated that the U/A-rich SNORD50A inhibits mRNA 3′ processing by blocking the Fip1-poly(A) site (PAS) interaction. Consistently, SNORD50A depletion altered the Fip1–RNA interaction landscape and changed the alternative polyadenylation (APA) profiles and/or transcript levels of a subset of genes. Taken together, our data revealed a novel function for snoRNAs and provided the first evidence that non-coding RNAs may play an important role in regulating mRNA 3′ processing.
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Affiliation(s)
- Chunliu Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Junjie Shi
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yibin Guo
- Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Weijun Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shanshan Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Siqi Ming
- Institute of Tuberculosis Control, Key laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Xingui Wu
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Rui Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Junjun Ding
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Department of Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Wei Zhao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jie Jia
- Department of Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xi Huang
- Institute of Tuberculosis Control, Key laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China.,Department of Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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10
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Berardocco M, Radeghieri A, Busatto S, Gallorini M, Raggi C, Gissi C, D'Agnano I, Bergese P, Felsani A, Berardi AC. RNA-seq reveals distinctive RNA profiles of small extracellular vesicles from different human liver cancer cell lines. Oncotarget 2017; 8:82920-82939. [PMID: 29137313 PMCID: PMC5669939 DOI: 10.18632/oncotarget.20503] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/29/2017] [Indexed: 12/20/2022] Open
Abstract
Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome. Here are reported genome wide data of the expression level of coding and non-coding transcripts, microRNAs, isomiRs and snoRNAs providing the first comprehensive overview of the extracellular-vesicle RNA cargo released from LC cell lines. The EV-RNA expression profiles of the four liver cancer cell lines share a similar background, but cell-specific features clearly emerge showing the marked heterogeneity of the EV-cargo among the individual cell lines, evident both for the coding and non-coding RNA species.
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Affiliation(s)
- Martina Berardocco
- U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy
| | - Annalisa Radeghieri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Sara Busatto
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Chiara Raggi
- Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Italy
| | - Clarissa Gissi
- U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy
| | - Igea D'Agnano
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Armando Felsani
- Institute of Cell Biology and Neurobiology, CNR, Monterotondo, Italy.,Genomnia Srl, Bresso, Italy
| | - Anna C Berardi
- U.O.C. of Immunohaematology and Transfusion Medicine, Laboratory of Stem Cells, Spirito Santo Hospital, Pescara, Italy
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11
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C/D-box snoRNA-derived RNA production is associated with malignant transformation and metastatic progression in prostate cancer. Oncotarget 2016; 6:17430-44. [PMID: 26041889 PMCID: PMC4627319 DOI: 10.18632/oncotarget.4172] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/02/2015] [Indexed: 12/14/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are dynamically regulated in different tissues and affected in disease. SnoRNAs are processed further to stable smaller RNAs. We sequenced the small RNA transcriptome of prostate cancer (PCa) at different PCa stages and generated a quantified catalogue of 3927 small non-coding RNAs (sncRNAs) detected in normal and malignant prostate tissue. From these, only 1524 are microRNAs. The remaining 2401 sncRNAs represent stable sncRNAs species that originate from snoRNA, tRNA and other sncRNAs. We show that snoRNA-derived RNAs (sdRNAs) display stronger differential expression than microRNAs and are massively upregulated in PCa. SdRNAs account for at least one third of all small RNAs with expression changes in tumor compared to normal adjacent tissue. Multiple sdRNAs can be produced from one snoRNA in a manner related to the conservation of structural snoRNA motifs. Q-PCR analysis in an independent patient cohort (n=106) confirmed the processing patterns of selected snoRNAs (SNORD44, SNORD78, SNORD74 and SNORD81) and the cancer-associated up-regulation of their sdRNAs observed in sequencing data. Importantly, expression of SNORD78 and its sdRNA is significantly higher in a subset of patients that developed metastatic disease demonstrating that snoRNA and sdRNAs may present as novel diagnostic and/or prognostic biomarkers for PCa.
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Dupuis-Sandoval F, Poirier M, Scott MS. The emerging landscape of small nucleolar RNAs in cell biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:381-97. [PMID: 25879954 PMCID: PMC4696412 DOI: 10.1002/wrna.1284] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/18/2015] [Accepted: 03/20/2015] [Indexed: 01/07/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are a large class of small noncoding RNAs present in all eukaryotes sequenced thus far. As a family, they have been well characterized as playing a central role in ribosome biogenesis, guiding either the sequence-specific chemical modification of pre-rRNA (ribosomal RNA) or its processing. However, in higher eukaryotes, numerous orphan snoRNAs were described over a decade ago, with no known target or ascribed function, suggesting the possibility of alternative cellular functionality. In recent years, thanks in great part to advances in sequencing methodologies, we have seen many examples of the diversity that exists in the snoRNA family on multiple levels. In this review, we discuss the identification of novel snoRNA members, of unexpected binding partners, as well as the clarification and extension of the snoRNA target space and the characterization of diverse new noncanonical functions, painting a new and extended picture of the snoRNA landscape. Under the deluge of novel features and functions that have recently come to light, snoRNAs emerge as a central, dynamic, and highly versatile group of small regulatory RNAs. WIREs RNA 2015, 6:381–397. doi: 10.1002/wrna.1284
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Affiliation(s)
- Fabien Dupuis-Sandoval
- Biochemistry Department, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
| | - Mikaël Poirier
- Biochemistry Department, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
| | - Michelle S Scott
- Biochemistry Department and RNA Group, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
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Abel Y, Clerget G, Bourguignon-Igel V, Salone V, Rederstorff M. Les petits ARN nucléolaires nous surprennent encore ! Med Sci (Paris) 2014; 30:297-302. [DOI: 10.1051/medsci/20143003018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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