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Wylie D, Wang X, Yao J, Xu H, Ferrick-Kiddie EA, Iwase T, Krishnamurthy S, Ueno NT, Lambowitz AM. TGIRT-seq of Inflammatory Breast Cancer Tumor and Blood Samples Reveals Widespread Enhanced Transcription Impacting RNA splicing and Intronic RNAs in Plasma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.05.26.23290469. [PMID: 37398275 PMCID: PMC10312853 DOI: 10.1101/2023.05.26.23290469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Inflammatory breast cancer (IBC) is the most aggressive and lethal breast cancer subtype but lacks unequivocal genomic differences or robust biomarkers that differentiate it from non-IBC. Here, Thermostable Group II intron Reverse Transcriptase RNA-sequencing (TGIRT-seq) revealed myriad differences in tumor samples, Peripheral Blood Mononuclear Cells (PBMCs), and plasma that distinguished IBC from non-IBC patients and healthy donors across all tested receptor-based subtypes. These included numerous differentially expressed protein-coding gene and non-coding RNAs in all three sample types, a granulocytic immune response in IBC PBMCs, and over-expression of repeat element and antisense RNAs, suggesting wide-spread enhanced transcription in both IBC tumors and PBMCs. By using TGIRT-seq to quantitate Intron-exon Depth Ratios (IDRs) and mapping reads to both genome and transcriptome reference sequences, we developed methods for parallel analysis of transcriptional and post-transcriptional gene regulation. This analysis identified numerous differentially and non-differentially expressed protein-coding genes in IBC tumors and PBMCs with high IDRs, reflecting rate-limiting RNA splicing that negatively impacts mRNA production. Mirroring gene expression differences in tumors and PBMCs, over-represented protein-coding gene RNAs in IBC patient plasma were largely intronic RNAs, while those in non-IBC patients and healthy donor plasma were largely mRNA fragments. Potential IBC biomarkers in plasma included T-cell receptor pre-mRNAs and intronic, LINE-1, and antisense RNAs. Our findings provide new insights into IBC and set the stage for monitoring disease progression and response to treatment by liquid biopsy. The methods developed for parallel transcriptional and post-transcriptional gene regulation analysis have potentially broad RNA-seq and clinical applications.
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Affiliation(s)
- Dennis Wylie
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712
| | - Xiaoping Wang
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Inflammatory Breast Cancer Research Program and Clinic, University of Hawai i Cancer Center, Honolulu, HI 96813
- Cancer Biology Research Program, University of Hawai i Cancer Center, Honolulu, HI 96813
| | - Jun Yao
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712
| | - Hengyi Xu
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712
| | | | - Toshiaki Iwase
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Inflammatory Breast Cancer Research Program and Clinic, University of Hawai i Cancer Center, Honolulu, HI 96813
- Translational Clinical Research Program, University of Hawai i Cancer Center, Honolulu, HI 96813
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
- Inflammatory Breast Cancer Research Program and Clinic, University of Hawai i Cancer Center, Honolulu, HI 96813
- Cancer Biology Research Program, University of Hawai i Cancer Center, Honolulu, HI 96813
- Translational Clinical Research Program, University of Hawai i Cancer Center, Honolulu, HI 96813
| | - Alan M Lambowitz
- Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX 78712
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Jalan A, Jayasree PJ, Karemore P, Narayan KP, Khandelia P. Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease. Mol Biotechnol 2024; 66:1581-1598. [PMID: 37341888 DOI: 10.1007/s12033-023-00792-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023]
Abstract
Cellular RNAs, both coding and noncoding are adorned by > 100 chemical modifications, which impact various facets of RNA metabolism and gene expression. Very often derailments in these modifications are associated with a plethora of human diseases. One of the most oldest of such modification is pseudouridylation of RNA, wherein uridine is converted to a pseudouridine (Ψ) via an isomerization reaction. When discovered, Ψ was referred to as the 'fifth nucleotide' and is chemically distinct from uridine and any other known nucleotides. Experimental evidence accumulated over the past six decades, coupled together with the recent technological advances in pseudouridine detection, suggest the presence of pseudouridine on messenger RNA, as well as on diverse classes of non-coding RNA in human cells. RNA pseudouridylation has widespread effects on cellular RNA metabolism and gene expression, primarily via stabilizing RNA conformations and destabilizing interactions with RNA-binding proteins. However, much remains to be understood about the RNA targets and their recognition by the pseudouridylation machinery, the regulation of RNA pseudouridylation, and its crosstalk with other RNA modifications and gene regulatory processes. In this review, we summarize the mechanism and molecular machinery involved in depositing pseudouridine on target RNAs, molecular functions of RNA pseudouridylation, tools to detect pseudouridines, the role of RNA pseudouridylation in human diseases like cancer, and finally, the potential of pseudouridine to serve as a biomarker and as an attractive therapeutic target.
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Affiliation(s)
- Abhishek Jalan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - P J Jayasree
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Pragati Karemore
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Kumar Pranav Narayan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India.
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3
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López J, Blanco S. Exploring the role of ribosomal RNA modifications in cancer. Curr Opin Genet Dev 2024; 86:102204. [PMID: 38759459 DOI: 10.1016/j.gde.2024.102204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/05/2024] [Accepted: 05/03/2024] [Indexed: 05/19/2024]
Abstract
Recent advances have highlighted the significant roles of post-transcriptional modifications in rRNA in various cancers. Evidence suggests that dysregulation of rRNA modifications acts as a common denominator in cancer development, with alterations in these modifications conferring competitive advantages to cancer cells. Specifically, rRNA modifications modulate protein synthesis and favor the specialized translation of oncogenic programs, thereby contributing to the formation of a protumorigenic proteome in cancer cells. These findings reveal a novel regulatory layer mediated by changes in the deposition of rRNA chemical modifications. Moreover, inhibition of these modifications in vitro and in preclinical studies demonstrates potential therapeutic applications. The recurrence of altered rRNA modification patterns across different types of cancer underscores their importance in cancer progression, proposing them as potential biomarkers and novel therapeutic targets. This review will highlight the latest insights into how post-transcriptional rRNA modifications contribute to cancer progression and summarize the main developments and ongoing challenges in this research area.
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Affiliation(s)
- Judith López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain. https://twitter.com/@judithlopezluis
| | - Sandra Blanco
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain.
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4
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Cui L, Zheng J, Lin Y, Lin P, Lu Y, Zheng Y, Guo B, Zhao X. Decoding the ribosome's hidden language: rRNA modifications as key players in cancer dynamics and targeted therapies. Clin Transl Med 2024; 14:e1705. [PMID: 38797935 PMCID: PMC11128715 DOI: 10.1002/ctm2.1705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Ribosomal RNA (rRNA) modifications, essential components of ribosome structure and function, significantly impact cellular proteomics and cancer biology. These chemical modifications transcend structural roles, critically shaping ribosome functionality and influencing cellular protein profiles. In this review, the mechanisms by which rRNA modifications regulate both rRNA functions and broader cellular physiological processes are critically discussed. Importantly, by altering the translational output, rRNA modifications can shift the cellular equilibrium towards oncogenesis, thus playing a key role in cancer development and progression. Moreover, a special focus is placed on the functions of mitochondrial rRNA modifications and their aberrant expression in cancer, an area with profound implications yet largely uncharted. Dysregulation in these modifications can lead to metabolic dysfunction and apoptosis resistance, hallmark traits of cancer cells. Furthermore, the current challenges and future perspectives in targeting rRNA modifications are highlighted as a therapeutic approach for cancer treatment. In conclusion, rRNA modifications represent a frontier in cancer research, offering novel insights and therapeutic possibilities. Understanding and harnessing these modifications can pave the way for breakthroughs in cancer treatment, potentially transforming the approach to combating this complex disease.
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Affiliation(s)
- Li Cui
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
- Division of Oral Biology and Medicine, School of DentistryUniversity of
California, Los AngelesLos AngelesUSA
| | - Jiarong Zheng
- Department of Dentistry, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Yunfan Lin
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Pei Lin
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Ye Lu
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Yucheng Zheng
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Bing Guo
- Department of Dentistry, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
| | - Xinyuan Zhao
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
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5
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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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6
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Gao L, Fan J, He J, Che X, Wang X, Han C. Small Nucleolar RNAs as Diagnostic and Prognostic Biomarkers in Cancer: A Systematic Review and Meta-Analysis. Technol Cancer Res Treat 2024; 23:15330338241245939. [PMID: 38752263 PMCID: PMC11102679 DOI: 10.1177/15330338241245939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 01/14/2024] [Accepted: 02/12/2024] [Indexed: 05/21/2024] Open
Abstract
OBJECTIVES Small nucleolar RNAs (snoRNAs) form clusters within the genome, representing a mysterious category of small non-coding RNAs. Research has demonstrated that aberrant snoRNAs can contribute to the development of various types of cancers. Recent studies have identified snoRNAs as potentially valuable biomarkers for the diagnosis or/and prognosis of cancers. However, there has been a lack of comprehensive reviews on prognostic and diagnostic snoRNAs across different types of cancers. METHODS We conducted a systematic search of various databases including Google Scholar, Medline, Cochrane, Scopus, PubMed, Embase, ScienceDirect, Ovid-Medline, Chinese National Knowledge Infrastructure, WanFang, and SinoMed with a time frame reception to December 30, 2022. A total of 49 relevant articles were included in our analysis, consisting of 21 articles focusing on diagnostic aspects and 41 articles focusing on prognostic aspects. Pooled odds ratio, 95% confidence intervals (CIs), and hazard ratio (HR) were utilized to evaluate clinical parameters and overall survival (OS), respectively. RESULT The findings indicated that area under the curve, sensitivity, and specificity were 0.85, 75%, and 80% in cancer, respectively. There was a possibility that snoRNAs had a positive impact on the diagnosis (risk ratio, RR = 2.95, 95% CI: 2.75-3.16, P = 0.000) and OS (HR = 1) in cancer. Additionally, abnormally expressed snoRNAs were associated with a positive impact on OS time for chronic lymphocytic leukemia (HR: 0.88, 95%Cl: 0.69-1.11, P < 0.00001), colon adenocarcinoma (HR: 0.97, 95%Cl: 0.91-1.03, P < 0.0001), and ovarian cancer (HR: 0.98, 95%Cl: 0.98-0.99, P < 0.00001). However, dysregulated snoRNAs of colon cancer and colorectal cancer had a negative impact on OS time (HR = 3.01 and 1.01 respectively, P < 0.0001). CONCLUSION The results strongly suggested that snoRNAs could serve as potential novel indicators for prognosis and diagnosis in cancers. This systematic review followed the guidelines of the Transparent Reporting of Systematic Review and Meta-Analyses (PROSPERO register: CRD42020209096).
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Affiliation(s)
- Liyun Gao
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
- Jiangxi Provincial Key Laboratory of Cell Precision Therapy, School of Basic Medical Sciences, Jiujiang University, China
| | - Junfei Fan
- School of Humanities, Shangluo University, Shangluo, China
| | - Jiayin He
- School of Literature and Journalism, South-central Minzu University, Wuhan, China
| | - Xiangxin Che
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Xin Wang
- Laboratory of Precision Preventive Medicine, School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Chunhua Han
- Internal Medicine, Jiujiang First People's Hospital, Jiujiang, China
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7
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Bergeron D, Faucher-Giguère L, Emmerichs AK, Choquet K, Song KS, Deschamps-Francoeur G, Fafard-Couture É, Rivera A, Couture S, Churchman LS, Heyd F, Abou Elela S, Scott MS. Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences. Genome Biol 2023; 24:160. [PMID: 37415181 PMCID: PMC10324135 DOI: 10.1186/s13059-023-03002-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Small nucleolar RNAs (snoRNAs) are abundant noncoding RNAs best known for their involvement in ribosomal RNA maturation. In mammals, most expressed snoRNAs are embedded in introns of longer genes and produced through transcription and splicing of their host. Intronic snoRNAs were long viewed as inert passengers with little effect on host expression. However, a recent study reported a snoRNA influencing the splicing and ultimate output of its host gene. Overall, the general contribution of intronic snoRNAs to host expression remains unclear. RESULTS Computational analysis of large-scale human RNA-RNA interaction datasets indicates that 30% of detected snoRNAs interact with their host transcripts. Many snoRNA-host duplexes are located near alternatively spliced exons and display high sequence conservation suggesting a possible role in splicing regulation. The study of the model SNORD2-EIF4A2 duplex indicates that the snoRNA interaction with the host intronic sequence conceals the branch point leading to decreased inclusion of the adjacent alternative exon. Extended SNORD2 sequence containing the interacting intronic region accumulates in sequencing datasets in a cell-type-specific manner. Antisense oligonucleotides and mutations that disrupt the formation of the snoRNA-intron structure promote the splicing of the alternative exon, shifting the EIF4A2 transcript ratio away from nonsense-mediated decay. CONCLUSIONS Many snoRNAs form RNA duplexes near alternative exons of their host transcripts, placing them in optimal positions to control host output as shown for the SNORD2-EIF4A2 model system. Overall, our study supports a more widespread role for intronic snoRNAs in the regulation of their host transcript maturation.
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Affiliation(s)
- Danny Bergeron
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Laurence Faucher-Giguère
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Ann-Kathrin Emmerichs
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Laboratory of RNA Biochemistry, Takustrasse 6, 14195, Berlin, Germany
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Kristina Sungeun Song
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Étienne Fafard-Couture
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Andrea Rivera
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Sonia Couture
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Florian Heyd
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Laboratory of RNA Biochemistry, Takustrasse 6, 14195, Berlin, Germany
| | - Sherif Abou Elela
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
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8
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Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023; 20:715-736. [PMID: 37796118 PMCID: PMC10557570 DOI: 10.1080/15476286.2023.2254540] [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] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in ribosome biogenesis, snoRNAs are also implicated in several other cellular activities including regulation of splicing, transcription, RNA editing, cellular trafficking, and miRNA-like functions. Mature snoRNAs must undergo a series of processing steps tightly regulated by transiently associating factors and coordinated with other cellular processes including transcription and splicing. In addition to their mature forms, snoRNAs can contribute to gene expression regulation through their derivatives and degradation products. Here, we review the current knowledge on mechanisms of snoRNA maturation, including the different pathways of processing, and the regulatory mechanisms that control snoRNA levels and complex assembly. We also discuss the significance of studying snoRNA maturation, highlight the gaps in the current knowledge and suggest directions for future research in this area.
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Affiliation(s)
- Sarah F. Webster
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
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9
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U5 snRNP Core Proteins Are Key Components of the Defense Response against Viral Infection through Their Roles in Programmed Cell Death and Interferon Induction. Viruses 2022; 14:v14122710. [PMID: 36560714 PMCID: PMC9785106 DOI: 10.3390/v14122710] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/11/2022] Open
Abstract
The spliceosome is a massive ribonucleoprotein structure composed of five small nuclear ribonucleoprotein (snRNP) complexes that catalyze the removal of introns from pre-mature RNA during constitutive and alternative splicing. EFTUD2, PRPF8, and SNRNP200 are core components of the U5 snRNP, which is crucial for spliceosome function as it coordinates and performs the last steps of the splicing reaction. Several studies have demonstrated U5 snRNP proteins as targeted during viral infection, with a limited understanding of their involvement in virus-host interactions. In the present study, we deciphered the respective impact of EFTUD2, PRPF8, and SNRNP200 on viral replication using mammalian reovirus as a model. Using a combination of RNA silencing, real-time cell analysis, cell death and viral replication assays, we discovered distinct and partially overlapping novel roles for EFTUD2, PRPF8, and SNRNP200 in cell survival, apoptosis, necroptosis, and the induction of the interferon response pathway. For instance, we demonstrated that EFTUD2 and SNRNP200 are required for both apoptosis and necroptosis, whereas EFTUD2 and PRPF8 are required for optimal interferon response against viral infection. Moreover, we demonstrated that EFTUD2 restricts viral replication, both in a single cycle and multiple cycles of viral replication. Altogether, these results establish U5 snRNP core components as key elements of the cellular antiviral response.
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10
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Bergeron D, Paraqindes H, Fafard-Couture É, Deschamps-Francoeur G, Faucher-Giguère L, Bouchard-Bourelle P, Abou Elela S, Catez F, Marcel V, Scott M. snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs. Nucleic Acids Res 2022; 51:D291-D296. [PMID: 36165892 PMCID: PMC9825428 DOI: 10.1093/nar/gkac835] [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: 08/09/2022] [Revised: 09/06/2022] [Accepted: 09/16/2022] [Indexed: 01/29/2023] Open
Abstract
snoDB is an interactive database of human small nucleolar RNAs (snoRNAs) that includes up-to-date information on snoRNA features, genomic location, conservation, host gene, snoRNA-RNA targets and snoRNA abundance and provides links to other resources. In the second edition of this database (snoDB 2.0), we added an entirely new section on ribosomal RNA (rRNA) chemical modifications guided by snoRNAs with easy navigation between the different rRNA versions used in the literature and experimentally measured levels of modification. We also included new layers of information, including snoRNA motifs, secondary structure prediction, snoRNA-protein interactions, copy annotations and low structure bias expression data in a wide panel of tissues and cell lines to bolster functional probing of snoRNA biology. Version 2.0 features updated identifiers, more links to external resources and duplicate entry resolution. As a result, snoDB 2.0, which is freely available at https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/, represents a one-stop shop for snoRNA features, rRNA modification targets, functional impact and potential regulators.
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Affiliation(s)
- Danny Bergeron
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Hermes Paraqindes
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France,Centre Léon Bérard, F-69008 Lyon, France,Université de Lyon 1, F-69000 Lyon, France
| | - Étienne Fafard-Couture
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Laurence Faucher-Giguère
- Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Philia Bouchard-Bourelle
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d’infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Frédéric Catez
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France,Centre Léon Bérard, F-69008 Lyon, France,Université de Lyon 1, F-69000 Lyon, France,Institut Convergence PLAsCAN, F-69373 Lyon, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France,Centre Léon Bérard, F-69008 Lyon, France,Université de Lyon 1, F-69000 Lyon, France,Institut Convergence PLAsCAN, F-69373 Lyon, France
| | - Michelle S Scott
- To whom correspondence should be addressed. Tel: +1 819 821 8000 (Ext 72123);
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Splicing inactivation generates hybrid mRNA-snoRNA transcripts targeted by cytoplasmic RNA decay. Proc Natl Acad Sci U S A 2022; 119:e2202473119. [PMID: 35878033 PMCID: PMC9351541 DOI: 10.1073/pnas.2202473119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many small nucleolar RNAs (snoRNA)s are processed from introns of host genes, but the importance of splicing for proper biogenesis and the fate of the snoRNAs is not well understood. Here, we show that inactivation of splicing factors or mutation of splicing signals leads to the accumulation of partially processed hybrid messenger RNA-snoRNA (hmsnoRNA) transcripts. hmsnoRNAs are processed to the mature 3' ends of the snoRNAs by the nuclear exosome and bound by small nucleolar ribonucleoproteins. hmsnoRNAs are unaffected by translation-coupled RNA quality-control pathways, but they are degraded by the major cytoplasmic exonuclease Xrn1p, due to their messenger RNA (mRNA)-like 5' extensions. These results show that completion of splicing is required to promote complete and accurate processing of intron-encoded snoRNAs and that splicing defects lead to degradation of hybrid mRNA-snoRNA species by cytoplasmic decay, underscoring the importance of splicing for the biogenesis of intron-encoded snoRNAs.
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Rai AK, Rajan KS, Bisserier M, Brojakowska A, Sebastian A, Evans AC, Coleman MA, Mills PJ, Arakelyan A, Uchida S, Hadri L, Goukassian DA, Garikipati VNS. Spaceflight-Associated Changes of snoRNAs in Peripheral Blood Mononuclear Cells and Plasma Exosomes-A Pilot Study. Front Cardiovasc Med 2022; 9:886689. [PMID: 35811715 PMCID: PMC9267956 DOI: 10.3389/fcvm.2022.886689] [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: 02/28/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
During spaceflight, astronauts are exposed to various physiological and psychological stressors that have been associated with adverse health effects. Therefore, there is an unmet need to develop novel diagnostic tools to predict early alterations in astronauts' health. Small nucleolar RNA (snoRNA) is a type of short non-coding RNA (60-300 nucleotides) known to guide 2'-O-methylation (Nm) or pseudouridine (ψ) of ribosomal RNA (rRNA), small nuclear RNA (snRNA), or messenger RNA (mRNA). Emerging evidence suggests that dysregulated snoRNAs may be key players in regulating fundamental cellular mechanisms and in the pathogenesis of cancer, heart, and neurological disease. Therefore, we sought to determine whether the spaceflight-induced snoRNA changes in astronaut's peripheral blood (PB) plasma extracellular vesicles (PB-EV) and peripheral blood mononuclear cells (PBMCs). Using unbiased small RNA sequencing (sRNAseq), we evaluated changes in PB-EV snoRNA content isolated from astronauts (n = 5/group) who underwent median 12-day long Shuttle missions between 1998 and 2001. Using stringent cutoff (fold change > 2 or log2-fold change >1, FDR < 0.05), we detected 21 down-and 9-up-regulated snoRNAs in PB-EVs 3 days after return (R + 3) compared to 10 days before launch (L-10). qPCR validation revealed that SNORA74A was significantly down-regulated at R + 3 compared to L-10. We next determined snoRNA expression levels in astronauts' PBMCs at R + 3 and L-10 (n = 6/group). qPCR analysis further confirmed a significant increase in SNORA19 and SNORA47 in astronauts' PBMCs at R + 3 compared to L-10. Notably, many downregulated snoRNA-guided rRNA modifications, including four Nms and five ψs. Our findings revealed that spaceflight induced changes in PB-EV and PBMCs snoRNA expression, thus suggesting snoRNAs may serve as potential novel biomarkers for monitoring astronauts' health.
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Affiliation(s)
- Amit Kumar Rai
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - K. Shanmugha Rajan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Malik Bisserier
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Agnieszka Brojakowska
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Aimy Sebastian
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Angela C. Evans
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA, United States
| | - Matthew A. Coleman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA, United States
| | - Paul J. Mills
- Center of Excellence for Research and Training in Integrative Health, University of California, San Diego, La Jolla, CA, United States
| | - Arsen Arakelyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Lahouaria Hadri
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David A. Goukassian
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Venkata Naga Srikanth Garikipati
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart Lung and Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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