1
|
Cai X, Wang H, Han Y, Huang H, Qian P. The essential roles of small non-coding RNAs and RNA modifications in normal and malignant hematopoiesis. Front Mol Biosci 2023; 10:1176416. [PMID: 37065445 PMCID: PMC10102602 DOI: 10.3389/fmolb.2023.1176416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Hematopoietic stem cells (HSCs) developing from mesoderm during embryogenesis are important for the blood circulatory system and immune system. Many factors such as genetic factors, chemical exposure, physical radiation, and viral infection, can lead to the dysfunction of HSCs. Hematological malignancies (involving leukemia, lymphoma, and myeloma) were diagnosed in more than 1.3 million people globally in 2021, taking up 7% of total newly-diagnosed cancer patients. Although many treatments like chemotherapy, bone marrow transplantation, and stem cell transplantation have been applied in clinical therapeutics, the average 5-year survival rate for leukemia, lymphoma, and myeloma is about 65%, 72%, and 54% respectively. Small non-coding RNAs play key roles in a variety of biological processes, including cell division and proliferation, immunological response and cell death. With the development of technologies in high-throughput sequencing and bioinformatic analysis, there is emerging research about modifications on small non-coding RNAs, as well as their functions in hematopoiesis and related diseases. In this study, we summarize the updated information of small non-coding RNAs and RNA modifications in normal and malignant hematopoiesis, which sheds lights into the future application of HSCs into the treatment of blood diseases.
Collapse
Affiliation(s)
- Xinyi Cai
- Center for 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 for 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 for 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
| | - Pengxu Qian
- Center for 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,
| |
Collapse
|
2
|
Song B, Wang X, Liang Z, Ma J, Huang D, Wang Y, de Magalhães JP, Rigden DJ, Meng J, Liu G, Chen K, Wei Z. RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. Nucleic Acids Res 2023; 51:D1388-D1396. [PMID: 36062570 PMCID: PMC9825452 DOI: 10.1093/nar/gkac750] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/02/2022] [Accepted: 08/24/2022] [Indexed: 01/30/2023] Open
Abstract
Recent advances in epitranscriptomics have unveiled functional associations between RNA modifications (RMs) and multiple human diseases, but distinguishing the functional or disease-related single nucleotide variants (SNVs) from the majority of 'silent' variants remains a major challenge. We previously developed the RMDisease database for unveiling the association between genetic variants and RMs concerning human disease pathogenesis. In this work, we present RMDisease v2.0, an updated database with expanded coverage. Using deep learning models and from 873 819 experimentally validated RM sites, we identified a total of 1 366 252 RM-associated variants that may affect (add or remove an RM site) 16 different types of RNA modifications (m6A, m5C, m1A, m5U, Ψ, m6Am, m7G, A-to-I, ac4C, Am, Cm, Um, Gm, hm5C, D and f5C) in 20 organisms (human, mouse, rat, zebrafish, maize, fruit fly, yeast, fission yeast, Arabidopsis, rice, chicken, goat, sheep, pig, cow, rhesus monkey, tomato, chimpanzee, green monkey and SARS-CoV-2). Among them, 14 749 disease- and 2441 trait-associated genetic variants may function via the perturbation of epitranscriptomic markers. RMDisease v2.0 should serve as a useful resource for studying the genetic drivers of phenotypes that lie within the epitranscriptome layer circuitry, and is freely accessible at: www.rnamd.org/rmdisease2.
Collapse
Affiliation(s)
- Bowen Song
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
- Department of Mathematical Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L7 8TX, UK
| | - Xuan Wang
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Zhanmin Liang
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Jiongming Ma
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L7 8TX, UK
| | - Daiyun Huang
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
- Department of Computer Science, University of Liverpool, Liverpool L7 8TX, UK
| | - Yue Wang
- Department of Mathematical Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
- Department of Computer Science, University of Liverpool, Liverpool L7 8TX, UK
| | - João Pedro de Magalhães
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L7 8TX, UK
| | - Jia Meng
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L7 8TX, UK
- AI University Research Centre, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Gang Liu
- Department of Mathematical Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
| | - Kunqi Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350004, China
| | - Zhen Wei
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, 215123, China
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| |
Collapse
|
3
|
Pichot F, Hogg MC, Marchand V, Bourguignon V, Jirström E, Farrell C, Gibriel HA, Prehn JH, Motorin Y, Helm M. Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines. Comput Struct Biotechnol J 2022; 21:401-417. [PMID: 36618980 PMCID: PMC9798144 DOI: 10.1016/j.csbj.2022.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always fully modified. Combinations and permutations of partially modified sites in tRNAs can generate a plethora of tRNA isoforms, termed modivariants. Here, we investigate the stoichiometry of incompletely modified sites in tRNAs from human cell lines for their information content. Using a panel of RNA modification mapping methods, we assess the stoichiometry of sites that contain the modifications 5-methylcytidine (m5C), 2'-O-ribose methylation (Nm), 3-methylcytidine (m3C), 7-methylguanosine (m7G), and Dihydrouridine (D). We discovered that up to 75% of sites can be incompletely modified and that the differential modification status of a cellular tRNA population holds information that allows to discriminate e.g. different cell lines. As a further aspect, we investigated potential causal connectivity between tRNA modification and its processing into tRNA fragments (tiRNAs and tRFs). Upon exposure of cultured living cells to cell-penetrating angiogenin, the modification patterns of the corresponding RNA populations was changed. Importantly, we also found that tsRNAs were significantly less modified than their parent tRNAs at numerous sites, suggesting that tsRNAs might derive chiefly from hypomodified tRNAs.
Collapse
Affiliation(s)
- Florian Pichot
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Marion C. Hogg
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Valérie Bourguignon
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Elisabeth Jirström
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Cliona Farrell
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Hesham A. Gibriel
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Jochen H.M. Prehn
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| |
Collapse
|
4
|
Meng J, Zuo Z, Lee TY, Liu Z, Huang Y. Bioinformatics resources for understanding RNA modifications. Methods 2022; 206:53-55. [PMID: 35988901 DOI: 10.1016/j.ymeth.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
|