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Cusenza VY, Tameni A, Neri A, Frazzi R. The lncRNA epigenetics: The significance of m6A and m5C lncRNA modifications in cancer. Front Oncol 2023; 13:1063636. [PMID: 36969033 PMCID: PMC10033960 DOI: 10.3389/fonc.2023.1063636] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/10/2023] [Indexed: 03/12/2023] Open
Abstract
Most of our transcribed RNAs are represented by non-coding sequences. Long non-coding RNAs (lncRNAs) are transcripts with no or very limited protein coding ability and a length >200nt. They can be epigenetically modified. N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 7-methylguanosine (m7G) and 2’-O-methylation (Nm) are some of the lncRNAs epigenetic modifications. The epigenetic modifications of RNA are controlled by three classes of enzymes, each playing a role in a specific phase of the modification. These enzymes are defined as “writers”, “readers” and “erasers”. m6A and m5C are the most studied epigenetic modifications in RNA. These modifications alter the structure and properties, thus modulating the functions and interactions of lncRNAs. The aberrant expression of several lncRNAs is linked to the development of a variety of cancers and the epigenetic signatures of m6A- or m5C-related lncRNAs are increasingly recognized as potential biomarkers of prognosis, predictors of disease stage and overall survival. In the present manuscript, the most up to date literature is reviewed with the focus on m6A and m5C modifications of lncRNAs and their significance in cancer.
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Affiliation(s)
- Vincenza Ylenia Cusenza
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Annalisa Tameni
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Antonino Neri
- Scientific Directorate, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Raffaele Frazzi
- Scientific Directorate, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy
- *Correspondence: Raffaele Frazzi,
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Li C, Zhao J, Qin T, Jin Y, Duan C, Wu T, Romani MD, Cao Y, Lu H, Hu J. Comprehensive analysis of m6A methylation modification in chronic spinal cord injury in mice. J Orthop Res 2022; 41:1320-1334. [PMID: 36205185 DOI: 10.1002/jor.25457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/06/2022] [Accepted: 10/01/2022] [Indexed: 02/04/2023]
Abstract
Chronic spinal cord injury (CSCI) is a catastrophic disease of the central nervous system (CNS), resulting in partial or complete loss of neurological function. N6-methyladenosine (m6A) is the most common form of reversible posttranslational modification at the RNA level. However, the role of m6A modification in CSCI remains unknown. In this study, we established a CSCI model using a water-absorbable polyurethane polymer, with behavioral assessment, electrophysiological analysis, and histochemical staining for validation. Methylated RNA immunoprecipitation sequencing (meRIP-seq) and messenger RNA sequencing (mRNA-seq) were jointly explored to compare the differences between CSCI spinal tissue and normal spinal tissue. Furthermore, real-time quantitative reverse transcription pcr (qRT-PCR), western blot analysis, and immunofluorescence staining were used to analyze m6A modification-related proteins. We found that water-absorbable polyurethane polymer simulated well chronic spinal cord compression. Basso mouse scale scores and electrophysiological analysis showed continuous neurological function decline after chronic compression of the spinal cord. meRIP-seq identified 642 differentially modified m6A genes, among which 263 genes were downregulated and 379 genes were upregulated. mRNA-seq showed that 1544 genes were upregulated and 290 genes were downregulated after CSCI. Gene Ontology terms and enriched Kyoto Encyclopedia of Genes and Genomes pathways were also identified. qRT-PCR, western blotting, and immunofluorescence staining showed that Mettl14, Ythdf1, and Ythdf3 were significantly upregulated after CSCI. Our study revealed a comprehensive profile of m6A modifications in CSCI which may act as a valuable key for future research on CSCI.
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Affiliation(s)
- Chengjun Li
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jinyun Zhao
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Tian Qin
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuxin Jin
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Chunyue Duan
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Tianding Wu
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Manini Daudi Romani
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yong Cao
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hongbin Lu
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Sports Medicine, Research Centre of Sports Medicine, Xiangya Hospital, Central South University, Changsha, China.,Hunan Engineering Research Center of Sports and Health, Changsha, China
| | - Jianzhong Hu
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Wu Z, Wang Y, Yan M, Liang Q, Li B, Hou G, Xia T, Lin Z, Xu W. Comprehensive analysis of the endoplasmic reticulum stress-related long non-coding RNA in bladder cancer. Front Oncol 2022; 12:951631. [PMID: 35992824 PMCID: PMC9386564 DOI: 10.3389/fonc.2022.951631] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022] Open
Abstract
Background Bladder cancer is ranked the second most frequent tumor among urological malignancies. The research strived to establish a prognostic model based on endoplasmic reticulum stress (ERS)-related long non-coding RNA (lncRNA) in bladder cancer. Methods We extracted the ERS-related genes from the published research and bladder cancer data from the Cancer Genome Atlas database. ERS-related lncRNAs with prognostic significance were screened by univariate Cox regression, least absolute shrinkage and selection operator regression analysis and Kaplan-Meier method. Multivariate Cox analysis was leveraged to establish the risk score model. Moreover, an independent dataset, GSE31684, was used to validate the model’s efficacy. The nomogram was constructed based on the risk score and clinical variables. Furthermore, the biological functions, gene mutations, and immune landscape were investigated to uncover the underlying mechanisms of the ERS-related signature. Finally, we employed external datasets (GSE55433 and GSE89006) and qRT-PCR to investigate the expression profile of these lncRNAs in bladder cancer tissues and cells. Results Six ERS-related lncRNAs were identified to be closely coupled with patients’ prognosis. On this foundation, a risk score model was created to generate the risk score for each patient. The ERS-related risk score was shown to be an independent prognostic factor. And the results of GSE31684 dataset also supported this conclusion. Then, a nomogram was constructed based on risk scores and clinical characteristics, and proven to have excellent predictive value. Moreover, the gene function analysis demonstrated that ERS-related lncRNAs were closely linked to fatty extracellular matrix, cytokines, cell adhesion, and tumor pathways. Further analysis revealed the association of the 6-lncRNAs signature with gene mutations and immunity in bladder cancer. Finally, the external datasets and qRT-PCR verified high expressions of the ERS-related lncRNAs in bladder cancer tissues and cells. Conclusions Overall, our findings indicated that ERS-related lncRNAs, which may affect tumor pathogenesis in a number of ways, might be exploited to assess the prognosis of bladder cancer patients.
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Affiliation(s)
- Zhenyu Wu
- Department of Urology, The First People’s Hospital of Foshan, Foshan, China
| | - Yue Wang
- The First Clinical Medical College, GuangDong Medical University, ZhanJiang, China
| | - Mengxin Yan
- The First Clinical Medical College, GuangDong Medical University, ZhanJiang, China
| | - Quan Liang
- Department of Urology, The First People’s Hospital of Foshan, Foshan, China
| | - Bin Li
- Department of Urology, The First People’s Hospital of Foshan, Foshan, China
| | - Guoliang Hou
- Department of Urology, The First People’s Hospital of Foshan, Foshan, China
| | - Taolin Xia
- Department of Urology, The First People’s Hospital of Foshan, Foshan, China
| | - Zhe Lin
- Department of Urology, The First People’s Hospital of Foshan, Foshan, China
- *Correspondence: Wenfeng Xu, ; Zhe Lin,
| | - Wenfeng Xu
- Department of Urology, The First People’s Hospital of Foshan, Foshan, China
- *Correspondence: Wenfeng Xu, ; Zhe Lin,
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