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Pan C, Lin J, Dai X, Jiao L, Liu J, Lin A. An m1A/m6A/m5C-associated long non-coding RNA signature: Prognostic and immunotherapeutic insights into cervical cancer. J Gene Med 2024; 26:e3618. [PMID: 37923390 DOI: 10.1002/jgm.3618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) remains a significant clinical challenge, even though its fatality rate has been declining in recent years. Particularly in developing countries, the prognosis for CC patients continues to be suboptimal despite numerous therapeutic advances. METHODS Using The Cancer Genome Atlas database, we extracted CC-related data. From this, 52 methylation-related genes (MRGs) were identified, leading to the selection of a 10 long non-coding RNA (lncRNA) signature co-expressed with these MRGs. R programming was employed to filter out the methylation-associated lncRNAs. Through univariate, least absolute shrinkage and selection operator (i.e. LASSO) and multivariate Cox regression analysis, an MRG-associated lncRNA model was constructed. The established risk model was further assessed via the Kaplan-Meier method, principal component analysis, functional enrichment annotation and a nomogram. Furthermore, we explored the potential of this model with respect to guiding immune therapeutic interventions and predicting drug sensitivities. RESULTS The derived 10-lncRNA signature, linked with MRGs, emerged as an independent prognostic factor. Segmenting patients based on their immunotherapy responses allowed for enhanced differentiation between patient subsets. Lastly, we highlighted potential compounds for distinguishing CC subtypes. CONCLUSIONS The risk model, associated with MRG-linked lncRNA, holds promise in forecasting clinical outcomes and gauging the efficacy of immunotherapies for CC patients.
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Affiliation(s)
- Chenxiang Pan
- Department of Gynaecology Oncology, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Jiali Lin
- Institute of Reproduction and Development, Affiliated Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaoxiao Dai
- Department of Gynaecology Oncology, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Lili Jiao
- Department of Gynaecology Oncology, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Jinsha Liu
- Department of Laboratory Medicine, Meizhou Meixian District Hospital of Traditional Chinese Medicine, Meizhou, China
| | - Aidi Lin
- Department of Gynaecology Oncology, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
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Cai L, Liu T, Hua H, Jiang X, Qian L. m6A modification patterns are associated with copy number burden and tumor immune landscape in thyroid cancer. BMC Endocr Disord 2023; 23:271. [PMID: 38057752 DOI: 10.1186/s12902-023-01510-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 11/09/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND The association involving N6-methyladenosine (m6A) modification, molecular subtype and specific immune cell group in tumor microenvironment has been the focus of recent studies. The underlying function of m6A modification in thyroid cancer (TC) remains elusive. METHODS The m6A modification regulations, molecular character and tumor immune profile of 461 TC patients were explored and then the correlation between them were comprehensively evaluated. The m6Ascore was established using principal component analysis (PCA) to quantify the m6A pattern of individual TC patients. The prognostic significance of the m6Ascore was evaluated by multivariate Cox regression analysis. RESULTS Four m6Aclusters (mc1, 2, 3, 4)-characterized by differences in extent of aneuploidy, expression of immunomodulatory genes, mRNA or lncRNA expression pattern and prognosis were identified. T Preliminary validation of m6Ascore was a potential independent prognostic factor of TC involving in mc3. Finally, the prognostic value of the m6Ascore and its association with copy number variation (CNV) and tumor immune microenvironment (TIME) of TC in mc3 were verified. CONCLUSIONS The correlation between m6A modification, the copy number burden and tumor immune landscape in TC was demonstrated. A m6Acluster-mc3 with low m6Ascore and high CNV molecular subtype was identified with poor clinical prognosis, low infiltrating immunocyte and weak effector T cell. A three-gene clinical prognosis model for TC based on 4 m6a cluster expression was established. Understanding of TIME is enhanced by comprehensive assessment of m6A patterns in individual TC patients and gives a new insight toward improved immunotherapy strategies for TC cancer patients.
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Affiliation(s)
- Liangliang Cai
- Institute of Translational Medicine, Medical College, Yangzhou University, No. 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, PR China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, 225001, PR China
| | - Tingting Liu
- Department of Orthopedics, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225000, PR China
| | - Hujia Hua
- Institute of Translational Medicine, Medical College, Yangzhou University, No. 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, PR China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, 225001, PR China
| | - Xingyu Jiang
- Institute of Translational Medicine, Medical College, Yangzhou University, No. 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, PR China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, 225001, PR China
| | - Li Qian
- Institute of Translational Medicine, Medical College, Yangzhou University, No. 48 East Wenhui Road, Yangzhou, Jiangsu, 225009, PR China.
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, 225001, PR China.
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Tang J, Zhang J, Lu Y, He J, Wang H, Liu B, Tu C, Li Z. Novel insights into the multifaceted roles of m 6A-modified LncRNAs in cancers: biological functions and therapeutic applications. Biomark Res 2023; 11:42. [PMID: 37069649 PMCID: PMC10111779 DOI: 10.1186/s40364-023-00484-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/11/2023] [Indexed: 04/19/2023] Open
Abstract
N6-methyladenosine (m6A) is considered as the most common and important internal transcript modification in several diseases like type 2 diabetes, schizophrenia and especially cancer. As a main target of m6A methylation, long non-coding RNAs (lncRNAs) have been proved to regulate cellular processes at various levels, including epigenetic modification, transcriptional, post-transcriptional, translational and post-translational regulation. Recently, accumulating evidence suggests that m6A-modified lncRNAs greatly participate in the tumorigenesis of cancers. In this review, we systematically summarized the biogenesis of m6A-modified lncRNAs and the identified m6A-lncRNAs in a variety of cancers, as well as their potential diagnostic and therapeutic applications as biomarkers and therapeutic targets, hoping to shed light on the novel strategies for cancer treatment.
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Affiliation(s)
- Jinxin Tang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Jinhui Zhang
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Yu Lu
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Jieyu He
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Hua Wang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410011, China
| | - Binfeng Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
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Cen J, Wang L, Zhang H, Guo Y. Analysis of the prognostic significance and potential mechanisms of lncRNAs related to m6A methylation in laryngeal cancer. Biotechnol Genet Eng Rev 2023:1-26. [PMID: 37053494 DOI: 10.1080/02648725.2023.2198630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Objective to investigate the prognostic significance and potential mechanism analysis of m6A methylation-associated lncRNAs in laryngeal cancer. Methods based on the expression of m6A-associated lncRNAs, the samples were divided into two clusters and least absolute value and selection operator (LASSO) regression analysis was performed to build and validate prognostic models. In addition, the relationships between risk scores, clusters, arginine synthase (SMS), tumor microenvironment, clinicopathological features, immune infiltration, immune checkpoints, and tumor mutation burden were analyzed. Finally, the relationship between SMS and m6A-associated IncRNAs was analyzed and SMS-associated pathways were enriched by gene set enrichment analysis (GSEA). Results a total of 95 lncRNAs were associated with the expression of 22 m6A methylation regulators in laryngeal cancer, 14 of which were prognostic lncRNAs. These lncRNAs were divided into two clusters and evaluated. Clinicopathological features did not show significant differences. However, the two clusters differed significantly in terms of naive B cells, memory B cells, naive CD4 T cells, T helper cells and immune score. lASSO regression analysis showed that risk score was a significant predictor of progression-free survival. Conclusion low expression of m6A-related lncRNAs involved in laryngeal cancer development in laryngeal cancer tissues can be used as an indicator to diagnose patients with laryngeal cancer, reduce patient prognosis, be an independent risk factor affecting patient prognosis and be able to assess patient prognosis.
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Affiliation(s)
- Jingtu Cen
- Shanghai Municipal Hospital of Traditional Chinese Medicine,ear-nose-throat department, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lihua Wang
- Shanghai Municipal Hospital of Traditional Chinese Medicine,ear-nose-throat department, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Haopeng Zhang
- Shanghai Municipal Hospital of Traditional Chinese Medicine,ear-nose-throat department, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yu Guo
- Shanghai Municipal Hospital of Traditional Chinese Medicine,ear-nose-throat department, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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