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Ye J, Liu F, Zhang L, Wu C, Jiang A, Xie T, Jiang H, Li Z, Luo P, Jiao J, Xiao J. MOCS, a novel classifier system integrated multimoics analysis refining molecular subtypes and prognosis for skin melanoma. J Biomol Struct Dyn 2024:1-17. [PMID: 38555737 DOI: 10.1080/07391102.2024.2329305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/08/2024] [Indexed: 04/02/2024]
Abstract
PURPOSE The present investigation focuses on Skin Cutaneous Melanoma (SKCM), a melanocytic carcinoma characterized by marked aggression, significant heterogeneity, and a complex etiological background, factors which collectively contribute to the challenge in prognostic determinations. We defined a novel classifier system specifically tailored for SKCM based on multiomics. METHODS We collected 423 SKCM samples with multi omics datasets to perform a consensus cluster analysis using 10 machine learning algorithms and verified in 2 independent cohorts. Clinical features, biological characteristics, immune infiltration pattern, therapeutic response and mutation landscape were compared between subtypes. RESULTS Based on consensus clustering algorithms, we identified two Multi-Omics-Based-Cancer-Subtypes (MOCS) in SKCM in TCGA project and validated in GSE19234 and GSE65904 cohorts. MOCS2 emerged as a subtype with poor prognosis, characterized by a complex immune microenvironment, dysfunctional anti-tumor immune state, high cancer stemness index, and genomic instability. MOCS2 exhibited resistance to chemotherapy agents like erlotinib and sunitinib while sensitive to rapamycin, NSC87877, MG132, and FH355. Additionally, ELSPBP1 was identified as the target involving in glycolysis and M2 macrophage infiltration in SKCM. CONCLUSIONS MOCS classification could stably predict prognosis of SKCM; patients with a high cancer stemness index combined with genomic instability may be predisposed to an immune exhaustion state.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Juelan Ye
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Fuchun Liu
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Luoshen Zhang
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Chunbiao Wu
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Tianying Xie
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Hao Jiang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Zhenxi Li
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Jiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
| | - Jianru Xiao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Orthopedic, Changzheng Hospital Affiliated to Naval Medical University (Second Military Medical University), Shanghai, China
- School of Health Science and Technology, University of Shanghai for Science and Technology, Shanghai, China
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Yang L, Yuan L. Identification of novel N7-methylguanine-related gene signatures associated with ulcerative colitis and the association with biological therapy. Inflamm Res 2023; 72:2169-2180. [PMID: 37889323 DOI: 10.1007/s00011-023-01806-z] [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: 07/23/2023] [Revised: 07/23/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
OBJECTIVE Ulcerative colitis (UC) is an inflammatory disease characterized by recurrent episodes of chronic intestinal inflammation. It is closely associated with immune dysregulation in the intestines. However, the mechanisms underlying the role of immune-related N7-methylguanosine (m7G) internal modification in UC remain unclear. METHODS We conducted a screening of differentially expressed genes (DEGs) associated with m7G and performed immune infiltration analysis. We then investigated the correlation between m7G-related DEGs and immune cells or pathways. To further explore the functional implications, we conducted functional enrichment analysis to identify gene modules that strongly correlated with hub gene expression. In addition, we constructed a miRNA regulatory network for the hub genes in UC. Furthermore, we examined the association between hub genes and disease remission in UC patients undergoing biologic therapy. RESULTS We obtained 13 m7G-related DEGs and conducted an in-depth analysis of immune infiltration. Among them, we identified five hub genes (NUDT7, NUDT12, POLR2H, QKI, and PRKCB) that showed diagnostic potential for UC. Through WGCNA and KEGG analysis, we found that gene modules strongly correlated with m7G hub gene expression were enriched in inflammation-related pathways. Furthermore, Kaplan-Meier survival analysis revealed a significant association between changes in hub gene expression levels and disease remission in UC patients undergoing biologic therapy. CONCLUSION The findings of this study demonstrate that five m7G-related DEGs, including the m7G-modified recognition protein QKI, play a key role in the occurrence and progression of UC intestinal inflammation, which is closely related to intestinal immunity. These results provide valuable insights into the mechanisms of m7G modification in UC development and offer new perspectives for exploring novel therapeutic targets for UC.
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Affiliation(s)
- Lichao Yang
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Lianwen Yuan
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
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Zhong S, Chen S, Lin H, Luo Y, He J. Selection of M7G-related lncRNAs in kidney renal clear cell carcinoma and their putative diagnostic and prognostic role. BMC Urol 2023; 23:186. [PMID: 37968670 PMCID: PMC10652602 DOI: 10.1186/s12894-023-01357-9] [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: 06/20/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Kidney renal clear cell carcinoma (KIRC) is a common malignant tumor of the urinary system. This study aims to develop new biomarkers for KIRC and explore the impact of biomarkers on the immunotherapeutic efficacy for KIRC, providing a theoretical basis for the treatment of KIRC patients. METHODS Transcriptome data for KIRC was obtained from the The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. Weighted gene co-expression network analysis identified KIRC-related modules of long noncoding RNAs (lncRNAs). Intersection analysis was performed differentially expressed lncRNAs between KIRC and normal control samples, and lncRNAs associated with N(7)-methylguanosine (m7G), resulting in differentially expressed m7G-associated lncRNAs in KIRC patients (DE-m7G-lncRNAs). Machine Learning was employed to select biomarkers for KIRC. The prognostic value of biomarkers and clinical features was evaluated using Kaplan-Meier (K-M) survival analysis, univariate and multivariate Cox regression analysis. A nomogram was constructed based on biomarkers and clinical features, and its efficacy was evaluated using calibration curves and decision curves. Functional enrichment analysis was performed to investigate the functional enrichment of biomarkers. Correlation analysis was conducted to explore the relationship between biomarkers and immune cell infiltration levels and common immune checkpoint in KIRC samples. RESULTS By intersecting 575 KIRC-related module lncRNAs, 1773 differentially expressed lncRNAs, and 62 m7G-related lncRNAs, we identified 42 DE-m7G-lncRNAs. Using XGBoost and Boruta algorithms, 8 biomarkers for KIRC were selected. Kaplan-Meier survival analysis showed significant survival differences in KIRC patients with high and low expression of the PTCSC3 and RP11-321G12.1. Univariate and multivariate Cox regression analyses showed that AP000696.2, PTCSC3 and clinical characteristics were independent prognostic factors for patients with KIRC. A nomogram based on these prognostic factors accurately predicted the prognosis of KIRC patients. The biomarkers showed associations with clinical features of KIRC patients, mainly localized in the cytoplasm and related to cytokine-mediated immune response. Furthermore, immune feature analysis demonstrated a significant decrease in immune cell infiltration levels in KIRC samples compared to normal samples, with a negative correlation observed between the biomarkers and most differentially infiltrating immune cells and common immune checkpoints. CONCLUSION In summary, this study discovered eight prognostic biomarkers associated with KIRC patients. These biomarkers showed significant correlations with clinical features, immune cell infiltration, and immune checkpoint expression in KIRC patients, laying a theoretical foundation for the diagnosis and treatment of KIRC.
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Affiliation(s)
- Shuangze Zhong
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
| | - Shangjin Chen
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
| | - Hansheng Lin
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
- Department of Urology, Yangjiang People's Hospital affiliated to Guangdong Medical University, Yangjiang, 42 Dongshan Road, Jiangcheng District, Guangdong Province, 529500, China
| | - Yuancheng Luo
- Guangdong Medical University, Zhanjiang City, 524023, Guangdong Province, China
| | - Jingwei He
- Department of Urology, Yangjiang People's Hospital affiliated to Guangdong Medical University, Yangjiang, 42 Dongshan Road, Jiangcheng District, Guangdong Province, 529500, China.
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Luo W, Lu J, Zheng X, Wang J, Qian S, Bai Z, Wu M. A novel prognostic N 7-methylguanosine-related long non-coding RNA signature in clear cell renal cell carcinoma. Sci Rep 2023; 13:18454. [PMID: 37891201 PMCID: PMC10611723 DOI: 10.1038/s41598-023-45287-w] [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: 02/03/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is regulated by methylation modifications and long noncoding RNAs (lncRNAs). However, knowledge of N7-methylguanosine (m7G)-related lncRNAs that predict ccRCC prognosis remains insufficient. A prognostic multi-lncRNA signature was created using LASSO regression to examine the differential expression of m7G-related lncRNAs in ccRCC. Furthermore, we performed Kaplan-Meier analysis and area under the curve (AUC) analysis for diagnosis. In all, a model based on five lncRNAs was developed. Principal component analysis (PCA) indicated that the risk model precisely separated the patients into different groups. The IC50 value for drug sensitivity divided patients into two risk groups. High-risk group of patients was more susceptible to A.443654, A.770041, ABT.888, AMG.706, and AZ628. Moreover, a lower tumor mutation burden combined with low-risk scores was associated with a better prognosis of ccRCC. Quantitative real-time polymerase chain reaction (qRT-PCR) exhibited that the expression levels of LINC01507, AC093278.2 were very high in all five ccRCC cell lines, AC084876.1 was upregulated in all ccRCC cell lines except 786-O, and the levels of AL118508.1 and DUXAP8 were upregulated in the Caki-1 cell line. This risk model may be promising for the clinical prediction of prognosis and immunotherapeutic responses in patients with ccRCC.
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Affiliation(s)
- Wang Luo
- School of Stomatology, Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - Jing Lu
- Department of Clinical, Zunyi Medical and Pharmaceutical College, Zunyi, 563000, Guizhou, China
| | - Xiang Zheng
- Department of Medical Genetics, Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - JinJing Wang
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - ShengYan Qian
- School of Stomatology, Zunyi Medical University, Zunyi, 563000, Guizhou, China
| | - ZhiXun Bai
- Department of Nephrology, the Second Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, Guizhou, China.
| | - MingSong Wu
- School of Stomatology, Zunyi Medical University, Zunyi, 563000, Guizhou, China.
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Lin Z, Wu Z, Yuan Y, Zhong W, Luo W. m7G-related genes predict prognosis and affect the immune microenvironment and drug sensitivity in osteosarcoma. Front Pharmacol 2023; 14:1158775. [PMID: 37654606 PMCID: PMC10466804 DOI: 10.3389/fphar.2023.1158775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 08/01/2023] [Indexed: 09/02/2023] Open
Abstract
Background: Osteosarcoma (OS), a primary malignant bone tumor, confronts therapeutic challenges rooted in multidrug resistance. Comprehensive understanding of disease occurrence and progression is imperative for advancing treatment strategies. m7G modification, an emerging post-transcriptional modification implicated in various diseases, may provide new insights to explore OS pathogenesis and progression. Methods: The m7G-related molecular landscape in OS was probed using diverse bioinformatics analyses, encompassing LASSO Cox regression, immune infiltration assessment, and drug sensitivity analysis. Furthermore, the therapeutic potential of AZD2014 for OS was investigated through cell apoptosis and cycle assays. Eventually, multivariate Cox analysis and experimental validations, were conducted to investigate the independent prognostic m7G-related genes. Results: A comprehensive m7G-related risk model incorporating eight signatures was established, with corresponding risk scores correlated with immune infiltration and drug sensitivity. Drug sensitivity analysis spotlighted AZD2014 as a potential therapeutic candidate for OS. Subsequent experiments corroborated AZD2014's capability to induce G1-phase cell cycle arrest and apoptosis in OS cells. Ultimately, multivariate Cox regression analysis unveiled the independent prognostic importance of CYFIP1 and EIF4A1, differential expressions of which were validated at histological and cytological levels. Conclusion: This study furnishes a profound understanding of the contribution of m7G-related genes to the pathogenesis of OS. The discerned therapeutic potential of AZD2014, in conjunction with the identification of CYFIP1 and EIF4A1 as independent risk factors, opens novel vistas for the treatment of OS.
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Affiliation(s)
- Zili Lin
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Ziyi Wu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yuhao Yuan
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Wei Zhong
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Wei Luo
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
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Yang J, Xu J, Wang W, Zhang B, Yu X, Shi S. Epigenetic regulation in the tumor microenvironment: molecular mechanisms and therapeutic targets. Signal Transduct Target Ther 2023; 8:210. [PMID: 37217462 DOI: 10.1038/s41392-023-01480-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/17/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Over decades, researchers have focused on the epigenetic control of DNA-templated processes. Histone modification, DNA methylation, chromatin remodeling, RNA modification, and noncoding RNAs modulate many biological processes that are crucial to the development of cancers. Dysregulation of the epigenome drives aberrant transcriptional programs. A growing body of evidence suggests that the mechanisms of epigenetic modification are dysregulated in human cancers and might be excellent targets for tumor treatment. Epigenetics has also been shown to influence tumor immunogenicity and immune cells involved in antitumor responses. Thus, the development and application of epigenetic therapy and cancer immunotherapy and their combinations may have important implications for cancer treatment. Here, we present an up-to-date and thorough description of how epigenetic modifications in tumor cells influence immune cell responses in the tumor microenvironment (TME) and how epigenetics influence immune cells internally to modify the TME. Additionally, we highlight the therapeutic potential of targeting epigenetic regulators for cancer immunotherapy. Harnessing the complex interplay between epigenetics and cancer immunology to develop therapeutics that combine thereof is challenging but could yield significant benefits. The purpose of this review is to assist researchers in understanding how epigenetics impact immune responses in the TME, so that better cancer immunotherapies can be developed.
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Affiliation(s)
- Jing Yang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Pancreatic Cancer Institute, Shanghai, China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Pancreatic Cancer Institute, Shanghai, China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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Lu J, Yang P, Yu L, Xie N, Wu Y, Li B. Identification of m7G-Related LncRNA Signature for Predicting Prognosis and Evaluating Tumor Immune Infiltration in Pancreatic Adenocarcinoma. Diagnostics (Basel) 2023; 13:diagnostics13101697. [PMID: 37238181 DOI: 10.3390/diagnostics13101697] [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: 02/27/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
N7-Methylguanosine (m7G) modification holds significant importance in regulating posttranscriptional gene expression in epigenetics. Long non-coding RNAs (lncRNAs) have been demonstrated to play a crucial role in cancer progression. m7G-related lncRNA may be involved in the progression of pancreatic cancer (PC), although the underlying mechanism of regulation remains obscure. We obtained RNA sequence transcriptome data and relevant clinical information from the TCGA and GTEx databases. Univariate and multivariate Cox proportional risk analyses were performed to build a twelve-m7G-associated lncRNA risk model with prognostic value. The model was verified using receiver operating characteristic curve analysis and Kaplan-Meier analysis. The expression level of m7G-related lncRNAs in vitro was validated. Knockdown of SNHG8 increased the proliferation and migration of PC cells. Differentially expressed genes between high- and low-risk groups were identified for gene set enrichment analysis, immune infiltration, and potential drug exploration. We conducted an m7G-related lncRNA predictive risk model for PC patients. The model had independent prognostic significance and offered an exact survival prediction. The research provided us with better knowledge of the regulation of tumor-infiltrating lymphocytes in PC. The m7G-related lncRNA risk model may serve as a precise prognostic tool and indicate prospective therapeutic targets for PC patients.
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Affiliation(s)
- Jiawei Lu
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Pusheng Yang
- Department of Obstetrics and Gynecology, Shanghai Key Laboratory of Gynecology Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lanting Yu
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Ni Xie
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Ying Wu
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Baiwen Li
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
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Ma C, Tu D, Xu Q, Wu Y, Song X, Guo Z, Zhao X. Identification of m 7G regulator-mediated RNA methylation modification patterns and related immune microenvironment regulation characteristics in heart failure. Clin Epigenetics 2023; 15:22. [PMID: 36782329 PMCID: PMC9926673 DOI: 10.1186/s13148-023-01439-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/05/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND N7-methylguanosine (m7G) modification has been reported to regulate RNA expression in multiple pathophysiological processes. However, little is known about its role and association with immune microenvironment in heart failure (HF). RESULTS One hundred twenty-four HF patients and 135 nonfailing donors (NFDs) from six microarray datasets in the gene expression omnibus (GEO) database were included to evaluate the expression profiles of m7G regulators. Results revealed that 14 m7G regulators were differentially expressed in heart tissues from HF patients and NFDs. Furthermore, a five-gene m7G regulator diagnostic signature, NUDT16, NUDT4, CYFIP1, LARP1, and DCP2, which can easily distinguish HF patients and NFDs, was established by cross-combination of three machine learning methods, including best subset regression, regularization techniques, and random forest algorithm. The diagnostic value of five-gene m7G regulator signature was further validated in human samples through quantitative reverse-transcription polymerase chain reaction (qRT-PCR). In addition, consensus clustering algorithms were used to categorize HF patients into distinct molecular subtypes. We identified two distinct m7G subtypes of HF with unique m7G modification pattern, functional enrichment, and immune characteristics. Additionally, two gene subgroups based on m7G subtype-related genes were further discovered. Single-sample gene-set enrichment analysis (ssGSEA) was utilized to assess the alterations of immune microenvironment. Finally, utilizing protein-protein interaction network and weighted gene co-expression network analysis (WGCNA), we identified UQCRC1, NDUFB6, and NDUFA13 as m7G methylation-associated hub genes with significant clinical relevance to cardiac functions. CONCLUSIONS Our study discovered for the first time that m7G RNA modification and immune microenvironment are closely correlated in HF development. A five-gene m7G regulator diagnostic signature for HF (NUDT16, NUDT4, CYFIP1, LARP1, and DCP2) and three m7G methylation-associated hub genes (UQCRC1, NDUFB6, and NDUFA13) were identified, providing new insights into the underlying mechanisms and effective treatments of HF.
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Affiliation(s)
- Chaoqun Ma
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, 110000, Liaoning, China
| | - Dingyuan Tu
- Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, 110000, Liaoning, China
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China
| | - Qiang Xu
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, Shanghai, 200052, China
| | - Yan Wu
- Department of Cardiology, Navy 905 Hospital, Naval Medical University, Shanghai, 200052, China
| | - Xiaowei Song
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China.
| | - Zhifu Guo
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China.
| | - Xianxian Zhao
- Department of Cardiology, Changhai Hospital, Naval Medical University, 168 Changhai Rd, Shanghai, 200433, China.
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Li DX, Feng DC, Wang XM, Wu RC, Zhu WZ, Chen K, Han P. M7G-related molecular subtypes can predict the prognosis and correlate with immunotherapy and chemotherapy responses in bladder cancer patients. Eur J Med Res 2023; 28:55. [PMID: 36732869 PMCID: PMC9893617 DOI: 10.1186/s40001-023-01012-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/26/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND N7-methylguanosine (m7G) is closely associated with tumor prognosis and immune response in many cancer types. The correlation between m7G and bladder cancer (BC) needs further study. We aimed to orchestrate molecular subtypes and identify key genes for BC from the perspective of m7G. METHODS RNA-seq and clinical data of BC patients were extracted from TCGA and GSE13507 datasets. The patients were subtyped by "ConsensusClusterPlus" and "limma." The clusters were validated by the Kaplan‒Meier curves, univariable and multivariate Cox regression models, the concordance index, and calibration curves. The immunotherapy response was evaluated by immune checkpoints, immune infiltration, TIDE score, and IMvigor210 cohort. Genomics of Drug Sensitivity in Cancer was utilized to predict the chemotherapy response between the clusters. RESULTS The m7G-related cluster was ultimately established by EIF4G1, NUDT11, NUDT10, and CCNB1. The independent prognostic value of the m7G-related cluster was validated by the TCGA and GSE13507 datasets. The cluster was involved in immune-associated pathways, such as neutrophil degranulation, antigen processing cross-presentation, and signaling by interleukins pathways. Meanwhile, cluster 2 was positively correlated with many immune checkpoints, such as CD274, CTLA4, HAVCR2, LAG3, PDCD1, and PDCD1LG2. The cluster 2 was significantly correlated with a higher TIDE score than the cluster 1. Furthermore, in the IMvigor210 cohort, patients in the cluster 1 had a higher response rate than those in the cluster 2. Patients in the cluster 2 were sensitive to many chemotherapies. CONCLUSIONS We successfully determined molecular subtypes and identified key genes for BC from the perspective of m7G, thereby providing a roadmap for the evolution of immunotherapy and precision medicine.
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Affiliation(s)
- Deng-xiong Li
- grid.13291.380000 0001 0807 1581Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, Guoxue Xiang #37, Chengdu, 610041 China
| | - De-chao Feng
- grid.13291.380000 0001 0807 1581Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, Guoxue Xiang #37, Chengdu, 610041 China
| | - Xiao-ming Wang
- grid.13291.380000 0001 0807 1581Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, Guoxue Xiang #37, Chengdu, 610041 China
| | - Rui-cheng Wu
- grid.13291.380000 0001 0807 1581Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, Guoxue Xiang #37, Chengdu, 610041 China
| | - Wei-zhen Zhu
- grid.13291.380000 0001 0807 1581Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, Guoxue Xiang #37, Chengdu, 610041 China
| | - Kai Chen
- grid.13291.380000 0001 0807 1581Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, Guoxue Xiang #37, Chengdu, 610041 China
| | - Ping Han
- grid.13291.380000 0001 0807 1581Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Sichuan Province, Guoxue Xiang #37, Chengdu, 610041 China
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The Multifaceted Role of Connexins in Tumor Microenvironment Initiation and Maintenance. BIOLOGY 2023; 12:biology12020204. [PMID: 36829482 PMCID: PMC9953436 DOI: 10.3390/biology12020204] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Today's research on the processes of carcinogenesis and the vital activity of tumor tissues implies more attention be paid to constituents of the tumor microenvironment and their interactions. These interactions between cells in the tumor microenvironment can be mediated via different types of protein junctions. Connexins are one of the major contributors to intercellular communication. They form the gap junctions responsible for the transfer of ions, metabolites, peptides, miRNA, etc., between neighboring tumor cells as well as between tumor and stromal cells. Connexin hemichannels mediate purinergic signaling and bidirectional molecular transport with the extracellular environment. Additionally, connexins have been reported to localize in tumor-derived exosomes and facilitate the release of their cargo. A large body of evidence implies that the role of connexins in cancer is multifaceted. The pro- or anti-tumorigenic properties of connexins are determined by their abundance, localization, and functionality as well as their channel assembly and non-channel functions. In this review, we have summarized the data on the contribution of connexins to the formation of the tumor microenvironment and to cancer initiation and progression.
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Jiang A, Song J, Fang X, Fang Y, Wang Z, Liu B, Wu Z, Qu L, Luo P, Wang L. A novel thinking: DDR axis refines the classification of ccRCC with distinctive prognosis, multi omics landscape and management strategy. Front Public Health 2022; 10:1029509. [PMID: 36478716 PMCID: PMC9720257 DOI: 10.3389/fpubh.2022.1029509] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/02/2022] [Indexed: 11/22/2022] Open
Abstract
Background DNA damage response and repair (DDR) related signatures play an important role in maintaining genome stability and other biological processes. It also affects the occurrence, development, and treatment of cancer. However, in renal cell carcinoma (RCC), especially clear cell renal carcinoma (ccRCC), the potential association between DDR-related signatures and tumor heterogeneity and tumor microenvironment (TME) remains unclear. Methods Utilizing unsupervised clustering algorithm, we divided RCC into two subgroups, DCS1 and DCS2, according to the differences in DDR gene expression, and compared the characteristics of the two subgroups through multiple dimensions. Results Compared with DCS1, DCS2 patients have higher clinical stage/grade and worse prognosis, which may be related to active metabolic status and immunosuppression status. At the same time, the high mutation rate in DCS2 may also be an important reason for the prognosis. We also analyzed the sensitivity of the two subgroups to different therapeutic agents and established a subtypes' biomarkers-based prognostic system with good validation results to provide ideas for clinical diagnosis and treatment. Finally, we identified a pivotal role for DDX1 in the DDR gene set, which may serve as a future therapeutic target. Conclusion This study showed that DDR has an important impact on the development and treatment of RCC. DCS2 subtypes have a poor prognosis, and more personalized treatment and follow-up programs may be needed. The assessment of DDR gene mutations in patients may be helpful for clinical decision-making. DDX1 may be one of the effective targets for RCC treatment in the future.
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Affiliation(s)
- Aimin Jiang
- Department of Urology, Changhai Hospital, Navel Medical University (Second Military Medical University), Shanghai, China
| | - Jiaao Song
- Department of Urology, Changhai Hospital, Navel Medical University (Second Military Medical University), Shanghai, China
| | - Xiao Fang
- Department of Urology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yu Fang
- Department of Urology, Changhai Hospital, Navel Medical University (Second Military Medical University), Shanghai, China
| | - Zheng Wang
- Department of Urology, Changhai Hospital, Navel Medical University (Second Military Medical University), Shanghai, China
| | - Bing Liu
- Department of Urology, The Third Affiliated Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Zhenjie Wu
- Department of Urology, Changhai Hospital, Navel Medical University (Second Military Medical University), Shanghai, China
| | - Le Qu
- Department of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China,*Correspondence: Le Qu
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China,Peng Luo
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Navel Medical University (Second Military Medical University), Shanghai, China,Linhui Wang
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12
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Lai G, Zhong X, Liu H, Deng J, Li K, Xie B. A Novel m7G-Related Genes-Based Signature with Prognostic Value and Predictive Ability to Select Patients Responsive to Personalized Treatment Strategies in Bladder Cancer. Cancers (Basel) 2022; 14:5346. [PMID: 36358764 PMCID: PMC9656096 DOI: 10.3390/cancers14215346] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 09/08/2023] Open
Abstract
Although N7-methylguanosine (m7G) modification serves as a tumor promoter in bladder cancer (BLCA), the comprehensive role of m7G-related characterization in BLCA remains unclear. In this study, we systematically evaluated the m7G-related clusters of 760 BLCA patients through consensus unsupervised clustering analysis. Next, we investigated the underlying m7G-related genes among these m7G-related clusters. Univariate Cox and LASSO regressions were used for screening out prognostic genes and for reducing the dimension, respectively. Finally, we developed a novel m7G-related scoring system via the GSVA algorithm. The correlation between tumor microenvironment, prediction of personalized therapies and this m7G-related signature was gradually revealed. We first identified three m7G-related clusters and 1108 differentially expressed genes relevant to the three clusters. Based on the profile of 1108 genes, we divided BLCA patients into two clusters, which were quantified by our established m7G-related scoring system. Patients with higher m7G-related scores tended to have a better OS and more chances to benefit from immunotherapy. A significantly negative connection between sensitivity to classic chemotherapeutic drugs and m7G-related signature was uncovered. In summary, our data show that m7G-related characterization of BLCA patients can be of value for prognostic stratification and for patient-oriented therapeutic options, designing personalized treatment strategies in the preclinical setting.
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Affiliation(s)
| | - Xiaoni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing 400016, China
| | | | | | | | - Biao Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing 400016, China
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13
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Wei W, Liu C, Wang C, Wang M, Jiang W, Zhou Y, Zhang S. Comprehensive pan-cancer analysis of N7-methylguanosine regulators: Expression features and potential implications in prognosis and immunotherapy. Front Genet 2022; 13:1016797. [PMID: 36339001 PMCID: PMC9633684 DOI: 10.3389/fgene.2022.1016797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/11/2022] [Indexed: 11/27/2022] Open
Abstract
Although immunotherapy has made great strides in cancer therapy, its effectiveness varies widely among individual patients as well as tumor types, and there is an urgent need to develop biomarkers for effectively assessing immunotherapy response. In recent years, RNA methylation regulators have demonstrated to be novel potential biomarkers for prognosis as well as immunotherapy of cancers, such as N6-methyladenine (m6A) and 5-methylcytosine (m5C). N7-methylguanosine (m7G) is a prevalent RNA modification in eukaryotes, but the relationship between m7G regulators and prognosis as well as tumor immune microenvironment is still unclear. In this study, a pan-cancer analysis of 26 m7G regulators across 17 cancer types was conducted based on the bioinformatics approach. On the one hand, a comprehensive analysis of expression features, genetic variations and epigenetic regulation of m7G regulators was carried out, and we found that the expression tendency of m7G regulators were different among tumors and their aberrant expression in cancers could be affected by single nucleotide variation (SNV), copy number variation (CNV), DNA methylation and microRNA (miRNA) separately or simultaneously. On the other hand, the m7Gscore was modeled based on single sample gene set enrichment analysis (ssGSEA) for evaluating the relationships between m7G regulators and cancer clinical features, hallmark pathways, tumor immune microenvironment, immunotherapy response as well as pharmacotherapy sensitivity, and we illustrated that the m7Gscore exhibited tight correlations with prognosis, several immune features, immunotherapy response and drug sensitivity in most cancers. In conclusion, our pan-cancer analysis revealed that m7G regulators may exert critical roles in the tumor progression and immune microenvironment, and have the potential as biomarkers for predicting prognosis, immunotherapy response as well as candidate drug compounds for cancer patients.
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Affiliation(s)
- Wei Wei
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Chao Liu
- Department of Vascular Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Caihong Wang
- Department of Pathology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Meng Wang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wei Jiang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yaqian Zhou
- College of Chemistry and Materials Science, Northwest University, Xi’an, Shaanxi, China
- *Correspondence: Shuqun Zhang, ; Yaqian Zhou,
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Shuqun Zhang, ; Yaqian Zhou,
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RNA modifications: importance in immune cell biology and related diseases. Signal Transduct Target Ther 2022; 7:334. [PMID: 36138023 PMCID: PMC9499983 DOI: 10.1038/s41392-022-01175-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
RNA modifications have become hot topics recently. By influencing RNA processes, including generation, transportation, function, and metabolization, they act as critical regulators of cell biology. The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years. Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells, including development, differentiation, activation, migration, and polarization, thereby modulating the immune responses and are involved in some immune related diseases. In this review, we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, and adenosine-to-inosine (A-to-I) RNA editing, and summarize their critical roles in immune cell biology. Via regulating the biological processes of immune cells, RNA modifications can participate in the pathogenesis of immune related diseases, such as cancers, infection, inflammatory and autoimmune diseases. We further highlight the challenges and future directions based on the existing knowledge. All in all, this review will provide helpful knowledge as well as novel ideas for the researchers in this area.
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