1
|
Fan W, Xing Y, Yan S, Liu W, Ning J, Tian F, Wang X, Zhan Y, Luo L, Cao M, Huang J, Cai L. DUSP5 regulated by YTHDF1-mediated m6A modification promotes epithelial-mesenchymal transition and EGFR-TKI resistance via the TGF-β/Smad signaling pathway in lung adenocarcinoma. Cancer Cell Int 2024; 24:208. [PMID: 38872157 DOI: 10.1186/s12935-024-03382-6] [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: 02/16/2024] [Accepted: 05/23/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) patients have a dismal survival rate because of cancer metastasis and drug resistance. The study aims to identify the genes that concurrently modulate EMT, metastasis and EGFR-TKI resistance, and to investigate the underlying regulatory mechanisms. METHODS Cox regression and Kaplan-Meier analyses were applied to identify prognostic oncogenes in LUAD. Gene set enrichment analysis (GSEA) was used to indicate the biological functions of the gene. Wound-healing and Transwell assays were used to detect migratory and invasive ability. EGFR-TKI sensitivity was evaluated by assessing the proliferation, clonogenic survival and metastatic capability of cancer cells with treatment with gefitinib. Methylated RNA immunoprecipitation (MeRIP) and RNA immunoprecipitation (RIP) analyses established the level of m6A modification present on the target gene and the protein's capability to interact with RNA, respectively. Single-sample gene set enrichment (ssGSEA) algorithm used to investigate levels of immune cell infiltration. RESULTS Our study identified dual-specificity phosphatase 5 (DUSP5) as a novel and powerful predictor of adverse outcomes for LUAD by using public datasets. Functional enrichment analysis found that DUSP5 was positively enriched in EMT and transforming growth factor-beta (TGF-β) signaling pathway, a prevailing pathway involved in the induction of EMT. As expected, DUSP5 knockdown suppressed EMT via inhibiting the canonical TGF-β/Smad signaling pathway in in vitro experiments. Consistently, knockdown of DUSP5 was first found to inhibit migratory ability and invasiveness of LUAD cells in in vitro and prevent lung metastasis in in vivo. DUSP5 knockdown re-sensitized gefitinib-resistant LUAD cells to gefitinib, accompanying reversion of EMT progress. In LUAD tissue samples, we found 14 cytosine-phosphate-guanine (CpG) sites of DUSP5 that were negatively associated with DUSP5 gene expression. Importantly, 5'Azacytidine (AZA), an FDA-approved DNA methyltransferase inhibitor, restored DUSP5 expression. Moreover, RIP experiments confirmed that YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), a m6A reader protein, could bind DUSP5 mRNA. YTHDF1 promoted DUSP5 expression and the malignant phenotype of LUAD cells. In addition, the DUSP5-derived genomic model revealed the two clusters with distinguishable immune features and tumor mutational burden (TMB). CONCLUSIONS Briefly, our study discovered DUSP5 which was regulated by epigenetic modification, might be a potential therapeutic target, especially in LUAD patients with acquired EGFR-TKI resistance.
Collapse
Affiliation(s)
- Weina Fan
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Ying Xing
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Shi Yan
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Wei Liu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Jinfeng Ning
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fanglin Tian
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Xin Wang
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Yuning Zhan
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Lixin Luo
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China
| | - Mengru Cao
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China.
| | - Jian Huang
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China.
| | - Li Cai
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Haping Road 150, Harbin, 150081, China.
| |
Collapse
|
2
|
Shen C, Jiang K, Zhang W, Su B, Wang Z, Chen X, Zheng B, He T. LASSO regression and WGCNA-based telomerase-associated lncRNA signaling predicts clear cell renal cell carcinoma prognosis and immunotherapy response. Aging (Albany NY) 2024; 16:9386-9409. [PMID: 38819232 PMCID: PMC11210217 DOI: 10.18632/aging.205871] [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: 01/08/2024] [Accepted: 04/16/2024] [Indexed: 06/01/2024]
Abstract
OBJECTIVE To investigate whether telomerase-associated lncRNA expression affects the prognosis and anti-tumor immunity of patients with renal clear cell carcinoma (ccRCC). METHODS A series of analyses were performed to establish a prognostic risk model and validate its accuracy. Immune-related analyses were performed to assess further the association between immune status, tumor microenvironment, and prognostic risk models. RESULTS Eight telomerase-associated lncRNAs associated with prognosis were identified and applied to establish a prognostic risk model. Overall survival was higher in the low-risk group. CONCLUSION The established prognostic risk model has a good predictive ability for the prognosis of ccRCC patients and provides a new possible therapeutic target for ccRCC.
Collapse
MESH Headings
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/mortality
- Carcinoma, Renal Cell/therapy
- Carcinoma, Renal Cell/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Humans
- Kidney Neoplasms/genetics
- Kidney Neoplasms/immunology
- Kidney Neoplasms/mortality
- Kidney Neoplasms/therapy
- Telomerase/genetics
- Telomerase/metabolism
- Prognosis
- Immunotherapy/methods
- Gene Expression Regulation, Neoplastic
- Tumor Microenvironment/immunology
- Tumor Microenvironment/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Signal Transduction/genetics
- Male
- Female
- Gene Regulatory Networks
Collapse
Affiliation(s)
- Cheng Shen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Kaiyao Jiang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Wei Zhang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Baohui Su
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Zhenyu Wang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xinfeng Chen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Bing Zheng
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Tao He
- Party Committe and Hospital Administration Office, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| |
Collapse
|
3
|
Yin Y, Yang S, Huang Z, Yang Z, Zhang C, He Y. RNA methylation-related genes INHBB and SOWAHA are associated with MSI status in colorectal cancer patients and may serve as prognostic markers for predicting immunotherapy efficacy. Carcinogenesis 2024; 45:337-350. [PMID: 38400766 DOI: 10.1093/carcin/bgae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/29/2023] [Accepted: 02/19/2024] [Indexed: 02/26/2024] Open
Abstract
The role of RNA methylation is vital in the advancement and spread of tumors. However, its exact role in microsatellite instability in colorectal cancer (CRC) is still not fully understood. To address this gap in knowledge, this study investigated the impact of genes associated with RNA methylation on the prognosis and response to immunotherapy in individuals diagnosed with low microsatellite instability (MSI-L) or microsatellite stable (MSS) CRC. The differentially expressed genes (DEGs) in two groups of patients: those with high microsatellite instability (MSI-H) and those with MSI-L/MSS was thoroughly investigated and compared with aims of exploring the association between them and the 60 RNA methylation regulators. We employed these genes and developed an MSI-RMscore to establish a risk signature capable of forecasting patient outcomes. Furthermore, an investigation of the immunophenotypic traits was conducted encompassing patients categorized as high-risk and low-risk. By combining the MSI-RMscore and clinicopathological features, a predictive nomogram was developed, which was subsequently validated using the GEO database. Furthermore, immunohistochemistry was employed to establish the correlation between INHBB and SOWAHA and the MSI status, as well as patient prognosis. Our findings indicated that the high-risk subgroup exhibited unfavorable overall survival rates, reduced responsiveness to immune checkpoint blockers, elevated estimate scores, and increased infiltration of macrophages and fibroblasts. We also confirmed that INHBB and SOWAHA were associated with CRC patient prognosis and MSI status, as well as immunotherapy response. These findings suggest that targeting INHBB and SOWAHA could be a promising strategy to enhance patient responsiveness to immunotherapy.
Collapse
Affiliation(s)
- Yuehan Yin
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Shangjiu Yang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Zhijian Huang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Pathology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Zheng Yang
- Department of Pathology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Changhua Zhang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yulong He
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| |
Collapse
|
4
|
Wang J, Shu J. Construction of RNA Methylation Modification-immune-related lncRNA Molecular Subtypes and Prognostic Scoring System in Lung Adenocarcinoma. Curr Med Chem 2024; 31:1539-1560. [PMID: 37680151 DOI: 10.2174/0929867331666230901110629] [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: 05/31/2023] [Revised: 07/13/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND RNA methylation modification is not only intimately interrelated with cancer development and progression but also actively influences immune cell infiltration in the tumor microenvironment (TME). RNA methylation modification genes influence the therapeutic progression of lung adenocarcinoma (LUAD), and mining RNA methylation modification prognosis-related markers in LUAD is crucial for its precise prognosis. METHODS RNA-Seq data and Gene sets were collected from online databases or published literature. Genomic variation analysis was conducted by the Maftools package. RNA methylation-immune-related lncRNAs were obtained by Pearson correlation analysis. Then, Consistent clustering analysis was performed to obtain RNA methylation modification- immune molecular subtypes (RMM-I Molecular subtypes) in LUAD based on selected lncRNAs. COX and random survival forest analysis were carried out to construct the RMM-I Score. The receiver operating characteristic (ROC) curve and Kaplan Meier survival analysis were used to assess survival differences. Tumor immune microenvironment was assessed through related gene signatures and CIBERSORT algorithm. In addition, drug sensitivity analysis was executed by the pRRophetic package. RESULTS Four RNA methylation modified-immune molecular subtypes (RMM-I1, RMM- I2, RMM-I3, RMM-I4) were presented in LUAD. Patients in RMM-I4 exhibited excellent survival advantages and immune activity. HAVCR2, CD274, and CTLA-4 expression were activated in RMM-I4, which might be heat tumors and a potential beneficial group for immunotherapy. OGFRP1, LINC01116, DLGAP1-AS2, CRNDE, LINC01137, MIR210HG, and CYP1B1-AS1 comprised the RMM-I Score. The RMM-I Score exhibited excellent accuracy in the prognostic assessment of LUAD, as patients with a low RMM- I Score exhibited remarkable survival advantage. Patients with a low RMM-I score might be more sensitive to treatment with Docetaxel, Vinorelbine, Paclitaxel, Cisplatin, and immunotherapy. CONCLUSION The RMM-I molecular subtype constituted the novel molecular characteristic subtype of LUAD, which complemented the existing pathological typing. More refined and accurate molecular subtypes provide help to reveal the mechanism of LUAD development. In addition, the RMM-I score offers a reliable tool for accurate prognosis of LUAD.
Collapse
Affiliation(s)
- Jiajing Wang
- Department of Clinical Laboratory, Beilun People's Hospital, Ningbo, 315000, China
| | - Jianfeng Shu
- Huamei Hospital, University of Chinese Academy of Sciences, Ningbo, 315000, China
| |
Collapse
|
5
|
Cao C, Luo Z, Zhang H, Yao S, Lu H, Zheng K, Wang Y, Zou M, Qin W, Xiong H, Yuan X, Wang Y, Pinheiro RN, Peixoto RD, Zou Y, Xiong H. A methylation-related signature for predicting prognosis and sensitivity to first-line therapies in gastric cancer. J Gastrointest Oncol 2023; 14:2354-2372. [PMID: 38196539 PMCID: PMC10772674 DOI: 10.21037/jgo-23-770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/16/2023] [Indexed: 01/11/2024] Open
Abstract
Background Methylation modification patterns play a crucial role in human cancer progression, especially in gastrointestinal cancers. We aimed to use methylation regulators to classify patients with gastric adenocarcinoma and build a model to predict prognosis, promoting the application of precision medicine. Methods We obtained RNA sequencing data and clinical data from The Cancer Genome Atlas (TCGA) database (n=335) and Gene Expression Omnibus (GEO) database (n=865). Unsupervised consensus clustering was used to identify subtypes of gastric adenocarcinoma. We performed functional enrichment analysis, immune infiltration analysis, drug sensitivity analysis, and molecular feature analysis to determine the clinical application for different subtypes. The univariate Cox regression analysis and the LASSO regression analysis were subsequently used to identify prognosis-related methylation regulators and construct a risk model. Results Through unsupervised consensus clustering, patients were divided into two subtypes (cluster A and cluster B) with different clinical outcomes. Cluster B included patients with a better prognosis outcome and who were more likely to respond to immunotherapy. We then successfully built a predictive model and found five methylation-related genes (CHAF1A, CPNE8, PHLDA3, SPARC, and EHF) potentially significant to the prognosis of patients. The 1-, 3-, and 5-year areas under the curve of the risk model were 0.712, 0.696, and 0.759, respectively. The risk score was an independent prognostic factor and had the highest concordance index among common clinical indicators. Meanwhile, the tumor microenvironment, sensitivity of chemotherapeutic drugs, molecular features, and oncogenic dedifferentiation differed significantly across the risk groups and subtypes. Conclusions We classified patients with gastric adenocarcinoma based on methylation regulators, which has positive implications for first-line clinical treatment. The prognostic model could predict the prognosis of patients and help to promote the development of precision medicine.
Collapse
Affiliation(s)
- Chenlin Cao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of the Second Clinical College, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyong Luo
- Division of Breast and Thyroid Surgery, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuo Yao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Lu
- Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Zheng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Man Zou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yihua Wang
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | | | - Renata D’Alpino Peixoto
- Department of Gastrointestinal Medical Oncology, Oncoclinicas, Av. Brigadeiro Faria Lima, São Paulo, Brazil
| | - Yanmei Zou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
6
|
Liu J, Dou M, Liu X, Lu Y, Lu W. A novel m6A/m5C/m1A score signature to evaluate prognosis and its immunotherapy value in colon cancer patients. J Cancer Res Clin Oncol 2023; 149:11995-12012. [PMID: 37421455 PMCID: PMC10465387 DOI: 10.1007/s00432-023-05033-1] [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: 06/14/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND Colon cancer features strong heterogeneity and invasiveness, with high incidence and mortality rates. Recently, RNA modifications involving m6A, m5C, and m1A play a vital part in tumorigenesis and immune cell infiltration. However, integrated analysis among various RNA modifications in colon cancer has not been performed. METHODS RNA-seq profiling, clinical data and mutation data were obtained from The Cancer Genome Atlas and Gene Expression Omnibus. We first explored the mutation status and expression levels of m6A/m5C/m1A regulators in colon cancer. Then, different m6A/m5C/m1A clusters and gene clusters were identified by consensus clustering analysis. We further constructed and validated a scoring system, which could be utilized to accurately assess the risk of individuals and guide personalized immunotherapy. Finally, m6A/m5C/m1A regulators were validated by immunohistochemical staining and RT-qPCR. RESULTS In our study, three m6A/m5C/m1A clusters and gene clusters were identified. Most importantly, we constructed a m6A/m5C/m1A scoring system to assess the clinical risk of the individuals. Besides, the prognostic value of the score was validated with three independent cohorts. Moreover, the level of the immunophenoscore of the low m6A/m5C/m1A score group increased significantly with CTLA-4/PD-1 immunotherapy. Finally, we validated that the mRNA and protein expression of VIRMA and DNMT3B increased in colon cancer tissues. CONCLUSIONS We constructed and validated a stable and powerful m6A/m5C/m1A score signature to assess the survival outcomes and immune infiltration characteristics of colon cancer patients, which further guides optimization of personalized treatment, making it valuable for clinical translation and implementation.
Collapse
Affiliation(s)
- Jinsong Liu
- Department of Oncology, Wujin Hospital Affiliated With Jiangsu University, Changzhou, 213017, Jiangsu, China
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine, Jiangsu University, Changzhou, 213017, Jiangsu, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou, 213017, Jiangsu, China
| | - Min Dou
- Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Xiuling Liu
- Department of Oncology, Wujin Hospital Affiliated With Jiangsu University, Changzhou, 213017, Jiangsu, China
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine, Jiangsu University, Changzhou, 213017, Jiangsu, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou, 213017, Jiangsu, China
| | - Yueyao Lu
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine, Jiangsu University, Changzhou, 213017, Jiangsu, China
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou, 213017, Jiangsu, China
- Department of Oncology, Changzhou Clinical Medical College, Nanjing Medical University, Changzhou, 213017, Jiangsu, China
| | - Wenbin Lu
- Department of Oncology, Wujin Hospital Affiliated With Jiangsu University, Changzhou, 213017, Jiangsu, China.
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine, Jiangsu University, Changzhou, 213017, Jiangsu, China.
- Changzhou Key Laboratory of Molecular Diagnostics and Precision Cancer Medicine, Changzhou, 213017, Jiangsu, China.
- Department of Oncology, Changzhou Clinical Medical College, Nanjing Medical University, Changzhou, 213017, Jiangsu, China.
- Department of Oncology, The Wujin Clinical College of Xuzhou Medical University, Changzhou, 213017, Jiangsu, China.
| |
Collapse
|
7
|
Zhao J, Han H, Wang R, Wang Y, Zhang Y, Li N, Wang B, Chu Z, Zhang Y, Zhang H. Identification of N1 methyladenosine-related biomarker predicting overall survival outcomes and experimental verification in ovarian cancer. J Obstet Gynaecol Res 2023; 49:2457-2467. [PMID: 37435915 DOI: 10.1111/jog.15745] [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: 12/05/2022] [Accepted: 07/04/2023] [Indexed: 07/13/2023]
Abstract
AIM This study aimed to construct a N1-methyladenosine (m1A)-related biomarker model for predicting the prognosis of ovarian cancer (OVCA). METHODS OVCA samples were clustered into two subtypes using the Non-Negative Matrix Factorization (NMF) algorithm, including TCGA (n = 374) as the training set and GSE26712 (n = 185) as the external validation set. Hub genes, which were screened to construct a risk model, and nomogram to predict the overall survival of OVCA were explored and validated through various bioinformatic analysis and quantitative real-time PCR. RESULTS Following bootstrap correction, the C-index of nomogram was 0.62515, showing reliable performance. The functions of DEGs in the high- and low-risk groups were mainly enriched in immune response, immune regulation, and immune-related diseases. The immune cells relevant to the expression of hub genes were explored, for example, Natural Killer (NK) cells, T cells, activated dendritic cells (aDC). CONCLUSIONS AADAC, CD38, CACNA1C, and ATP1A3 might be used as m1A-related biomarkers for OVCA, and the nomogram labeled with m1A for the first time had excellent performance for predicting overall survival in OVCA.
Collapse
Affiliation(s)
- Jing Zhao
- Department of Obstetrics and Gynecology, The First Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Hua Han
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Runfang Wang
- Department of Obstetrics, Hebei General Hospital, Shijiazhuang, China
| | - Yazhuo Wang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Yuan Zhang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Na Li
- Department of Oncology, Hebei General Hospital, Shijiazhuang, China
| | - Bei Wang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Zhaoping Chu
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Yunxia Zhang
- Department of Gynecology, Hebei General Hospital, Shijiazhuang, China
| | - Hongzhen Zhang
- Department of Obstetrics and Gynecology, The First Hospital of Hebei Medical University, Shijiazhuang, China
| |
Collapse
|
8
|
Deng K, Li JX, Yang R, Mou ZQ, Yang L, Yang QQ. Identification and validation of a novel prognostic model for gastric cancer based on m7G-related genes. Transl Cancer Res 2023; 12:1836-1851. [PMID: 37588749 PMCID: PMC10425669 DOI: 10.21037/tcr-22-2614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/06/2023] [Indexed: 08/18/2023]
Abstract
Background The role of N7-methyladenosine (m7G)-related genes in the progression and prognosis of gastric cancer (GC) remains unclear. This study aimed to explore prognostic biomarkers for GC based on m7G methylation regulators and to construct a prognostic risk model. Methods RNA sequencing profiles with corresponding clinicopathological information associated with GC of which the histological type was stomach adenocarcinoma (STAD) were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), respectively. A total of 29 m7G regulators were extracted from previous studies. According to the expression similarity of m7G regulators, the GC samples obtained from TCGA were further classified into 2 clusters demonstrating different overall survival (OS) rates and genetic heterogeneity, and the differentially expressed genes (DEGs) between these 2 clusters were defined as m7G-related genes. Univariate regression analysis and regression analysis were then used to obtain the prognostic m7G-related genes. The samples in TCGA and Genotype-Tissue Expression (GTEx) were used to verify the differential expression and prognostic value of these m7G-related genes contained in the prognostic model. Subsequently, the risk score was combined with other prognostic factors to develop a nomogram. The predictive ability of the nomogram was evaluated by the standard receiver operating characteristic (ROC) curve. Gene set enrichment analysis (GSEA) was used to identify activation pathways in both groups. Finally, the association between the prognostic model and the immune characteristics of GC were appraised. Results A prognostic model consisting of 11 m7G-related genes was constructed. GC patients in the high-risk group were shown to have a poor prognosis and this result was further demonstrated in each group. The risk model can be applied for patients with different clinical features. The results of GSEA showed that cell adhesion, cell junction, and focal adhesion were highly enriched in the high-risk group. In addition, we found that the expression of programmed cell death ligand 1 (PD-L1) was significantly elevated in the low-risk group, whereas programmed cell death ligand 2 (PD-L2) and tumor necrosis factor receptor superfamily member 4 (TNFRSF4) were overexpressed in the high-risk group. Conclusions We successfully built and verified a m7G relevant prognostic model for predicting prognosis and providing a new train of thought for improving the treatment of GC.
Collapse
Affiliation(s)
- Kun Deng
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jian-Xin Li
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Rui Yang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhi-Qiang Mou
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Li Yang
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qing-Qiang Yang
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China
| |
Collapse
|
9
|
Li D, Shi Z, Liu X, Jin S, Chen P, Zhang Y, Chen G, Fan X, Yang J, Lin H. Identification and development of a novel risk model based on cuproptosis-associated RNA methylation regulators for predicting prognosis and characterizing immune status in hepatocellular carcinoma. Hepatol Int 2023; 17:112-130. [PMID: 36598701 DOI: 10.1007/s12072-022-10460-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/12/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Cuproptosis, a novel cell death caused by excess copper, is quite obscure in hepatocellular carcinoma (HCC) and needs more investigation. METHODS RNA-seq and clinical data of HCC patients TCGA database were analyzed to establish a predictive model through LASSO Cox regression analysis. External dataset ICGC was used for the verification. GSEA and CIBERSORT were applied to investigate the molecular mechanisms and immune microenvironment of HCC. Cuproptosis induced by elesclomol was confirmed via various in vitro experiments. The expression of prognostic genes was verified in HCC tissues using qRT-PCR analysis. RESULTS Initially, 18 cuproptosis-associated RNA methylation regulators (CARMRs) were selected for prognostic analysis. A nine-gene signature was created by applying the LASSO Cox regression method. Survival and ROC assays were carried out to validate the model using TCGA and ICGC database. Moreover, there exhibited obvious differences in drug sensitivity in terms of common drugs. A higher tumor mutation burden was shown in the high-risk group. Additionally, significant discrepancies were found between the two groups in metabolic pathways and RNA processing via GSEA analysis. Meanwhile, CIBERSORT analysis indicated different infiltrating levels of various immune cells between the two groups. Elesclomol treatment caused a unique form of programmed cell death accompanied by loss of lipoylated mitochondrial proteins and Fe-S cluster protein. The results of qRT-PCR indicated that most prognostic genes were differentially expressed in the HCC tissues. CONCLUSION Overall, our predictive signature displayed potential value in the prediction of overall survival of HCC patients and might provide valuable clues for personalized therapies.
Collapse
Affiliation(s)
- Duguang Li
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China
| | - Zhaoqi Shi
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China
| | - Xiaolong Liu
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China
| | - Shengxi Jin
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China
| | - Peng Chen
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China
| | - Yiyin Zhang
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China
| | - Guoqiao Chen
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China
| | - Xiaoxiao Fan
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China.
| | - Jing Yang
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China.
| | - Hui Lin
- Department of General Surgery, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, 3 East Qingchun Rd, Hangzhou, 310016, People's Republic of China. .,Zhejiang Engineering Research Center of Cognitive Healthcare, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, People's Republic of China. .,College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, People's Republic of China.
| |
Collapse
|
10
|
Identification and validation of RNA methylation-related alternative splicing gene signature for low-grade glioma to predict survival and immune landscapes. J Cancer Res Clin Oncol 2023; 149:47-62. [PMID: 36528831 DOI: 10.1007/s00432-022-04431-1] [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: 09/18/2022] [Accepted: 10/18/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Low-grade glioma (LGG) is a crucial pathological type of glioma. The present study aimed to explore multiple RNA methylation regulator-related AS events and investigate their prognostic values in LGG. METHODS The prognostic model for low-grade glioma was established using the LASSO regression analysis. To validate prognostic value, we performed Kaplan-Maier survival analysis, ROC curves and nomograms. The ESTIMATE algorithm, the CIBERSORT algorithm and the ssGSEA algorithm were utilized to explore the role of the immune microenvironment in LGG. Subsequently, we then used GO, KEGG and GSEA enrichment analysis to explore the functional roles of these genes. In addition, we employed the GDSC database to screen potential chemotherapeutic agents. RESULTS Eight RNA methylation related AS events were involved in construct a survival and prognosis model, which had good ability of independent prediction for patients with LGG. Patients in the high-risk group had shorter life expectancy and higher mortality, while patients in the low-risk group had a better prognosis. We constructed a nomogram which showed an excellent predictive performance for individual OS. The risk score exhibited a close correlation with some immune cells and expression of immune checkpoints. Patients in high-risk group were characterized by immunosuppressive microenvironment and poor response to immunotherapy, and were sensitive to more chemotherapeutic drugs. Pathway and functional enrichment analyses further confirmed that significant differences existed in immune landscape between the two subgroups. CONCLUSION The prognostic RNA methylation-related alternative splicing signature constructed could constitute a promising prognostic biomarker, which could serve to optimize treatment regimens.
Collapse
|
11
|
Feng J, Tang X, Song L, Zhou Z, Jiang Y, Huang Y. A telomerase regulation-related lncRNA signature predicts prognosis and immunotherapy response for gastric cancer. J Cancer Res Clin Oncol 2023; 149:135-146. [PMID: 36333566 DOI: 10.1007/s00432-022-04456-6] [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: 09/10/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Telomeres are involved in the development and progression of gastric cancer (GC). However, the association of telomerase regulation-related lncRNAs with prognosis and immunotherapy responsiveness in gastric cancer is unclear. METHODS This study systematically evaluated the relationship between lncRNAs co-expressed with 67 telomerase regulatory genes and gastric cancer prognosis. The risk scores of the samples were calculated based on telomerase regulation-related lncRNAs with prognostic value, and the samples were classified into high-/low-risk groups. The prognostic value of risk groups was then evaluated, a GC prognostic prediction model based on risk groups and clinical characteristics was established, and the prediction accuracy of the model was clarified by receiving operating characteristic (ROC) curves and calibration curves. Finally, the value of risk grouping in GC immunotherapy sensitivity was predicted by comparing MSI status and tumor mutation load between the high- and low-risk groups. RESULTS We identified 13 lncRNAs with prognostic value co-expressed with telomerase regulatory genes and observed that the prognosis of the low-risk group was significantly better than that of the high-risk group. Meanwhile, a GC overall survival (OS) prediction model based on risk grouping and clinical characteristics was developed, and ROC curves and calibration curves confirmed the good predictive ability of the model. In addition, the low-risk group exhibited a higher tumor mutation load and MSI-H, suggesting a possible benefit of immunotherapy. CONCLUSION We found that telomerase regulation-related lncRNAs have prognostic value in GC patients and contribute to the exploration of more effective immunotherapeutic strategies.
Collapse
Affiliation(s)
- Jinggao Feng
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China.
| | - Xiayu Tang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Liusong Song
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Zhipeng Zhou
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Yuan Jiang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Yao Huang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| |
Collapse
|
12
|
Ye X, Wang R, Yu X, Wang Z, Hu H, Zhang H. m6A/ m1A /m5C/m7G-related methylation modification patterns and immune characterization in prostate cancer. Front Pharmacol 2022; 13:1030766. [PMID: 36313300 PMCID: PMC9596993 DOI: 10.3389/fphar.2022.1030766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022] Open
Abstract
Methylation has a close relationship with immune reactions, metastasis, and cancer cell growth. Additionally, RNA methylation-related proteins have emerged as potential cancer therapeutic targets. The connection between the tumor microenvironment (TME) and methylation-related genes (MRGs) remains unclear. We explored the expression patterns of the MRGs in the genome and transcriptional fields of 796 prostate cancer (PCa) samples using two separate data sets. We identified a relationship between patient clinicopathological characteristics, prognosis, TME cell infiltrating qualities, and different MRG changes, as well as the identification of two distinct molecular groupings. Then, we formed an MRGs model to predict overall survival (OS), and we tested the accuracy of the model in patients with PCa. In addition, we developed a very accurate nomogram to improve the MRG model’s clinical applicability. The low-risk group had fewer tumor mutational burden (TMB), greater tumor immune dysfunction and exclusion (TIDE) ratings, fewer mutant genes, and better OS prospects. We discuss how MGRs may affect the prognosis, clinically important traits, TME, and immunotherapy responsiveness in PCa. In order to get a better understanding of MRGs in PCa, we could further explore the prognosis and create more effective immunotherapy regimens to open new avenues.
Collapse
Affiliation(s)
- Xin Ye
- Department of Urology, Institute of Urology, West China Hospital of Sichuan University, Chengdu, China
| | - Ruyi Wang
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, China
| | - Xiaoqian Yu
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zili Wang
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, China
| | - Haifeng Hu
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, China
| | - Hanchao Zhang
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, China
- Medical College of Soochow University, Suzhou, China
- *Correspondence: Hanchao Zhang,
| |
Collapse
|
13
|
RNA Modification in Inflammatory Bowel Diseases. Biomedicines 2022; 10:biomedicines10071695. [PMID: 35885000 PMCID: PMC9313455 DOI: 10.3390/biomedicines10071695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 12/02/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disorder characterized by damage to the intestinal mucosa, which is caused by a combination of factors. These include genetic and epigenetic alterations, environmental influence, microorganism interactions, and immune conditions. Some populations with IBD show a cancer-prone phenotype. Recent studies have provided insight into the involvement of RNA modifications in the specific pathogenesis of IBD through regulation of RNA biology in epithelial and immune cells. Studies of several RNA modification-targeting reagents have shown preferable outcomes in patients with colitis. Here, we note a new awareness of RNA modification in the targeting of IBD and related diseases, which will contribute to early diagnosis, disease monitoring, and possible control by innovative therapeutic approaches.
Collapse
|