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Peng B, Lin Y, Yi G, Lin M, Xiao Y, Qiu Y, Yao W, Zhou X, Liu Z. Comprehensive landscape of m6A regulator-related gene patterns and tumor microenvironment infiltration characterization in gastric cancer. Sci Rep 2024; 14:16404. [PMID: 39013954 PMCID: PMC11252343 DOI: 10.1038/s41598-024-66744-0] [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: 02/22/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
The epigenetic regulation of N6-methyladenosine (m6A) has attracted considerable interest in tumor research, but the potential roles of m6A regulator-related genes, remain largely unknown within the context of gastric cancer (GC) and tumor microenvironment (TME). Here, a comprehensive strategy of data mining and computational biology utilizing multiple datasets based on 28 m6A regulators (including novel anti-readers) was employed to identify m6A regulator-related genes and patterns and elucidate their underlying mechanisms in GC. Subsequently, a scoring system was constructed to evaluate individual prognosis and immunotherapy response. Three distinct m6A regulator-related patterns were identified through the unsupervised clustering of 56 m6A regulator-related genes (all significantly associated with GC prognosis). TME characterization revealed that these patterns highly corresponded to immune-inflamed, immune-excluded, and immune-desert phenotypes, and their TME characteristics were highly consistent with different clinical outcomes and biological processes. Additionally, an m6A-related scoring system was developed to quantify the m6A modification pattern of individual samples. Low scores indicated high survival rates and high levels of immune activation, whereas high scores indicated stromal activation and tumor malignancy. Furthermore, the m6A-related scores were correlated with tumor mutation loads and various clinical traits, including molecular or histological subtypes and clinical stage or grade, and the score had predictive values across all digestive system tumors and even in all tumor types. Notably, a low score was linked to improved responses to anti-PD-1/L1 and anti-CTLA4 immunotherapy in three independent cohorts. This study has expanded the important role of m6A regulator-related genes in shaping TME diversity and clinical/biological traits of GC. The developed scoring system could help develop more effective immunotherapy strategies and personalized treatment guidance.
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Affiliation(s)
- Bin Peng
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, State Key Laboratory of Respiratory Disease, The Fifth Affiliated Hospital, Guangzhou Medical University, The Fifth Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Yinglin Lin
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, State Key Laboratory of Respiratory Disease, The Fifth Affiliated Hospital, Guangzhou Medical University, The Fifth Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Gao Yi
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, State Key Laboratory of Respiratory Disease, The Fifth Affiliated Hospital, Guangzhou Medical University, The Fifth Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Mingzhen Lin
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, State Key Laboratory of Respiratory Disease, The Fifth Affiliated Hospital, Guangzhou Medical University, The Fifth Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Yao Xiao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, State Key Laboratory of Respiratory Disease, The Fifth Affiliated Hospital, Guangzhou Medical University, The Fifth Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Yezhenghong Qiu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, State Key Laboratory of Respiratory Disease, The Fifth Affiliated Hospital, Guangzhou Medical University, The Fifth Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Wenxia Yao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, State Key Laboratory of Respiratory Disease, The Fifth Affiliated Hospital, Guangzhou Medical University, The Fifth Clinical College of Guangzhou Medical University, Guangzhou, China.
| | - Xinke Zhou
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, State Key Laboratory of Respiratory Disease, The Fifth Affiliated Hospital, Guangzhou Medical University, The Fifth Clinical College of Guangzhou Medical University, Guangzhou, China.
| | - Zhaoyu Liu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, State Key Laboratory of Respiratory Disease, The Fifth Affiliated Hospital, Guangzhou Medical University, The Fifth Clinical College of Guangzhou Medical University, Guangzhou, China.
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Xiong H, Lin C, Huang X, Wang H. A novel mitochondrial-related lncRNA signature mediated prediction of overall survival, immune landscape, and the chemotherapeutic outcomes for bladder cancer patients. Discov Oncol 2024; 15:239. [PMID: 38907134 PMCID: PMC11192708 DOI: 10.1007/s12672-024-01108-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024] Open
Abstract
OBJECTIVE To develop a prognostic risk model for Bladder Cancer (BLCA) based on mitochondrial-related long non-coding RNAs (lncRNAs). METHODS Transcriptome and clinical data of BLCA patients were retrieved from the TCGA database. Mitochondrial-related lncRNAs with independent prognostic significance were screened to develop a prognostic risk model. Patients were categorized into high- and low-risk groups using the model. Various methods including Kaplan-Meier (KM) analysis, ROC curve analysis, Gene Set Enrichment Analysis (GSEA), immune analysis, and chemotherapy drug analysis were used to verify and evaluate the model. RESULTS A mitochondrial-associated lncRNA prognostic risk model with independent prognostic significance was developed. High-risk group (HRG) patients exhibited significantly shorter survival periods compared to low-risk group (LRG) patients (P < 0.01). The risk score from the model was an independent predictor of BLCA prognosis, correlating with tumor grade, pathological stage, and lymph node metastasis (P < 0.05). The HRG showed significant positive correlations with high expressions of immune checkpoints (CTLA4, LAG3, PD-1, TIGIT, PD-L1, PD-L2, and TIM-3) and lower IC50 for chemotherapy drugs (cisplatin, docetaxel, paclitaxel, methotrexate, and vinblastine) (P < 0.001). CONCLUSIONS The mitochondrial-related lncRNA-based prognostic risk model effectively predicts BLCA prognosis and can guide individualized treatment for BLCA patients.
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Affiliation(s)
- Hao Xiong
- Department of Urology, Nanping First Hospital Affiliated to Fujian Medical University, Nanping, 353000, China
| | - Cheng Lin
- Department of Urology, Nanping First Hospital Affiliated to Fujian Medical University, Nanping, 353000, China
| | - Xiang Huang
- Department of Urology, Nanping First Hospital Affiliated to Fujian Medical University, Nanping, 353000, China
| | - Hao Wang
- Department of Urology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China.
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Yang M, Wei Y, He X, Xia C. The deubiquitinating protein OTUD6B promotes lung adenocarcinoma progression by stabilizing RIPK1. Biol Direct 2024; 19:46. [PMID: 38880876 PMCID: PMC11181667 DOI: 10.1186/s13062-024-00489-8] [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: 04/19/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND There is growing evidence indicating that deubiquitinating enzymes may contribute to tumor progression and can serve as promising therapeutic targets. METHODS The overexpression of deubiquitinase OTUD6B in lung adenocarcinoma (LUAD) and its adjacent tissues was analyzed by immunohistochemistry and TCGA/GO database. Survival analysis further supported OTUD6B as a potential target for LUAD treatment. We assessed the effect of OTUD6B on LUAD cell growth using cell viability assays and conducted TUNEL staining, migration, and invasion experiments to investigate the impact of OTUD6B on the apoptosis and metastasis of LUAD cells. Additionally, we established a transplanted tumor model in nude mice to validate our findings in vivo. Finally, using IP mass spectrometry and co-IP experiments, we screened and confirmed the influence of RIPK1 as a substrate of OTUD6B in LUAD. RESULTS OTUD6B is highly overexpressed in human LUAD and predicts poor prognosis in LUAD patients. OTUD6B knockdown inhibited the proliferation of LUAD cells and enhanced apoptosis and inhibited metastasis in LUAD cells suppressed. A549 xenografts revealed that OTUD6B deletion can slow down tumour growth. Additionally, OTUD6B can bind to RIPK1, reduce its ubiquitination level and increase its protein stability. CONCLUSIONS Our results suggest that OTUD6B is a promising clinical target for LUAD treatment and that targeting OTUD6B may constitute an effective anti-LUAD strategy.
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Affiliation(s)
- Miaomiao Yang
- Department of Nephrology, Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial Clinical Research Center for Kidney Disease, Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450053, Henan, China.
| | - Yujie Wei
- National Engineering Laboratory for Internet Medical Systems and Applications, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, No. 1 Jianshe Road, Erqi District, Zhengzhou, 450052, Henan, China
| | - Xin He
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Zhengzhou University, No.3 Kangfuqian Street, Erqi District, Zhengzhou, China
| | - Changwei Xia
- Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital and Central China Branch of National Center Fuwai Cardiovascular Diseases, Zhengzhou, China.
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Wang W, Liu D, Yao J, Yuan Z, Yan L, Cao B. ANXA5: A Key Regulator of Immune Cell Infiltration in Hepatocellular Carcinoma. Med Sci Monit 2024; 30:e943523. [PMID: 38824386 PMCID: PMC11155417 DOI: 10.12659/msm.943523] [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: 12/16/2023] [Accepted: 04/10/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) poses a significant threat to human life and is the most prevalent form of liver cancer. The intricate interplay between apoptosis, a common form of programmed cell death, and its role in immune regulation stands as a crucial mechanism influencing tumor metastasis. MATERIAL AND METHODS Utilizing HCC samples from the TCGA database and 61 anoikis-related genes (ARGs) sourced from GeneCards, we analyzed the relationship between ARGs and immune cell infiltration in HCC. Subsequently, we identified long non-coding RNAs (lncRNAs) associated with ARGs, using the least absolute shrinkage and selection operator (LASSO) regression analysis to construct a robust prognostic model. The predictive capabilities of the model were then validated through examination in a single-cell dataset. RESULTS Our constructed prognostic model, derived from lncRNAs linked to ARGs, comprised 11 significant lncRNAs: NRAV, MCM3AP-AS1, OTUD6B-AS1, AC026356.1, AC009133.1, DDX11-AS1, AC108463.2, MIR4435-2HG, WARS2-AS1, LINC01094, and HCG18. The risk score assigned to HCC samples demonstrated associations with immune indicators and the infiltration of immune cells. Further, we identified Annexin A5 (ANXA5) as the pivotal gene among ARGs, with it exerting a prominent role in regulating the lncRNA gene signature. Our validation in a single-cell database elucidated the involvement of ANXA5 in immune cell infiltration, specifically in the regulation of mononuclear cells. CONCLUSIONS This study delves into the intricate correlation between ARGs and immune cell infiltration in HCC, culminating in the development of a novel prognostic model reliant on 11 ARGs-associated lncRNAs. Furthermore, our findings highlight ANXA5 as a promising target for immune regulation in HCC, offering new perspectives for immune therapy in the context of HCC.
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Zheng B, Zhou B, Ye D, Wang Y, Zheng W, Wang X, Liu D, Qian F, Zhou X, Yan T, Li Y, Fang L. LINC01572 promotes triple-negative breast cancer progression through EIF4A3-mediated β-catenin mRNA nuclear exportation. ENVIRONMENTAL TOXICOLOGY 2024; 39:3026-3039. [PMID: 38317508 DOI: 10.1002/tox.24171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/08/2024] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
Long noncoding RNAs have been reported to be involved in the development of breast cancer. LINC01572 was previously reported to promote the development of various tumors. However, the potential biological function of LINC01572 in breast cancer remains largely unknown. R language was used to perform bioinformatic analysis of The Cancer Genome Atlas data. The expression level of RNAs was examined by RT-qPCR. The effect of knocking down or overexpression LINC01572 in triple-negative breast cancer (TNBC) cell lines was evaluated by detecting cell proliferation, migrant action. RNA immunoprecipitation assay and RNA pull-down assay were performed to explore the regulatory relationship between LINC01572, EIF4A3, and β-catenin. Bioinformatics analysis identifies LINC01572 as an oncogene of breast cancer. LINC01572 is over-expressed in TNBC tissues and cell lines, correlated with poor clinical prognosis in BC patients. Cell function studies confirmed that LINC01572 facilitated the proliferation and migration of TNBC cells in both vivo and vitro. Mechanistically, β-catenin mRNA and EIF4A3 combine spatially to form a complex, LINC01572 helps transport this complex from the nucleus to the cytoplasm, thereby facilitating the translation of β-catenin. Our findings confirm that LINC01572 acts as a tumor promoter and may act as a biomarker in TNBC. In addition, novel molecular regulatory relationships involving LINC01572/EIF4A3/β-catenin are critical to the development of TNBC, which led to a new understanding of the mechanisms of TNBC progression and shows a new target for precision treatment for TNBC.
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Affiliation(s)
- Bowen Zheng
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Baian Zhou
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Danrong Ye
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Yuying Wang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Wenfang Zheng
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Xuehui Wang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Diya Liu
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Fengyuan Qian
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Xiqian Zhou
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Tao Yan
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
- Medical College, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Yating Li
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
- Medical College, Anhui University of Science and Technology, Huainan, People's Republic of China
| | - Lin Fang
- Department of Breast and Thyroid Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
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Yin Q, Qu Z, Mathew R, Zeng L, Du Z, Xue Y, Liu D, Zheng X. Epitranscriptomic orchestrations: Unveiling the regulatory paradigm of m6A, A-to-I editing, and m5C in breast cancer via long noncoding RNAs and microRNAs. Cell Biochem Funct 2024; 42:e3996. [PMID: 38561942 DOI: 10.1002/cbf.3996] [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: 01/31/2024] [Revised: 03/09/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Breast cancer (BC) poses a persistent global health challenge, particularly in countries with elevated human development indices linked to factors such as increased life expectancy, education, and wealth. Despite therapeutic progress, challenges persist, and the role of epitranscriptomic RNA modifications in BC remains inadequately understood. The epitranscriptome, comprising diverse posttranscriptional modifications on RNA molecules, holds the potential to intricately modulate RNA function and regulation, implicating dysregulation in various diseases, including BC. Noncoding RNAs (ncRNAs), acting as posttranscriptional regulators, influence physiological and pathological processes, including cancer. RNA modifications in long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) add an extra layer to gene expression control. This review delves into recent insights into epitranscriptomic RNA modifications, such as N-6-methyladenosine (m6A), adenine-to-inosine (A-to-I) editing, and 5-methylcytosine (m5C), specifically in the context of lncRNA and miRNAs in BC, highlighting their potential implications in BC development and progression. Understanding this intricate regulatory landscape is vital for deciphering the molecular mechanisms underlying BC and identifying potential therapeutic targets.
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Affiliation(s)
- Qinan Yin
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Zhifeng Qu
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Regina Mathew
- Department of Chemistry and Biochemistry, California State University, Los Angeles, California, USA
| | - Li Zeng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Zhe Du
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Yun Xue
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Dechun Liu
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Xuewei Zheng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
- Henan Engineering Research Center of Digital Pathology and Artificial Intelligence Diagnosis, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
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Wang Y, Bu N, Luan XF, Song QQ, Ma BF, Hao W, Yan JJ, Wang L, Zheng XL, Maimaitiyiming Y. Harnessing the potential of long non-coding RNAs in breast cancer: from etiology to treatment resistance and clinical applications. Front Oncol 2024; 14:1337579. [PMID: 38505593 PMCID: PMC10949897 DOI: 10.3389/fonc.2024.1337579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Breast cancer (BC) is the most common malignancy among women and a leading cause of cancer-related deaths of females worldwide. It is a complex and molecularly heterogeneous disease, with various subtypes that require different treatment strategies. Despite advances in high-resolution single-cell and multinomial technologies, distant metastasis and therapeutic resistance remain major challenges for BC treatment. Long non-coding RNAs (lncRNAs) are non-coding RNAs with more than 200 nucleotides in length. They act as competing endogenous RNAs (ceRNAs) to regulate post-transcriptional gene stability and modulate protein-protein, protein-DNA, and protein-RNA interactions to regulate various biological processes. Emerging evidence suggests that lncRNAs play essential roles in human cancers, including BC. In this review, we focus on the roles and mechanisms of lncRNAs in BC progression, metastasis, and treatment resistance, and discuss their potential value as therapeutic targets. Specifically, we summarize how lncRNAs are involved in the initiation and progression of BC, as well as their roles in metastasis and the development of therapeutic resistance. We also recapitulate the potential of lncRNAs as diagnostic biomarkers and discuss their potential use in personalized medicine. Finally, we provide lncRNA-based strategies to promote the prognosis of breast cancer patients in clinical settings, including the development of novel lncRNA-targeted therapies.
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Affiliation(s)
- Yun Wang
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Na Bu
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-fei Luan
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian-qian Song
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ba-Fang Ma
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Wenhui Hao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Jing-jing Yan
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Wang
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-ling Zheng
- Department of Pharmacy, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yasen Maimaitiyiming
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Cancer Center, Zhejiang University School of Medicine, Hangzhou, China
- Women’s Hospital, Institute of Genetics, and Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi, China
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Li F, Yang Y, Zhang X, Yu J, Yu Y. A novel prognostic model of breast cancer based on cuproptosis-related lncRNAs. Discov Oncol 2024; 15:35. [PMID: 38353835 PMCID: PMC10866837 DOI: 10.1007/s12672-024-00888-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/08/2024] [Indexed: 02/17/2024] Open
Abstract
OBJECTIVE Breast cancer (BC) is a deadly form of malignancy responsible for the death of a large number of women every year. Cuproptosis is a newly discovered form of cell death that may have implications for the prognosis of BC. Long non-coding RNAs (lncRNAs) have been shown to be involved in the progression and development of BC. Here within, a novel model capable of predicting the prognosis of patients with BC was established based on cuproptosis-related lncRNAs. METHODS Data of breast cancer patients was downloaded, including clinical information from The Cancer Genome Atlas (TCGA) database and lncRNAs related to cuproptosis were isolated. In total, nine lncRNAs related to copper death were obtained by Cox regression model based on Least Absolute Shrinkage and Selector Operation (LASSO) algorithm for model construction. The model was verified by overall survival (OS), progression-free survival (PFS) and receiver operating characteristic (ROC) curve. The differences in immune function, tumor mutation burden (TMB) and tumor immune dysfunction and exclusion (TIDE) between patients with different risk scores were analyzed. RESULTS Based on cuproptosis-related lncRNAs, a prognostic model for predicting BC was constructed. Each patient was assigned a risk score based on our model formula. We found that patients with higher risk scores had significantly lower OS and PFS, increased TMB, and higher sensitivity to immunotherapy. CONCLUSIONS The model established in this study based on cuproptosis-related lncRNAs may be capable of improving the OS of patients with BC.
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Affiliation(s)
- Feixiang Li
- Department of Anesthesiology, Tianjin Medical University General Hospital, NO.154, Anshan Road, Heping District, Tianjin, 300052, China
- Tianjin Research Institute of Anesthesiology, Tianjin, China
| | - Yongyan Yang
- Department of Anesthesiology, Tianjin Medical University General Hospital, NO.154, Anshan Road, Heping District, Tianjin, 300052, China
- Tianjin Research Institute of Anesthesiology, Tianjin, China
| | - Xuan Zhang
- Department of Anesthesiology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jiafeng Yu
- Department of Anesthesiology, Tianjin Medical University General Hospital, NO.154, Anshan Road, Heping District, Tianjin, 300052, China
- Tianjin Research Institute of Anesthesiology, Tianjin, China
| | - Yonghao Yu
- Department of Anesthesiology, Tianjin Medical University General Hospital, NO.154, Anshan Road, Heping District, Tianjin, 300052, China.
- Tianjin Research Institute of Anesthesiology, Tianjin, China.
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Li XQ, Yin SQ, Chen L, Tulamaiti A, Xiao SY, Zhang XL, Shi L, Miao XC, Yang Y, Xing X. Identification of a novel m6A-related lncRNAs signature and immunotherapeutic drug sensitivity in pancreatic adenocarcinoma. BMC Cancer 2024; 24:116. [PMID: 38262966 PMCID: PMC10804632 DOI: 10.1186/s12885-024-11885-8] [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: 08/10/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma (PDAC) ranks as the fourth leading cause for cancer-related deaths worldwide. N6-methyladenosine (m6A) and long non-coding RNAs (lncRNAs) are closely related with poor prognosis and immunotherapeutic effect in PDAC. The aim of this study is to construct and validate a m6A-related lncRNAs signature and assess immunotherapeutic drug sensitivity in PDAC. METHODS RNA-seq data for 178 cases of PDAC patients and 167 cases of normal pancreatic tissue were obtained from TCGA and GTEx databases, respectively. A set of 21 m6A-related genes were downloaded based on the previous report. Co-expression network was conducted to identify m6A-related lncRNAs in PDAC. Cox analyses and least absolute shrinkage and selection operator (Lasso) regression model were used to construct a risk prognosis model. The relationship between signature genes and immune function was explored by single-sample GSEA (ssGSEA). The tumor immune dysfunction and exclusion (TIDE) score and tumor mutation burden (TMB) were utilized to evaluate the response to immunotherapy. Furthermore, the expression levels of 4 m6A-related lncRNAs on PDAC cell lines were measured by the quantitative real-time PCR (qPCR). The drug sensitivity between the high- and low-risk groups was validated using PDAC cell lines by Cell-Counting Kit 8 (CCK8). RESULTS The risk prognosis model was successfully constructed based on 4 m6A-related lncRNAs, and PDAC patients were divided into the high- and low-risk groups. The overall survival (OS) of the high-risk groups was more unfavorable compared with the low-risk groups. Receiver operating characteristic (ROC) curves demonstrated that the risk prognosis model reasonably predicted the 2-, 3- and 5-year OS of PDAC patients. qPCR analysis confirmed the decreased expression levels of 4 m6A-related lncRNAs in PDAC cells compared to the normal pancreatic cells. Furthermore, CCK8 assay revealed that Phenformin exhibited higher sensitivity in the high-risk groups, while Pyrimethamine exhibited higher sensitivity in the low-risk groups. CONCLUSION The prognosis of patients with PDAC were well predicted in the risk prognosis model based on m6A-related lncRNAs, and selected immunotherapy drugs have potential values for the treatment of pancreatic cancer.
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Affiliation(s)
- Xia-Qing Li
- Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, China
| | - Shi-Qi Yin
- Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, China
| | - Lin Chen
- Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, Shanghai, China
| | - Aziguli Tulamaiti
- State Key Laboratory of Systems Medicine for Cancer, Ren Ji Hospital, School of Medicine, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Shu-Yu Xiao
- State Key Laboratory of Systems Medicine for Cancer, Ren Ji Hospital, School of Medicine, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Li Zhang
- State Key Laboratory of Systems Medicine for Cancer, Ren Ji Hospital, School of Medicine, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Shi
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Xiao-Cao Miao
- State Key Laboratory of Systems Medicine for Cancer, Ren Ji Hospital, School of Medicine, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Yang
- State Key Laboratory of Systems Medicine for Cancer, Ren Ji Hospital, School of Medicine, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China.
| | - Xin Xing
- Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Shanghai, China.
- Shanghai University of Medicine and Health Sciences Affiliated Sixth People's Hospital South Campus, Shanghai, China.
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Yang S, Li K, Zhang J, Liu J, Liu L, Tan Y, Xu C. Link between m6A modification and infiltration characterization of tumor microenvironment in lung adenocarcinoma. Exp Biol Med (Maywood) 2023; 248:2273-2288. [PMID: 38166412 PMCID: PMC10903232 DOI: 10.1177/15353702231214266] [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: 05/11/2023] [Accepted: 08/30/2023] [Indexed: 01/04/2024] Open
Abstract
N6-methyladenosine (m6A) RNA methylation plays a pivotal role in immune responses and the onset and advancement of cancer. Nonetheless, the precise impact of m6A modification in lung adenocarcinoma (LUAD) and its associated tumor microenvironment (TME) remains to be fully elucidated. Here, we distinguished distinct m6A modification patterns within two separate LUAD cohorts using a set of 21 m6A regulators. The TME characteristics associated with these two patterns align with the immune-inflamed and immune-excluded phenotypes, respectively. We identified 2064 m6A-related genes, which were used as a basis to divide all LUAD samples into three distinct m6A gene clusters. We applied a scoring system to evaluate the m6A gene signature of the m6A modification pattern in individual patients. To authenticate the categorization significance of m6A modification patterns, we established a correlation between m6A score and TME infiltration profiling, tumor somatic mutations, and responses to immunotherapy. A high level of m6A modification may be associated with the aggressiveness and poor prognosis of LUAD. Further studies should investigate the mechanism of action of m6A regulators and m6A-related genes to improve the diagnosis and treatment of patients with LUAD.
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Affiliation(s)
- Sha Yang
- Guizhou University Medical College, Guiyang 550025, China
| | - Ke Li
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Jiqin Zhang
- Department of Anesthesiology, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Jian Liu
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Lin Liu
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Ying Tan
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Chuan Xu
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
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Chen Y, Chen C, Gao G, Zeng C, Chen Z, Lin G, Yao G, Nian S, Chen X, Weng S, Gu X, Lin C. Identification and validation of N6-methyladenosine (m6A)-related lncRNAs signature for predicting the prognosis of laryngeal carcinoma, especially for smoking patients. Front Genet 2023; 14:1292164. [PMID: 38028627 PMCID: PMC10666777 DOI: 10.3389/fgene.2023.1292164] [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: 09/11/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Laryngeal cancer (LC), a highly fatal tumor in the head and neck region, has been the focus of research in recent years. The study of LC has primarily focused on the role of long non-coding RNAs (lncRNAs) in regulating gene expression, as they have emerged as pivotal factors in this biological process. Additionally, a reversible RNA modification called N6-methyladenosine (m6A) has been observed to have a significant impact on gene expression as well. The purpose of this research is to investigate the impact of m6A-related lncRNAs on the prognosis of laryngeal squamous cell carcinoma (LSCC). Specifically, this investigation analyzed the m6A-related regulators' patterns of expression and mutation, encompassing a total of 15 regulators. Drawing upon the expression levels of prognostic m6A-regulated lncRNAs, two distinct lncRNA clusters were identified. Further analysis revealed differentially expressed lncRNAs between these clusters. In addition to studying the expression of lncRNAs, the researchers also examined the distribution of clinical characteristics and the tumor microenvironment (TME) in relation to the identified lncRNA clusters. This provided valuable insights into potential associations between lncRNA expression patterns and the clinical features of LSCC. Through the establishment of a risk model associated with lncRNAs, we were able to further investigate their clinical features, prognosis, and immune status. Additionally, we conducted a separate analysis of LINC00528, a lncRNA associated with smoking, examining its expression, overall survival time, correlated mRNAs, and conducting enrichment of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), as well as determining the sensitivity of related drugs. RT-qPCR results also indicated an increase in LINC00528 expression among smoking LSCC patients. The findings suggest that a high expression level of LINC00528 in LSCC patients may lead to a more favorable prognosis, providing new insights for the management and treatment of LSCC patients, particularly those with high expression of LINC00528. Overall, this research sheds light on the prognostic impact of m6A-regulated lncRNAs in LSCC. The implications of these findings for the advancement of innovative therapeutic approaches for LSCC patients are noteworthy.
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Affiliation(s)
- Yuqing Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Chenyu Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Gufeng Gao
- Department of Geriatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Chaojun Zeng
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Zhifeng Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Gongbiao Lin
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Guangnan Yao
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Shenqing Nian
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Xihang Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Simin Weng
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Xi Gu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
| | - Chang Lin
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Otorhinolaryngology, Head and Neck Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Fujian Provincial Clinical Medical Research Center for Ear, Nose and Throat Difficulty Diseases, Fuzhou, Fujian, China
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Xiong Y, Kong X, Fang K, Sun G, Tu S, Wei Y, Ouyang Y, Wan R, Xiao W. Establishment of a novel signature to predict prognosis and immune characteristics of pancreatic cancer based on necroptosis-related long non-coding RNA. Mol Biol Rep 2023; 50:7405-7419. [PMID: 37452900 DOI: 10.1007/s11033-023-08663-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Necroptosis plays an important role in tumorigenesis and tumour progression. Long noncoding RNAs (lncRNAs) have been proven to be regulatory factors of necroptosis in various tumours. However, the real role of necroptosis-related lncRNAs (NRLs) and their potential to predict the prognosis of pancreatic cancer (PC) remain largely unclear. The goal of this study was to identify NRLs and create a predictive risk signature in PC, explore its prognostic predictive performance, and further assess immunotherapy and chemotherapy responses. METHODS RNA sequencing data, tumour mutation burden (TMB) data, and clinical profiles of 178 PC patients were downloaded from The Cancer Genome Atlas (TCGA) database. NRLs were identified using Pearson correlation analysis. Then, patients were divided into the training set and the validation set at a 1:1 ratio. Subsequently, Cox and LASSO regression analyses were conducted to establish a prognostic NRL signature in the training set and validation set. The predictive efficacy of the 5-NRL signature was assessed by survival analysis, nomogram, Cox regression, clinicopathological feature correlation analysis, and receiver operating characteristic (ROC) curve analysis. Furthermore, correlations between the risk score (RS) and immune cell infiltration, immune checkpoint molecules, somatic gene mutations, and anticancer drug sensitivity were analysed. Finally, we used quantitative reverse transcription polymerase chain reaction (qRT-PCR) to validate the 5-NRLs. RESULTS A 5-NRL signature was established to predict the prognosis of PC, including LINC00857, AL672291.1, PTPRN2-AS1, AC141930.2, and MEG9. The 5-NRL signature demonstrated a high degree of predictive power according to ROC and Kaplan‒Meier curves and was revealed to be an independent prognostic risk factor via stratified survival analysis. Nomogram and calibration curves indicated the clinical adaptability of the signature. Immune-related pathways were linked to the 5-NRL signature according to enrichment analysis. Additionally, immune cell infiltration, immune checkpoint molecules, somatic gene mutations and the half-maximal inhibitory concentration (IC50) of chemotherapeutic agents were significantly different between the two risk subgroups. These results suggested that our model can be used to evaluate the effectiveness of immunotherapy and chemotherapy, providing a potential new strategy for treating PC. CONCLUSIONS The novel 5-NRL signature is helpful for assessing the prognosis of PC patients and improving therapy options, so it can be further applied clinically.
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Affiliation(s)
- Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xiaoyu Kong
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Kang Fang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Gen Sun
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Shuju Tu
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yongyang Wei
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yonghao Ouyang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Renhua Wan
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Weidong Xiao
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
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Wang YW, Liu C, Chen YD, Yang B, Chen X, Ma G, Tian YR, Bo X, Zhang K. An angiogenesis-related lncRNA signature predicts the immune microenvironment and prognosis of breast cancer. Aging (Albany NY) 2023; 15:7616-7636. [PMID: 37543427 PMCID: PMC10457060 DOI: 10.18632/aging.204930] [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: 03/01/2023] [Accepted: 07/17/2023] [Indexed: 08/07/2023]
Abstract
Both angiogenesis and lncRNAs play crucial roles in the development and progression of breast cancer. Considering the unknown association of angiogenesis and lncRNAs in breast cancer, we aim to identify angiogenesis-related lncRNAs (ARLs) and explore their prognostic value. Here, based on analysis of The Cancer Genome Atlas database, the correlation between ARL and the prognosis and immune infiltration landscape of breast cancer were investigated. Eight ARLs (MAFG-DT, AC097478.1, AL357054.4, AL118556.1, SNHG10, MED14OS, OTUD6B-AS1, and CYTOR) were selected to construct the risk model as a prognostic signature. The survival rate of the patients in the high-risk group was lower than that in the low-risk group. The ARL signature was an independent prognostic predictor, and areas under the curve of 1-, 3-, and 5-year survival were 0.745, 0.695, and 0.699, respectively. The prognostic ARLs were associated with the immune infiltration landscape and could indicate the immune status, immune response, tumor mutational burden, and drug sensitivity of patients with breast cancer. Furthermore, qRT-PCR of clinical samples revealed that OTUD6B-AS1 was correlated with prognostic pathological parameters. OTUD6B-AS1 promoted breast cancer cell proliferation, wound healing, migration, invasion, and human umbilical vein endothelial cells tube formation. Mechanistically, OTUD6B-AS1 regulated EMT- and angiogenesis-related molecules. Taken together, we constructed and verified a robust signature of eight ARLs for the prediction of survival in patients with breast cancer, and the characterization of the immune infiltration landscape. Our findings suggest that OTUD6B-AS1 could be a therapeutic target for patients with breast cancer.
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Affiliation(s)
- Ya-Wen Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, People’s Republic of China
| | - Can Liu
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, People’s Republic of China
| | - Yan-Duo Chen
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, People’s Republic of China
| | - Bin Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, People’s Republic of China
| | - Xu Chen
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, People’s Republic of China
| | - Guangxin Ma
- Hematology and Oncology Unit, Department of Geriatrics, Qilu Hospital of Shandong University, Jinan, People’s Republic of China
| | - Ya-Ru Tian
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, People’s Republic of China
| | - Xiangkun Bo
- Department of General Surgery, Affiliated Haian Hospital of Nantong University, Nantong, People’s Republic of China
| | - Kai Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, People’s Republic of China
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Deng X, Qing Y, Horne D, Huang H, Chen J. The roles and implications of RNA m 6A modification in cancer. Nat Rev Clin Oncol 2023; 20:507-526. [PMID: 37221357 DOI: 10.1038/s41571-023-00774-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
N6-Methyladenosine (m6A), the most prevalent internal modification in eukaryotic mRNA, has been extensively and increasingly studied over the past decade. Dysregulation of RNA m6A modification and its associated machinery, including writers, erasers and readers, is frequently observed in various cancer types, and the dysregulation profiles might serve as diagnostic, prognostic and/or predictive biomarkers. Dysregulated m6A modifiers have been shown to function as oncoproteins or tumour suppressors with essential roles in cancer initiation, progression, metastasis, metabolism, therapy resistance and immune evasion as well as in cancer stem cell self-renewal and the tumour microenvironment, highlighting the therapeutic potential of targeting the dysregulated m6A machinery for cancer treatment. In this Review, we discuss the mechanisms by which m6A modifiers determine the fate of target RNAs and thereby influence protein expression, molecular pathways and cell phenotypes. We also describe the state-of-the-art methodologies for mapping global m6A epitranscriptomes in cancer. We further summarize discoveries regarding the dysregulation of m6A modifiers and modifications in cancer, their pathological roles, and the underlying molecular mechanisms. Finally, we discuss m6A-related prognostic and predictive molecular biomarkers in cancer as well as the development of small-molecule inhibitors targeting oncogenic m6A modifiers and their activity in preclinical models.
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Affiliation(s)
- Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - David Horne
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
- Gehr Family Center for Leukemia Research & City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
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Liu Z, Ren C, Cai J, Yin B, Yuan J, Ding R, Ming W, Sun Y, Li Y. A Novel Aging-Related Prognostic lncRNA Signature Correlated with Immune Cell Infiltration and Response to Immunotherapy in Breast Cancer. Molecules 2023; 28:molecules28083283. [PMID: 37110517 PMCID: PMC10141963 DOI: 10.3390/molecules28083283] [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: 01/20/2023] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Breast cancer (BC) is among the most universal malignant tumors in women worldwide. Aging is a complex phenomenon, caused by a variety of factors, that plays a significant role in tumor development. Consequently, it is crucial to screen for prognostic aging-related long non-coding RNAs (lncRNAs) in BC. The BC samples from the breast-invasive carcinoma cohort were downloaded from The Cancer Genome Atlas (TCGA) database. The differential expression of aging-related lncRNAs (DEarlncRNAs) was screened by Pearson correlation analysis. Univariate Cox regression, LASSO-Cox analysis, and multivariate Cox analysis were performed to construct an aging-related lncRNA signature. The signature was validated in the GSE20685 dataset from the Gene Expression Omnibus (GEO) database. Subsequently, a nomogram was constructed to predict survival in BC patients. The accuracy of prediction performance was assessed through the time-dependent receiver operating characteristic (ROC) curves, Kaplan-Meier analysis, principal component analyses, decision curve analysis, calibration curve, and concordance index. Finally, differences in tumor mutational burden, tumor-infiltrating immune cells, and patients' response to chemotherapy and immunotherapy between the high- and low-risk score groups were explored. Analysis of the TCGA cohort revealed a six aging-related lncRNA signature consisting of MCF2L-AS1, USP30-AS1, OTUD6B-AS1, MAPT-AS1, PRR34-AS1, and DLGAP1-AS1. The time-dependent ROC curve proved the optimal predictability for prognosis in BC patients with areas under curves (AUCs) of 0.753, 0.772, and 0.722 in 1, 3, and 5 years, respectively. Patients in the low-risk group had better overall survival and significantly lower total tumor mutational burden. Meanwhile, the high-risk group had a lower proportion of tumor-killing immune cells. The low-risk group could benefit more from immunotherapy and some chemotherapeutics than the high-risk group. The aging-related lncRNA signature can provide new perspectives and methods for early BC diagnosis and therapeutic targets, especially tumor immunotherapy.
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Affiliation(s)
- Zhixin Liu
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
- Department of Orthopedics, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Chongkang Ren
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Jinyi Cai
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Baohui Yin
- Department of Pediatrics, Yantai Affiliated Hospital of Binzhou Medical University, Yantai 264100, China
| | - Jingjie Yuan
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Rongjuan Ding
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Wenzhuo Ming
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
| | - Yunxiao Sun
- Department of Pediatrics, Yantai Affiliated Hospital of Binzhou Medical University, Yantai 264100, China
| | - Youjie Li
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, China
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Deng Y, Wang F, Wu X, Du K, Yang Q, Xia T. The m6A-regulation and single cell effect pattern in sunitinib resistance on clear cell renal cell carcinoma: Identification and validation of targets. Front Pharmacol 2023; 14:1131610. [PMID: 37063301 PMCID: PMC10102343 DOI: 10.3389/fphar.2023.1131610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Background: Sunitinib is the main target drug for clear cell renal cell carcinoma. However, the effect of sunitinib is often limited by acquired drug resistance.Methods: The open-accessed data used in this study were obtained from different online public databases, which were analyzed using the R software. The RNA level of specific genes was detected using quantitative Real-Time PCR. Sunitinib-resistant cell lines were constructed based on protocol get from the previous study. Colony formation and Cell Counting Kit-8 assays were applied to detect cell proliferation ability.Results: In this study, through publicly available data and high-quality analysis, we deeply explored the potential biological mechanisms that affect the resistance of sunitinib. Detailed, data from GSE64052, GSE76068 and The Cancer Genome Atlas were extracted. We identified the IFITM1, IL6, MX2, PCOLCE2, RSAD2 and SLC2A3 were associated with sunitinib resistance. Single-cell analysis, prognosis analysis and m6A regulatory network were conducted to investigate their role. Moreover, the MX2 was selected for further analysis, including its biological role and effect on the ccRCC microenvironment. Interestingly, we noticed that MX2 might be an immune-related gene that could affect the response rate of immunotherapy. Then, in vitro experiments validated the overexpression of MX2 in sunitinib-resistance cells. Colony formation assay indicated that the knockdown of MX2 could remarkably inhibit the proliferation ability of 786-O-Res and Caki-1-Res when exposed to sunitinib.Conclusion: In summary, through publicly available data and high-quality analysis, we deeply explored the potential biological mechanisms that affect the resistance of sunitinib. MX2 was selected for further analysis, including its biological role and effect on the ccRCC microenvironment. Finally, in vitro experiments were used to validate its role in ccRCC.
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Affiliation(s)
- Yanxi Deng
- Clinical Laboratory, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Fang Wang
- Clinical Laboratory, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xinhui Wu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Kangming Du
- Department of Cardiothoracic Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qing Yang
- Department of Cardiothoracic Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Qing Yang, ; Ting Xia,
| | - Ting Xia
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Qing Yang, ; Ting Xia,
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17
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Yang Z, Zheng Y, Wu H, Xie H, Zhao J, Chen Z, Li L, Yue X, Zhao B, Bian E. Integrative analysis of a novel super-enhancer-associated lncRNA prognostic signature and identifying LINC00945 in aggravating glioma progression. Hum Genomics 2023; 17:33. [PMID: 37004060 PMCID: PMC10064652 DOI: 10.1186/s40246-023-00480-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/25/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Super-enhancers (SEs), driving high-level expression of genes with tumor-promoting functions, have been investigated recently. However, the roles of super-enhancer-associated lncRNAs (SE-lncRNAs) in tumors remain undetermined, especially in gliomas. We here established a SE-lncRNAs expression-based prognostic signature to choose the effective treatment of glioma and identify a novel therapeutic target. METHODS Combined analysis of RNA sequencing (RNA-seq) data and ChIP sequencing (ChIP-seq) data of glioma patient-derived glioma stem cells (GSCs) screened SE-lncRNAs. Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets served to construct and validate SE-lncRNA prognostic signature. The immune profiles and potential immuno- and chemotherapies response prediction value of the signature were also explored. Moreover, we verified the epigenetic activation mechanism of LINC00945 via the ChIP assay, and its effect on glioma was determined by performing the functional assay and a mouse xenograft model. RESULTS 6 SE-lncRNAs were obtained and identified three subgroups of glioma patients with different prognostic and clinical features. A risk signature was further constructed and demonstrated to be an independent prognostic factor. The high-risk group exhibited an immunosuppressive microenvironment and was higher enrichment of M2 macrophage, regulatory T cells (Tregs), and Cancer-associated fibroblasts (CAFs). Patients in the high-risk group were better candidates for immunotherapy and chemotherapeutics. The SE of LINC00945 was further verified via ChIP assay. Mechanistically, BRD4 may mediate epigenetic activation of LINC00945. Additionally, overexpression of LINC00945 promoted glioma cell proliferation, EMT, migration, and invasion in vitro and xenograft tumor formation in vivo. CONCLUSION Our study constructed the first prognostic SE-lncRNA signature with the ability to optimize the choice of patients receiving immuno- and chemotherapies and provided a potential therapeutic target for glioma.
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Affiliation(s)
- Zhihao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Yinfei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Haoyuan Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Han Xie
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Jiajia Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Lianxin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
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18
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Cusenza VY, Tameni A, Neri A, Frazzi R. The lncRNA epigenetics: The significance of m6A and m5C lncRNA modifications in cancer. Front Oncol 2023; 13:1063636. [PMID: 36969033 PMCID: PMC10033960 DOI: 10.3389/fonc.2023.1063636] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/10/2023] [Indexed: 03/12/2023] Open
Abstract
Most of our transcribed RNAs are represented by non-coding sequences. Long non-coding RNAs (lncRNAs) are transcripts with no or very limited protein coding ability and a length >200nt. They can be epigenetically modified. N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 7-methylguanosine (m7G) and 2’-O-methylation (Nm) are some of the lncRNAs epigenetic modifications. The epigenetic modifications of RNA are controlled by three classes of enzymes, each playing a role in a specific phase of the modification. These enzymes are defined as “writers”, “readers” and “erasers”. m6A and m5C are the most studied epigenetic modifications in RNA. These modifications alter the structure and properties, thus modulating the functions and interactions of lncRNAs. The aberrant expression of several lncRNAs is linked to the development of a variety of cancers and the epigenetic signatures of m6A- or m5C-related lncRNAs are increasingly recognized as potential biomarkers of prognosis, predictors of disease stage and overall survival. In the present manuscript, the most up to date literature is reviewed with the focus on m6A and m5C modifications of lncRNAs and their significance in cancer.
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Affiliation(s)
- Vincenza Ylenia Cusenza
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Annalisa Tameni
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Antonino Neri
- Scientific Directorate, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Raffaele Frazzi
- Scientific Directorate, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy
- *Correspondence: Raffaele Frazzi,
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19
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Zhang YY, Li XW, Li XD, Zhou TT, Chen C, Liu JW, Wang L, Jiang X, Wang L, Liu M, Zhao YG, Li SD. Comprehensive analysis of anoikis-related long non-coding RNA immune infiltration in patients with bladder cancer and immunotherapy. Front Immunol 2022; 13:1055304. [PMID: 36505486 PMCID: PMC9732092 DOI: 10.3389/fimmu.2022.1055304] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Background Anoikis is a form of programmed cell death or programmed cell death(PCD) for short. Studies suggest that anoikis involves in the decisive steps of tumor progression and cancer cell metastasis and spread, but what part it plays in bladder cancer remains unclear. We sought to screen for anoikis-correlated long non-coding RNA (lncRNA) so that we can build a risk model to understand its ability to predict bladder cancer prognosis and the immune landscape. Methods We screened seven anoikis-related lncRNAs (arlncRNAs) from The Cancer Genome Atlas (TCGA) and designed a risk model. It was validated through ROC curves and clinicopathological correlation analysis, and demonstrated to be an independent factor of prognosis prediction by uni- and multi-COX regression. In the meantime, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, immune infiltration, and half-maximal inhibitory concentration prediction (IC50) were implemented with the model. Moreover, we divided bladder cancer patients into three subtypes by consensus clustering analysis to further study the differences in prognosis, immune infiltration level, immune checkpoints, and drug susceptibility. Result We designed a risk model of seven arlncRNAs, and proved its accuracy using ROC curves. COX regression indicated that the model might be an independent prediction factor of bladder cancer prognosis. KEGG enrichment analysis showed it was enriched in tumors and immune-related pathways among the people at high risk. Immune correlation analysis and drug susceptibility results indicated that it had higher immune infiltration and might have a better immunotherapy efficacy for high-risk groups. Of the three subtypes classified by consensus clustering analysis, cluster 3 revealed a positive prognosis, and cluster 2 showed the highest level of immune infiltration and was sensitive to most chemistries. This is helpful for us to discover more precise immunotherapy for bladder cancer patients. Conclusion In a nutshell, we found seven arlncRNAs and built a risk model that can identify different bladder cancer subtypes and predict the prognosis of bladder cancer patients. Immune-related and drug sensitivity researches demonstrate it can provide individual therapeutic schedule with greater precision for bladder cancer patients.
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Affiliation(s)
- Yao-Yu Zhang
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China,Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiao-Wei Li
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China
| | - Xiao-Dong Li
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China,Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ting-Ting Zhou
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China
| | - Chao Chen
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China
| | - Ji-Wen Liu
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China
| | - Li Wang
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China
| | - Xin Jiang
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China
| | - Liang Wang
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China
| | - Ming Liu
- Department of Urology, Xuanhan Chinese Medicine Hospital, Dazhou, China
| | - You-Guang Zhao
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China,*Correspondence: You-Guang Zhao, ; Sha-dan Li,
| | - Sha-dan Li
- Department of Urology, The General Hospital of Western Theater Command, Chengdu, China,Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China,*Correspondence: You-Guang Zhao, ; Sha-dan Li,
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20
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Wang Z, Zhou J, Zhang H, Ge L, Li J, Wang H. RNA m 6 A methylation in cancer. Mol Oncol 2022; 17:195-229. [PMID: 36260366 PMCID: PMC9892831 DOI: 10.1002/1878-0261.13326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/28/2022] [Accepted: 10/18/2022] [Indexed: 02/04/2023] Open
Abstract
N6 -methyladenosine (m6 A) is one of the most abundant internal modifications in eukaryotic messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). It is a reversible and dynamic RNA modification that has been observed in both internal coding segments and untranslated regions. Studies indicate that m6 A modifications play important roles in translation, RNA splicing, export, degradation and ncRNA processing control. In this review, we focus on the profiles and biological functions of RNA m6 A methylation on both mRNAs and ncRNAs. The dynamic modification of m6 A and its potential roles in cancer development are discussed. Moreover, we discuss the possibility of m6 A modifications serving as potential biomarkers for cancer diagnosis and targets for therapy.
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Affiliation(s)
- Zhaotong Wang
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Jiawang Zhou
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Haisheng Zhang
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Lichen Ge
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Jiexin Li
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Hongsheng Wang
- School of Pharmaceutical SciencesSun Yat‐sen UniversityGuangzhouChina
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21
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Cao J, Liang Y, Gu JJ, Huang Y, Wang B. Construction of prognostic signature of breast cancer based on N7-Methylguanosine-Related LncRNAs and prediction of immune response. Front Genet 2022; 13:991162. [PMID: 36353118 PMCID: PMC9639662 DOI: 10.3389/fgene.2022.991162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Long non-coding RNA (LncRNA) is a prognostic factor for malignancies, and N7-Methylguanosine (m7G) is crucial in the occurrence and progression of tumors. However, it has not been documented how well m7G-related LncRNAs predict the development of breast cancer (BC). This study aims to develop a predictive signature based on long non-coding RNAs (LncRNAs) associated with m7G to predict the prognosis of breast cancer patients. Methods: The Cancer Genome Atlas (TCGA) database provided us with the RNA-seq data and matching clinical information of individuals with breast cancer. To identify the signature of N7-Methylguanosine-Related LncRNAs and create a prognostic model, we employed co-expression network analysis, least absolute shrinkage selection operator (LASSO) regression analysis, univariate Cox regression analysis, and multivariate Cox regression analysis. The signature was assessed using the Kaplan-Meier analysis and Receiver Operating Characteristic (ROC) curve. A nomogram and principal component analysis (PCA) were employed to confirm the predictive signature’s usefulness. Then, we examined the drug sensitivity between the two risk groups and utilized single-sample gene set enrichment analysis (ssGSEA) to investigate the association between predictive factors and the tumor immune microenvironment in high-risk and low-risk groups. Results: Nine m7G-related LncRNAs (LINC01871, AP003469.4, Z68871.1, AC245297.3, EGOT, TFAP2A-AS1, AL136531.1, SEMA3B-AS1, AL606834.2) that are independently associated with the overall survival time (OS) of BC patients make up the signature we developed. For predicting 1-, 3-, and 5-year survival rates, the areas under the ROC curve (AUC) were 0.715, 0.724, and 0.726, respectively. The Kaplan-Meier analysis revealed that the prognosis of BC patients in the high-risk group was worse than that of those in the low-risk group. When compared to clinicopathological variables, multiple regression analysis demonstrated that risk score was a significant independent predictive factor for BC patients. The results of the ssGSEA study revealed a substantial correlation between the predictive traits and the BC patients’ immunological status, low-risk BC patients had more active immune systems, and they responded better to PD1/L1 immunotherapy. Conclusion: The prognostic signature, which is based on m7G-related LncRNAs, can be utilized to inform patients’ customized treatment plans by independently predicting their prognosis and how well they would respond to immunotherapy.
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Affiliation(s)
- Jin Cao
- Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yichen Liang
- Institute of Oncology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
- Department of Oncology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
| | - J. Juan Gu
- Medical College, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Oncology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
- Department of Oncology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
| | - Yuxiang Huang
- Institute of Oncology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
- Department of Oncology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
| | - Buhai Wang
- Medical College, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Oncology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
- Department of Oncology, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
- *Correspondence: Buhai Wang,
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22
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Definition of a Novel Cuproptosis-Relevant lncRNA Signature for Uncovering Distinct Survival, Genomic Alterations, and Treatment Implications in Lung Adenocarcinoma. J Immunol Res 2022; 2022:2756611. [PMID: 36281357 PMCID: PMC9587678 DOI: 10.1155/2022/2756611] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/04/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Objective Cuproptosis is a newly discovered copper-independent cell death modality, and limited evidence suggests the critical implications in human cancers. Nonetheless, the clinical impacts of cuproptosis-relevant lncRNAs in lung adenocarcinoma (LUAD) remain largely ill-defined. The present study was aimed at defining a cuproptosis-relevant lncRNA signature for LUAD and discuss the clinical utility. Methods We collected transcriptome expression profiling, clinical information, somatic mutation, and copy number variations from TCGA-LUAD cohort retrospectively. The genetic alterations of cuproptosis genes were systematically assessed across LUAD, and cuproptosis-relevant lncRNAs were screened for defining a LASSO prognostic model. Genomic alterations, immunological and stemness features, and therapeutic sensitivity were studied with a series of computational approaches. Results Cuproptosis genes displayed aberrant expression and widespread genomic alterations across LUAD, potentially modulated by m6A/m5C/m1A RNA modification mechanisms. We defined a cuproptosis-relevant lncRNA signature, with a reliable efficacy in predicting clinical outcomes. High-risk subset displayed higher somatic mutations, CNVs, TMB, SNV neoantigens, aneuploidy score, CTA score, homologous recombination defects, and intratumor heterogeneity, cytolytic activity, CD8+ T effector, and antigen processing machinery, proving that this subset might benefit from immunotherapy. Increased stemness indexes and activity of oncogenic pathways might contribute to undesirable prognostic outcomes for high-risk subset. Additionally, high-risk patients generally exhibited higher response to chemotherapeutic agents (cisplatin, etc.). We also predicted several small molecule compounds (GSK461364, KX2-391, etc.) for treating this subset. Conclusion Accordingly, this cuproptosis-relevant lncRNA signature offers an efficient approach to identify and characterize diverse prognosis, genomic alterations, and treatment outcomes in LUAD, thus potentially assisting personalized therapy.
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23
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Li J, Zhang Y, Li C, Wu H, Feng C, Wang W, Liu X, Zhang Y, Cai Y, Jia Y, Qiao H, Wu F, Zhang S. A lactate-related LncRNA model for predicting prognosis, immune landscape and therapeutic response in breast cancer. Front Genet 2022; 13:956246. [DOI: 10.3389/fgene.2022.956246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer (BC) has the highest incidence rate of all cancers globally, with high heterogeneity. Increasing evidence shows that lactate and long non-coding RNA (lncRNA) play a critical role in tumor occurrence, maintenance, therapeutic response, and immune microenvironment. We aimed to construct a lactate-related lncRNAs prognostic signature (LRLPS) for BC patients to predict prognosis, tumor microenvironment, and treatment responses. The BC data download from the Cancer Genome Atlas (TCGA) database was the entire cohort, and it was randomly assigned to the training and test cohorts at a 1:1 ratio. Difference analysis and Pearson correlation analysis identified 196 differentially expressed lactate-related lncRNAs (LRLs). The univariate Cox regression analysis, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analysis were used to construct the LRLPS, which consisted of 7 LRLs. Patients could be assigned into high-risk and low-risk groups based on the medium-risk sore in the training cohort. Then, we performed the Kaplan–Meier survival analysis, time-dependent receiver operating characteristic (ROC) curves, and univariate and multivariate analyses. The results indicated that the prognosis prediction ability of the LRLPS was excellent, robust, and independent. Furthermore, a nomogram was constructed based on the LRLPS risk score and clinical factors to predict the 3-, 5-, and 10-year survival probability. The GO/KEGG and GSEA indicated that immune-related pathways differed between the two-risk group. CIBERSORT, ESTIMATE, Tumor Immune Dysfunction and Exclusion (TIDE), and Immunophenoscore (IPS) showed that low-risk patients had higher levels of immune infiltration and better immunotherapeutic response. The pRRophetic and CellMiner databases indicated that many common chemotherapeutic drugs were more effective for low-risk patients. In conclusion, we developed a novel LRLPS for BC that could predict the prognosis, immune landscape, and treatment response.
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24
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Zhou M, Dong M, Yang X, Gong J, Liao X, Zhang Q, Liu Z. The emerging roles and mechanism of m6a in breast cancer progression. Front Genet 2022; 13:983564. [PMID: 36035182 PMCID: PMC9399344 DOI: 10.3389/fgene.2022.983564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/18/2022] [Indexed: 12/30/2022] Open
Abstract
Breast cancer (BC) has continued to be the leading cause of cancer deaths in women, accompanied by highly molecular heterogeneity. N6-methyladenosine (m6A), a methylation that happens on adenosine N6, is the most abundant internal mRNA modification type in eukaryotic cells. Functionally, m6A methylation is a reversible modification process and is regulated by 3 enzymes with different functions, namely “writer”, “reader”, and “eraser”. Abnormal m6A modifications trigger the expression, activation, or inhibition of key signaling molecules in critical signaling pathways and the regulatory factors acting on them in BC. These m6A-related enzymes can not only be used as markers for accurate diagnosis, prediction of prognosis, and risk model construction, but also as effective targets for BC treatment. Here, we have emphasized the roles of different types of m6A-related enzymes reported in BC proliferation, invasion, and metastasis, as well as immune regulation. The comprehensive and in-depth exploration of the molecular mechanisms related to m6A will benefit in finding effective potential targets and effective stratified management of BC.
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Affiliation(s)
- Mengying Zhou
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, China
| | - Menglu Dong
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xue Yang
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Gong
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinghua Liao
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, China
- *Correspondence: Xinghua Liao, ; Qi Zhang, ; Zeming Liu,
| | - Qi Zhang
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Xinghua Liao, ; Qi Zhang, ; Zeming Liu,
| | - Zeming Liu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Xinghua Liao, ; Qi Zhang, ; Zeming Liu,
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25
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Liu Y, Zhu T, Jiang Y, Bu J, Zhu X, Gu X. The Key Role of RNA Modification in Breast Cancer. Front Cell Dev Biol 2022; 10:885133. [PMID: 35721510 PMCID: PMC9198488 DOI: 10.3389/fcell.2022.885133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/25/2022] [Indexed: 12/09/2022] Open
Abstract
The modulation of the function and expression of epigenetic regulators of RNA modification has gradually become the hotspot of cancer research. Studies have shown that alteration of epigenetic modifications can promote the development and metastasis of breast cancer. This review highlights the progress in characterization of the link between RNA modification and the prognosis, carcinogenesis and treatment of breast cancer, which may provide a new theoretical basis for development of effective strategies for monitoring of breast cancer based on epigenetics.
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Chen F, Yang J, Fang M, Wu Y, Su D, Sheng Y. Necroptosis-related lncRNA to establish novel prognostic signature and predict the immunotherapy response in breast cancer. J Clin Lab Anal 2022; 36:e24302. [PMID: 35229919 PMCID: PMC8993638 DOI: 10.1002/jcla.24302] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background Necroptosis is a type of programmed cell death, and recent researches have showed that lncRNAs could regulate the process of necroptosis in multiple cancers. We tried to screen necroptosis‐related lncRNAs and investigate the immune landscape in breast cancer (BC). Methods The samples of breast normal and cancer tissue were acquired from TCGA and GTEx databases. A risk prognostic model was constructed based on the identified necroptosis‐related lncRNAs by Cox regression and least absolute shrinkage and selection operator (LASSO) method. Moreover, the forecast performance of this model was verified and accredited by synthetic approach. Subsequently, an accurate nomogram was constructed to predict the prognosis of BC patients. The biological differences were investigated through GO, GSEA, and immune analysis. The immunotherapy response was estimated through tumor mutation burden (TMB) and tumor immune dysfunction and exclusion (TIDE) score. Results A total of 251 necroptosis‐related lncRNAs were identified by differential coexpression analysis, and SH3BP5‐AS1, AC012073.1, AC120114.1, LINC00377, AL133467.1, AC036108.3, and AC020663.2 were involved in the risk model, which had an excellent concordance with the prediction. The pathway analyses showed that immune‐related pathways were relevant to the necroptosis‐related lncRNAs risk model. And the risk score was significantly correlated with immune cell infiltration, as well as the ESTIMATE score. Most notably, the patients of higher risk score were characterized with increased TMB and decreased TIDE score, indicating that these patients showed better immune checkpoint blockade response. Conclusion These findings were conducive to understand the function of necroptosis‐related lncRNAs in BC and provide a potential promising therapeutic strategy for BC.
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Affiliation(s)
- Fangyue Chen
- Department of General Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Jun Yang
- Department of General Surgery, 63650 Military Hospital, China
| | - Min Fang
- Department of General Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Yanmei Wu
- Department of General Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Dongwei Su
- Department of General Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
| | - Yuan Sheng
- Department of General Surgery, Changhai Hospital, Navy Military Medical University, Shanghai, China
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