1
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Lv L, Yi L, Huang B, Zhou C, Zhang L. Hsa_circ_0071589 aggravates stemness and oxaliplatin resistance in colorectal cancer through sponging miR-133b to upregulate SOX13 expression. Mol Cell Biochem 2024; 479:2055-2068. [PMID: 37522976 DOI: 10.1007/s11010-023-04819-8] [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: 02/20/2023] [Accepted: 07/16/2023] [Indexed: 08/01/2023]
Abstract
Hsa_circ_0071589 can exacerbate the malignant behavior of colorectal cancer (CRC) cells. However, its function in stemness and oxaliplatin (OXP) resistance of CRC cells remains unclear. To assess the function of hsa_circ_0071589 in stemness and OXP resistance of CRC cells. Western blotting and qRT-PCR were applied to assess protein and mRNA levels. The association between hsa_circ_0071589, miR-133b and SOX13 was explored via a correlation analysis. Sphere formation was used to assess cell stemness. Meanwhile, the viability of CRC cells and OXP-resistant CRC cells was evaluated with the MTT assay. Cell stemness marker (CD133) levels and apoptosis of CRC cells and OXP-resistant CRC cells were tested using flow cytometry. The ALDH level was investigated using the related detection kit. In addition, the association between hsa_circ_0071589 and miR-133b and SOX13 was investigated using the RIP and dual luciferase assay. Finally, in vivo experiments were performed to detect the function of hsa_circ_0071589 in CRC, and the levels of SOX13, Ki67, and CD44 in mice were evaluated via immunohistochemistry staining. The expression of hsa_circ_0071589 and SOX13 was upregulated in CRC, whereas the expression of miR-133b was downregulated. Hsa_circ_0071589 knockdown significantly inhibited CRC stemness via the mediation of miR-133b. Moreover, hsa_circ_0071589 silencing significantly sensitized CRC cells to OXP by upregulating miR-133b. SOX13 was the direct target of miR-133b, and miR-133b could attenuate stemness and OXP resistance in CRC cells by targeting SOX13. Notably, hsa_circ_0071589 knockdown inhibited tumor growth and decreased OXP resistance in mice with CRC. Hsa_circ_0071589 aggravates stemness and OXP resistance by sponging miR-133b to indirectly target SOX13 in CRC. Thus, our study might present a novel treatment strategy against OXP-resistant CRC.
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MESH Headings
- Animals
- Humans
- Mice
- Cell Line, Tumor
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Colorectal Neoplasms/metabolism
- Drug Resistance, Neoplasm
- Gene Expression Regulation, Neoplastic/drug effects
- Mice, Inbred BALB C
- Mice, Nude
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oxaliplatin/pharmacology
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- RNA, Neoplasm/biosynthesis
- Up-Regulation
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Affiliation(s)
- Lv Lv
- Department of Breast and Thyroid Surgery, Liuzhou People's Hospital, NO.8, Wenchang Road, Liuzhou, 545006, Guangxi, People's Republic of China
| | - Lu Yi
- Department of Dermatology & Venerology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Bojie Huang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Cong Zhou
- Clinical Medical College of Guilin Medical University, Guilin, 541001, Guangxi, People's Republic of China
| | - Lei Zhang
- Department of Emergency and Trauma Surgery, Affiliated Hospital of Guilin Medical University, NO.15 Lequn Road, Guilin, 541001, Guangxi, People's Republic of China.
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2
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Wei Q, Xue C, Li M, Wei J, Zheng L, Chen S, Duan Y, Deng H, Tang F, Xiong W, Zhou M. Ferroptosis: a critical mechanism of N 6-methyladenosine modification involved in carcinogenesis and tumor progression. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1119-1132. [PMID: 38811442 DOI: 10.1007/s11427-023-2474-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/23/2023] [Indexed: 05/31/2024]
Abstract
Ferroptosis is an iron-dependent regulatory cell necrosis induced by iron overload and lipid peroxidation. It occurs when multiple redox-active enzymes are ectopically expressed or show abnormal function. Hence, the precise regulation of ferroptosis-related molecules is mediated across multiple levels, including transcriptional, posttranscriptional, translational, and epigenetic levels. N6-methyladenosine (m6A) is a highly evolutionarily conserved epigenetic modification in mammals. The m6A modification is commonly linked to tumor proliferation, progression, and therapy resistance because it is involved in RNA metabolic processes. Intriguingly, accumulating evidence suggests that dysregulated ferroptosis caused by the m6A modification drives tumor development. In this review, we summarized the roles of m6A regulators in ferroptosis-mediated malignant tumor progression and outlined the m6A regulatory mechanism involved in ferroptosis pathways. We also analyzed the potential value and application strategies of targeting m6A/ferroptosis pathway in the clinical diagnosis and therapy of tumors.
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Affiliation(s)
- Qingqing Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Lemei Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Shipeng Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Yumei Duan
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Hongyu Deng
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Faqing Tang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
- Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China.
- Hunan Key Laboratory of Oncotarget Gene, Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
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3
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Povedano E, Ruiz-Valdepeñas Montiel V, Sebuyoya R, Torrente-Rodríguez RM, Garranzo-Asensio M, Montero-Calle A, Pingarrón JM, Barderas R, Bartosik M, Campuzano S. Bringing to Light the Importance of the miRNA Methylome in Colorectal Cancer Prognosis Through Electrochemical Bioplatforms. Anal Chem 2024; 96:4580-4588. [PMID: 38348822 PMCID: PMC10955513 DOI: 10.1021/acs.analchem.3c05474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
This work reports the first electrochemical bioplatforms developed for the determination of the total contents of either target miRNA or methylated target miRNA. The bioplatforms are based on the hybridization of the target miRNA with a synthetic biotinylated DNA probe, the capture of the formed DNA/miRNA heterohybrids on the surface of magnetic microcarriers, and their recognition with an antibody selective to these heterohybrids or to the N6-methyladenosine (m6A) epimark. The determination of the total or methylated target miRNA was accomplished by labeling such secondary antibodies with the horseradish peroxidase (HRP) enzyme. In both cases, amperometric transduction was performed on the surface of disposable electrodes after capturing the resulting HRP-tagged magnetic bioconjugates. Because of their increasing relevance in colorectal cancer (CRC) diagnosis and prognosis, miRNA let-7a and m6A methylation were selected. The proposed electrochemical bioplatforms showed attractive analytical and operational characteristics for the determination of the total and m6A-methylated target miRNA in less than 75 min. These bioplatforms, innovative in design and application, were applied to the analysis of total RNA samples extracted from cultured cancer cells with different metastatic profiles and from paired healthy and tumor tissues of patients diagnosed with CRC at different stages. The obtained results demonstrated, for the first time using electrochemical platforms, the potential of interrogating the target miRNA methylation level to discriminate the metastatic capacities of cancer cells and to identify tumor tissues and, in a pioneering way, the potential of the m6A methylation in miRNA let-7a to serve as a prognostic biomarker for CRC.
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Affiliation(s)
- Eloy Povedano
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
| | - Víctor Ruiz-Valdepeñas Montiel
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
| | - Ravery Sebuyoya
- Research
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Zluty kopec 7, Brno 656
53, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Rebeca M. Torrente-Rodríguez
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
| | - Maria Garranzo-Asensio
- Chronic
Disease Programme, UFIEC, Institute of Health
Carlos III, Majadahonda, Madrid 28220, Spain
| | - Ana Montero-Calle
- Chronic
Disease Programme, UFIEC, Institute of Health
Carlos III, Majadahonda, Madrid 28220, Spain
| | - José M. Pingarrón
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
| | - Rodrigo Barderas
- Chronic
Disease Programme, UFIEC, Institute of Health
Carlos III, Majadahonda, Madrid 28220, Spain
| | - Martin Bartosik
- Research
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Zluty kopec 7, Brno 656
53, Czech Republic
| | - Susana Campuzano
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
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4
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Wu Q, Fu X, He X, Liu J, Li Y, Ou C. Experimental prognostic model integrating N6-methyladenosine-related programmed cell death genes in colorectal cancer. iScience 2024; 27:108720. [PMID: 38299031 PMCID: PMC10829884 DOI: 10.1016/j.isci.2023.108720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/30/2023] [Accepted: 12/11/2023] [Indexed: 02/02/2024] Open
Abstract
Colorectal cancer (CRC) intricacies, involving dysregulated cellular processes and programmed cell death (PCD), are explored in the context of N6-methyladenosine (m6A) RNA modification. Utilizing the TCGA-COADREAD/CRC cohort, 854 m6A-related PCD genes are identified, forming the basis for a robust 10-gene risk model (CDRS) established through LASSO Cox regression. qPCR experiments using CRC cell lines and fresh tissues was performed for validation. The CDRS served as an independent risk factor for CRC and showed significant associations with clinical features, molecular subtypes, and overall survival in multiple datasets. Moreover, CDRS surpasses other predictors, unveiling distinct genomic profiles, pathway activations, and associations with the tumor microenvironment. Notably, CDRS exhibits predictive potential for drug sensitivity, presenting a novel paradigm for CRC risk stratification and personalized treatment avenues.
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Affiliation(s)
- Qihui Wu
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaodan Fu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jiaxin Liu
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha 410078, China
| | - Yimin Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha 410008, China
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5
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Cheng J, Lyu Y, Cheng Z. Comprehensive Investigation of m6A Regulators for Prognosis in Head and Neck Squamous Cell Carcinoma. J Environ Pathol Toxicol Oncol 2024; 43:45-60. [PMID: 37824369 DOI: 10.1615/jenvironpatholtoxicoloncol.2023047701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
The early detection of head and neck squamous cell carcinoma (HNSCC) has an important impact on the clinical prognosis. N6-methyladenosine (m6A) is involved in the post-transcriptional regulation of tumorigenesis and development. In this study, the prognosis and biological functions of m6A regulator targets in HNSCC were explored. RNA-Seq expression data and clinical information from TCGA-HNSCC and GSE23036 datasets were collected. The mRNA levels of IGF2BP2 and IGF2BP3 in tumor tissues were significantly up-regulated. Differential expression and functional enrichment analysis of potential targets for IGF2BP2 and IGF2BP3 obtained from the m6A2Target database showed that they were significantly enriched in cell cycle-related pathways. The Cox regression analysis was performed to establish a three-mRNA signature including PLAU, LPIN1 and AURKA. The prognostic effect was verified in the external dataset GSE41613. Further studies revealed that the three-mRNA signature was significantly associated with survival in the clinical subgroup. The ROC curve, Harrell consistency index and decision curve comparison used to compare the predictive effect of the three-mRNA signature and the other signatures in previous studies showed that the three-mRNA signature had better predictive effect on the prognosis of HNSCC patients. The three-mRNA signature expression were verified in HNSCC cell lines with qRT-PCR and Western blot. Sequence analysis showed that m6A-modification sites existed on PLAU, LPIN1 and AURKA genes. In conclusion, the three-mRNA signature has been proved to be useful on evaluating the prognosis and contributing to the personalized treatment of HNSCC, and IGB2BP2/3 were related to the cell cycle in HNSCC.
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Affiliation(s)
- Jingning Cheng
- Department of ENT Head-Neck Surgery, China‑Japan Friendship Hospital, Beijing 100029, P.R. China
| | - Yong Lyu
- Department of ENT Head-Neck Surgery, China‑Japan Friendship Hospital, Beijing 100029, P.R. China
| | - Ziyan Cheng
- The Experimental High School Attached to Beijing Normal University, Beijing 100032, P.R. China
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6
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Li M, Song J, Wang L, Wang Q, Huang Q, Mo D. Natural killer cell-related prognosis signature predicts immune response in colon cancer patients. Front Pharmacol 2023; 14:1253169. [PMID: 38026928 PMCID: PMC10679416 DOI: 10.3389/fphar.2023.1253169] [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: 07/05/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Natural killer (NK) cells are crucial components of the innate immune system that fight tumors and viral infections. Patients with colorectal cancer (CRC) have a poor prognosis, and immunotherapeutic tools play a key role in the treatment of CRC. Methods: Public data on CRC patients was collected from the TCGA and the GEO databases. Tissue data of CRC patients were collected from Guangxi Medical University Affiliated Cancer Hospital. An NK-related prognostic model was developed by the least absolute shrinkage and selection operator (LASSO) and Cox regression method. Validation data were collected from different clinical subgroups and an external independent validation cohort to verify the model's accuracy. In addition, multiple external independent immunotherapy datasets were collected to further examine the value of NK-related risk scores (NKRS) in the prediction of immunotherapy response. Potential biological functions of key genes were examined by methods of cell proliferation, apoptosis and Western blotting. Results: A novel prognostic model for CRC patients based on NK-related genes was developed and NKRS was generated. There was a significantly poorer prognosis among the high-NKRS group. Based on immune response prediction, patients with low NKRS may be more suitable for immunotherapy and they are more sensitive to immunotherapy. The proliferation rate of CRC cells was significantly reduced and apoptosis of CRC cells was increased after SLC2A3 was knocked down. SLC2A3 was also found to be associated with the TGF-β signaling pathway. Conclusion: NKRS has potential applications for predicting prognostic status and response to immunotherapy in CRC patients. SLC2A3 has potential as a therapeutic target for CRC.
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Affiliation(s)
- Meiqin Li
- Department of Clinical Laboratory, Guang Xi Medical University Cancer Hospital, Nanning, China
| | - Jingqing Song
- Department of Gastrointestinal Surgery, Guang Xi Medical University Cancer Hospital, Nanning, China
| | - Lin Wang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
- School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Qi Wang
- Department of Basic Medicine, Guangxi Health Science College, Nanning, China
| | - Qinghua Huang
- Department of Breast Surgery, Wuzhou Red Cross Hospital, Wuzhou, China
| | - Dan Mo
- Department of Breast, Maternal and Child Healthcare Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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7
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Zhang D, Wu G, Yang L, Wu Q, Yuan L. The predictive significance of a 5-m6A RNA methylation regulator signature in colorectal cancer. Heliyon 2023; 9:e20172. [PMID: 37810844 PMCID: PMC10550633 DOI: 10.1016/j.heliyon.2023.e20172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Colorectal cancer attacks the colon or rectum, with increasing morbidity and mortality globally. The RNA modification 6-methyladenine (m6A) is related to RNA modifications, playing a critical role in colorectal cancer. We aimed to identify prognostic signatures for colorectal cancer using risk prediction algorithms, and to validate these signatures using independent datasets and clinical samples. In this study, 175 cases in GSE17536 were assigned into two clusters using consistent clustering and PCA analysis. A multivariate Cox risk regression model revealed that among 21 m6A RNA methylation regulators, RBM15B, FTO, IGF2BP2, ZCCHC4, and KIAA1429 were remarkably associated with colorectal cancer patients' overall survival (OS); however, Kaplan-Meier (KM) survival assessment showed no significant association between these five regulators and colorectal cancer patients' prognosis. A 5-m6A RNA methylation regulator signature was established using LASSO algorithm. Risk scores of cases in GSE17536, GSE17537 and GSE75500 were calculated, and lower risk scores were associated with better DSS/OS. receiver operating characteristic (ROC) curve and the nomogram revealed the satisfactory predictive efficiency of the risk score model. The risk score could distinguish cases in Cluster1 and Cluster2 and normal and tumor tissues based on GSE37182. The prognostic variables for colorectal cancer patients were assessed using both univariate and multivariate Cox's proportional hazard regression models, which revealed that the stage and risk score were significant risk factors. In this study, a comprehensive set of integrative bioinformatics analyses was conducted to investigate the prognostic and diagnostic potential of a panel of 5 m6A RNA methylated regulators in colorectal cancer patients. The conducted studies included the use of several statistical methods, such as the LASSO regression model, KM survival evaluation, ROC curve, and univariate and multivariate Cox's proportional hazard regression analyses. The findings from these analyses collectively established the prognostic marker, highlighting its significance in predicting patient outcomes and diagnosing colorectal cancer.
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Affiliation(s)
- Dan Zhang
- Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, PR China
| | - Guotao Wu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lichao Yang
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiang Wu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lianwen Yuan
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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8
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Jiang S, Wang T, Zhang KH. Data-driven decision-making for precision diagnosis of digestive diseases. Biomed Eng Online 2023; 22:87. [PMID: 37658345 PMCID: PMC10472739 DOI: 10.1186/s12938-023-01148-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 08/15/2023] [Indexed: 09/03/2023] Open
Abstract
Modern omics technologies can generate massive amounts of biomedical data, providing unprecedented opportunities for individualized precision medicine. However, traditional statistical methods cannot effectively process and utilize such big data. To meet this new challenge, machine learning algorithms have been developed and applied rapidly in recent years, which are capable of reducing dimensionality, extracting features, organizing data and forming automatable data-driven clinical decision systems. Data-driven clinical decision-making have promising applications in precision medicine and has been studied in digestive diseases, including early diagnosis and screening, molecular typing, staging and stratification of digestive malignancies, as well as precise diagnosis of Crohn's disease, auxiliary diagnosis of imaging and endoscopy, differential diagnosis of cystic lesions, etiology discrimination of acute abdominal pain, stratification of upper gastrointestinal bleeding (UGIB), and real-time diagnosis of esophageal motility function, showing good application prospects. Herein, we reviewed the recent progress of data-driven clinical decision making in precision diagnosis of digestive diseases and discussed the limitations of data-driven decision making after a brief introduction of methods for data-driven decision making.
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Affiliation(s)
- Song Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zheng Street, Nanchang, 330006 China
- Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, 330006 China
| | - Ting Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zheng Street, Nanchang, 330006 China
- Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, 330006 China
| | - Kun-He Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zheng Street, Nanchang, 330006 China
- Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, 330006 China
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9
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Zou QT, Lin Y, Luo QY. miR-138-5p inhibits the progression of colorectal cancer via regulating SP1/LGR5 axis. Cell Biol Int 2023; 47:273-282. [PMID: 36317454 DOI: 10.1002/cbin.11926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/06/2022]
Abstract
Colorectal cancer (CRC) is one of the main malignancies that seriously threaten human health. Considering the high mortality and morbidity associated with this disease, even surgical resection and chemotherapy may not be sufficient in certain cases. This study aimed to explore the molecular mechanisms of miR-138-5p in regulating CRC progression. Quantitative reverse transcriptase polymerase chain reaction and western blot were performed to assess the levels of mRNA and proteins, including miR-138-5p, leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5), SP1, β-catenin, cyclin D1, and c-myc. The bioactivities of LoVo and HCT116 cells were assessed via MTT assay, flow cytometry, and transwell assay. StarBase was used to identify the downstream targets of genes. Double luciferase reporter and RIP assays revealed the direct binding of miR-138-5p to SP1 and of SP1 to LGR5. Our results illustrated that miR-138-5p was downregulated in CRC and its knockdown accelerated CRC progression. Conversely, SP1 was upregulated in CRC and its knockdown inhibited CRC progression. SP1 is also targeted by miR-138-5p and binds to LGR5. This study showed that miR-138-5p inhibits LoVo and HCT116 cell proliferation, migration, and invasion. Overall, miR-138-5p regulates CRC progression and promotes apoptosis via the SP1/LGR5 axis. This study indicates that miR-138-5p is involved in regulating CRC progression.
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Affiliation(s)
- Qing-Tao Zou
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Yi Lin
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Qing-Yu Luo
- Department of Gastroenterology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, Guangdong Province, China
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10
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Li J, Xu J, Zheng S, Cheng S. LncRNA LINC02535 Induces Colorectal Adenocarcinoma Progression via Modulating miR-30d-5p/CHD1. Mol Biotechnol 2022:10.1007/s12033-022-00628-4. [PMID: 36577835 DOI: 10.1007/s12033-022-00628-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/28/2022] [Indexed: 12/29/2022]
Abstract
Growing evidence has suggested that lncRNAs play a significant role in the development of colorectal adenocarcinoma. LncRNA LINC02535 was a potential novel lncRNA marker of neoplastic processes of the colon. Nevertheless, the function and mechanisms of LINC02535 in colorectal adenocarcinoma remain unclear. Proteins levels were measured by western blotting. EdU, CCK-8, Transwell, and wound healing assays were performed to investigate the function of LINC02535 in colorectal adenocarcinoma. The distribution of LINC02535 in cells was evaluated by subcellular fractionation assay. The interaction among RNAs was identified by luciferase reporter and RIP assays. In this study, our findings revealed that LINC02535 was highly expressed in colorectal adenocarcinoma cells. Knockdown of LINC02535 inhibited colorectal adenocarcinoma cell proliferation, migration, and invasion. Mechanistically, LINC02535 bound with miR-30d-5p and worked as a competing endogenous RNA to facilitate the expression of messenger RNA chromodomain helicase DNA-binding protein 1 (CHD1). miR-30d-5p directly targeted the sequence of CHD1 3'-untranslated region. Notably, CHD1 upregulation abolished the suppressive influence of LINC02535 inhibition on the malignant phenotypes of colorectal adenocarcinoma cells. Overall, it was disclosed that LINC02535 played an oncogenic role in colorectal adenocarcinoma progression by sponging miR-30d-5p to upregulate CHD1 expression.
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Affiliation(s)
- Jiguang Li
- Department of Anorectal Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, 437100, Hubei, China
| | - Jianhua Xu
- Department of Gastrointestinal Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xian'an District, No. 228, Jingui Road, Xianning, 437100, Hubei, China
| | - Sen Zheng
- Department of Gastrointestinal Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xian'an District, No. 228, Jingui Road, Xianning, 437100, Hubei, China.
| | - Si Cheng
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xian'an District, No. 228, Jingui Road, Xianning, 437100, Hubei, China.
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11
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Niu M, Chen C, Gao X, Guo Y, Zhang B, Wang X, Chen S, Niu X, Zhang C, Li L, Li Z, Zhao Z, Jiang X. Comprehensive analysis of the differences between left- and right-side colorectal cancer and respective prognostic prediction. BMC Gastroenterol 2022; 22:482. [DOI: 10.1186/s12876-022-02585-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Previous studies have reported that the tumor heterogeneity and complex oncogenic mechanisms of proximal and distal colon cancer (CRC) are divergent. Therefore, we aim to analyze the differences between left-sided CRC (L_cancer) and right-sided CRC (R_cancer), as well as constructing respective nomograms.
Methods
We enrolled 335 colon cancer patients (146 L_cancer patients and 189 R_cancer patients) from The Cancer Genome Atlas (TCGA) data sets, and 102 pairs of color cancer tissue and adjacent normal tissue (51 L_cancer patients and 51 R_cancer patients) from our hospital. Firstly, we analyzed the differences between the L_cancer patients and R_cancer patients, and then established the L_cancer and R_cancer prognostic models using LASSO Cox.
Results
R_cancer patients had lower survival than L_cancer patients. R_cancer patients had higher ESTIMATE and immune scores and lower tumor purity. These patterns of expression of immune checkpoint-related genes and TMB level were higher in R_cancer than in L_cancer patients. Finally, we using Lasso Cox regression analyses established a prognostic model for L_cancer patients and a prognostic model for R_cancer patients. The AUC values of the risk score for OS in L_cancer were 0.862 in the training set and 0.914 in the testing set, while those in R_cancer were 0.835 in the training set and 0.857 in the testing set. The AUC values in fivefold cross-validation were between 0.727 and 0.978, proving that the two prognostic models have great stability. The nomogram of L_cancer included prognostic genes, age, pathological M, pathological stage, and gender, the AUC values of which were 0.800 in the training set and 0.905 in the testing set. Meanwhile, the nomogram of R_cancer comprised prognostic genes, pathological N, pathological T, and age, the AUC values of which were 0.836 in the training set and 0.850 in the testing set. In the R_cancer patients, high-risk patients had a lower proportion of ‘B cells memory’, ‘Dendritic cells resting’, immune score, ESTIMATE score, immune checkpoint-related genes, and HLA-family genes, and a higher proportion of ‘T cells follicular helper’, ‘Dendritic cells activated’, and ‘Mast cells activated’.
Conclusions
We found significant differences between L_cancer and R_cancer patients and established a clinical predictive nomogram for L_cancer patients and a nomogram for R_cancer patients. Additionally, R_cancer patients in low-risk groups may be more beneficial from immunotherapy.
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12
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Zhang X, Li MJ, Xia L, Zhang H. The biological function of m6A methyltransferase KIAA1429 and its role in human disease. PeerJ 2022; 10:e14334. [PMID: 36389416 PMCID: PMC9657180 DOI: 10.7717/peerj.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/12/2022] [Indexed: 11/11/2022] Open
Abstract
KIAA1429 is a major m6A methyltransferase, which plays important biological and pharmacological roles in both human cancer or non-cancer diseases. KIAA1429 produce a tumorigenic role in various cancers through regulating DAPK3, ID2, GATA3, SMC1A, CDK1, SIRT1 and other targets, promoting cell proliferation, migration, invasion, metastasis and tumor growth . At the same time, KIAA1429 is also effective in non-tumor diseases, such as reproductive system and cardiovascular system diseases. The potential regulatory mechanism of KIAA1429 dependent on m6A modification is related to mRNA, lncRNA, circRNA and miRNAs. In this review, we summarized the current evidence on KIAA1429 in various human cancers or non-cancer diseases and its potential as a prognostic target.
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Affiliation(s)
- Xiaoyu Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Meng jiao Li
- Liaocheng Vocational and Technical College, Liaocheng, China
| | - Lei Xia
- Shandong University of Traditional Chinese Medicine, Department of Pathology, Jinan, China
| | - Hairong Zhang
- Shandong Provincial Third Hospital, Department of Obstetrics and Gynecology, Jinan, China
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13
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Zhou M, Lv S, Hou Y, Zhang R, Wang W, Yan Z, Li T, Gan W, Zeng Z, Zhang F, Yang M. Characterization of sialylation-related long noncoding RNAs to develop a novel signature for predicting prognosis, immune landscape, and chemotherapy response in colorectal cancer. Front Immunol 2022; 13:994874. [PMID: 36330513 PMCID: PMC9623420 DOI: 10.3389/fimmu.2022.994874] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/03/2022] [Indexed: 08/22/2023] Open
Abstract
Aberrant sialylation plays a key biological role in tumorigenesis and metastasis, including tumor cell survival and invasion, immune evasion, angiogenesis, and resistance to therapy. It has been proposed as a possible cancer biomarker and a potential therapeutic target of tumors. Nevertheless, the prognostic significance and biological features of sialylation-related long noncoding RNAs (lncRNAs) in colorectal cancer (CRC) remain unclear. This study aimed to develop a novel sialylation-related lncRNA signature to accurately evaluate the prognosis of patients with CRC and explore the potential molecular mechanisms of the sialylation-related lncRNAs. Here, we identified sialylation-related lncRNAs using the Pearson correlation analysis on The Cancer Genome Atlas (TCGA) dataset. Univariate and stepwise multivariable Cox analysis were used to establish a signature based on seven sialylation-related lncRNAs in the TCGA dataset, and the risk model was validated in the Gene Expression Omnibus dataset. Kaplan-Meier curve analysis revealed that CRC patients in the low-risk subgroup had a better survival outcome than those in the high-risk subgroup in the training set, testing set, and overall set. Multivariate analysis demonstrated that the sialylation-related lncRNA signature was an independent prognostic factor for overall survival, progression-free survival, and disease-specific survival prediction. The sialylation lncRNA signature-based nomogram exhibited a robust prognostic performance. Furthermore, enrichment analysis showed that cancer hallmarks and oncogenic signaling were enriched in the high-risk group, while inflammatory responses and immune-related pathways were enriched in the low-risk group. The comprehensive analysis suggested that low-risk patients had higher activity of immune response pathways, greater immune cell infiltration, and higher expression of immune stimulators. In addition, we determined the sialylation level in normal colonic cells and CRC cell lines by flow cytometry combined with immunofluorescence, and verified the expression levels of seven lncRNAs using real-time quantitative polymerase chain reaction. Finally, combined drug sensitivity analysis using the Genomics of Drug Sensitivity in Cancer, Cancer Therapeutics Response Portal, and Profiling Relative Inhibition Simultaneously in Mixtures indicated that the sialylation-related lncRNA signature could serve as a potential predictor for chemosensitivity. Collectively, this is the first sialylation lncRNA-based signature for predicting the prognosis, immune landscape, and chemotherapeutic response in CRC, and may provide vital guidance to facilitate risk stratification and optimize individualized therapy for CRC patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Min Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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14
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Ding P, Gao Y, Wang J, Xiang H, Zhang C, Wang L, Ji G, Wu T. Progress and challenges of multidrug resistance proteins in diseases. Am J Cancer Res 2022; 12:4483-4501. [PMID: 36381332 PMCID: PMC9641395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023] Open
Abstract
Chemotherapy remains the first choice for patients with advanced cancers when other treatments are ineffective. Multidrug resistance (MDR) is an unavoidable factor that negatively affects the effectiveness of cancer chemotherapy drugs. Researchers are trying to reduce MDR, improve the effectiveness of chemotherapeutic drugs, and alleviate patient suffering to positively contribute to disease treatment. MDR also occurs in inflammation and genetic disorders, which increases the difficulty of clinically beneficial treatments. The ATP-binding cassette (ABC) is an active transporter that plays an important role in the barrier and secretory functions of many normal cells. As the C subfamily in the ABC family, multidrug resistance proteins (MRPs/ABCCs) export a variety of antitumour drugs and are expressed in a variety of cancers. The present review summarises the role of MRPs in cancer and other diseases and recent research progress of MRP inhibitors to better examine the mechanism and function of MRPs, and establish a good relationship with clinical treatment.
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Affiliation(s)
- Peilun Ding
- Department of Hepatology, Longhua Hospital, Shanghai University of Traditional Chinese MedicineShanghai 200032, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese MedicineShanghai 201203, China
| | - Ying Gao
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese MedicineShanghai 201203, China
| | - Junmin Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese MedicineShanghai 201203, China
| | - Hongjiao Xiang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese MedicineShanghai 201203, China
| | - Caiyun Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese MedicineShanghai 201203, China
| | - Lei Wang
- Department of Hepatology, Longhua Hospital, Shanghai University of Traditional Chinese MedicineShanghai 200032, China
| | - Guang Ji
- Institute of Digestive Disease, Longhua Hospital, Shanghai University of Traditional Chinese MedicineShanghai 200032, China
| | - Tao Wu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese MedicineShanghai 201203, China
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15
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Li H, Lin D, Wang X, Feng Z, Zhang J, Wang K. The development of a novel signature based on the m6A RNA methylation regulator-related ceRNA network to predict prognosis and therapy response in sarcomas. Front Genet 2022; 13:894080. [PMID: 36313417 PMCID: PMC9597465 DOI: 10.3389/fgene.2022.894080] [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: 03/11/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Background: N6 methyladenosine (m6A)-related noncoding RNAs (including lncRNAs and miRNAs) are closely related to the development of cancer. However, the gene signature and prognostic value of m6A regulators and m6A-associated RNAs in regulating sarcoma (SARC) development and progression remain largely unexplored. Therefore, further research is required. Methods: We obtained expression data for RNA sequencing (RNA-seq) and miRNAs of SARC from The Cancer Genome Atlas (TCGA) datasets. Correlation analysis and two target gene prediction databases (miRTarBase and LncBase v.2) were used to deduce m6A-related miRNAs and lncRNAs, and Cytoscape software was used to construct ceRNA-regulating networks. Based on univariate Cox regression and least absolute shrinkage and selection operator (LASSO) Cox regression analyses, an m6A-associated RNA risk signature (m6Ascore) model was established. Prognostic differences between subgroups were explored using Kaplan–Meier (KM) analysis. Risk score-related biological phenotypes were analyzed in terms of functional enrichment, tumor immune signature, and tumor mutation signature. Finally, potential immunotherapy features and drug sensitivity predictions for this model were also discussed. Results: A total of 16 miRNAs, 104 lncRNAs, and 11 mRNAs were incorporated into the ceRNA network. The risk score was obtained based on RP11-283I3.6, hsa-miR-455-3p, and CBLL1. Patients were divided into two risk groups using the risk score, with patients in the low-risk group having longer overall survival (OS) than those in the high-risk group. The receiver operating characteristic (ROC) curves indicated that risk characteristic performed well in predicting the prognosis of patients with SARC. In addition, lower m6Ascore was also positively correlated with the abundance of immune cells such as monocytes and mast cells activated, and several immune checkpoint genes were highly expressed in the low-m6Ascore group. According to our analysis, lower m6Ascore may lead to better immunotherapy response and OS outcomes. The risk signature was significantly associated with the chemosensitivity of SARC. Finally, a nomogram was constructed to predict the OS in patients with SARC. The concordance index (C-index) for the nomogram was 0.744 (95% CI: 0.707–0.784). The decision curve analysis (DCA), calibration plot, and ROC curve all showed that this nomogram had good predictive performance. Conclusion: This m6Ascore risk model based on m6A RNA methylation regulator-related RNAs may be promising for clinical prediction of prognosis and might contain potential biomarkers for treatment response prediction for SARC patients.
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Affiliation(s)
- Huling Li
- School of Public Health, Xinjiang Medical University, Urumqi, China
| | - Dandan Lin
- School of Public Health, Xinjiang Medical University, Urumqi, China
| | - Xiaoyan Wang
- School of Public Health, Xinjiang Medical University, Urumqi, China
| | - Zhiwei Feng
- School of Continuing Education, Xinjiang Medical University, Urumqi, China
| | - Jing Zhang
- School of Public Health, Xinjiang Medical University, Urumqi, China
| | - Kai Wang
- Department of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, China
- *Correspondence: Kai Wang,
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16
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The functions of N6-methyladenosine (m6A) RNA modifications in colorectal cancer. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:235. [PMID: 36175777 DOI: 10.1007/s12032-022-01827-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/17/2022] [Indexed: 10/14/2022]
Abstract
Colorectal cancers (CRC), which includes colon cancer (CC) and rectal cancer (RC), are some of the most common malignant tumors that are prone to distant metastasis. Its high incidence rate and high mortality rate have attracted much attention. In recent years, epigenetics has attracted increasing attention and has been the focus of many research studies. N6-methyladenosine(m6A) RNA modifications can modify eukaryotic mRNA to impact metabolism. The changes in the m6A regulatory genes are related to the occurrence and development of CRC and play an important role in the pathogenesis of CRC. The effect of m6A RNA modification is regulated by its related regulatory factors ("writer", "eraser", "reader"). In this review, we comprehensively analyzed the effect of m6A methylation on CRC and the relationship between the expression of related regulatory factors and the development and occurrence of CRC. Then, we summarized the roles of m6A and its regulatory factors in CRC and its potential clinical value, which provides a basis for further research on the mechanism of m6A methylation in CRC.
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17
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Xu Q, Lu X, Li J, Feng Y, Tang J, Zhang T, Mao Y, Lan Y, Luo H, Zeng L, Xiang Y, Hu L, Zhang Y, Li Q, Deng L, He X, Tang B, Mao X, Zeng D. Fusobacterium nucleatum induces excess METTL3-mediated miR-4717-3p maturation to promote colorectal cancer cell proliferation. Cancer Sci 2022; 113:3787-3800. [PMID: 35984699 DOI: 10.1111/cas.15536] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/02/2022] [Accepted: 08/06/2022] [Indexed: 12/01/2022] Open
Abstract
Fusobacterium nucleatum (F. nucleatum) infection plays vital roles in colorectal cancer (CRC) progression. Over-expression of miR-4717-3p (miR-4717) has been previously up-regulated in F. nucleatum positive CRC tissues, however, the underlying mechanism is unknown. In this study, we found that miR-4717 promoted CRC cell proliferation in vitro and growth of CRC in vivo upon F. nucleatum infection. MiR-4717 suppressed the expression of mitogen-activated protein kinase kinase 4 (MAP2K4), a tumor suppressor, by directly targeting its 3'UTR. Furthermore, we confirmed that methyltransferase-like 3 (METTL3) -dependent m6 A methylation could methylate pri-miR-4717, which further promoted the maturation of pri-miR-4717, and METTL3 positively regulated CRC cell proliferation through miR-4717/MAP2K4 pathways. In conclusion, F. nucleatum-induced miR-4717 excessive maturation via METTL3-dependent m6 A modification promotes CRC cell proliferation, which provides a potential therapeutic target and diagnostic biomarker for CRC.
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Affiliation(s)
- Qiaolin Xu
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Xiaoxue Lu
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Medical Laboratory, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jing Li
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Yuyang Feng
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Medical Laboratory, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jie Tang
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Tao Zhang
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Yilan Mao
- Class of 2021 undergraduate, Nursing College of Chongqing Medical University, Chongqing, PR China
| | - Yuanzhi Lan
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Huaxing Luo
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Linghai Zeng
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Yuanyuan Xiang
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Lv Hu
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Yan Zhang
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Qian Li
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Medical Laboratory, Army Medical University (Third Military Medical University), Chongqing, China
| | - Ling Deng
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Medical Laboratory, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xiaoyi He
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Medical Laboratory, Army Medical University (Third Military Medical University), Chongqing, China
| | - Bin Tang
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
| | - Xuhu Mao
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Medical Laboratory, Army Medical University (Third Military Medical University), Chongqing, China
| | - Dongzhu Zeng
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, China
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18
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m6A RNA methylation-mediated NDUFA4 promotes cell proliferation and metabolism in gastric cancer. Cell Death Dis 2022; 13:715. [PMID: 35977935 PMCID: PMC9385701 DOI: 10.1038/s41419-022-05132-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 01/21/2023]
Abstract
Gastric cancer (GC) is a malignancy with poor prognosis. NDUFA4 is reported to correlate with the progression of GC. However, its underlying mechanism in GC is unknown. Our study was to reveal the pathogenic mechanism of NDUFA4 in GC. NDUFA4 expression was explored in single-cell and bulk RNA-seq data as well as GC tissue microarray. Mitochondrial respiration and glycolysis were estimated by oxygen consumption rate and extracellular acidification rate, respectively. The interaction between NDUFA4 and METTL3 was validated by RNA immunoprecipitation. Flow cytometry was used to estimate cell cycle, apoptosis and mitochondrial activities. NDUFA4 was highly expressed in GC and its high expression indicated a poor prognosis. The knockdown of NDUFA4 could reduce cell proliferation and inhibit tumor growth. Meanwhile, NDUFA4 could promote glycolytic and oxidative metabolism in GC cells, whereas the inhibition of glycolysis suppressed the proliferation and tumor growth of GC. Besides, NDUFA4 inhibited ROS level and promoted MMP level in GC cells, whereas the inhibition of mitochondrial fission could reverse NDUFA4-induced glycolytic and oxidative metabolism and tumor growth of GC. Additionally, METTL3 could increase the m6A level of NDUFA4 mRNA via the m6A reader IGF2BP1 to promote NDUFA4 expression in GC cells. Our study revealed that NDUFA4 was increased by m6A methylation and could promote GC development via enhancing cell glycolysis and mitochondrial fission. NDUFA4 was a potential target for GC treatment.
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19
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Zhang Y, Li L, Chu F, Xiao X, Zhang L, Li K, Wu H. Identification and Validation of an m6A-Related LncRNA Signature to Predict Progression-Free Survival in Colorectal Cancer. Pathol Oncol Res 2022; 28:1610536. [PMID: 36032659 PMCID: PMC9407446 DOI: 10.3389/pore.2022.1610536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/10/2022] [Indexed: 12/16/2022]
Abstract
The RNA methylation of N6 adenosine (m6A) plays a crucial role in various biological processes. Strong evidence reveals that the dysregulation of long non-coding RNAs (lncRNA) brings about the abnormality of downstream signaling in multiple ways, thus influencing tumor initiation and progression. Currently, it is essential to discover effective and succinct molecular biomarkers for predicting colorectal cancer (CRC) prognosis. However, the prognostic value of m6A-related lncRNAs for CRC remains unclear, especially for progression-free survival (PFS). Here, we screened 24 m6A-related lncRNAs in 622 CRC patients and identified five lncRNAs (SLCO4A1-AS1, MELTF-AS1, SH3PXD2A-AS1, H19 and PCAT6) associated with patient PFS. Compared to normal samples, their expression was up-regulated in CRC tumors from TCGA dataset, which was validated in 55 CRC patients from our in-house cohort. We established an m6A-Lnc signature for predicting patient PFS, which was an independent prognostic factor by classification analysis of clinicopathologic features. Moreover, the signature was validated in 1,077 patients from six independent datasets (GSE17538, GSE39582, GSE33113, GSE31595, GSE29621, and GSE17536), and it showed better performance than three known lncRNA signatures for predicting PFS. In summary, our study demonstrates that the m6A-Lnc signature is a promising biomarker for forecasting patient PFS in CRC.
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Affiliation(s)
- Yong Zhang
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- Branch Center of Advanced Medical Research Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Lu Li
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Feifei Chu
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xingguo Xiao
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Li Zhang
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Kunkun Li
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Huili Wu
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
- *Correspondence: Huili Wu,
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20
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Liu T, Tang W, Chen Y, Liu Y, Xu D, Jiang Y, Zhou S, Qin X, Ren L, Chang W, Xu J. The m6A RNA Modification Quantity and the Prognostic Effect of Reader YTHDC2 in Colorectal Cancer. Clin Med Insights Oncol 2022; 16:11795549221104441. [PMID: 35898390 PMCID: PMC9310211 DOI: 10.1177/11795549221104441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/15/2022] [Indexed: 11/17/2022] Open
Abstract
Background: N6-methyladenosine (m6A) modification plays crucial roles in cancers. However, its alteration in colorectal cancer (CRC) is still poorly described. The purpose of this study is to explore the change of m6A modification and the function of m6A binding protein YTHDC2 in CRC. Methods: The global level of m6A modification was detected by mass spectrometry and dot blotting assay. The expression of YTHDC2 was investigated using The Cancer Genome Atlas and using real-time polymerase chain reaction (RT-qPCR), western blotting, and immunohistochemistry based on CRC tissues. Kaplan–Meier analysis and Cox proportional hazards regression were performed to analyze the prognostic value of YTHDC2. RNA immunoprecipitation (RIP)-seq and m6A immunoprecipitation (MeRIP)-seq were used to explore the direct targets of YTHDC2. Gene oncology (GO) and Gene Set Enrichment Analysis (GSEA) were used to explore the pathways that could be influenced by YTHDC2. Results: No significant difference was observed in the global level of m6A modification on total RNA or mRNA between CRC and adjacent nontumor tissues. We further found a significant decreasing of YTHDC2 in CRC tissues. Kaplan–Meier analysis indicated that lower expression of YTHDC2 was related to the worse disease-free survival and overall survival. In addition, lower expression of YTHDC2 was an independent worse prognostic factor in univariate and multivariate Cox regression analysis. Using YTHDC2-RIP-seq and MeRIP-seq, we identified that YTHDC2 could participate in several important biological signal pathways. Conclusions: In summary, this study suggested that the global level of m6A did not change in CRC and identified that lower YTHDC2 as a prognostic marker for worse survival of CRC.
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Affiliation(s)
- Tianyu Liu
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wentao Tang
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
| | - Yijiao Chen
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu Liu
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Donghao Xu
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yudong Jiang
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shizhao Zhou
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaorui Qin
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Ren
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
| | - Wenju Chang
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China.,General Surgery Department, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianmin Xu
- Colorectal Cancer Center, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Colorectal Cancer Minimally Invasive Technology, Shanghai, China
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21
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Characterization of m6A Methylation Modification Patterns in Colorectal Cancer Determines Prognosis and Tumor Microenvironment Infiltration. J Immunol Res 2022; 2022:8766735. [PMID: 35692505 PMCID: PMC9177296 DOI: 10.1155/2022/8766735] [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: 02/18/2022] [Accepted: 04/21/2022] [Indexed: 12/04/2022] Open
Abstract
Cumulative studies have suggested that dysregulation of m6A regulators and immunity is highly linked to the prognosis of patients with cancer. However, the potential contribution of m6A modification patterns to the tumor microenvironment (TME) and the therapeutic efficacy of immunotherapy for colorectal cancer (CRC) remain elusive. A comprehensive analysis of the m6A modification profiles of 458 patients with CRC was performed by clustering 21 genes encoding m6A methylation regulators and linking the m6A modification pattern with TME characteristics. Using principal component analysis (PCA), a risk model was constructed to quantify individual m6A modification patterns in patients with CRC. The results indicated that the expression profiles and genetic mutations of 21 genes encoding m6A methylation regulators in CRC were characterized by a high degree of heterogeneity. Three m6A clusters had significant differences in prognosis, m6A modification patterns, and TME characteristics. Furthermore, a risk model, termed m6Ascore, was developed by PCA to quality m6A methylation patterns at an individual level. The m6Ascore could stratify patients into high- and low-m6Ascore groups. Further analyses demonstrated that the m6Ascore had a good predictive performance for overall survival and clinical efficacy of immunotherapy in patients with CRC. Finally, the predictive value of the model was validated by external cohorts. In conclusion, the comprehensive characterization of m6A methylation modification patterns might contribute to our understanding of the TME in CRC and the development of personalized antitumor immunotherapy in the future.
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22
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Serelli-Lee V, Ito K, Koibuchi A, Tanigawa T, Ueno T, Matsushima N, Imai Y. A State-of-the-Art Roadmap for Biomarker-Driven Drug Development in the Era of Personalized Therapies. J Pers Med 2022; 12:jpm12050669. [PMID: 35629092 PMCID: PMC9143954 DOI: 10.3390/jpm12050669] [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: 01/26/2022] [Revised: 03/30/2022] [Accepted: 04/15/2022] [Indexed: 02/05/2023] Open
Abstract
Advances in biotechnology have enabled us to assay human tissue and cells to a depth and resolution that was never possible before, redefining what we know as the “biomarker”, and how we define a “disease”. This comes along with the shift of focus from a “one-drug-fits-all” to a “personalized approach”, placing the drug development industry in a highly dynamic landscape, having to navigate such disruptive trends. In response to this, innovative clinical trial designs have been key in realizing biomarker-driven drug development. Regulatory approvals of cancer genome sequencing panels and associated targeted therapies has brought personalized medicines to the clinic. Increasing availability of sophisticated biotechnologies such as next-generation sequencing (NGS) has also led to a massive outflux of real-world genomic data. This review summarizes the current state of biomarker-driven drug development and highlights examples showing the utility and importance of the application of real-world data in the process. We also propose that all stakeholders in drug development should (1) be conscious of and efficiently utilize real-world evidence and (2) re-vamp the way the industry approaches drug development in this era of personalized medicines.
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Affiliation(s)
- Victoria Serelli-Lee
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Eli Lilly Japan K.K., 5-1-28 Isogamidori, Chuo-ku, Kobe 651-0086, Japan
- Correspondence: (V.S.-L.); (Y.I.)
| | - Kazumi Ito
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan;
| | - Akira Koibuchi
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Astellas Pharma Inc., 2-5-1 Nihonbashi-Honcho, Chuo-ku, Tokyo 103-8411, Japan
| | - Takahiko Tanigawa
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Bayer Yakuhin Ltd., 2-4-9, Umeda, Kita-ku, Osaka 530-0001, Japan
| | - Takayo Ueno
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Bristol Myers Squibb K.K., 6-5-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 163-1334, Japan
| | - Nobuko Matsushima
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Janssen Pharmaceutical K.K., 3-5-2, Nishikanda, Chiyoda-ku, Tokyo 101-0065, Japan
| | - Yasuhiko Imai
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Bristol Myers Squibb K.K., 6-5-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 163-1334, Japan
- Correspondence: (V.S.-L.); (Y.I.)
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23
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Tu B, Jia Y, Qian J. Bioinformatics Analysis Identified Five Widely Expressed Genes Associated with Prognosis in Sarcoma. Int J Gen Med 2022; 15:3711-3725. [PMID: 35414751 PMCID: PMC8995039 DOI: 10.2147/ijgm.s352048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/16/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Bizhi Tu
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
| | - Yaya Jia
- Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Jun Qian
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
- Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui, People’s Republic of China, Tel +86-13955116514, Fax +86-551-62922025, Email
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24
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Zhang L, Tang X, Wan J, Zhang X, Zheng T, Lin Z, Liu T. Construction of a Novel Signature and Prediction of the Immune Landscape in Soft Tissue Sarcomas Based on N6-Methylandenosine-Related LncRNAs. Front Mol Biosci 2021; 8:715764. [PMID: 34733885 PMCID: PMC8559337 DOI: 10.3389/fmolb.2021.715764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/28/2021] [Indexed: 12/21/2022] Open
Abstract
Background: N6-methylandenosine-related long non-coding RNAs (m6A-related lncRNAs) are critically involved in cancer development. However, the roles and clinical significance of m6A-related lncRNAs in soft tissue sarcomas (STS) are inconclusive, thereby warranting further investigations. Methods: Transcriptome profiling data were extracted from The Cancer Genome Atlas (TCGA) database and Genotype-Tissue Expression (GTEx). Consensus clustering was employed to divide patients into clusters and Kaplan–Meier analysis was used to explore the prognostic differences between the subgroups. Gene set enrichment analysis (GSEA) was conducted to identify the biological processes and signaling pathways associated with m6A-Related lncRNAs. Finally, patients were randomly divided into training and validation cohorts, and least absolute shrinkage and selection operator (LASSO) Cox regression was conducted to establish the m6A-related lncRNA-based risk signature. Results: A total of 259 STS patients from TCGA-SARC dataset were enrolled in our study. Thirteen m6A-Related lncRNAs were identified to be closely related to the prognosis of STS patients. Patients were divided into two clusters, and patients in cluster 2 had a better overall survival (OS) than those in cluster 1. Patients in different clusters also showed differences in immune scores, infiltrating immune cells, and immune checkpoint expression. Patients were further classified into high-risk and low-risk subgroups according to risk scores, and high-risk patients were found to have a worse prognosis. The receiver operating characteristic (ROC) curve indicated that the risk signature displayed excellent performance at predicting the prognosis of patients with STS. Further, the risk signature was remarkably connected with the immune microenvironment and chemosensitivity in STS. Conclusion: Our study demonstrated that m6A-related lncRNAs were significantly associated with prognosis and tumor immune microenvironment and could function as independent prognosis-specific predictors in STS, thereby providing novel insights into the roles of m6A-related lncRNAs in STS.
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Affiliation(s)
- Li Zhang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China.,Department of Endocrinology, The Fifth Central Hospital of Tianjin, Tianjin, China
| | - Xianzhe Tang
- Department of Orthopedics, Chenzhou No. 1 People's Hospital, Chenzhou, China
| | - Jia Wan
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xianghong Zhang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Tao Zheng
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhengjun Lin
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
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25
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Ye F, Hu Y, Gao J, Liang Y, Liu Y, Ou Y, Cheng Z, Jiang H. Radiogenomics Map Reveals the Landscape of m6A Methylation Modification Pattern in Bladder Cancer. Front Immunol 2021; 12:722642. [PMID: 34733275 PMCID: PMC8559436 DOI: 10.3389/fimmu.2021.722642] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
We aimed to develop a noninvasive radiomics approach to reveal the m6A methylation status and predict survival outcomes and therapeutic responses in patients. A total of 25 m6A regulators were selected for further analysis, we confirmed that expression level and genomic mutations rate of m6A regulators were significantly different between cancer and normal tissues. Besides, we constructed methylation modification models and explored the immune infiltration and biological pathway alteration among different models. The m6A subtypes identified in this study can effectively predict the clinical outcome of bladder cancer (including m6AClusters, geneClusters, and m6Ascore models). In addition, we observed that immune response markers such as PD1 and CTLA4 were significantly corelated with the m6Ascore. Subsequently, a total of 98 obtained digital images were processed to capture the image signature and construct image prediction models based on the m6Ascore classification using a radiomics algorithm. We constructed seven signature radiogenomics models to reveal the m6A methylation status, and the model achieved an area under curve (AUC) degree of 0.887 and 0.762 for the training and test datasets, respectively. The presented radiogenomics models, a noninvasive prediction approach that combined the radiomics signatures and genomics characteristics, displayed satisfactory effective performance for predicting survival outcomes and therapeutic responses of patients. In the future, more interdisciplinary fields concerning the combination of medicine and electronics remains to be explored.
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Affiliation(s)
- Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yun Hu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiahao Gao
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yingchun Liang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yufei Liu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuxi Ou
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhang Cheng
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
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26
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Ge Y, Liu T, Wang C, Zhang Y, Xu S, Ren Y, Feng Y, Yin L, Pu Y, Liang G. N6-methyladenosine RNA modification and its interaction with regulatory non-coding RNAs in colorectal cancer. RNA Biol 2021; 18:551-561. [PMID: 34674600 DOI: 10.1080/15476286.2021.1974749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
As one of the most common forms of RNA modification, N6-methyladenosine (m6A) RNA modification has attracted increasing research interest in recent years. This reversible RNA modification added a new dimension to the post-transcriptional regulation of gene expression. In colorectal cancer (CRC), the role of m6A modification has been extensively studied, not only on mRNAs but also on non-coding RNAs (ncRNAs). In the present review, we depicted the role of m6A modification in CRC, systematically elaborate the interaction between m6A modification and regulatory ncRNAs in function and mechanism. Moreover, we discussed the potential applications in clinical.
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Affiliation(s)
- Yiling Ge
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, PR China
| | - Tong Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, PR China
| | - Chuntao Wang
- Science and technology department, Jiangsu Vocational College of Medicine, Yancheng, Jiangsu, PR China
| | - Yanqiu Zhang
- Department of Environmental Occupational Health, Taizhou Center for Disease Control and Prevention, Taizhou, PR China
| | - Siyi Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, PR China
| | - Yiyi Ren
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, PR China
| | - Yanlu Feng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, PR China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, PR China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, PR China
| | - Geyu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, PR China
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27
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Wu X, Dai M, Li J, Cai J, Zuo Z, Ni S, Zhang Q, Zhou Z. m(6)A demethylase ALKBH5 inhibits cell proliferation and the metastasis of colorectal cancer by regulating the FOXO3/miR-21/SPRY2 axis. Am J Transl Res 2021; 13:11209-11222. [PMID: 34786052 PMCID: PMC8581846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE Colorectal cancer is a common malignancy worldwide. This research aimed to investigate the role of α-ketoglutarate-dependent dioxygenase alkB homologue 5 (ALKBH5), a N6-methyladenosine (m(6)A) demethylase, on the cell proliferation and metastasis of colorectal cancer. METHODS The interaction relationship between FOXO3, miR-21, and SPRY2 were predicted by starBase 2.0 and determined using RIP, CHIP, and dual-luciferase reporter assays. Quantitative reverse transcription PCR (RT-qPCR) and western blot were used to measure the gene and miRNA expressions of ALKBH5, FOXO3, miR-21, and SPRY2. The cell proliferation was determined using CCK8 and colony formation assays. The metastatic abilities were measured using wound healing and transwell assays. RESULTS In colorectal cancer, downregulated ALKBH5 is related to poor prognosis. Rescued ALKBH5 suppresses the proliferation and metastasis of colorectal cancer cells. The role of ALKBH5 is achieved by reducing the m(6)A modification of forkhead box O3 (FOXO3), which enhances its stability. FOXO3 targets miR-21 and increases the SPRY2 expressions. The antitumor effects of ALKBH5 can be blocked by FOXO3 knockdown, which is reversed by the miR-21 inhibitor. CONCLUSION ALKBH5 plays an antitumor role in colorectal cancer by regulating the FOXO3/miR-21/SPRY2 axis, providing a new direction for colorectal cancer therapy.
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Affiliation(s)
- Xiangbin Wu
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325000, Zhejiang Province, China
| | - Minzhi Dai
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325000, Zhejiang Province, China
| | - Jinlei Li
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325000, Zhejiang Province, China
| | - Jianhui Cai
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325000, Zhejiang Province, China
| | - Zhigui Zuo
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325000, Zhejiang Province, China
| | - Shichang Ni
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325000, Zhejiang Province, China
| | - Qiyu Zhang
- Department of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325000, Zhejiang Province, China
| | - Zhenhua Zhou
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325000, Zhejiang Province, China
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28
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Tan X, Li Q, Zhang Q, Fan G, Liu Z, Zhou K. Integrative Analysis Reveals Potentially Functional N6-Methylandenosine-Related Long Noncoding RNAs in Colon Adenocarcinoma. Front Genet 2021; 12:739344. [PMID: 34603397 PMCID: PMC8484874 DOI: 10.3389/fgene.2021.739344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/07/2021] [Indexed: 01/23/2023] Open
Abstract
N6-methyladenosine (m6A) is one of the most prevalent RNA modifications in mRNA and non-coding RNA. In this study, we identified 10 upregulated m6A regulators at both mRNA and protein levels, and 2,479 m6A-related lncRNAs. Moreover, the m6A-related long noncoding RNAs (lncRNAs) could clearly stratify the colon adenocarcinoma (COAD) samples into three subtypes. The subtype 2 had nearly 40% of samples with microsatellite instability (MSI), significantly higher than the two other subtypes. In accordance with this finding, the inflammatory response-related pathways were highly activated in this subtype. The subtype-3 had a shorter overall survival and a higher proportion of patients with advanced stage than subtypes 1 and 2 (p-value < 0.05). Pathway analysis suggested that the energy metabolism-related pathways might be aberrantly activated in subtype 3. In addition, we observed that most of the m6A readers and m6A-related lncRNAs were upregulated in subtype 3, suggesting that the m6A readers and the m6A-related lncRNAs might be associated with metabolic reprogramming and unfavorable outcome in COAD. Among the m6A-related lncRNAs in subtype 3, four were predicted as prognostically relevant. Functional inference suggested that CTD-3184A7.4, RP11-458F8.4, and RP11-108L7.15 were positively correlated with the energy metabolism-related pathways, further suggesting that these lncRNAs might be involved in energy metabolism-related pathways. In summary, we conducted a systematic data analysis to identify the key m6A regulators and m6A-related lncRNAs, and evaluated their clinical and functional importance in COAD, which may provide important evidences for further m6A-related researches.
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Affiliation(s)
- Xinjie Tan
- School of Medicine, Nankai University, Tianjin, China
| | - Qian Li
- Department of Pediatrics, The Second Affiliated Hospital of Zheng Zhou University, Zhengzhou, China
| | - Qinya Zhang
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany.,Department of Anesthesiology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Gang Fan
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China.,Department of Urology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Zhuo Liu
- Third Department of General Surgery, The Central Hospital of Xiangtan, Xiangtan, China
| | - Kunyan Zhou
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
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29
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Liu C, Yang S, Zhang Y, Wang C, Du D, Wang X, Liu T, Liang G. Emerging Roles of N6-Methyladenosine Demethylases and Its Interaction with Environmental Toxicants in Digestive System Cancers. Cancer Manag Res 2021; 13:7101-7114. [PMID: 34526822 PMCID: PMC8437382 DOI: 10.2147/cmar.s328188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/19/2021] [Indexed: 01/02/2023] Open
Abstract
Digestive system cancers are common cancers with high cancer deaths worldwide. They have become a major threat to public health and economic burden. As one of the most universal RNA modifications in eukaryotes, the N6-methyladenosine (m6A) modification is involved in the occurrence, development, prognosis, and treatment response of various cancers, including digestive system cancers. M6A demethylases shape the m6A landscape dynamically, playing important roles in cancers. In addition, accumulating evidence reveal that many environmental toxicants are the established risk factors for digestive system cancers and associated with m6A modification. In this review, we summarize the multiple functions of M6A demethylases (fat mass and obesity-associated protein (FTO), AlkB homolog 5 (ALKBH5) and AlkB homolog 3 (ALKBH3)) in digestive system cancers, which are aberrantly expressed and affect cancer progression. We also discuss the potential roles of m6A demethylases in the assessment of environmental exposure, the signature for prevention and diagnosis of digestive system cancers.
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Affiliation(s)
- Caiping Liu
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Sheng Yang
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Yanqiu Zhang
- Department of Environmental Occupational Health, Taizhou Center for Disease Control and Prevention, Taizhou, 225300, Jiangsu, People's Republic of China
| | - Chuntao Wang
- Jiangsu Vocational College of Medicine, Yancheng, 224000, Jiangsu, People's Republic of China
| | - Dandan Du
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Xian Wang
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Tong Liu
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Geyu Liang
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
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30
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Xie Z, Li M, Hong H, Xu Q, He Z, Peng Z. Expression of N 6-methyladenosine (m 6A) regulators correlates with immune microenvironment characteristics and predicts prognosis in diffuse large cell lymphoma (DLBCL). Bioengineered 2021; 12:6115-6133. [PMID: 34482808 PMCID: PMC8806613 DOI: 10.1080/21655979.2021.1972644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
This study conducted a comprehensive analysis of the clinical significance of N6-methyladenosine (m6A) regulators and their relationship with immune microenvironment characteristics in diffuse large cell lymphoma (DLBCL). Consensus clustering was performed to molecularly discriminate DLBCL subtypesbased on m6A regulators’ expression. Using the Cox and Lasso regression algorithm, survival-associated m6A regulators were identified, and a m6A-based prognostic signature was established. The influence of m6A risk on immune cell infiltration, immune checkpoint genes, cancer immunity cycle, and immunotherapeutic response was evaluated. Potential molecular pathways related to m6A risk were investigated using gene set enrichment analysis. The m6A regulators showed satisfactory performance in distinguishing DLBCL subgroups with distinct clinical traits and outcomes. A six m6A regulator-based prognostic signature was established and validated as an independent predictor, which separated patients into low- and high-risk groups. High-risk m6A indicated worse survival. The B cells naïve, T cells gamma delta, and NK cells resting were the three most affected immune cells by m6A risk. Up-regulated (PDCD1 and KIR3DL1) and down-regulated (TIGIT, IDO1, and BTLA) immune checkpoint genes in the high-risk group were identified. The m6A risk was found to influence several steps in the cancer immunity cycle. Patients with high-risk m6A were more likely to benefit from immunotherapy. Biological function enrichment analysis revealed that high-risk m6A to be tended related to malignant tumor characteristics, while low-risk m6A showed trend to be related to defensive response processes. Collectively, the m6A-based prognostic signature could be a practical prognostic predictor for DLBCL and immune microenvironment characteristics affected by m6A may be part of the mechanism.
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Affiliation(s)
- Zucheng Xie
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Meiwei Li
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Haoyuan Hong
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Qingyuan Xu
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Zhendong He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Zhigang Peng
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
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Liu J, Zhou Z, Ma L, Li C, Lin Y, Yu T, Wei JF, Zhu L, Yao G. Effects of RNA methylation N6-methyladenosine regulators on malignant progression and prognosis of melanoma. Cancer Cell Int 2021; 21:453. [PMID: 34446007 PMCID: PMC8393813 DOI: 10.1186/s12935-021-02163-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/18/2021] [Indexed: 12/14/2022] Open
Abstract
Background Melanoma is an extremely aggressive type of skin cancer and experiencing a expeditiously rising mortality in a current year. Exploring new potential prognostic biomarkers and therapeutic targets of melanoma are urgently needed. The ambition of this research was to identify genetic markers and assess prognostic performance of N6-methyladenosine (m6A) regulators in melanoma. Methods Gene expression data and corresponding clinical informations of melanoma patients as well as sequence data of normal controls are collected from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. Quantitative real-time PCR (qRT-PCR) analysis was carried out to detect the RNA expression of IGF2BP3 in A375 cell line, melanoma tissues, and normal tissues. Western blot, cell proliferation, and migration assays were performed to assess the ability of IGF2BP3 in A375 cell line. Results Differently expressed m6A regulators between tumor samples and normal samples were analyzed. A three-gene prognostic signature including IGF2BP3, RBM15B, and METTL16 was constructed, and the risk score of this signature was identified to be an independent prognostic indicator for melanoma. In addition, IGF2BP3 was verified to promote melanoma cell proliferation and migration in vitro and associate with lymph node metastasis in clinical samples. Moreover, risk score and the expression of IGF2BP3 were positively associated with the infiltrating immune cells and these hub genes made excellent potential drug targets in melanoma. Conclusion We identified the genetic changes in m6A regulatory genes and constructed a three-gene risk signature with distinct prognostic value in melanoma. This research provided new insights into the epigenetic understanding of m6A regulators and novel therapeutic strategies in melanoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02163-9.
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Affiliation(s)
- Jinfang Liu
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Zijian Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Ling Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Chujun Li
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Yu Lin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Ting Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Lingjun Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Gang Yao
- Department of Plastic and Burns Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
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Huang J, Shao Y, Gu W. Function and clinical significance of N6-methyladenosine in digestive system tumours. Exp Hematol Oncol 2021; 10:40. [PMID: 34246319 PMCID: PMC8272376 DOI: 10.1186/s40164-021-00234-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/03/2021] [Indexed: 12/21/2022] Open
Abstract
RNA modification, like DNA methylation, histone modification, non-coding RNA modification and chromatin rearrangement, plays an important role in tumours. N6-methyladenosine (m6A) is the most abundant RNA modification in cells, and it regulates RNA transcription, processing, splicing, degradation, and translation. m6A-associated proteins have been used as new biomarkers and therapeutic targets for tumour prediction and monitoring. There are three main types of proteins involved in m6A methylation: methyltransferases (METTL3, METTL14, WTAP, RBM15, ZC3H13 and KIAA1429), demethylases (FTO, ALKBH5 and ALKBH3) and RNA-binding proteins (YTHDF1-3, YTHDC1-2, IGF2BPs and HNRNPs). This article reviews the origins, characteristics and functions of m6A and its relationship with digestive system tumours based on recent research. The expression of m6A regulators can be used as an evaluation indicator of tumour growth and progression and as a prognostic indicator. In-depth research on m6A methylation in digestive system tumours may provide new directions for clinical prediction and further treatment.
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Affiliation(s)
- Junchao Huang
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
| | - Yingjie Shao
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
| | - Wendong Gu
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, 185 Juqian Street, Changzhou, 213003 China
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Feng ZY, Wang T, Su X, Guo S. Identification of the m 6A RNA Methylation Regulators WTAP as a Novel Prognostic Biomarker and Genomic Alterations in Cutaneous Melanoma. Front Mol Biosci 2021; 8:665222. [PMID: 34291082 PMCID: PMC8287526 DOI: 10.3389/fmolb.2021.665222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/22/2021] [Indexed: 02/03/2023] Open
Abstract
Background: The purpose of our research was to establish a gene signature and determine the prognostic value of m6A methylation regulators in cutaneous melanoma and WTAP as a protective gene in cutaneous melanoma prognosis, we also evaluated gene mutations in cutaneous melanoma. Methods: We downloaded the RNA-seq transcriptome data and the clinical information for cutaneous melanoma patients from the GTEx and TCGA databases. Consensus clustering analysis was applied to divide the samples into two groups. Then the least absolute shrinkage and selection operator (LASSO) analyses were conducted to construct a risk signature, and we use external and internal datasets to verify its predictive value. We further searched the cBioPortal tools to detect genomic alterations and WTAP mutations. Finally, WTAP was further identified as a prognostic factor, and the related mechanisms mediated by WTAP were predicted by gene set enrichment analysis (GSEA). Experimental validations and have been further carried out. Results: Notably, m6A RNA methylation regulators play significant roles in tumorigenesis and development. In total, we selected three subtypes of cutaneous melanoma according to consensus clustering of the m6A RNA methylation regulators, and the stage of cutaneous melanoma was proven to be related to the subtypes. The Cox regression and LASSO analyses built a risk signature including ELF3, ZC3H13 and WTAP. The prognostic value of the risk signature in internal and external datasets have been proven then. The whole-genome and selected gene WTAP mutations were further explored. WTAP as a single prognostic factor was also explored and found to serve as an independent protective prognostic factor. Conclusions: Our study constructed a stable risk signature composed of m6A RNA methylation regulators in cutaneous melanoma. Moreover, WTAP was identified as a valuable prognostic factor and potential molecular target for cutaneous melanoma treatment.
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Affiliation(s)
- Zi-Yi Feng
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ting Wang
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xin Su
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Shu Guo
- Department of Plastic Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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Feng ZY, Gao HY, Feng TD. Immune Infiltrates of m 6A RNA Methylation-Related lncRNAs and Identification of PD-L1 in Patients With Primary Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:672248. [PMID: 34178999 PMCID: PMC8220827 DOI: 10.3389/fcell.2021.672248] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
Background: The purpose of this study was to determine the association between m6A-modified lncRNAs, immune infiltration, and PD-L1 expression in patients with primary head and neck squamous cell carcinoma (HNSCC) and the prognostic value of m6A RNA methylation-related lncRNAs in HNSCC. Methods: We downloaded the RNA-seq transcriptome data and the clinical information for HNSCC from the TCGA databases and used consensus clustering analysis to divide the samples into two groups. To identify a risk signature, least absolute shrinkage and selection operator (LASSO) analyses were conducted. the association between m6A-modified lncRNAs, immune infiltration, and PD-L1 expression were detected by using the R packages. What is more, we used cBioPortal tools to identify genomic alterations and PD-L1 mutations and Gene set enrichment analysis (GSEA) was utilized to predict downstream access of two clusters. Results: Notably, lncRNAs play significant roles in tumorigenesis and development. In total, we identified two subtypes of HNSCC according to consensus clustering of the m6A RNA methylation-related lncRNAs, and the T, grade and age were proven to be related to the subtypes. The Cox regression and LASSO analyses identified a risk signature including GRHL3-AS1, AL121845.4, AC116914.2, AL513190.1. The prognostic value of the risk signature was then proven. The selected gene PD-L1 mutations and the immune infiltration in both groups were further explored. Conclusion: Collectively, our study elucidated the important role of m6A RNA methylation- related lncRNAs in tumor microenvironment of HNSCC. The proposed m6A RNA methylation- related lncRNAs might serve as crucial mediators of tumor microenvironment of HNSCC, representing promising therapeutic targets in improving immunotherapeutic efficacy.
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Affiliation(s)
- Zi-Yi Feng
- Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Hao-Yu Gao
- Department of Students, The First Hospital of China Medical University, Shenyang, China
| | - Tian-Da Feng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
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Fang Z, Hu Y, Hu J, Huang Y, Zheng S, Guo C. The crucial roles of N 6-methyladenosine (m 6A) modification in the carcinogenesis and progression of colorectal cancer. Cell Biosci 2021; 11:72. [PMID: 33836813 PMCID: PMC8034132 DOI: 10.1186/s13578-021-00583-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022] Open
Abstract
As the predominant modification in RNA, N6-methyladenosine (m6A) has attracted increasing attention in the past few years since it plays vital roles in many biological processes. This chemical modification is dynamic, reversible and regulated by several methyltransferases, demethylases and proteins that recognize m6A modification. M6A modification exists in messenger RNA and affects their splicing, nuclear export, stability, decay, and translation, thereby modulating gene expression. Besides, the existence of m6A in noncoding RNAs (ncRNAs) could also directly or indirectly regulated gene expression. Colorectal cancer (CRC) is a common cancer around the world and of high mortality. Increasing evidence have shown that the changes of m6A level and the dysregulation of m6A regulatory proteins have been implicated in CRC carcinogenesis and progression. However, the underlying regulation laws of m6A modification to CRC remain elusive and better understanding of these mechanisms will benefit the diagnosis and therapy. In the present review, the latest studies about the dysregulation of m6A and its regulators in CRC have been summarized. We will focus on the crucial roles of m6A modification in the carcinogenesis and development of CRC. Moreover, we will also discuss the potential applications of m6A modification in CRC diagnosis and therapeutics.
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Affiliation(s)
- Zhihao Fang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yiqiu Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Jinhui Hu
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
| | - Yanqin Huang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
| | - Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
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Gao C, Zhuang J, Li H, Liu C, Zhou C, Liu L, Feng F, Sun C. Gene signatures of 6-methyladenine regulators in women with lung adenocarcinoma and development of a risk scoring system: a retrospective study using the cancer genome atlas database. Aging (Albany NY) 2021; 13:3957-3968. [PMID: 33428597 PMCID: PMC7906130 DOI: 10.18632/aging.202364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/23/2020] [Indexed: 01/22/2023]
Abstract
Although the emergence of new treatments has improved the prognosis of women with lung adenocarcinoma (LUAD), the emergence of drug resistance limits their clinical efficacy. Therefore, there is an urgent need to identify new targets and develop a risk scoring system to evaluate the prognosis of patients. 6-methyladenine (M6A), as the most common methyl modification in RNA modification, its clinicopathological features, diagnosis and prognostic value in lung cancer, especially in LUAD remain to be discussed. We analyzed the clinical and sequencing data of the female LUAD cohort from The Cancer Genome Atlas (TCGA), evaluated the expression profiles of 16 M6A regulation-related genes in the cohort and the relationships between genetic changes and clinical characteristics, developed an M6A-related risk scoring system using Cox analysis. Finally, the copy number variations (CNVs) of the related genes in the samples were analyzed and verified using the cBioPortal platform. Compared with other clinical factors, this risk scoring system showed a higher predictive sensitivity and specificity. The M6A-related risk scoring system developed in this study may help to improve the screening of female patients at high risk of LUAD and provides important theoretical bioinformatics support for evaluating the prognosis of such patients.
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Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, Shandong, PR China
| | - Jing Zhuang
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China
| | - Huayao Li
- College of Basic Medical Sciences, Shandong University of Traditional Chinese Medicine, Jinan 250014, Shandong, PR China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, Shandong, PR China
| | - Chao Zhou
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China
| | - Lijuan Liu
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China
| | - Fubin Feng
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China
| | - Changgang Sun
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China.,Cancer and Immunology Institute, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
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Wang X, Ye X, Zhang Y, Ji F. Flurbiprofen suppresses the inflammation, proliferation, invasion and migration of colorectal cancer cells via COX2. Oncol Lett 2020; 20:132. [PMID: 32934701 PMCID: PMC7471702 DOI: 10.3892/ol.2020.11993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer is an aggressive disease with a poor prognosis and low survival rate at the advanced stage, therefore new innovative targets are urgently required. Flurbiprofen has been reported to exhibit therapeutic effects in other types of cancer, such as esophageal cancer, breast cancer and colorectal cancer. Therefore, the present study aimed to investigate the function of flurbiprofen in colorectal cancer. SW620 colorectal cancer cells were treated with different concentrations of flurbiprofen to determine the optimum concentration. Subsequently, COX2 expression affected by flurbiprofen was tested using western blotting, reverse transcription-quantitative PCR and immunofluorescence. Enzyme-linked immunosorbent assay was used to determine the levels of tumor necrosis factor-α, interleukin (IL)-6 and IL-1β. Cell Counting Kit-8, colony formation and flow cytometry assays were used to assess the proliferation and apoptosis of SW620 cells in various groups. Western blotting was performed to investigate the expression of proliferation-, apoptosis- and migration-related proteins after different treatments. Wound healing and Transwell assays were performed to measure the invasion and migration of colorectal cancer cells, respectively. The results demonstrated that flurbiprofen inhibited colorectal cancer cell proliferation. Furthermore, it was identified that flurbiprofen inhibited the expression of COX2. Notably, flurbiprofen suppressed the expression of inflammatory factors by inhibiting COX2. Moreover, flurbiprofen inhibited the proliferation, invasion and migration of colorectal cancer cells by inhibiting COX2. In conclusion, the present study revealed that flurbiprofen inhibited COX2 expression in colorectal cancer, and affected the proliferation, invasion, migration and apoptosis of colorectal cancer cells. These results expand the understanding of the function of COX2 in colorectal cancer and the effect of flurbiprofen on COX2 expression.
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Affiliation(s)
- Xiaobo Wang
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Xuxing Ye
- Traditional Medicine Center, Jinhua Hospital, Zhejiang University, Jinhua, Zhejiang 321000, P.R. China
| | - Yili Zhang
- Physical Examination Center, Jinhua Hospital, Zhejiang University, Jinhua, Zhejiang 321000, P.R. China
| | - Feng Ji
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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