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Ji F, Lu Y, Chen S, Lin X, Yu Y, Zhu Y, Luo X. m 6A methyltransferase METTL3-mediated lncRNA FOXD2-AS1 promotes the tumorigenesis of cervical cancer. MOLECULAR THERAPY-ONCOLYTICS 2021; 22:574-581. [PMID: 34589576 PMCID: PMC8450180 DOI: 10.1016/j.omto.2021.07.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/14/2021] [Indexed: 01/04/2023]
Abstract
Recent studies have indicated that long noncoding RNA (lncRNA) and N6-methyladenosine (m6A) methylation modification play critical roles in human cancers; however, their regulation on cervical cancer is largely unclear. Here, our study tries to investigate the underlying mechanisms by which lncRNA FOXD2 adjacent opposite strand RNA 1 (FOXD2-AS1) modulates cervical cancer tumorigenesis. Results illuminated that FOXD2-AS1 expression was significantly upregulated in cervical cancer cells and tissue, which was closely correlated to the unfavorable prognosis. Functionally, gain and loss-of-function assays showed that FOXD2-AS1 promoted the migration and proliferation of cervical cancer cells. Besides, FOXD2-AS1 silencing repressed the tumor growth in vivo. Mechanistically, m6A methyltransferase methyltransferase-like 3 (METTL3) enhanced the stability of FOXD2-AS1 and maintained its expression. Moreover, FOXD2-AS1 recruited lysine-specific demethylase 1 (LSD1) to the promoter region of p21 to silence its transcription abundance. In conclusion, these findings support that METTL3/FOXD2-AS1 accelerates cervical cancer progression via a m6A-dependent modality, which may serve as a potential therapeutic target for cervical cancer.
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Affiliation(s)
- Fei Ji
- Department of Obstetrics and Gynecology, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen 518102, China.,The First Clinical Medical College of Jinan University, Guangzhou 510632, China
| | - Yang Lu
- Department of Obstetrics and Gynecology, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen 518102, China
| | - Shaoyun Chen
- Maternal-Fetal Medicine Institute, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen 518102, China
| | - Xiaoling Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou 510632, China
| | - Yan Yu
- Department of Obstetrics and Gynecology, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen 518102, China
| | - Yuanfang Zhu
- Department of Obstetrics and Gynecology, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen 518102, China
| | - Xin Luo
- The First Clinical Medical College of Jinan University, Guangzhou 510632, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou 510632, China
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52
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Wang Y, Li N, Tian D, Zhou CW, Wang YH, Yang C, Zeng MS. Analysis of m6A-Related lncRNAs for Prognosis Value and Response to Immune Checkpoint Inhibitors Therapy in Hepatocellular Carcinoma. Cancer Manag Res 2021; 13:6451-6471. [PMID: 34429653 PMCID: PMC8379396 DOI: 10.2147/cmar.s322179] [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: 06/08/2021] [Accepted: 07/29/2021] [Indexed: 01/03/2023] Open
Abstract
Introduction N6-methyladenosine (m6A) modification and long non-coding RNAs (lncRNAs) play pivotal roles in the progression of hepatocellular carcinoma (HCC). However, how their interaction is involved in the prognostic value of HCC and immune checkpoint inhibitors (ICIs) therapy remains unclear. Methods The RNA sequencing and clinical data of HCC patients were collected from TCGA database. The prognostic m6A-related lncRNAs were screened out with Pearson correlation test, univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression. Patients with HCC were classified into 2 subtypes by consensus clustering. Survival analyses were performed to assess the prognostic value of different clusters and risk models. Potential tumor correlated biological pathways correlated with different clusters were explored through gene set enrichment analysis. We also identified the relationship of the risk model and clusters with response to immune checkpoint inhibitors (ICIs) therapy and tumor microenvironment (TME). Furthermore, the prognostic value of the 9 m6A-related lncRNAs was validated in the external cohort. Finally, the role of SNHG4 was explored by silencing and overexpression of SNHG4 through conducting proliferation, migration and invasion experiments. Results Patients from 2 clusters and different risk groups based on m6A-related lncRNAs had significantly different clinicopathological characteristics and overall survival outcomes. Tumor-correlated biological pathways were found to be correlated with Cluster 2 through GSEA. Moreover, we found that patients from different clusters and risk groups expressed higher levels of immune checkpoint genes and had distinct TME and different responses for ICIs therapy. Prognostic value of this risk model was further confirmed in the external cohort. Finally, consistent with the discovery, SNHG4 played an oncogenic role in vitro. Conclusion Our study demonstrated that the 9 m6A-related lncRNA signature may serve as a novel predictor in the prognosis of HCC and optimize (ICIs) therapy. SNHG4 plays an oncogenic role in HCC.
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Affiliation(s)
- Yi Wang
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - Na Li
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - Di Tian
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - Chang-Wu Zhou
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - You-Hua Wang
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, People's Republic of China
| | - Chun Yang
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - Meng-Su Zeng
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
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Ma YS, Cao YF, Liu JB, Li W, Deng J, Yang XL, Xin R, Shi Y, Zhang DD, Lv ZW, Fu D. The power and the promise of circRNAs for cancer precision medicine with functional diagnostics and prognostic prediction. Carcinogenesis 2021; 42:1305-1313. [PMID: 34313732 DOI: 10.1093/carcin/bgab071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a large class of covalently closed circular RNA. As a member of competitive endogenous RNA (ceRNA), it participates in the regulation of circRNA-miRNA-mRNA network and plays an important role in the regulation of physiology and pathology. CircRNA is produced by the reverse splicing of exon, intron or both, forming exon or intron circRNA. Studies have shown that circRNA is a ubiquitous molecule, which exceeds the linear mRNA distributed in human cells. Because of its covalent closed-loop structure, circRNA is resistant to RNase R, which is more stable than linear mRNA; circRNA is highly conserved in different species. It was found that circRNA competitively adsorbs miRNA, as a miRNA sponge, to involve in the expression regulation of a variety of genes and plays an important role in tumor development, invasion, metastasis and other processes. These molecules offer new potential opportunities for therapeutic intervention and serve as biomarkers for diagnosis. In this paper, the origin, characteristics and functions of circRNA and its role in tumor development, invasion and metastasis, diagnosis and prognosis are reviewed.
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Affiliation(s)
- Yu-Shui Ma
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.,Department of Tumor, Affiliated Tumor Hospital of Nantong University, Nantong 226300, China.,International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, National Center for Liver Cancer, the Second Military Medical University, Shanghai 200433, China.,Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yong-Feng Cao
- Department of Tumor, Affiliated Tumor Hospital of Nantong University, Nantong 226300, China
| | - Ji-Bin Liu
- Department of Tumor, Affiliated Tumor Hospital of Nantong University, Nantong 226300, China
| | - Wen Li
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Jing Deng
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Xiao-Li Yang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Rui Xin
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yi Shi
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.,Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Dan-Dan Zhang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Zhong-Wei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Da Fu
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.,Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
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Zhang P, Liu G, Lu L. N6-Methylandenosine-Related lncRNA Signature Is a Novel Biomarkers of Prognosis and Immune Response in Colon Adenocarcinoma Patients. Front Cell Dev Biol 2021; 9:703629. [PMID: 34336856 PMCID: PMC8321625 DOI: 10.3389/fcell.2021.703629] [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: 04/30/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is the most common type of colon cancer. To date, however, the prognostic values of m6A RNA methylation-related long non-coding RNAs (lncRNAs) in COAD are largely unknown. Materials and Methods The m6A-related lncRNAs were identified from The Cancer Genome Atlas (TCGA) data set. Univariate and multivariate Cox regression analyses were performed to explore the prognostic m6A-related lncRNAs. Consistent clustering analysis was performed to classify the COAD patients into different subgroups based on the expression of m6A-related lncRNAs. The potential biological functions as well as differences in the stemness index and tumor immune microenvironment between different subgroups were analyzed. The prognostic m6A-related lncRNAs were used to establish an m6A-related lncRNA risk model to predict prognosis and survival status. Results We identified 31 m6A-associated lncRNAs with prognostic values from the TCGA data set. Based on the expression of prognostic m6A-associated lncRNAs, TCGA-COAD patients were classified into three clusters using consistent clustering analysis. There was a low correlation of tumor stemness between the three clusters but a significant correlation with the tumor immune microenvironment as well as the tumor mutational load. Thirty-one prognostic-related m6A-associated lncRNAs were used to construct a risk model, which was further determined by survival analysis, receiver operating characteristic (ROC) curve, and univariate and multifactor Cox analysis. The m6A-related risk model demonstrates good performance in predicting prognosis and survival status. The model-based high-risk group exhibited poorer overall survival (OS) compared with the low-risk group. Conclusion In this study, we construct a risk model that consists of 31 m6A-related lncRNAs with independent prognostic values in COAD. Our study shows the critical roles of these 31 m6A-related lncRNAs in the tumor immune microenvironment, indicating the prospect of informing prognostic stratification and the development of immunotherapeutic strategies for COAD patients.
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Affiliation(s)
- Peiling Zhang
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Guolong Liu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lin Lu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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55
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Tang J, Han T, Tong W, Zhao J, Wang W. N 6-methyladenosine (m 6A) methyltransferase KIAA1429 accelerates the gefitinib resistance of non-small-cell lung cancer. Cell Death Discov 2021; 7:108. [PMID: 34001850 PMCID: PMC8128911 DOI: 10.1038/s41420-021-00488-y] [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: 01/29/2021] [Revised: 03/19/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A) modification has been convincingly identified to be a critical regulator in human cancer. However, the contribution of m6A to NSCLC gefitinib resistance is still largely unknown. Here, we screened and identified that m6A methyltransferase KIAA1429 was highly expressed in gefitinib-resistant NSCLC cells (PC9-GR), tissues, and closely related to unfavorable survival. Functionally, KIAA1429 accelerated the gefitinib resistance of NSCLC in vitro. Depletion of KIAA1429 repressed the tumor growth of PC9-GR cells in vivo. Mechanistically, KIAA1429 enhanced the mRNA stability of HOXA1 through targeting its 3'-untranslated regions (3'-UTR). Overall, our findings indicate that KIAA1429 plays essential oncogenic roles in NSCLC gefitinib resistance, which may provide a feasible therapeutic target for NSCLC.
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Affiliation(s)
- Jun Tang
- No. 1 Department of Tuberculosis, Chest Hospital, Shenyang, Liaoning Province, 110044, China
| | - Tianci Han
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, 110042, China
- Department of Thoracic Surgery, Liaoning Cancer Hospital, Shenyang, Liaoning Province, 110042, China
| | - Wei Tong
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, 110042, China
- Department of Thoracic Surgery, Liaoning Cancer Hospital, Shenyang, Liaoning Province, 110042, China
| | - Jian Zhao
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, 110042, China
- Department of Thoracic Surgery, Liaoning Cancer Hospital, Shenyang, Liaoning Province, 110042, China
| | - Wei Wang
- Department of Thoracic Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning Province, 110042, China.
- Department of Thoracic Surgery, Liaoning Cancer Hospital, Shenyang, Liaoning Province, 110042, China.
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56
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Epigenetics: Roles and therapeutic implications of non-coding RNA modifications in human cancers. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:67-82. [PMID: 34188972 PMCID: PMC8217334 DOI: 10.1016/j.omtn.2021.04.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As next-generation sequencing (NGS) is leaping forward, more than 160 covalent RNA modification processes have been reported, and they are widely present in every organism and overall RNA type. Many modification processes of RNA introduce a new layer to the gene regulation process, resulting in novel RNA epigenetics. The commonest RNA modification includes pseudouridine (Ψ), N 7-methylguanosine (m7G), 5-hydroxymethylcytosine (hm5C), 5-methylcytosine (m5C), N 1-methyladenosine (m1A), N 6-methyladenosine (m6A), and others. In this study, we focus on non-coding RNAs (ncRNAs) to summarize the epigenetic consequences of RNA modifications, and the pathogenesis of cancer, as diagnostic markers and therapeutic targets for cancer, as well as the mechanisms affecting the immune environment of cancer. In addition, we summarize the current status of epigenetic drugs for tumor therapy based on ncRNA modifications and the progress of bioinformatics methods in elucidating RNA modifications in recent years.
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57
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Wu P, Fang X, Liu Y, Tang Y, Wang W, Li X, Fan Y. N6-methyladenosine modification of circCUX1 confers radioresistance of hypopharyngeal squamous cell carcinoma through caspase1 pathway. Cell Death Dis 2021; 12:298. [PMID: 33741902 PMCID: PMC7979824 DOI: 10.1038/s41419-021-03558-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 02/08/2023]
Abstract
Hypopharyngeal squamous cell carcinoma (HPSCC) is one of the most common malignant tumors in otolaryngology head and neck surgery and is one of the worst prognostic malignant tumors. Endogenous circular RNA (circRNA) is more stable than mRNA, microRNA (miRNA), and long non-coding RNA (LncRNA) in exosomes, plasma, and urine, and participates in gene expression regulation to perform different functions. Therefore, circRNA is expected to become a biomarker and therapy target for many tumors. However, the expression and function of circRNA regulated by N6-methyladenosine (m6A) are still unclear in HNSCC. In this study, we demonstrated that a specific circRNA, circCUX1, was upregulated in HPSCC patients who are resistant to radiotherapy and predicts poor survival outcome. We further found that methyltransferase like 3 (METTL3) mediated the m6A methylation of circCUX1 and stabilizes its expression. Knockdown circCUX1 promotes the sensitivity of hypopharyngeal cancer cells to radiotherapy. In addition, circCUX1 binds to Caspase1 and inhibits its expression, resulting in a decrease in the release of inflammatory factors, thereby developing tolerance to radiotherapy. Our findings indicate that circCUX1 is a potential therapeutic target for radiotherapy tolerance in HPSCC patients.
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Affiliation(s)
- Ping Wu
- Department of Otorhinolaryngology Head & Neck Surgery; Province Key Laboratory of Otolaryngology Critical Diseases, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Xing Fang
- Department of Otorhinolaryngology Head & Neck Surgery; Province Key Laboratory of Otolaryngology Critical Diseases, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yalan Liu
- Department of Otorhinolaryngology Head & Neck Surgery; Province Key Laboratory of Otolaryngology Critical Diseases, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yaoyun Tang
- Department of Otorhinolaryngology Head & Neck Surgery; Province Key Laboratory of Otolaryngology Critical Diseases, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Wei Wang
- Department of Otorhinolaryngology Head & Neck Surgery; Province Key Laboratory of Otolaryngology Critical Diseases, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Xin Li
- Department of Otorhinolaryngology Head & Neck Surgery; Province Key Laboratory of Otolaryngology Critical Diseases, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yuhua Fan
- Department of Otorhinolaryngology Head & Neck Surgery; Province Key Laboratory of Otolaryngology Critical Diseases, Xiangya Hospital, Central South University, Changsha, 410008, China
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58
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Geng X, Zhang Y, Zeng Z, Zhu Z, Wang H, Yu W, Li Q. Molecular Characteristics, Prognostic Value, and Immune Characteristics of m 6A Regulators Identified in Head and Neck Squamous Cell Carcinoma. Front Oncol 2021; 11:629718. [PMID: 33816266 PMCID: PMC8014089 DOI: 10.3389/fonc.2021.629718] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine (m6A) plays crucial roles in a diverse range of physiological and pathological processes, and it is believed that it tremendously promotes neoplasia and progression. However, knowledge of the molecular characteristics of m6A modification, its prognostic value, and the infiltration of immune cell populations in head and neck squamous cell carcinoma (HNSCC) is still insufficient. Therefore, a pan-cancer genomic analysis was systematically performed here by examining m6A regulators at the molecular level within 33 multiple cancer types, and the correlations between the expression of m6A molecules were researched using datasets from The Cancer Genome Atlas (TCGA). Based on the above analysis, insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) is upregulated in HNSCC and may serve as an independent prognostic factor of overall survival, thus showing potential as a prognostic biomarker in HNSCC. Genetic alteration analyses elucidated the reasons for the abnormal upregulation of IGF2BP2 in HNSCC. As a result, IGF2BP2 was selected for further univariate and multivariate analyses. The functions of the related genes were annotated through gene set enrichment analysis, and the activation states of multiple biological pathways were shown by gene set variation analysis. We found that LRRC59 and STIP1 may act as IGF2BP2-associated genes to have a regulatory function in the m6A modification. In addition, we found that the status of immune cell infiltration was correlated with the level of IGF2BP2 gene expression. Our results provide supplementation at the molecular level for epigenetic regulation in HNSCC and insight into effective immunotherapy targets and strategies.
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Affiliation(s)
- Xiuchao Geng
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang, China.,Hebei Key Laboratory of Chinese Medicine Research on Cardio-cerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yuhao Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China.,School of Clinical Medicine, Hebei University, Baoding, China
| | - Zhaomu Zeng
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China.,School of Clinical Medicine, Hebei University, Baoding, China
| | - Zhongrui Zhu
- Faculty of Acupuncture-Moxibustion and Tuina, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Hong Wang
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang, China.,Hebei Key Laboratory of Chinese Medicine Research on Cardio-cerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China.,Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China.,School of Clinical Medicine, Hebei University, Baoding, China
| | - Wentao Yu
- Hebei Key Laboratory of Chinese Medicine Research on Cardio-cerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China.,Faculty of Acupuncture-Moxibustion and Tuina, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Qiang Li
- Faculty of Acupuncture-Moxibustion and Tuina, Hebei University of Chinese Medicine, Shijiazhuang, China
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Li L, Miao H, Chang Y, Yao H, Zhao Y, Wu F, Song X. Multidimensional crosstalk between RNA-binding proteins and noncoding RNAs in cancer biology. Semin Cancer Biol 2021; 75:84-96. [PMID: 33722631 DOI: 10.1016/j.semcancer.2021.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 02/09/2023]
Abstract
RNA-binding proteins (RBPs) are well-known to bind RNA via a set of RNA-binding domains (RBDs) and determine the fate and function of their RNA targets; inversely, some RBPs, in certain cases, may be modulated by the bound RNAs rather than regulate their RNA partners. Current proteome-wide studies reveal that almost half of RBPs have no canonical RBDs, and the discovery of tens of thousands of noncoding RNAs (ncRNAs), especially those with the size larger than 200 nt (namely long noncoding RNAs, lncRNAs), makes the crosstalk between RBPs and RNAs more complicated. It is clear that macromolecular complexes formed by RBP and RNA are not only a form of existence of their RBP and RNA components in cells, but also represent a functional entity through which those RBPs and regulatory ncRNAs participate in the construction of regulatory networks in organism. In this review, we summarize the multidimensional crosstalk between RBPs and ncRNAs in cancer and discuss how RBPs achieve their function via the bound ncRNAs in different aspects of gene expression as well as how RBPs direct modification and processing of ncRNAs, in order to better understand tumor biology and provide new insights into development of strategies for cancer therapy and early detection.
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Affiliation(s)
- Ling Li
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Hui Miao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yanbo Chang
- Sichuan Institute for Food and Drug Control, Department of Forensic Analytical Toxicology, West China School of Basic Medical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Hong Yao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yongyun Zhao
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Fan Wu
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xu Song
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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60
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Zhao H, Xu Y, Xie Y, Zhang L, Gao M, Li S, Wang F. m6A Regulators Is Differently Expressed and Correlated With Immune Response of Esophageal Cancer. Front Cell Dev Biol 2021; 9:650023. [PMID: 33748145 PMCID: PMC7970005 DOI: 10.3389/fcell.2021.650023] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
N6 methyladenosine (m6A) RNA methylation regulators play an important role in the development of tumors. However, their function in esophageal cancer (EC) has not been fully elucidated. Here, we analyzed the gene expression data of 24 major m6A RNA methylation regulators from 775 patients with EC from TCGA dataset. The present study showed the aberrations of m6A regulators in genome were correlated to prognosis in human ECs. Meanwhile, 17 m6A regulators showed increased expression in EC samples, including YTHDC1, IGF2BP2, FTO, METTL14, YTHDF3, RBM15, WTAP, HNRNPA2B1, HNRNPC, ALKBH5, YTHDF2, METTL16, IGF2BP3, VIRMA, RBM15B, YTHDF1, KIAA1429, HAKAI, and ZC3H13. Among them, we found HNRNPC, YTHDC2, WTAP, VIRMA, IGF2BP3, and HNRNPA2B1 were significantly correlated to worse outcomes and advanced stage in EC. Furthermore, we showed levels of m6A regulators is correlated with the expression of Immuno-regulators (Immunoinhibitors, Immunostimulators, and MHC molecules) and immune infiltration levels in EC. Bioinformatics further confirm m6A regulators were involved in regulating RNA splicing, RNA stability, and cell proliferation. Our study showed m6A regulators are promising targets and biomarkers for cancer immunotherapy in EC.
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Affiliation(s)
- Huaying Zhao
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yue Xu
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yilin Xie
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Lan Zhang
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ming Gao
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shenglei Li
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Feng Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Lv W, Liu S, Zhang Q, Hu W, Wu Y, Ren Y. Circular RNA CircCOL5A1 Sponges the MiR-7-5p/Epac1 Axis to Promote the Progression of Keloids Through Regulating PI3K/Akt Signaling Pathway. Front Cell Dev Biol 2021; 9:626027. [PMID: 33553184 PMCID: PMC7859531 DOI: 10.3389/fcell.2021.626027] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/04/2021] [Indexed: 01/25/2023] Open
Abstract
Keloids, as a result of abnormal wound healing in susceptible individuals, are characterized by the hyper-proliferation of fibroblasts and exaggerated deposition of extracellular matrix. Current surgical and therapeutic modalities provide limited satisfactory results. Growing evidence has highlighted the roles of circRNAs in acting as miRNA sponges. However, up to date, the regulatory mechanism of circRNAs in the pathological process of keloids has rarely been reported. In this study, cell proliferation, cell migration, flow cytometry, western blotting, fluorescence in situ hybridization, dual-luciferase activity, and immunohistochemistry assays were applied to explore the roles and mechanisms of the circCOL5A1/miR-7-5p/Epac1 axis in the keloid. The therapeutic potential of circCOL5A1 was investigated by establishing keloid implantation models. The RT-qPCR result revealed that circCOL5A1 expression was obviously higher in keloid tissues and keloid fibroblasts. Subsequent cellular experiments demonstrated that circCOL5A1 knockdown repressed the proliferation, migration, extracellular matrix (ECM) deposition, whereas promoted cell apoptosis, through the PI3K/Akt signaling pathway. Furthermore, RNA-fluorescence in situ hybridization (RNA-FISH) illustrated that both circCOL5A1 and miR-7-5p were located in the cytoplasm. The luciferase reporter gene assay confirmed that exact binding sites were present between circCOL5A1 and miR-7-5p, as well as between miR-7-5p and Epac1. Collectively, the present study revealed that circCOL5A1 functioned as competing endogenous RNA (ceRNA) by adsorbing miR-7-5p to release Epac1, which contributed to pathological hyperplasia of keloids through activating the PI3K/Akt signaling pathway. Our data indicated that circCOL5A1 might serve as a novel promising therapeutic target and represent a new avenue to understand underlying pathogenesis for keloids.
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Affiliation(s)
- Wenchang Lv
- Department of Plastic and Aesthetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Shengxuan Liu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Qi Zhang
- Department of Plastic and Aesthetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Weijie Hu
- Department of Plastic and Aesthetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Yiping Wu
- Department of Plastic and Aesthetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Yuping Ren
- Department of Plastic and Aesthetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
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Geng X, Zhang Y, Li Q, Xi W, Yu W, Shi L, Lin X, Sun S, Wang H. Screening and functional prediction of differentially expressed circular RNAs in human glioma of different grades. Aging (Albany NY) 2020; 13:1989-2014. [PMID: 33323543 PMCID: PMC7880344 DOI: 10.18632/aging.202192] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) have a critical regulatory function in human glioma. However, novel circRNAs related to different pathological grades of glioma and their crucial potential function are worth screening and prediction. CircRNA expression profiling was performed for 6 paired high- and low-grade glioma tissues and 5 adjacent normal brain tissues through next-generation sequencing. Quantitative real-time PCR (qRT-PCR) was conducted to validate circRNA expression. Bioinformatics analysis was performed, and circRNA-miRNA-mRNA networks were constructed. The expression and survival data of miRNAs and target genes were examined by GEPIA, Chinese Glioma Genome Atlas (CGGA), ONCOMINE, and cBioPortal databases. The RNA binding proteins (RBPs), open reading frames (ORFs) and N6-methyladenosine (m6A) modifications of the identified circRNAs were also predicted. Through multilevel research screening, 4 circRNAs (hsa_circ_0000915, hsa_circ_0127664, hsa_circ_0008362, and hsa_circ_0001467) were associated with glioma of different pathological grades and could be preferred candidates for subsequent functional analysis. Therefore, circRNAs are associated with the different pathological grades of glioma and reveal their potential critical regulatory function. CircRNAs might provide vital molecular biomarkers and potential therapeutic targets for glioma.
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Affiliation(s)
- Xiuchao Geng
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang 050091, PR China.,Hebei Key Laboratory of Chinese Medicine Research on Cardio-cerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang 050091, PR China
| | - Yuhao Zhang
- School of Clinical Medicine, Hebei University, Baoding 071000, PR China.,Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding 071000, PR China
| | - Qiang Li
- Faculty of Acupuncture-Moxibustion and Tuina, Hebei University of Chinese Medicine, Shijiazhuang 050200, PR China
| | - Wang Xi
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, PR China
| | - Wentao Yu
- Faculty of Acupuncture-Moxibustion and Tuina, Hebei University of Chinese Medicine, Shijiazhuang 050200, PR China
| | - Liang Shi
- Endoscope Room, Department of General Surgery, Cangzhou Central Hospital, Cangzhou 061001, PR China
| | - Xiaomeng Lin
- Departments of Breast Surgery, Affiliated Hospital of Hebei University, Baoding 071000, PR China
| | - Shaoguang Sun
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Hong Wang
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang 050091, PR China.,Hebei Key Laboratory of Chinese Medicine Research on Cardio-cerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang 050091, PR China.,School of Clinical Medicine, Hebei University, Baoding 071000, PR China
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