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Xu B, Liu D, Wang Z, Tian R, Zuo Y. Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family. Cell Mol Life Sci 2021; 78:129-141. [PMID: 32642789 PMCID: PMC11072825 DOI: 10.1007/s00018-020-03594-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022]
Abstract
AlkB homologs (ALKBH) are a family of specific demethylases that depend on Fe2+ and α-ketoglutarate to catalyze demethylation on different substrates, including ssDNA, dsDNA, mRNA, tRNA, and proteins. Previous studies have made great progress in determining the sequence, structure, and molecular mechanism of the ALKBH family. Here, we first review the multi-substrate selectivity of the ALKBH demethylase family from the perspective of sequence and structural evolution. The construction of the phylogenetic tree and the comparison of key loops and non-homologous domains indicate that the paralogs with close evolutionary relationship have similar domain compositions. The structures show that the lack and variations of four key loops change the shape of clefts to cause the differences in substrate affinity, and non-homologous domains may be related to the compatibility of multiple substrates. We anticipate that the new insights into selectivity determinants of the ALKBH family are useful for understanding the demethylation mechanisms.
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Affiliation(s)
- Baofang Xu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Dongyang Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zerong Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ruixia Tian
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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302
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Jia CY, Xiang W, Liu JB, Jiang GX, Sun F, Wu JJ, Yang XL, Xin R, Shi Y, Zhang DD, Li W, Zuberi Z, Zhang J, Lu GX, Wang HM, Wang PY, Yu F, Lv ZW, Ma YS, Fu D. MiR-9-1 Suppresses Cell Proliferation and Promotes Apoptosis by Targeting UHRF1 in Lung Cancer. Technol Cancer Res Treat 2021; 20:15330338211041191. [PMID: 34520284 PMCID: PMC8445543 DOI: 10.1177/15330338211041191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 07/30/2021] [Indexed: 12/29/2022] Open
Abstract
Lung cancer is listed as the most common reason for cancer-related death all over the world despite diagnostic improvements and the development of chemotherapy and targeted therapies. MicroRNAs control both physiological and pathological processes including development and cancer. A microRNA-9 to 1 (miR-9 to 1) overexpression model in lung cancer cell lines was established and miR-9 to 1 was found to significantly suppress the proliferation rate in lung cancer cell lines, colony formation in vitro, and tumorigenicity in nude mice of A549 cells. Ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) was then identified to direct target of miR-9 to 1. The inhibition of UHRF1 by miR-9 to 1 causes G1 arrest and p15, p16, and p21 were re-expressed in miR-9 to 1 group in mRNA level and protein level. Silence of UHRF1 expression in A549 cells resulted in the similar re-expression of p15, p16, p21 which is similar with miR-9 to 1 infection. Therefore, we concluded that UHRF1 is a new target for miR-9 to 1 to suppress cell proliferation by re-expression of tumor suppressors p15, p16, and p21 mediated by UHRF1.
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Affiliation(s)
- Cheng-You Jia
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Xiang
- Shanghai Punan Hospital, Shanghai, China
| | - Ji-Bin Liu
- Cancer Institute, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Geng-Xi Jiang
- Navy Military Medical University Affiliated Changhai Hospital, Shanghai, China
| | - Feng Sun
- Cancer Institute, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Jian-Jun Wu
- Nantong Haimen Yuelai Health Centre, Haimen, China
| | - Xiao-Li Yang
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rui Xin
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Shi
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dan-Dan Zhang
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wen Li
- Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Zavuga Zuberi
- Dares Salaam Institute of Technology, Salaam, Tanzania
| | - Jie Zhang
- School of Medicine, Nantong University, Nantong, China
| | - Gai-Xia Lu
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hui-Min Wang
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Pei-Yao Wang
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fei Yu
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhong-Wei Lv
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yu-Shui Ma
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Eastern Hepatobiliary Surgery Hospital/Institute, National Center for Liver Cancer, the Second Military Medical University, Shanghai, China
| | - Da Fu
- Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
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303
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Qin B, Dong M, Wang Z, Wan J, Xie Y, Jiao Y, Yan D. Long non‑coding RNA CASC15 facilitates esophageal squamous cell carcinoma tumorigenesis via decreasing SIM2 stability via FTO‑mediated demethylation. Oncol Rep 2020; 45:1059-1071. [PMID: 33650646 PMCID: PMC7860005 DOI: 10.3892/or.2020.7917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/27/2020] [Indexed: 01/18/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in the regulation of esophageal squamous cell carcinoma (ESCC) progression. However, the function and mechanism of lncRNA cancer susceptibility candidate 15 (CASC15) are poorly defined. In the present study, tumor and normal adjacent tissues were collected from 45 patients with ESCC. Expression levels of CASC15, fat mass and obesity-associated (FTO) protein and single-minded 2 (SIM2) were examined via reverse transcription-quantitative PCR and western blot assays. Cell proliferation and apoptosis were evaluated via MTT, flow cytometry and caspase-3 activity assays, respectively. Additionally, an ESCC mouse xenograft model was used to assess the function of CASC15 in vivo. The interaction between FTO and CASC15/SIM2 was analyzed via RNA immunoprecipitation and RNA pull-down assays. The results revealed that CASC15 expression was elevated in ESCC tissues, and patients with ESCC exhibiting high CASC15 expression had a poor prognosis. CASC15-knockdown inhibited ESCC cell proliferation and facilitated apoptosis. Additionally, CASC15-knockdown decreased the growth of ESCC xenograft tumors. CASC15 decreased SIM2 stability via FTO-mediated demethylation. Additionally, FTO loss markedly weakened CASC15-mediated pro-proliferative and anti-apoptotic effects in ESCC cells. SIM2 downregulation weakened the effect of CASC15-knockdown on cell proliferation and inhibited the increase of the apoptotic rate and caspase-3 activity induced by CASC15 depletion in ESCC cells. In conclusion, CASC15 promoted ESCC tumorigenesis by decreasing SIM2 stability via FTO-mediated demethylation.
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Affiliation(s)
- Bo Qin
- Translational Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Meng Dong
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Zhengyang Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Jiajia Wan
- Medical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yingying Xie
- Translational Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yi Jiao
- Yongcheng Coal & Electricity Holding Group Co., Ltd., Shangqiu, Henan 476000, P.R. China
| | - Dan Yan
- Translational Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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304
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Kowalski-Chauvel A, Lacore MG, Arnauduc F, Delmas C, Toulas C, Cohen-Jonathan-Moyal E, Seva C. The m6A RNA Demethylase ALKBH5 Promotes Radioresistance and Invasion Capability of Glioma Stem Cells. Cancers (Basel) 2020; 13:cancers13010040. [PMID: 33375621 PMCID: PMC7795604 DOI: 10.3390/cancers13010040] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Glioblastoma stem cells (GBMSCs), which are particularly radio-resistant and invasive, are responsible for the high recurrence of glioblastoma (GBM). Therefore, there is a real need for a better understanding of the mechanisms involved in these processes and to identify new factors that might be targeted to radiosensitize GBMSC and decrease their invasive capability. Here, we report that the m6A RNA demethylase ALKBH5, which is overexpressed in GBMSCs, promotes their radioresistance by controlling the homologous repair. ALKBH5 was also involved in GBMSC invasion. These data suggest that ALKBH5 inhibition might be a novel approach to radiosensitize GBMSCs and to overcome their invasiveness. Abstract Recurrence of GBM is thought to be due to GBMSCs, which are particularly chemo-radioresistant and characterized by a high capacity to invade normal brain. Evidence is emerging that modulation of m6A RNA methylation plays an important role in tumor progression. However, the impact of this mRNA modification in GBM is poorly studied. We used patient-derived GBMSCs to demonstrate that high expression of the RNA demethylase, ALKBH5, increases radioresistance by regulating homologous recombination (HR). In cells downregulated for ALKBH5, we observed a decrease in GBMSC survival after irradiation likely due to a defect in DNA-damage repair. Indeed, we observed a decrease in the expression of several genes involved in the HR, including CHK1 and RAD51, as well as a persistence of γ-H2AX staining after IR. We also demonstrated in this study that ALKBH5 contributes to the aggressiveness of GBM by favoring the invasion of GBMSCs. Indeed, GBMSCs deficient for ALKBH5 exhibited a significant reduced invasion capability relative to control cells. Our data suggest that ALKBH5 is an attractive therapeutic target to overcome radioresistance and invasiveness of GBMSCs.
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Affiliation(s)
- Aline Kowalski-Chauvel
- INSERM UMR.1037-Cancer Research Center of Toulouse (CRCT)/University Paul Sabatier Toulouse III, 31100 Toulouse, France; (A.K.-C.); (M.G.L.); (F.A.); (C.D.); (C.T.); (E.C.-J.-M.)
| | - Marie Géraldine Lacore
- INSERM UMR.1037-Cancer Research Center of Toulouse (CRCT)/University Paul Sabatier Toulouse III, 31100 Toulouse, France; (A.K.-C.); (M.G.L.); (F.A.); (C.D.); (C.T.); (E.C.-J.-M.)
| | - Florent Arnauduc
- INSERM UMR.1037-Cancer Research Center of Toulouse (CRCT)/University Paul Sabatier Toulouse III, 31100 Toulouse, France; (A.K.-C.); (M.G.L.); (F.A.); (C.D.); (C.T.); (E.C.-J.-M.)
| | - Caroline Delmas
- INSERM UMR.1037-Cancer Research Center of Toulouse (CRCT)/University Paul Sabatier Toulouse III, 31100 Toulouse, France; (A.K.-C.); (M.G.L.); (F.A.); (C.D.); (C.T.); (E.C.-J.-M.)
- IUCT-Oncopole Toulouse, 31000 Tolouse, France
| | - Christine Toulas
- INSERM UMR.1037-Cancer Research Center of Toulouse (CRCT)/University Paul Sabatier Toulouse III, 31100 Toulouse, France; (A.K.-C.); (M.G.L.); (F.A.); (C.D.); (C.T.); (E.C.-J.-M.)
- IUCT-Oncopole Toulouse, 31000 Tolouse, France
| | - Elizabeth Cohen-Jonathan-Moyal
- INSERM UMR.1037-Cancer Research Center of Toulouse (CRCT)/University Paul Sabatier Toulouse III, 31100 Toulouse, France; (A.K.-C.); (M.G.L.); (F.A.); (C.D.); (C.T.); (E.C.-J.-M.)
- IUCT-Oncopole Toulouse, 31000 Tolouse, France
| | - Catherine Seva
- INSERM UMR.1037-Cancer Research Center of Toulouse (CRCT)/University Paul Sabatier Toulouse III, 31100 Toulouse, France; (A.K.-C.); (M.G.L.); (F.A.); (C.D.); (C.T.); (E.C.-J.-M.)
- Correspondence: ; Tel.: +33-(5)82741604
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305
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Shi Y, Zhuang Y, Zhang J, Chen M, Wu S. METTL14 Inhibits Hepatocellular Carcinoma Metastasis Through Regulating EGFR/PI3K/AKT Signaling Pathway in an m6A-Dependent Manner. Cancer Manag Res 2020; 12:13173-13184. [PMID: 33380825 PMCID: PMC7767748 DOI: 10.2147/cmar.s286275] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/10/2020] [Indexed: 12/18/2022] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) ranks as the fourth leading cause of cancer-related deaths worldwide. N6-methyladenosine (m6A) RNA methylation is the most common modification of messenger RNAs (mRNAs). The prognosis of HCC patients with metastasis remains poor. Our study aimed to elucidate the regulatory role of m6A on HCC metastasis. Patients and Methods All HCC patients were enrolled from The Affiliated Huai’an No. 1 People’s Hospital of Nanjing Medical University. The expression levels of gene were tested by quantitative polymerase chain reaction (qPCR), Western blot, or immunohistochemistry (IHC) analysis. Wound healing assay, Transwell invasion assay, and lung metastasis model were implemented to investigate the migration and invasion ability of HCC cells. Candidate targets were selected by a comprehensive analysis of RNA-sequencing and m6A-sequencing of HepG2 cells. Results In this study, we demonstrated that METTL14 was significantly downregulated in HCC and significantly associated with the prognosis of HCC patients. METTL14 knockdown promoted the migration, invasion, and epithelial–mesenchymal transition (EMT) of HCC cells in vitro and in vivo. In addition, overlapping RNA-sequencing and m6A-sequencing data, we identified EGFR as a direct target of METTL14 in HCC. Mechanistically, METTL14 was found to inhibit HCC cell migration, invasion, and EMT through modulating EGFR/PI3K/AKT signaling pathway in an m6A-dependent manner. Conclusion Targeting METTL14/EGFR/PI3K/AKT signaling pathway may facilitate the development of a new treatment strategy against the metastasis of HCC.
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Affiliation(s)
- Yuntao Shi
- Department of Gastroenterology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, People's Republic of China
| | - Yingying Zhuang
- Department of Medical Imaging, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, People's Republic of China
| | - Jialing Zhang
- Department of Gastroenterology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, People's Republic of China
| | - Mengxue Chen
- Department of Gastroenterology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, People's Republic of China
| | - Shangnong Wu
- Department of Gastroenterology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, People's Republic of China
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306
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Wang JY, Chen LJ, Qiang P. The Potential Role of N6-Methyladenosine (m6A) Demethylase Fat Mass and Obesity-Associated Gene (FTO) in Human Cancers. Onco Targets Ther 2020; 13:12845-12856. [PMID: 33364780 PMCID: PMC7751723 DOI: 10.2147/ott.s283417] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A) demethylase fat mass and obesity-associated gene(FTO), previously recognized to be related with obesity and diabetes, was gradually discovered to be dysregulated in multiple cancers and plays an oncogenic or tumor-suppressive role. However, the specific expression and pro- or anti-cancer role of FTO in various cancers remained controversial. In this review, through summarizing the available literature, we found that FTO single nucleotide polymorphisms (SNPs) were closely related with cancer risk. Additionally, the dysregulation of FTO was implicated in multiple biological processes, such as cancer cell apoptosis, proliferation, migration, invasion, metastasis, cell-cycle, differentiation, stem cell self-renewal and so on. These modulations mostly relied on the communications between FTO and specific signaling pathways, including PI3K/AKT, MAPK and mTOR signaling pathways. Furthermore, FTO had great potential for clinical application by serving as a prognostic biomarker.
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Affiliation(s)
- Jin-Yan Wang
- Department of Obstetrics and Gynecology, Zhangjiagang First People's Hospital, Zhangjiagang Jiangsu 215600, People's Republic of China.,Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Li-Juan Chen
- Department of Obstetrics and Gynecology, Zhangjiagang First People's Hospital, Zhangjiagang Jiangsu 215600, People's Republic of China
| | - Ping Qiang
- Department of Gynecology, Zhangjiagang First People's Hospital, Zhangjiagang Affiliated Hospital of Soochow University, Zhangjiagang, Jiangsu 215600, People's Republic of China
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307
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He W, Jin H, Liu Q, Sun Q. miR‑182‑5p contributes to radioresistance in nasopharyngeal carcinoma by regulating BNIP3 expression. Mol Med Rep 2020; 23:130. [PMID: 33313953 PMCID: PMC7751459 DOI: 10.3892/mmr.2020.11769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
Radioresistance is the primary roadblock limiting the success of treatment of nasopharyngeal carcinoma (NPC). microRNA (miRNA/miR)-182-5p has been reported to affect the sensitivity of cancer cells to irradiation; however, the role of miR-182-5p in NPC has not been assessed. The aim of the present study was to investigate the contribution of miR-182-5p to the radioresistance of NPC cells. The key mRNA and miRNA involved in NPC radioresistance were identified using bioinformatics analysis. The two cell lines used in the present study were 5–8F cells (radio-sensitive) and 5–8F-R cells (radioresistant). A dual-luciferase reporter assay system was used to validate the binding between BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (BNIP3) mRNA and miR-182-5p. Reverse transcription-quantitative PCR and western blotting were used to determine the RNA and protein expression levels. To obtain a deeper insight into the effects of the BNIP3/miR-182-5p axis on NPC radioresistance, Cell Counting Kit-8, wound healing, Transwell invasion and colony formation assays, as well as flow cytometry analysis were performed. The results showed that miR-182-5p and BNIP3 were up and downregulated, respectively, in 5–8F-R cells. BNIP3 was also confirmed to be the target of miR-182-5p, and miR-182-5p reversed the inhibitory effect of BNIP3 in 5–8F-R cells. The cellular experiments showed that upregulation of BNIP3 not only inhibited cell proliferation, viability, invasion and migration, but also promoted the apoptosis of 5–8F-R cells. However, the effects of BNIP3 were attenuated by the simultaneous upregulation of miR-182-5p. Thus, through downregulation of BNIP3, miR-182-5p contributed to radiation resistance of NPC cells.
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Affiliation(s)
- Wei He
- Department of Oncology, Wuhan Puren Hospital, Puren Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Hongyan Jin
- Department of Oncology, Wuhan Puren Hospital, Puren Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Qian Liu
- Department of Oncology, Wuhan Puren Hospital, Puren Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Quanxin Sun
- Department of Oncology, The Third People's Hospital of Hubei Province Affiliated to Jianghan University, Wuhan, Hubei 430033, P.R. China
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308
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Ao C, Yu L, Zou Q. Prediction of bio-sequence modifications and the associations with diseases. Brief Funct Genomics 2020; 20:1-18. [PMID: 33313647 DOI: 10.1093/bfgp/elaa023] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/22/2022] Open
Abstract
Modifications of protein, RNA and DNA play an important role in many biological processes and are related to some diseases. Therefore, accurate identification and comprehensive understanding of protein, RNA and DNA modification sites can promote research on disease treatment and prevention. With the development of sequencing technology, the number of known sequences has continued to increase. In the past decade, many computational tools that can be used to predict protein, RNA and DNA modification sites have been developed. In this review, we comprehensively summarized the modification site predictors for three different biological sequences and the association with diseases. The relevant web server is accessible at http://lab.malab.cn/∼acy/PTM_data/ some sample data on protein, RNA and DNA modification can be downloaded from that website.
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309
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Gong PJ, Shao YC, Yang Y, Song WJ, He X, Zeng YF, Huang SR, Wei L, Zhang JW. Analysis of N6-Methyladenosine Methyltransferase Reveals METTL14 and ZC3H13 as Tumor Suppressor Genes in Breast Cancer. Front Oncol 2020; 10:578963. [PMID: 33363011 PMCID: PMC7757663 DOI: 10.3389/fonc.2020.578963] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/06/2020] [Indexed: 12/21/2022] Open
Abstract
Objectives Recently, an increasing number of studies have revealed that N6-methyladenosine (m6A) functions as a significant post-transcriptional modification which plays a critical role in the occurrence and progression of enriched tumors by regulating coding and non-coding RNA biogenesis. However, the biological function of m6A in breast cancer remains largely unclear. Materials and Methods In this study, we used a series of bioinformatic databases and tools to jointly analyze the expression of m6A methylation transferases (METTL3, METTL14, WTAP, RBM15, RBM15B and ZC3H13) and investigate the prognostic value of METTL14 and ZC3H13 in breast cancer. Besides, we analyzed the downstream carcinogenic molecular mechanisms related to METTL14 and ZC3H13 and their relationship with immune infiltration in breast tumor tissues. Results The results showed that METTL14 and ZC3H13 were the down-regulated m6A methylation transferases in breast cancer. Survival outcome analysis suggested that abnormally low expression of METTL14 and ZC3H13 could predict unfavorable prognosis in four breast cancer subtypes. Moreover, their down-regulation was associated with ER-, PR- and triple-negative breast cancer patients, as well as tumor progression (increased Scarff, Bloom and Richardson grade status and Nottingham Prognostic Index classification). Co-expression analysis revealed that METTL14 and ZC3H13 had a strong positive correlation with APC, an antagonist of the Wnt signaling pathway, indicating they might cooperate in regulating proliferation, invasion, and metastasis of tumor cells. METTL14, ZC3H13, and APC expression levels had significant positive correlation with infiltrating levels of CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells, and negative correlation with Treg cells in breast cancer. Conclusions This study demonstrated that down-regulation of METTL14 and ZC3H13 which act as two tumor suppressor genes was found in breast cancer and predicted poor prognosis. Their abnormal expression promoted breast cancer invasion by affecting pathways related to tumor progression and mediating immunosuppression.
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Affiliation(s)
- Peng-Ju Gong
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - You-Cheng Shao
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yan Yang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Wen-Jing Song
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Xin He
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Yi-Fan Zeng
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Si-Rui Huang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
| | - Lei Wei
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jing-Wei Zhang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan University, Wuhan, China
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310
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Li D, Zhu X, Li Y, Zeng X. Novel insights into the roles of RNA N 6-methyladenosine modification in regulating gene expression during environmental exposures. CHEMOSPHERE 2020; 261:127757. [PMID: 32726721 DOI: 10.1016/j.chemosphere.2020.127757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 05/26/2023]
Abstract
N6-methyladenosine (m6A) is one of the most common RNA modifications in eukaryotes involved in the regulation of post-transcriptional gene expression, as well as the occurrence and development of diseases related to environmental exposures. Adverse factors produced by environmental exposures, such as reactive oxygen species, inflammation, and cyclobutane pyrimidine dimers, mediate m6A modification, thereby regulating downstream gene and protein expression, and signaling pathways, such as FTO/m6A RNA/p53 axis, PI3K/AKT/mTOR pathway, and PARP/METTL3/m6A RNA/Pol κ pathway. Moreover, an imbalance in m6A methylation levels directly mediates disease pathogenesis. To date, some studies have detailed the mechanisms underlying environmental exposure-mediated global changes in RNA m6A methylation. Based on our current understanding, we aimed to elaborate on the molecular mechanisms through which RNA m6A methylation regulates gene expression under environmental exposures. In this review, we outline the biogenesis and functions of RNA m6A modification. Furthermore, we focus on the effects of environmental exposures on m6A levels and highlight the relationships between environmental exposures (doses and time) and m6A levels. Although the molecular mechanisms regulating gene expression remains to be elucidated, m6A has potential applications as a disease biomarker.
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Affiliation(s)
- Dong Li
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China
| | - Xiaohua Zhu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan, 637009, China
| | - Yunxiang Li
- College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan, 637009, China
| | - Xianyin Zeng
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
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311
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Gu C, Shi X, Dai C, Shen F, Rocco G, Chen J, Huang Z, Chen C, He C, Huang T, Chen C. RNA m 6A Modification in Cancers: Molecular Mechanisms and Potential Clinical Applications. Innovation (N Y) 2020; 1:100066. [PMID: 34557726 PMCID: PMC8454620 DOI: 10.1016/j.xinn.2020.100066] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
N6-Methyladenosine (m6A) RNA modification brings a new dawn for RNA modification researches in recent years. This posttranscriptional RNA modification is dynamic and reversible, and is regulated by methylases ("writers"), demethylases ("erasers"), and proteins that preferentially recognize m6A modifications ("readers"). The change of RNA m6A modification regulates RNA metabolism in eucaryon, including translation, splicing, exporting, decay, and processing. Thereby the dysregulation of m6A may lead to tumorigenesis and progression. Given the tumorigenic role of abnormal m6A expression, m6A regulators may function as potential clinical therapeutic targets for cancers. In this review, we emphasize on the underlying mechanisms of m6A modifications in tumorigenesis and further introduce the potential m6A regulators-associated therapeutic targets for tumor therapy.
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Affiliation(s)
- Chang Gu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chenyang Dai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jiafei Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Zhengyu Huang
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Chunji Chen
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Medical Scientist Training Program/Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
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312
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Wang Y, Zhang Y, Du Y, Zhou M, Hu Y, Zhang S. Emerging roles of N6-methyladenosine (m 6A) modification in breast cancer. Cell Biosci 2020; 10:136. [PMID: 33292526 PMCID: PMC7690038 DOI: 10.1186/s13578-020-00502-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant, dynamic, and reversible epigenetic RNA modification that is found in coding and non-coding RNAs. Emerging studies have shown that m6A and its regulators affect multiple steps in RNA metabolism and play broad roles in various cancers. Worldwide, breast cancer is the most prevalent cancer in female. It is a very heterogeneous disease characterized by genetic and epigenetic variations in tumor cells. Increasing evidence has shown that the dysregulation of m6A-related effectors, as methyltransferases, demethylases, and m6A binding proteins, is pivotal in breast cancer pathogenesis. In this review, we have summarized the most up-to-date research on the biological functions of m6A modification in breast cancer and have discussed the potential clinical applications and future directions of m6A modification as a biomarker as well as a therapeutic target of breast cancer.
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Affiliation(s)
- Yanyan Wang
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
| | - Yujie Zhang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Meiqi Zhou
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yue Hu
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Suzhan Zhang
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
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313
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Sun X, Zhang Y, Hu Y, An J, Li L, Wang Y, Zhang X. Decreased expression of m 6A demethylase FTO in ovarian aging. Arch Gynecol Obstet 2020; 303:1363-1369. [PMID: 33221958 DOI: 10.1007/s00404-020-05895-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/09/2020] [Indexed: 11/30/2022]
Abstract
PURPOSE N6-methyladenosine (m6A) and demethylase fat mass and obesity-associated protein (FTO) were reported to be associated with oocyte development and maturation. But the relationship between FTO and ovarian aging was still unclear. This study was aimed at investigating the FTO expression level and the m6A content during ovarian aging. METHODS The expression level of FTO and the content of m6A RNA methylation in human follicular fluid (FF), granulosa cells (GCs) and mouse ovary from different age groups were studied by ELISA, WB, qRT-PCR, IHC and m6A Colorimetric. RESULTS Human FF ELISA quantified that the level of FTO protein decreased with age (P = 0.025). QRT-PCR results showed that the relative expression of FTO in human GCs was lower in the elderly group than in the young group (P = 0.012). FTO mRNA and protein expression levels were lower in the ovary of 32-week-old mice than in 3- and 8-week-old mice (P < 0.05). Immunohistochemistry showed FTO was relatively decreased in 32-week-old mice (P < 0.05). The m6A content in total RNA from old human GCs and ovary from 32-week-old mice was significantly higher compared with the younger ones. CONCLUSIONS In human FF, GCs and mouse ovary, the expression of FTO decreased while the content of m6A increased with aging. However, the inner mechanism still needs further investigation.
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Affiliation(s)
- Xiaoyan Sun
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, China.,The Reproductive Medicine Special Hospital of the First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Yigan Zhang
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, China
| | - Yuping Hu
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, China.,The Reproductive Medicine Special Hospital of the First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Junxia An
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, China.,The Reproductive Medicine Special Hospital of the First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Lifei Li
- The First School of Clinical Medicine of Lanzhou University, Lanzhou, China.,The Reproductive Medicine Special Hospital of the First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Yiqing Wang
- The Reproductive Medicine Special Hospital of the First Hospital of Lanzhou University, Lanzhou, 730000, China.,Gansu Key Laboratory of Reproductive Medicine and Embryology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xuehong Zhang
- The Reproductive Medicine Special Hospital of the First Hospital of Lanzhou University, Lanzhou, 730000, China. .,Gansu Key Laboratory of Reproductive Medicine and Embryology, The First Hospital of Lanzhou University, Lanzhou, China.
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314
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RNA methylations in human cancers. Semin Cancer Biol 2020; 75:97-115. [DOI: 10.1016/j.semcancer.2020.11.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/23/2020] [Accepted: 11/08/2020] [Indexed: 12/24/2022]
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315
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Hypoxia and Oxygen-Sensing Signaling in Gene Regulation and Cancer Progression. Int J Mol Sci 2020; 21:ijms21218162. [PMID: 33142830 PMCID: PMC7663541 DOI: 10.3390/ijms21218162] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
Oxygen homeostasis regulation is the most fundamental cellular process for adjusting physiological oxygen variations, and its irregularity leads to various human diseases, including cancer. Hypoxia is closely associated with cancer development, and hypoxia/oxygen-sensing signaling plays critical roles in the modulation of cancer progression. The key molecules of the hypoxia/oxygen-sensing signaling include the transcriptional regulator hypoxia-inducible factor (HIF) which widely controls oxygen responsive genes, the central members of the 2-oxoglutarate (2-OG)-dependent dioxygenases, such as prolyl hydroxylase (PHD or EglN), and an E3 ubiquitin ligase component for HIF degeneration called von Hippel–Lindau (encoding protein pVHL). In this review, we summarize the current knowledge about the canonical hypoxia signaling, HIF transcription factors, and pVHL. In addition, the role of 2-OG-dependent enzymes, such as DNA/RNA-modifying enzymes, JmjC domain-containing enzymes, and prolyl hydroxylases, in gene regulation of cancer progression, is specifically reviewed. We also discuss the therapeutic advancement of targeting hypoxia and oxygen sensing pathways in cancer.
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316
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Wang Q, Guo X, Li L, Gao Z, Su X, Ji M, Liu J. N 6-methyladenosine METTL3 promotes cervical cancer tumorigenesis and Warburg effect through YTHDF1/HK2 modification. Cell Death Dis 2020; 11:911. [PMID: 33099572 PMCID: PMC7585578 DOI: 10.1038/s41419-020-03071-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022]
Abstract
N6-methyladenosine (m6A) serves as the most common and conserved internal transcriptional modification. However, the roles of m6A on cervical cancer (CC) tumorigenesis are still unclear. Here, results indicated that METTL3 was significantly upregulated in CC tissue and cells, which was closely correlated with the lymph node metastasis and poor prognosis of CC patients. MeRIP-Seq analysis revealed the m6A profiles in CC cells. Functionally, METTL3 promoted the proliferation and Warburg effect (aerobic glycolysis) of CC cells. Mechanistically, METTL3 targeted the 3’-Untranslated Region (3’-UTR) of hexokinase 2 (HK2) mRNA. Moreover, METTL3 recruited YTHDF1, a m6A reader, to enhance HK2 stability. These findings demonstrated that METTL3 enhanced the HK2 stability through YTHDF1-mediated m6A modification, thereby promoting the Warburg effect of CC, which might promote a novel insight for the CC treatment.
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Affiliation(s)
- Qianqing Wang
- Department of Gynecology, Xinxiang Central Hospital, 453000, Xinxiang, Henan, China
| | - Xiangcui Guo
- Department of Gynecology, Xinxiang Central Hospital, 453000, Xinxiang, Henan, China
| | - Li Li
- Department of Gynecology, Xinxiang Central Hospital, 453000, Xinxiang, Henan, China
| | - Zhihui Gao
- Department of Gynecology, Xinxiang Central Hospital, 453000, Xinxiang, Henan, China
| | - Xiaoke Su
- Department of Gynecology, Xinxiang Central Hospital, 453000, Xinxiang, Henan, China
| | - Mei Ji
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University, 450003, Zhengzhou, China.
| | - Juan Liu
- Department of Gynecology, Third Affiliated Hospital Guangzhou Medical University, 510080, Guangdong, China.
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317
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Xiao L, Zhao Q, Hu B, Wang J, Liu C, Xu H. METTL3 promotes IL-1β-induced degeneration of endplate chondrocytes by driving m6A-dependent maturation of miR-126-5p. J Cell Mol Med 2020; 24:14013-14025. [PMID: 33098220 PMCID: PMC7754036 DOI: 10.1111/jcmm.16012] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
METTL3 is an important regulatory molecule in the process of RNA biosynthesis. It mainly regulates mRNA translation, alternative splicing and microRNA maturation by mediating m6A‐dependent methylation. Interleukin 1β (IL‐1β) is an important inducer of cartilage degeneration that can induce an inflammatory cascade reaction in chondrocytes and inhibit the normal biological function of cells. However, it is unclear whether IL‐1β is related to METTL3 expression or plays a regulatory role in endplate cartilage degeneration. In this study, we found that the expression level of METTL3 and methylation level of m6A in human endplate cartilage with different degrees of degeneration were significantly different, indicating that the methylation modification of m6A mediated by METTL3 was closely related to the degeneration of human endplate cartilage. Next, through a series of functional experiments, we found that miR‐126‐5p can play a significant role in IL‐1β–induced degeneration of endplate chondrocytes. Moreover, we found that miR‐126‐5p can inhibit the PI3K/Akt signalling pathway by targeting PIK3R2 gene, leading to the disorder of cell vitality and functional metabolism. To further determine whether METTL3 could regulate miR‐126‐5p maturation, we first confirmed that METTL3 can bind the key protein underlying pri‐miRNA processing, DGCR8. Additionally, when METTL3 expression was inhibited, the miR‐126‐5p maturation process was blocked. Therefore, we hypothesized that METTL3 can promote cleavage of pri‐miR‐126‐5p and form mature miR‐126‐5p by combining with DGCR8.
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Affiliation(s)
- Liang Xiao
- Reseach center of Spine Surgery, Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution (Wannan Medical College), Department of Spine Surgery, Yijishan Hospital, The First Affliated Hospital of Wannan Medical College, Wuhu, China
| | - Quanlai Zhao
- Reseach center of Spine Surgery, Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution (Wannan Medical College), Department of Spine Surgery, Yijishan Hospital, The First Affliated Hospital of Wannan Medical College, Wuhu, China
| | - Bo Hu
- Reseach center of Spine Surgery, Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution (Wannan Medical College), Department of Spine Surgery, Yijishan Hospital, The First Affliated Hospital of Wannan Medical College, Wuhu, China
| | - Jing Wang
- Reseach center of Spine Surgery, Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution (Wannan Medical College), Department of Spine Surgery, Yijishan Hospital, The First Affliated Hospital of Wannan Medical College, Wuhu, China
| | - Chen Liu
- Reseach center of Spine Surgery, Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution (Wannan Medical College), Department of Spine Surgery, Yijishan Hospital, The First Affliated Hospital of Wannan Medical College, Wuhu, China
| | - Hongguang Xu
- Reseach center of Spine Surgery, Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution (Wannan Medical College), Department of Spine Surgery, Yijishan Hospital, The First Affliated Hospital of Wannan Medical College, Wuhu, China
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318
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Yu H, Yang X, Tang J, Si S, Zhou Z, Lu J, Han J, Yuan B, Wu Q, Lu Q, Yang H. ALKBH5 Inhibited Cell Proliferation and Sensitized Bladder Cancer Cells to Cisplatin by m6A-CK2α-Mediated Glycolysis. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 23:27-41. [PMID: 33376625 PMCID: PMC7744648 DOI: 10.1016/j.omtn.2020.10.031] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 10/17/2020] [Indexed: 12/19/2022]
Abstract
N6-methyladenosine (m6A) is the most commonly occurring internal RNA modification to be found in eukaryotic mRNA and serves an important role in various physiological events. AlkB homolog 5 RNA demethylase (ALKBH5), an m6A demethylase, belongs to the AlkB family of dioxygenases and has been shown to specifically demethylate m6A in RNA, which is associated with a variety of tumors. However, its function in bladder cancer remains largely unclear. In the present study, we found that the expression of ALKBH5 was downregulated in bladder cancer tissues and cell lines. Low expression of ALKBH5 was correlated with the worse prognosis of bladder cancer patients. Furthermore, functional assays revealed that knockdown of ALKBH5 promoted bladder cancer cell proliferation, migration, invasion, and decreased cisplatin chemosensitivity in the 5637 and T24 bladder cancer cell lines in vivo and in vitro, whereas ALKBH5 overexpression led to the opposite results. Finally, ALKBH5 inhibited the progression and sensitized bladder cancer cells to cisplatin through a casein kinase 2 (CK2)α-mediated glycolysis pathway in an m6A-dependent manner. Taken together, these findings might provide fresh insights into bladder cancer therapy.
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Affiliation(s)
- Hao Yu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Xiao Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Jinyuan Tang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Shuhui Si
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Zijian Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Jiancheng Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Jie Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Baorui Yuan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Qikai Wu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Qiang Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
| | - Haiwei Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, PR China
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319
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Han X, Wang L, Han Q. Advances in the role of m 6A RNA modification in cancer metabolic reprogramming. Cell Biosci 2020; 10:117. [PMID: 33062255 PMCID: PMC7552565 DOI: 10.1186/s13578-020-00479-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/24/2020] [Indexed: 01/10/2023] Open
Abstract
N6-methyladenosine (m6A) modification is the most common internal modification of eukaryotic mRNA and is widely involved in many cellular processes, such as RNA transcription, splicing, nuclear transport, degradation, and translation. m6A has been shown to plays important roles in the initiation and progression of various cancers. The altered metabolic programming of cancer cells promotes their cell-autonomous proliferation and survival, leading to an indispensable hallmark of cancers. Accumulating evidence has demonstrated that this epigenetic modification exerts extensive effects on the cancer metabolic network by either directly regulating the expression of metabolic genes or modulating metabolism-associated signaling pathways. In this review, we summarized the regulatory mechanisms and biological functions of m6A and its role in cancer metabolic reprogramming.
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Affiliation(s)
- Xiu Han
- Center of Clinical Laboratory, Suzhou Dushu Lake Public Hospital, 9#, Chongwen Road, Suzhou, 215000 People’s Republic of China
| | - Lin Wang
- Center of Clinical Laboratory, Suzhou Dushu Lake Public Hospital, 9#, Chongwen Road, Suzhou, 215000 People’s Republic of China
| | - Qingzhen Han
- Center of Clinical Laboratory, Suzhou Dushu Lake Public Hospital, 9#, Chongwen Road, Suzhou, 215000 People’s Republic of China
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320
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Huo FC, Zhu ZM, Pei DS. N 6 -methyladenosine (m 6 A) RNA modification in human cancer. Cell Prolif 2020; 53:e12921. [PMID: 33029866 PMCID: PMC7653258 DOI: 10.1111/cpr.12921] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/04/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
N6 -methyladenosine (m6 A) RNA modification, first discovered in 1974, is the most prevalent, abundant and penetrating messenger RNA (mRNA) modification in eukaryotes. This governs the fate of modified transcripts, regulates RNA metabolism and biological processes, and participates in pathogenesis of numerous human diseases, especially in cancer through the reciprocal regulation of m6 A methyltransferases ("writers") and demethylases ("erasers") and the binding proteins decoding m6 A methylation ("readers"). Accumulating evidence indicates a complicated regulation network of m6 A modification involving multiple m6 A-associated regulatory proteins whose biological functions have been further analysed. This review aimed to summarize the current knowledge on the potential significance and molecular mechanisms of m6 A RNA modification in the initiation and progression of cancer.
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Affiliation(s)
- Fu-Chun Huo
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
| | - Zhi-Man Zhu
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
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321
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Xu Z, Peng B, Cai Y, Wu G, Huang J, Gao M, Guo G, Zeng S, Gong Z, Yan Y. N6-methyladenosine RNA modification in cancer therapeutic resistance: Current status and perspectives. Biochem Pharmacol 2020; 182:114258. [PMID: 33017575 DOI: 10.1016/j.bcp.2020.114258] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 02/05/2023]
Abstract
Several strategies, including chemotherapy and radiotherapy, have improved therapeutic outcomes among cancer patients in clinical practice. However, due to their heterogeneity, cancer cells frequently display primary or acquired therapeutic resistance, thereby resulting in treatment failure. The mechanisms underlying cancer therapeutic resistance are complex and varied. Among them, N6-methyladenosine (m6A) RNA modification has gained increasing attention as a potential determinant of therapy resistance within various cancers. In this review, we primarily describe evidence for the effect of the m6A epitranscriptome on RNA homeostasis modulation, which has been shown to alter multiple cellular pathways in cancer research and treatment. Additionally, we discuss the profiles and biological implications of m6A RNA methylation, which is undergoing intensive investigation for its effect on the control of therapeutic resistance.
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Affiliation(s)
- Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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322
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Wang P, Wang X, Zheng L, Zhuang C. Gene Signatures and Prognostic Values of m6A Regulators in Hepatocellular Carcinoma. Front Genet 2020; 11:540186. [PMID: 33133142 PMCID: PMC7567013 DOI: 10.3389/fgene.2020.540186] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification in mammals and has been implicated in various biological processes. However, its role in hepatocellular carcinoma (HCC) remains largely unknown. In this study, we investigated the alterations of 19 main m6A regulatory genes in HCC and their association with clinicopathological features, including survival. The mutation, copy number variation (CNV) and clinical data of HCC patients were retrieved from The Cancer Genome Atlas (TCGA) database. We found that the m6A regulators had high frequent alterations in HCC. The alterations of m6A regulators were significantly associated with clinicopathological features as well as TP53 alteration. Patients with any mutation of the m6A regulatory genes had worse overall survival (OS) and disease free survival (DFS). Deletion of METTL16 or ALKBH5 predicted poor OS and DFS of HCC patients. Moreover, deletion of METTL16 was an independent risk factor for DFS. Low METT16 expression was association with activation of multiple metabolic pathways in HCC. Finally, by RT-PCR, we confirmed that METTL16 was downregulated in HCC, and that lower METTL16 expression was associated with poor OS. In conclusion, we reported a significant association between alterations of m6A regulators and clinicopathological features, and highlighted the importance of METTL16 among the 19 m6A regulators in HCC pathogenesis. These findings will provide new insights into the role of m6A modification in HCC.
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Affiliation(s)
- Pei Wang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaotong Wang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Zheng
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunbo Zhuang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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323
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m6A RNA methylation regulators can contribute to malignant progression and impact the prognosis of bladder cancer. Biosci Rep 2020; 39:221434. [PMID: 31808521 PMCID: PMC6923333 DOI: 10.1042/bsr20192892] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/24/2019] [Accepted: 12/05/2019] [Indexed: 01/01/2023] Open
Abstract
N6-methyladenosine (m6A) is the most common form of messenger RNA (mRNA) modification. An increasing number of studies have proven that m6A RNA methylation regulators are overexpressed in many cancers and participate in the development of cancer through the dynamic regulation of m6A RNA methylation regulators. However, the prognostic role of m6A RNA methylation regulators in bladder cancer (BC) is poorly understood. In the present study, we downloaded the mRNA expression data from The Cancer Genome Atlas (TCGA) database and the corresponding clinical and prognostic information. The relationship between m6A RNA methylation regulators and clinicopathological variables of BC patients was assessed by the Kolmogorov–Smirnov test. The expression of the m6A RNA methylation regulators was differentially associated with different clinicopathological variables of BC patients. The least absolute shrinkage and selection operator (LASSO) Cox regression model was then applied to identify three m6A RNA methylation regulators. The risk signature was constructed as follows: 0.164FTO − (0.081YTHDC1+0.032WTAP). Based on the risk signature, the risk score of each patient was calculated, and the patients were divided into a high-risk group and a low-risk group. The overall survival (OS) rate of the high-risk group was significantly lower than that of the low-risk group. The risk signature was not only an independent prognostic marker for BC patients but also a predictor of clinicopathological variables. In conclusion, m6A RNA methylation regulators can participate in the malignant progression of BC, and a risk signature with three selected m6A RNA methylation regulators may be a promising prognostic biomarker to guide personalized treatment for BC patients.
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324
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Sun H, Chen D, Zhan S, Wu W, Xu H, Luo C, Su H, Feng Y, Shao W, Wan A, Zhou B, Wan G, Bu X. Design and Discovery of Natural Cyclopeptide Skeleton Based Programmed Death Ligand 1 Inhibitor as Immune Modulator for Cancer Therapy. J Med Chem 2020; 63:11286-11301. [PMID: 32844651 DOI: 10.1021/acs.jmedchem.0c01262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Blockade of immune checkpoint PD-1/PD-L1 facilitates the rescue of immune escapes of tumor cells. Though various monoclonal antibodies have been approved for clinical therapy, the development of small molecular inhibitors lags behind antibodies partially owing to the challenges of protein-protein interaction (PPI) blocker design. In this work, we adopted the skeleton of natural cyclopeptidic antibiotics gramicidin S as the start point for PD-1/PD-L1 inhibitor exploring and discovered a series of novel cyclopeptides that could interfere with the PPI of PD-1/PD-L1 based on several rounds of structural design and optimization. The representative active cyclopeptide 66 can bind two PD-L1 and efficiently block the PD-1/PD-L1 interaction, recruit the immune cells to the tumor cells, enhance their killing against tumor cells by promoting the release of granzyme B and perforin, and display significant CD8+ T cell-dependent tumor suppression activity in vivo.
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Affiliation(s)
- Haixia Sun
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Daoyuan Chen
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Guangzhou 519041, China
| | - Siyue Zhan
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Weijian Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Huiying Xu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Chunxiang Luo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Hui Su
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yanqiao Feng
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Weiyan Shao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Arabella Wan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Binhua Zhou
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China.,School of Chinese Pharmacy, Guizhou Minzu University, Guiyang 550025, China
| | - Guohui Wan
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China.,National-Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Sun Yat-Sen University, Guangzhou 510006, China
| | - Xianzhang Bu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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325
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Zhou Y, Kong Y, Fan W, Tao T, Xiao Q, Li N, Zhu X. Principles of RNA methylation and their implications for biology and medicine. Biomed Pharmacother 2020; 131:110731. [PMID: 32920520 DOI: 10.1016/j.biopha.2020.110731] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023] Open
Abstract
RNA methylation is a post-transcriptional level of regulation. At present, more than 150 kinds of RNA modifications have been identified. They are widely distributed in messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), noncoding small RNA (sncRNA) and long-chain non-coding RNA (lncRNA). In recent years, with the discovery of RNA methylation related proteins and the development of high-throughput sequencing technology, the mystery of RNA methylation has been gradually revealed, and its biological function and application value have gradually emerged. In this review, a large number of research results of RNA methylation in recent years are collected. Through systematic summary and refinement, this review introduced RNA methylation modification-related proteins and RNA methylation sequencing technologies, as well as the biological functions of RNA methylation, expressions and applications of RNA methylation-related genes in physiological or pathological states such as cancer, immunity and virus infection, and discussed the potential therapeutic strategies.
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Affiliation(s)
- Yujia Zhou
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
| | - Ying Kong
- Department of Clinical Laboratory, Hubei No.3 People's Hospital of Jianghan University, Wuhan, China
| | - Wenguo Fan
- Department of Anesthesiology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, China.
| | - Qin Xiao
- Department of Blood Transfusion, Peking University Shenzhen Hospital, Shenzhen, China
| | - Na Li
- College of Basic Medicine, Chongqing Medical University, Chongqing, China.
| | - Xiao Zhu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China; The Key Lab of Zhanjiang for R&D Marine Microbial Resources in the Beibu Gulf Rim, Guangdong Medical University, Zhanjiang, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China.
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326
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Li Y, Ge YZ, Xu L, Xu Z, Dou Q, Jia R. The Potential Roles of RNA N6-Methyladenosine in Urological Tumors. Front Cell Dev Biol 2020; 8:579919. [PMID: 33015074 PMCID: PMC7510505 DOI: 10.3389/fcell.2020.579919] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is regarded as the most abundant, prevalent and conserved internal mRNA modification in mammalian cells. M6A can be catalyzed by m6A methyltransferases METTL3, METTL14 and WTAP (writers), reverted by demethylases ALKBH5 and FTO (erasers), and recognized by m6A -binding proteins such as YTHDF1/2/3, IGF2BP1/2/3 and HNRNPA2B1 (readers). Emerging evidence suggests that m6A modification is significant for regulating many biological and cellular processes and participates in the pathological development of various diseases, including tumors. This article reviews recent studies on the biological function of m6A modification and the methylation modification of m6A in urological tumors.
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Affiliation(s)
- Yang Li
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yu-Zheng Ge
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Luwei Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zheng Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Quanliang Dou
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ruipeng Jia
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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327
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Xiao Y, Thakkar KN, Zhao H, Broughton J, Li Y, Seoane JA, Diep AN, Metzner TJ, von Eyben R, Dill DL, Brooks JD, Curtis C, Leppert JT, Ye J, Peehl DM, Giaccia AJ, Sinha S, Rankin EB. The m 6A RNA demethylase FTO is a HIF-independent synthetic lethal partner with the VHL tumor suppressor. Proc Natl Acad Sci U S A 2020; 117:21441-21449. [PMID: 32817424 PMCID: PMC7474618 DOI: 10.1073/pnas.2000516117] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Loss of the von Hippel-Lindau (VHL) tumor suppressor is a hallmark feature of renal clear cell carcinoma. VHL inactivation results in the constitutive activation of the hypoxia-inducible factors (HIFs) HIF-1 and HIF-2 and their downstream targets, including the proangiogenic factors VEGF and PDGF. However, antiangiogenic agents and HIF-2 inhibitors have limited efficacy in cancer therapy due to the development of resistance. Here we employed an innovative computational platform, Mining of Synthetic Lethals (MiSL), to identify synthetic lethal interactions with the loss of VHL through analysis of primary tumor genomic and transcriptomic data. Using this approach, we identified a synthetic lethal interaction between VHL and the m6A RNA demethylase FTO in renal cell carcinoma. MiSL identified FTO as a synthetic lethal partner of VHL because deletions of FTO are mutually exclusive with VHL loss in pan cancer datasets. Moreover, FTO expression is increased in VHL-deficient ccRCC tumors compared to normal adjacent tissue. Genetic inactivation of FTO using multiple orthogonal approaches revealed that FTO inhibition selectively reduces the growth and survival of VHL-deficient cells in vitro and in vivo. Notably, FTO inhibition reduced the survival of both HIF wild type and HIF-deficient tumors, identifying FTO as an HIF-independent vulnerability of VHL-deficient cancers. Integrated analysis of transcriptome-wide m6A-seq and mRNA-seq analysis identified the glutamine transporter SLC1A5 as an FTO target that promotes metabolic reprogramming and survival of VHL-deficient ccRCC cells. These findings identify FTO as a potential HIF-independent therapeutic target for the treatment of VHL-deficient renal cell carcinoma.
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Affiliation(s)
- Yiren Xiao
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305
| | - Kaushik N Thakkar
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305
| | - Hongjuan Zhao
- Department of Urology, Stanford University, Stanford, CA 94305
| | | | - Yang Li
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305
| | - Jose A Seoane
- Department of Medicine, Stanford University, Stanford, CA 94305
- Deparment of Genetics, Stanford University, Stanford, CA 94305
| | - Anh N Diep
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305
| | | | - Rie von Eyben
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305
| | - David L Dill
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | - James D Brooks
- Department of Urology, Stanford University, Stanford, CA 94305
| | - Christina Curtis
- Department of Medicine, Stanford University, Stanford, CA 94305
- Deparment of Genetics, Stanford University, Stanford, CA 94305
| | - John T Leppert
- Department of Urology, Stanford University, Stanford, CA 94305
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305
| | - Donna M Peehl
- Deparment of Genetics, Stanford University, Stanford, CA 94305
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158
| | - Amato J Giaccia
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305
| | - Subarna Sinha
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | - Erinn B Rankin
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305;
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305
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328
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Cheng Y, Fu Y, Wang Y, Wang J. The m6A Methyltransferase METTL3 Is Functionally Implicated in DLBCL Development by Regulating m6A Modification in PEDF. Front Genet 2020; 11:955. [PMID: 33061938 PMCID: PMC7481464 DOI: 10.3389/fgene.2020.00955] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/30/2020] [Indexed: 12/22/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of lymphoma, whose treatment still has a major challenge of achieving a satisfactory curative effect. The underlying mechanisms also have not been fully illustrated. N6-Methyladenosine (m6A) has been identified as the most prevalent internal modification of mRNAs present in eukaryotes, which is involved in the pathogenesis of cancers. It remains unclear how m6A mRNA methylation is functionally linked to the pathogenesis of DLBCL. In this study, we sought to explore the roles of METTL3 on DLBCL development. The results showed that m6A level for RNA methylation and the expression level of METTL3 were upregulated in DLBCL tissues and cell lines. Functionally, downregulated METTL3 expression in DLBCL cells inhibited the cell proliferation ability. Further mechanism analysis indicated that METTL3 knockdown abates the m6A methylation and total mRNA level of pigment epithelium-derived factor (PEDF). However, Wnt/β-catenin signaling was not thus activated. Overexpressed PEDF abrogates the inhibition of cell proliferation in DLBCL cells that is caused by METTL3 silence. In summary, the above-mentioned results demonstrated that the METTL3 promotes DLBCL progression by regulating the m6A level of PEDF.
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Affiliation(s)
- Yingying Cheng
- Department of Hematology, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Yuanyuan Fu
- Department of Hematology, Changzhou Traditional Chinese Medicine Hospital, Changzhou, China
| | - Ying Wang
- Department of Hematology, Changzhou Traditional Chinese Medicine Hospital, Changzhou, China
| | - Jinbi Wang
- Department of Hematology, Changzhou Traditional Chinese Medicine Hospital, Changzhou, China
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329
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Sher G, Salman NA, Khan AQ, Prabhu KS, Raza A, Kulinski M, Dermime S, Haris M, Junejo K, Uddin S. Epigenetic and breast cancer therapy: Promising diagnostic and therapeutic applications. Semin Cancer Biol 2020; 83:152-165. [PMID: 32858230 DOI: 10.1016/j.semcancer.2020.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
The global burden of breast cancer (BC) is increasing significantly. This trend is caused by several factors such as late diagnosis, limited treatment options for certain BC subtypes, drug resistance which all lead to poor clinical outcomes. Recent research has reported the role of epigenetic alterations in the mechanism of BC pathogenesis and its hallmarks include drug resistance and stemness features. The understanding of these modifications and their significance in the management of BC carcinogenesis is challenging and requires further attention. Nevertheless, it promises to provide novel insight needed for utilizing these alterations as potential diagnostic, prognostic markers, predict treatment efficacy, as well as therapeutic agents. This highlights the importance of continuing research development to further advance the existing knowledge on epigenetics and BC carcinogenesis to overcome the current challenges. Hence, this review aims to shed light and discuss the current state of epigenetics research in the diagnosis and management of BC.
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Affiliation(s)
- Gulab Sher
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Nadia Aziz Salman
- Kingston University London, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston, upon Thames, London, KT1 2EE, UK
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Afsheen Raza
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Said Dermime
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Mohammad Haris
- Functional and Molecular Imaging Laboratory, Sidra Medicine, P.O. Box 26999, Qatar; Laboratory Animal Research Center, Qatar University, Doha, P.O. Box 2713, Qatar
| | - Kulsoom Junejo
- General Surgery Department, Hamad General Hospital, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar.
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330
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Li F, Wang H, Huang H, Zhang L, Wang D, Wan Y. m6A RNA Methylation Regulators Participate in the Malignant Progression and Have Clinical Prognostic Value in Lung Adenocarcinoma. Front Genet 2020; 11:994. [PMID: 33193582 PMCID: PMC7477360 DOI: 10.3389/fgene.2020.00994] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
Abnormal methylation of N6 adenosine (m6A) in RNA plays a crucial role in the pathogenesis of many types of tumors. However, little is known about m6A RNA methylation in lung adenocarcinoma. This study aimed to identify the value of m6A RNA methylation regulators in the malignant progression and clinical prognosis of lung adenocarcinoma. The RNA-seq transcriptome data and corresponding clinical information of lung adenocarcinoma were downloaded from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database. Then the identification of differentially expressed m6A RNA methylation regulators between cancer samples and normal control samples, different subgroups by consensus expression of these regulators and the prognostic signature were achieved using R software with multiple corresponding packages. The results showed that the expression levels of HNRNPC, YTHDF1, KIAA1429, RBM15, YTHDF2, and METTL3 in cancer group were significantly up-regulated (P < 0.05), while expression levels of FTO, ZC3H13, METTL14, YTHDC1 and WTAP in cancer group were significantly down-regulated (P < 0.05) compared with control group. Two subgroups identified by consensus expression of these regulators were closely related to the clinicopathological features, clinical outcomes and malignancy of lung adenocarcinoma. In addition, a 3-gene risk signature including KIAA1429, RBM15, and HNRNPC was constructed and the lung adenocarcinoma patients in TCGA database were divided into high-risk group and low-risk group based on the median risk score. In conclusion, the prognostic signature-based risk score calculated according to the expression levels of KIAA1429, RBM15, and HNRNPC, was not only strongly associated with clinical outcomes and clinicopathological features, but also an independent prognostic factor in lung adenocarcinoma.
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Affiliation(s)
- Fangwei Li
- Department of Respiratory Medicine, Lanzhou University Second Hospital, Lanzhou, China
| | - Hong Wang
- Department of Respiratory Medicine, Lanzhou University Second Hospital, Lanzhou, China
| | - Huirong Huang
- Department of Respiratory Medicine, Lanzhou University Second Hospital, Lanzhou, China
| | - Li Zhang
- Department of Respiratory Medicine, Lanzhou University Second Hospital, Lanzhou, China
| | - Dan Wang
- Department of Respiratory Medicine, Lanzhou University Second Hospital, Lanzhou, China
| | - Yixin Wan
- Department of Respiratory Medicine, Lanzhou University Second Hospital, Lanzhou, China
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331
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Karthiya R, Khandelia P. m6A RNA Methylation: Ramifications for Gene Expression and Human Health. Mol Biotechnol 2020; 62:467-484. [PMID: 32840728 DOI: 10.1007/s12033-020-00269-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
Cellular transcriptomes are frequently adorned by a variety of chemical modification marks, which in turn have a profound influence on its functioning. Of these modifications, the one which has invited a lot of attention in the recent years is m6A RNA methylation, leading to the development of RNA epigenetics or epitranscriptomics as a frontier research area. m6A RNA methylation is one of the most abundant reversible internal modification seen in cellular RNAs. Studies in the last few years have not only shed light on the molecular machinery involved in m6A RNA methylation but also on the impact of this modification in regulating gene expression and hence biological processes. In this review, we will emphasize the biological impact of this modification in normal organismal development and diseases.
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Affiliation(s)
- R Karthiya
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India.
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332
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Chen S, Li Y, Zhi S, Ding Z, Wang W, Peng Y, Huang Y, Zheng R, Yu H, Wang J, Hu M, Miao J, Li J. WTAP promotes osteosarcoma tumorigenesis by repressing HMBOX1 expression in an m 6A-dependent manner. Cell Death Dis 2020; 11:659. [PMID: 32814762 PMCID: PMC7438489 DOI: 10.1038/s41419-020-02847-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
N6-methyladenosine (m6A) regulators are involved in the progression of various cancers via regulating m6A modification. However, the potential role and mechanism of the m6A modification in osteosarcoma remains obscure. In this study, WTAP was found to be highly expressed in osteosarcoma tissue and it was an independent prognostic factor for overall survival in osteosarcoma. Functionally, WTAP, as an oncogene, was involved in the proliferation and metastasis of osteosarcoma in vitro and vivo. Mechanistically, M6A dot blot, RNA-seq and MeRIP-seq, MeRIP-qRT-PCR and luciferase reporter assays showed that HMBOX1 was identified as the target gene of WTAP, which regulated HMBOX1 stability depending on m6A modification at the 3′UTR of HMBOX1 mRNA. In addition, HMBOX1 expression was downregulated in osteosarcoma and was an independent prognostic factor for overall survival in osteosarcoma patients. Silenced HMBOX1 evidently attenuated shWTAP-mediated suppression on osteosarcoma growth and metastasis in vivo and vitro. Finally, WTAP/HMBOX1 regulated osteosarcoma growth and metastasis via PI3K/AKT pathway. In conclusion, this study demonstrated the critical role of the WTAP-mediated m6A modification in the progression of osteosarcoma, which could provide novel insights into osteosarcoma treatment.
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Affiliation(s)
- Shijie Chen
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China.,Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yuezhan Li
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Shuang Zhi
- Four Gynecological Wards, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Zhiyu Ding
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Weiguo Wang
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Yi Peng
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Yan Huang
- The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ruping Zheng
- School of Basic Medical Science, Central South University, Changsha, China
| | - Haiyang Yu
- School of Basic Medical Science, Central South University, Changsha, China
| | - Jianlong Wang
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Minghua Hu
- Department of Anatomy, Histology and Embryology, Changsha Medical University, Changsha, China
| | - Jinglei Miao
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China.
| | - Jinsong Li
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China.
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Xu Y, Ye S, Zhang N, Zheng S, Liu H, Zhou K, Wang L, Cao Y, Sun P, Wang T. The FTO/miR-181b-3p/ARL5B signaling pathway regulates cell migration and invasion in breast cancer. Cancer Commun (Lond) 2020; 40:484-500. [PMID: 32805088 PMCID: PMC7571404 DOI: 10.1002/cac2.12075] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 04/22/2020] [Accepted: 06/27/2020] [Indexed: 12/20/2022] Open
Abstract
Background N6‐methyladenosine (m6A) RNA modification has been demonstrated to be a significant regulatory process in the progression of various tumors, including breast cancer. Fat mass and obesity‐associated (FTO) enzyme, initially known as the obesity‐related protein, is the first identified m6A demethylase. However, the relationship between FTO and breast cancer remains controversial. In this study, we aimed to elucidate the role and clinical significance of FTO in breast cancer and to explore the underlying mechanism. Methods We first investigated the expression of FTO in breast cancer cell lines and tissues by quantitative reverse transcription‐PCR (qRT‐PCR), Western blotting, and immunohistochemistry. Wound healing assay and Transwell assay were performed to determine the migration and invasion abilities of SKBR3 and MDA‐MB453 cells with either knockdown or overexpression of FTO. RNA sequencing (RNA‐seq) was conducted to decipher the downstream targets of FTO. qRT‐PCR, luciferase reporter assay, and Western blotting were employed to confirm the existence of the FTO/miR‐181b‐3p/ARL5B axis. The biological function of ADP ribosylation factor like GTPase 5B (ARL5B) in breast cancer cells was evaluated by wound healing assay and Transwell invasion assay. Results High FTO expression was observed in human epidermal growth factor receptor 2 (HER2)‐positive breast cancer, predicting advanced progression (tumor size [P < 0.001], nuclear grade [P = 0.001], peritumoral lymphovascular invasion [P < 0.001), lymph node metastasis [P = 0.002], and TNM stage [P = 0.001]) and poor prognosis. Moreover, FTO promoted cell invasion and migration in vitro. Mechanistically, RNA‐seq and further confirmation studies suggested that FTO up‐regulated ARL5B by inhibiting miR‐181b‐3p. We further verified that ARL5B also displayed carcinogenic activity in breast cancer cells. Conclusion Our work demonstrated the carcinogenic activity of FTO in promoting the invasion and migration of breast cancer cells via the FTO/miR‐181b‐3p/ARL5B signaling pathway.
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Affiliation(s)
- Yuanyuan Xu
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Shuang Ye
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Nan Zhang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Shuhui Zheng
- Research Center for Translational Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Huatao Liu
- Department of Clinical Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Kewen Zhou
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Ling Wang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Yue Cao
- Department of Basic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Peng Sun
- Department of Pathology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Tinghuai Wang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
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Dai F, Wu Y, Lu Y, An C, Zheng X, Dai L, Guo Y, Zhang L, Li H, Xu W, Gao W. Crosstalk between RNA m 6A Modification and Non-coding RNA Contributes to Cancer Growth and Progression. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:62-71. [PMID: 32911345 PMCID: PMC7486578 DOI: 10.1016/j.omtn.2020.08.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/04/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022]
Abstract
N6-methyladenosine (m6A) is the most common RNA modification and has an important role in normal development and tumorigenesis. The abnormal expression of m6A regulators can lead to an imbalance in m6A levels in cancer cells, leading to the dysregulated expression of oncogenes and tumor suppressor genes that may contribute to cancer development, patient response to chemoradiotherapy, and clinical prognosis. Recent studies demonstrate that non-coding RNAs are involved in epigenetic modification of both DNA and RNA in tumor cells, and may also affect the development and progression of cancer by targeting m6A regulators. In this review, we describe the functional crosstalk between m6A and non-coding RNAs, particularly microRNA, long non-coding RNA, and circular RNA, and illustrate their roles in tumor regulation. Finally, we discuss the significance of non-coding RNA and m6A modification in the diagnosis, treatment, and prognosis of cancer patients, as well as potential future research directions.
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Affiliation(s)
- Fengsheng Dai
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Yongyan Wu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, P. R. China.
| | - Yan Lu
- Department of Otolaryngology Head & Neck Surgery, The First Hospital of Jinzhou Medical University, Jinzhou 121001, P. R. China
| | - Changming An
- Department of Head and Neck Surgery, Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P. R. China
| | - Xiwang Zheng
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Li Dai
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Yujia Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Linshi Zhang
- Department of Thyroid Surgery, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, P. R. China
| | - Huizheng Li
- Department of Otolaryngology Head & Neck Surgery, Dalian Municipal Friendship Hospital of Dalian Medical University, Dalian 116100, P. R. China
| | - Wei Xu
- Department of Head & Neck Surgery, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan 250022, P. R. China; Shandong Provincial Institute of Otolaryngology, Jinan 250022, P. R. China; Key Laboratory of Otolaryngology, Ministry of Health, Shandong University, Jinan 250022, P. R. China.
| | - Wei Gao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, P. R. China.
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Expression pattern of m 6A regulators is significantly correlated with malignancy and antitumor immune response of breast cancer. Cancer Gene Ther 2020; 28:188-196. [PMID: 32759989 DOI: 10.1038/s41417-020-00208-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 11/08/2022]
Abstract
More than 24 regulators have been revealed to dynamically participant in N6-methyladenosine (m6A) RNA methylation, and play critical roles in tumorigenesis and development of cancers. However, their functional roles have not been comprehensively clarified in breast cancer. Here we systematically analyzed the RNA sequencing data of 24 main m6A RNA methylation regulators in 775 breast cancer patients from The Cancer Genome Atlas dataset. Consensus clustering of the 24 m6A regulators was carried out and identified two patient subgroups, RNA methylation 1/2 (RM1/2). RM1 demonstrated generally lower RNA methylation modification than that of RM2, and had significantly shorter overall survival. The hallmarks of PI3K/AKT signaling in cancer, KRAS signaling and angiogenesis were significantly enriched in RM1. Moreover, the association between m6A regulators and antitumor immune response was also investigated in this study and revealed that RM2 was associated with significantly higher expressions of HLA-A, higher numbers of tumor-infiltrating CD8+ T cells, helper T cells and activated NK cells, but lower expressions of PD-L1, PD-L2, TIM3, and CCR4 than RM1. In conclusion, the expression pattern of m6A regulators was significantly correlated with the malignancy, prognosis and antitumor immune response in breast cancer, which might serve as potential targets and biomarkers for immunotherapy.
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336
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Tsuruta N, Tsuchihashi K, Ohmura H, Yamaguchi K, Ito M, Ariyama H, Kusaba H, Akashi K, Baba E. RNA N6-methyladenosine demethylase FTO regulates PD-L1 expression in colon cancer cells. Biochem Biophys Res Commun 2020; 530:235-239. [PMID: 32828292 DOI: 10.1016/j.bbrc.2020.06.153] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 01/26/2023]
Abstract
Fat mass and obesity-associated protein (FTO) is an enzyme that demethylates N6-methyladenosine (m6A), the most abundant RNA modifications in a cell. The upregulated expression of FTO promotes the progression of various types of cancer by modulating cell-intrinsic genes which relate to malignant potential. However, the impact of FTO on the expression of immune-checkpoint molecules in the tumor cells, which are important for immune escape, has not been well understood. We examined the relevance of FTO to programmed cell death-ligand 1 (PD-L1) expression in colon cancer cells. HCT-116 cells showed high expression of both FTO and PD-L1 proteins. The knockdown of FTO by small interfering RNA decreased mRNA and protein levels of PD-L1 in HCT-116 cells. To elucidate the underlying mechanism by which FTO regulates the expression of PD-L1, we depleted FTO in HCT-116 in the presence of IFN-γ, which is a major stimulus to upregulate PD-L1 expression. Depletion of FTO reduced PD-L1 expression in an IFN-γ signaling-independent manner. RNA immunoprecipitation assay revealed the m6A modification of the PD-L1 mRNA and the binding of FTO to the PD-L1 mRNA in HCT-116. Taken together, our results indicated that FTO could regulate PD-L1 expression in colon cancer cells and provides new insights into the regulation of PD-L1 expression by RNA modification.
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Affiliation(s)
- Nobuhiro Tsuruta
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenji Tsuchihashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hirofumi Ohmura
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kyoko Yamaguchi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Mamoru Ito
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hiroshi Ariyama
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hitoshi Kusaba
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Eishi Baba
- Department of Oncology and Social Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
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Anita R, Paramasivam A, Priyadharsini JV, Chitra S. The m6A readers YTHDF1 and YTHDF3 aberrations associated with metastasis and predict poor prognosis in breast cancer patients. Am J Cancer Res 2020; 10:2546-2554. [PMID: 32905518 PMCID: PMC7471347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023] Open
Abstract
N6-Methyladenosine (m6A) is the most common RNA modification in eukaryotic mRNAs and growing evidence suggests the crucial roles of m6A and its regulators in human tumorigenesis. Recent studies have shown that the m6A regulators promote tumorigenesis of various types of cancer. However, the underlying molecular mechanisms of m6A regulators in breast cancer remain largely unknown. We therefore assessed the genetic alterations, expression and prognostic role of m6A regulators in breast cancer using openly available data from The Cancer Genome Atlas (TCGA). Analysis of TCGA data revealed that m6A regulators including KIAA1429, YTHDF1, and YTHDF3 were upregulated in breast cancer tissues, and the expression level significantly correlated with intrinsic subclasses and nodal metastasis. Importantly, we found for the first time that YTHDF1 and YTHDF3 were frequently amplified which contribute to the overexpression of YTHDF1 and YTHDF3 transcripts, thereby promoting breast cancer progression. Moreover, overexpression of YTHDF1 and YTHDF3 were associated with poor prognosis of breast cancer patients. Therefore, YTHDF1 and YTHDF3 serve a crucial role in the pathogenesis of breast cancer, which are potentially useful for prognosis stratification and therapeutic target for breast cancer.
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Affiliation(s)
- Ramesh Anita
- Department of Medical Oncology, Saveetha Medical College Hospital, Saveetha UniversityChennai, India
| | - Arumugam Paramasivam
- BRULAC-DRC, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha UniversityChennai, India
| | - Jayaseelan Vijayashree Priyadharsini
- BRULAC-DRC, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha UniversityChennai, India
| | - Srinivasan Chitra
- Department of Pathology, Saveetha Medical College Hospital, Saveetha UniversityChennai, India
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338
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Li N, Zhan X. Identification of pathology-specific regulators of m 6A RNA modification to optimize lung cancer management in the context of predictive, preventive, and personalized medicine. EPMA J 2020; 11:485-504. [PMID: 32849929 DOI: 10.1007/s13167-020-00220-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
Abstract
Relevance Lung cancer is the most common malignant tumor with high morbidity (11.6% of the total diagnosed cancer cases) and mortality (18.4% of the total cancer deaths), and its 5-year survival rate is very low (20%). Clarification of any molecular events and the discovery of effective biomarkers will offer increasing promise for lung canner management. N6-methyladenosine (m6A) modification is one of the important RNA modifications that are closely associated with lung cancer, and are tightly regulated by m6A regulators. Elucidation of pathology-specific m6A regulators will directly contribute to lung cancer medical services in the context of predictive, preventive, and personalized medicine (PPPM). Purpose To investigate pathology-specific regulators of m6A RNA modifications in lung cancer and further inspect the m6A regulator gene signature as useful tools for PPPM in lung cancers. Methods The gene expression data of 19 m6A regulators (m6A-methyltransferases-ZC3H13, KIAA1429, RBM15/15B, WTAP, and METTL3/14; demethylases-FTO and ALKBH5; and m6A-binding proteins-HNRNPC, YTHDF1/2/3, YTHDC1/2, IGF2BP1/2/3, and HNRNPA2B1) and clinical data of 1013 lung cancer patients [511 lung adenocarcinoma (LUAD) and 502 lung squamous carcinoma (LUSC)] and 109 controls (Con) were obtained from the TCGA database. Quantitative real-time PCR (qRT-PCR) was used to verify m6A regulators in lung cancer cell lines. Protein-protein interaction (PPI), gene co-expression, survival analysis, and heatmap were used to analyze these m6A regulators in this set of lung cancer clinical data. Lasso regression was used to optimize the pathology-specific m6A regulator gene signature. Gene set enrichment analysis (GSEA) was used to reveal the functional characteristics of m6A regulators. Results Those 19 m6A regulator profiling was significantly differentially expressed in lung cancer tissues relative to control tissues, which was also verified in lung cancer cell lines. Those m6A regulators interacted mutually, and those regulator-based sample clusters were correlated with clinical traits, including survival status, gender, tobacco smoking history, primary disease, and pathologic stage. Further, lasso regression based on the 19 m6A regulators optimized and identified a three-m6A-regulator signature (KIAA1429, METTL3, and IGF2BP1) as independent prognostic factor, which classified 1013 lung cancer patients into high-risk and low-risk groups according to median value (0.84) of the lasso regression risk scores. This three-m6A-regulator signature profiling was significantly related to lung cancer overall survival, cancer status, and the above-described clinical traits. Further, GSEA revealed that KIAA1429, METTL3, and IGF2BP1 were significantly related to multiple biological behaviors, including proliferation, apoptosis, metastasis, energy metabolism, drug resistance, and recurrence, and that KIAA1429 and IGF2BP1 had potential target genes, including E2F3, WTAP, CCND1, CDK4, EGR2, YBX1, and TLX, which were associated with cancers. Conclusion This study provided the first view of the pathology-specific regulators of m6A RNA modification in lung cancers and identified the three-m6A-regulator signature (KIAA1429, METTL3, and IGF2BP1) as an independent prognostic model to classify lung cancers into high- and low-risk groups for patient stratification, prognostic assessment, and personalized treatment toward PPPM in lung cancers.
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Affiliation(s)
- Na Li
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, 250117 Shandong People's Republic of China.,Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China.,State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, 250117 Shandong People's Republic of China.,Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China.,State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China.,Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan People's Republic of China
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339
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Wang J, Lin H, Zhou M, Xiang Q, Deng Y, Luo L, Liu Y, Zhu Z, Zhao Z. The m6A methylation regulator-based signature for predicting the prognosis of prostate cancer. Future Oncol 2020; 16:2421-2432. [PMID: 32687727 DOI: 10.2217/fon-2020-0330] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To construct a survival prediction signature for prostate cancer (PC) based on the RNA N6-methyladenosine (m6A) methylation regulator. Materials & methods: This paper explores the interaction network of differentially expressed m6A RNA methylation regulators in PC by Pearson correlation analysis. Univariate Cox risk regression and LASSO regression analysis were used to construct a predictive signature of PC. Kaplan-Meier survival analysis compared the overall survival of the high- and low-risk groups. Results & Conclusion: We first constructed a prognostic two gene signature for PC based on the m6A RNA methylation regulators MRTTL14 and YTHDF2. The interaction network of m6A RNA methylation regulators in PC was also established.
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Affiliation(s)
- Jiamin Wang
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Han Lin
- Department of Gynecology of Traditional Chinese Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Mingda Zhou
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Qian Xiang
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Yihan Deng
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Lianmin Luo
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Yangzhou Liu
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Zhiguo Zhu
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Zhigang Zhao
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
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340
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Guo F, Li S, Guo C, Xu X, Zhou X, Ma D, Cao Z, Bing Z, Cui Y. Circular RNA circMAGI3 accelerates the glycolysis of non-small cell lung cancer through miR-515-5p/HDGF. Am J Transl Res 2020; 12:3953-3963. [PMID: 32774748 PMCID: PMC7407684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
The emerging roles of circular RNAs (circRNAs) in non-small cell lung cancer (NSCLC) have been convincingly proved. However, there are still numerous unknown circRNAs needing exploration. Here, present research performed a circRNA microarray analysis for the expression profile and identified a novel circRNA (circMAGI3, hsa_circ_0110498). Clinically, circMAGI3 was significantly up-regulated in NSCLC tissue and cells, which was closely correlated with unfavorable outcome for NSCLC patients. Functionally, circMAGI3 promoted the glycolysis and proliferation of NSCLC cells. Mechanistically, circMAGI3 functioned as a sponge for miR-515-5p to relieve its target gene HDGF expression, thereby accelerating the glycolysis of NSCLC. Collectively, this research identified the oncogenic role of circMAGI3 in the tumorigenesis through miR-515-5p/HDGF axis, providing a vital theoretical basis for treatment of NSCLC.
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Affiliation(s)
- Feng Guo
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730, China
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730, China
| | - Chao Guo
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730, China
| | - Xiaohui Xu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730, China
| | - Xiaoyun Zhou
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730, China
| | - Dongjie Ma
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730, China
| | - Zhili Cao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730, China
| | - Zhongxing Bing
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730, China
| | - Yushang Cui
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730, China
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341
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Shi Y, Zheng C, Jin Y, Bao B, Wang D, Hou K, Feng J, Tang S, Qu X, Liu Y, Che X, Teng Y. Reduced Expression of METTL3 Promotes Metastasis of Triple-Negative Breast Cancer by m6A Methylation-Mediated COL3A1 Up-Regulation. Front Oncol 2020; 10:1126. [PMID: 32766145 PMCID: PMC7381173 DOI: 10.3389/fonc.2020.01126] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
The abnormal m6A modification caused by m6A modulators is a common feature of various tumors; however, little is known about which m6A modulator plays the most important role in triple-negative breast cancer (TNBC). In this study, when analyzing the influence of m6A modulators (METTL3, METTL14, WTAP, FTO, and ALKBH5) on the prognosis of breast cancer, especially in TNBC using several on-line databases, methyltransferase-like 3 (METTL3) was found to have low expression in breast cancer, and was closely associated with short-distance-metastasis-free survival in TNBC. Further investigation showed that knockdown of METTL3 could enhance the ability of migration, invasion, and adhesion by decreasing m6A level in TNBC cell lines. Collagen type III alpha 1 chain (COL3A1) was identified and verified as a target gene of METTL3. METTL3 could down-regulate the expression of COL3A1 by increasing its m6A methylation, ultimately inhibiting the metastasis of TNBC cells. Finally, with immunohistochemistry staining in breast cancer tissues, it was proved that METTL3 expression was negatively correlated with COL3A1 in TNBC, but not in non-TNBC. This study demonstrated the potential mechanism of m6A modification in metastasis and provided potential targets for treatment in TNBC.
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Affiliation(s)
- Yu Shi
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Chunlei Zheng
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Yue Jin
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Bowen Bao
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Duo Wang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Kezuo Hou
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Jing Feng
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Shiying Tang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Xiujuan Qu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Yunpeng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Xiaofang Che
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
| | - Yuee Teng
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, China Medical University, Shenyang, China
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Su R, Dong L, Li Y, Gao M, Han L, Wunderlich M, Deng X, Li H, Huang Y, Gao L, Li C, Zhao Z, Robinson S, Tan B, Qing Y, Qin X, Prince E, Xie J, Qin H, Li W, Shen C, Sun J, Kulkarni P, Weng H, Huang H, Chen Z, Zhang B, Wu X, Olsen MJ, Müschen M, Marcucci G, Salgia R, Li L, Fathi AT, Li Z, Mulloy JC, Wei M, Horne D, Chen J. Targeting FTO Suppresses Cancer Stem Cell Maintenance and Immune Evasion. Cancer Cell 2020; 38:79-96.e11. [PMID: 32531268 PMCID: PMC7363590 DOI: 10.1016/j.ccell.2020.04.017] [Citation(s) in RCA: 411] [Impact Index Per Article: 102.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/19/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022]
Abstract
Fat mass and obesity-associated protein (FTO), an RNA N6-methyladenosine (m6A) demethylase, plays oncogenic roles in various cancers, presenting an opportunity for the development of effective targeted therapeutics. Here, we report two potent small-molecule FTO inhibitors that exhibit strong anti-tumor effects in multiple types of cancers. We show that genetic depletion and pharmacological inhibition of FTO dramatically attenuate leukemia stem/initiating cell self-renewal and reprogram immune response by suppressing expression of immune checkpoint genes, especially LILRB4. FTO inhibition sensitizes leukemia cells to T cell cytotoxicity and overcomes hypomethylating agent-induced immune evasion. Our study demonstrates that FTO plays critical roles in cancer stem cell self-renewal and immune evasion and highlights the broad potential of targeting FTO for cancer therapy.
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Affiliation(s)
- Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Yangchan Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Min Gao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; School of Pharmaceutical Science and Technology, Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, and Collaborative Innovation Center of Chemical Science and Engineer (Tianjin), Tianjin University, Tianjin 300072, China
| | - Li Han
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; School of Pharmacy, China Medical University, Shenyang, Liaoning 110001, China
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yue Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lei Gao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of Pathology and Genomic Medicine, Houston Methodist, Houston, TX 77030, USA
| | - Chenying Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of Hematology, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 31003, China
| | - Zhicong Zhao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Sean Robinson
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Brandon Tan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Xi Qin
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Emily Prince
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Jun Xie
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Hanjun Qin
- The Integrative Genomics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Jie Sun
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA 91010, USA
| | - Hengyou Weng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Huilin Huang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Bin Zhang
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA
| | - Xiwei Wu
- The Integrative Genomics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Mark J Olsen
- Department of Pharmaceutical Sciences, College of Pharmacy-Glendale, Midwestern University, Glendale, AZ 85308, USA
| | - Markus Müschen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA
| | - Guido Marcucci
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA 91010, USA
| | - Ling Li
- Department of Hematologic Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA
| | - Amir T Fathi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist, Houston, TX 77030, USA
| | - James C Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Minjie Wei
- School of Pharmacy, China Medical University, Shenyang, Liaoning 110001, China
| | - David Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA.
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343
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Hou J, Wang Z, Li H, Zhang H, Luo L. Gene Signature and Identification of Clinical Trait-Related m 6 A Regulators in Pancreatic Cancer. Front Genet 2020; 11:522. [PMID: 32754191 PMCID: PMC7367043 DOI: 10.3389/fgene.2020.00522] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/29/2020] [Indexed: 12/30/2022] Open
Abstract
Pancreatic cancer (PC) has a very poor prognosis and is usually diagnosed only at an advanced stage. The discovery of new biomarkers for PC will help in early diagnosis and a better prognosis for patients. Recently, N6-methyladenosine (m6A) RNA modifications and their regulators have been implicated in the development of many cancers. To investigate the functions and mechanisms of m6A modifications in the development of PC, 19 m6A regulators, including m6A-methyltransferases (ZC3H13, RBM15/15B, WTAP, KIAA1429, and METTL3/14), demethylases (FTO and ALKBH5), and binding proteins (YTHDF1/2/3, YTHDC1/2, IGF2BP1/2/3, HNRNPC, and HNRNPA2B1) were analyzed in 178 PC tissues from the cancer genome atlas (TCGA) database. The results were verified in PC cell lines Mia-PaCa-2, BXPC-3, and the control cell line HDE-CT. The m6A regulators-based sample clusters were significantly related to overall survival (OS). Further, lasso regression identified a six-m6A-regulator-signature prognostic model (KIAA1429, HNRNPC, METTL3, YTHDF1, IGF2BP2, and IGF2BP3). Model-based high-risk and low-risk groups were significantly correlated with OS and clinical traits (pathologic M, N, and clinical stages and vital status). The risk signature was verified as an independent prognostic marker for patients with PC. Finally, gene set enrichment analysis revealed m6A regulators (KIAA1429, HNRNPC, and IGF2BP2) were related to multiple biological behaviors in PC, including adipocytokine signaling, the well vs. poorly differentiated tumor pathway, tumor metastasis pathway, epithelial mesenchymal transition pathway, gemcitabine resistance pathway, and stemness pathway. In summary, the m6A regulatory factors which related to clinical characteristics can be involved in the malignant progression of PC, and the constructed risk markers may be a promising prognostic biomarker that can guide the individualized treatment of PC patients.
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Affiliation(s)
- Jie Hou
- The People's Hospital of Baoan Shenzhen, The 8th people's Hospital of Shenzhen, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, China
| | - Zhan Wang
- The People's Hospital of Baoan Shenzhen, The 8th people's Hospital of Shenzhen, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, China
| | - Hong Li
- The People's Hospital of Baoan Shenzhen, The 8th people's Hospital of Shenzhen, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, China
| | - Hongzhi Zhang
- The People's Hospital of Baoan Shenzhen, The 8th people's Hospital of Shenzhen, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, China
| | - Lan Luo
- The People's Hospital of Baoan Shenzhen, The 8th people's Hospital of Shenzhen, The Affiliated Baoan Hospital of Southern Medical University, Shenzhen, China
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344
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Meng Z, Yuan Q, Zhao J, Wang B, Li S, Offringa R, Jin X, Wu H. The m 6A-Related mRNA Signature Predicts the Prognosis of Pancreatic Cancer Patients. Mol Ther Oncolytics 2020; 17:460-470. [PMID: 32490170 PMCID: PMC7256444 DOI: 10.1016/j.omto.2020.04.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/23/2020] [Indexed: 12/19/2022] Open
Abstract
N6-methyladenosine (m6A) has an important epitranscriptomic modification that controls cancer self-renewal and cell fate. The addition of m6A to mRNA is a reversible modification. The deposition of m6A is encoded by a methyltransferase complex involving three homologous factors, jargonized as "writers," "erasers," and "readers." However, their roles in pancreatic adenocarcinoma (PAAD) are underexploited. With the use of The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases, we provided an mRNA signature that may improve the prognostic prediction of PAAD patients based on the genetic status of m6A regulators. PAAD patients with genetic alteration of m6A regulators had worse disease-free and overall survival. After comparing PAAD groups with/without genetic alteration of m6A regulators, we identified 196 differentially expressed genes (DEGs). Then, we generated a 16-mRNA signature score system through least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Multivariate cox regression analysis demonstrated that a high-risk score significantly correlates with poor prognosis. Moreover, time-dependent receiver operating characteristic (ROC) curves revealed it was effective in predicting the overall survival in both training and validation sets. PAH, ZPLD1, PPFIA3, and TNNT1 from our signature also exhibited an independent prognostic value. Collectively, these findings can improve the understanding of m6A modifications in PAAD and potentially guide therapies in PAAD patients.
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Affiliation(s)
- Zibo Meng
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Qingchen Yuan
- Key Lab of Molecular Biological Targeted Therapies of the Ministry of Education, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jingyuan Zhao
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Bo Wang
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shoukang Li
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Rienk Offringa
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Heidelberg, Germany
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Xin Jin
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Heshui Wu
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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345
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Yang J, Chen J, Fei X, Wang X, Wang K. N6-methyladenine RNA modification and cancer. Oncol Lett 2020; 20:1504-1512. [PMID: 32724392 DOI: 10.3892/ol.2020.11739] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) in messenger RNA (mRNA) is regulated by m6A methyltransferases and demethylases. Modifications of m6A are dynamic and reversible, may regulate gene expression levels and serve vital roles in numerous life processes, such as cell cycle regulation, cell fate decision and cell differentiation. In recent years, m6A modifications have been reported to exhibit functions in human cancers via regulation of RNA stability, microRNA processing, mRNA splicing and mRNA translation, including lung cancer, breast tumor and acute myeloid leukemia. In the present review, the roles of m6A modifications in the onset and progression of cancer were summarized. These modifications display an oncogenic role in certain types of cancer, whereas in other types of cancer they exhibit a tumor suppressor role. Therefore, understanding the biological functions performed by m6A in different types of tumors and identifying pivotal m6A target genes to deduce the potential mechanisms underlying the progression of cancer may assist in the development of novel therapeutics.
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Affiliation(s)
- Jun Yang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Junwen Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Xiang Fei
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
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346
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Zhou Z, Lv J, Yu H, Han J, Yang X, Feng D, Wu Q, Yuan B, Lu Q, Yang H. Mechanism of RNA modification N6-methyladenosine in human cancer. Mol Cancer 2020; 19:104. [PMID: 32513173 PMCID: PMC7278081 DOI: 10.1186/s12943-020-01216-3] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/13/2020] [Indexed: 01/08/2023] Open
Abstract
Since the breakthrough discoveries of DNA and histone modifications, the field of RNA modifications has gained increasing interest in the scientific community. The discovery of N6-methyladenosine (m6A), a predominantly internal epigenetic modification in eukaryotes mRNA, heralded the creation of the field of epi-transcriptomics. This post-transcriptional RNA modification is dynamic and reversible, and is regulated by methylases, demethylases and proteins that preferentially recognize m6A modifications. Altered m6A levels affect RNA processing, degradation and translation, thereby disrupting gene expression and key cellular processes, ultimately resulting in tumor initiation and progression. Furthermore, inhibitors and regulators of m6A-related factors have been explored as therapeutic approaches for treating cancer. In the present review, the mechanisms of m6A RNA modification, the clinicopathological relevance of m6A alterations, the type and frequency of alterations and the multiple functions it regulates in different types of cancer are discussed.
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Affiliation(s)
- Zijian Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Jiancheng Lv
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Hao Yu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Jie Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Xiao Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Dexiang Feng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Qikai Wu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Baorui Yuan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Qiang Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
| | - Haiwei Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
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347
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Wang X, Fu X, Zhang J, Xiong C, Zhang S, Lv Y. Identification and validation of m 6A RNA methylation regulators with clinical prognostic value in Papillary thyroid cancer. Cancer Cell Int 2020; 20:203. [PMID: 32514248 PMCID: PMC7260751 DOI: 10.1186/s12935-020-01283-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/22/2020] [Indexed: 02/09/2023] Open
Abstract
Background Papillary thyroid cancer (PTC) is a type of malignant tumor with excellent prognosis, accounting for more than 80% of thyroid cancer. Recently, numerous studies illustrated the importance of N6-methyladenosine (m6A) RNA modification to tumorigenesis, but it has never been reported in PTC. Methods We downloaded data from The Cancer Genome Atlas (TCGA) and analyzed RNA expression, single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) of 19 m6A RNA methylation regulators in PTC. Then we used nonnegative matrix factorization (NMF) to cluster patients into two m6A subtypes and compared them in overall survival (OS) and disease-free survival (DFS). The Weighted correlation network analysis (WGCNA) and univariate Cox proportional hazard model (CoxPH) were used to select genes for the construction of a m6A-related signature. The accuracy and prognostic value of this signature were validated by using receiver operating characteristic (ROC) curves, K-M (Kaplan–Meier) survival analysis, univariant and multivariant analyses. Results CNVs and differential expression of m6A regulators were observed in PTC patients. Especially IGF2BP2 (Insulin-like growth factor 2 mRNA binding protein 2), which was most significantly overexpressed in tumor tissue. We chose 4 genes in the m6A-related module from WGCNA: IGF2BP2, STT3A, MTHFD1 and GSTM4, and used them to construct a m6A-related signature. The prognostic value of this signature was validated, and risk scores provided by the signature was the independent prognostic factor for PTC. A nomogram was also provided for clinical usage. Conclusions We performed a comprehensive evaluation of the m6A RNA modification landscape of PTC and explored its underlying mechanisms. Our m6A-related signature was of great significance in predicting the DFS of patients with PTC. And IGF2BP2 was a gene worthy for further analysis as its strong correlation with DFS and clinical phenotypes of PTC.
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Affiliation(s)
- Xinyi Wang
- Queen Mary College, Medical Department, Nanchang University, Nanchang, Jiangxi People's Republic of China
| | - Xiaorui Fu
- Queen Mary College, Medical Department, Nanchang University, Nanchang, Jiangxi People's Republic of China
| | - Junjia Zhang
- Department of Breast and Endocrine Surgical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8574 Japan
| | - Chengfeng Xiong
- Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi People's Republic of China
| | - Shuyong Zhang
- Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi People's Republic of China
| | - Yunxia Lv
- Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi People's Republic of China
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348
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Chen M, Zhang S, Nie Z, Wen X, Gao Y. Identification of an Autophagy-Related Prognostic Signature for Clear Cell Renal Cell Carcinoma. Front Oncol 2020; 10:873. [PMID: 32547955 PMCID: PMC7274034 DOI: 10.3389/fonc.2020.00873] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/04/2020] [Indexed: 12/23/2022] Open
Abstract
Abnormal autophagy is closely related to the development of cancer. Many studies have demonstrated that autophagy plays an important role in biological function in clear cell renal cell carcinoma (ccRCC). This study aimed to construct a prognostic signature for ccRCC based on autophagy-related genes (ARGs) to predict the prognosis of ccRCC. Differentially expressed ARGs were obtained from ccRCC RNA-seq data in The Cancer Genome Atlas (TCGA) database. ARGs were enriched by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The prognostic ARGs used to construct the risk score models for overall survival (OS) and disease-free survival (DFS) were identified by Cox regression analyses. According to the median value of the risk score, patients were divided into a high-risk group and a low-risk group. The OS and DFS were analyzed by the Kaplan-Meier method. The predictive accuracy was determined by a receiver operating characteristic (ROC) curve analysis. Additionally, we performed stratification analyses based on different clinical variables and evaluated the correlation between the risk score and the clinical variables. The differentially expressed ARGs were mainly enriched in the platinum drug resistance pathway. The prognostic signatures based on 11 ARGs for OS and 5 ARGs for DFS were constructed and showed that the survive time was significantly shorter in the high-risk group than in the low-risk group (P < 0.001). The ROC curve for OS exhibited good predictive accuracy, with an area under the curve value of 0.738. In the stratification analyses, the OS time of the high-risk group was shorter than that of the low-risk group stratified by different clinical variables. In conclusion, an autophagy-related signature for OS we constructed can independently predict the prognosis of ccRCC patient, and provide a deep understanding of the potential biological mechanisms of autophagy in ccRCC.
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Affiliation(s)
- Mei Chen
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, China
| | - Shufang Zhang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, China
| | - Zhenyu Nie
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, China
| | - Xiaohong Wen
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, China
| | - Yuanhui Gao
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, China
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349
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Wang T, Kong S, Tao M, Ju S. The potential role of RNA N6-methyladenosine in Cancer progression. Mol Cancer 2020; 19:88. [PMID: 32398132 PMCID: PMC7216508 DOI: 10.1186/s12943-020-01204-7] [Citation(s) in RCA: 550] [Impact Index Per Article: 137.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) is considered the most common, abundant, and conserved internal transcript modification, especially in eukaryotic messenger RNA (mRNA). m6A is installed by m6A methyltransferases (METTL3/14, WTAP, RBM15/15B, VIRMA and ZC3H13, termed “writers”), removed by demethylases (FTO, ALKBH5, and ALKBH3, termed “erasers”), and recognized by m6A-binding proteins (YTHDC1/2, YTHDF1/2/3, IGF2BP1/2/3, HNRNP, and eIF3, termed “readers”). Accumulating evidence suggests that m6A RNA methylation greatly impacts RNA metabolism and is involved in the pathogenesis of many kinds of diseases, including cancers. In this review, we focus on the physiological functions of m6A modification and its related regulators, as well as on the potential biological roles of these elements in human tumors.
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Affiliation(s)
- Tianyi Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Shan Kong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Mei Tao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China. .,School of Public Health, Nantong University, NO 9, Seyuan Road, Nantong, 226019, Jiangsu, China.
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350
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Lin Z, Niu Y, Wan A, Chen D, Liang H, Chen X, Sun L, Zhan S, Chen L, Cheng C, Zhang X, Bu X, He W, Wan G. RNA m 6 A methylation regulates sorafenib resistance in liver cancer through FOXO3-mediated autophagy. EMBO J 2020; 39:e103181. [PMID: 32368828 PMCID: PMC7298296 DOI: 10.15252/embj.2019103181] [Citation(s) in RCA: 257] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/25/2020] [Accepted: 04/03/2020] [Indexed: 12/31/2022] Open
Abstract
N6‐methyladenosine (m6A) is an abundant nucleotide modification in mRNA, known to regulate mRNA stability, splicing, and translation, but it is unclear whether it is also has a physiological role in the intratumoral microenvironment and cancer drug resistance. Here, we find that METTL3, a primary m6A methyltransferase, is significantly down‐regulated in human sorafenib‐resistant hepatocellular carcinoma (HCC). Depletion of METTL3 under hypoxia promotes sorafenib resistance and expression of angiogenesis genes in cultured HCC cells and activates autophagy‐associated pathways. Mechanistically, we have identified FOXO3 as a key downstream target of METTL3, with m6A modification of the FOXO3 mRNA 3′‐untranslated region increasing its stability through a YTHDF1‐dependent mechanism. Analysis of clinical samples furthermore showed that METTL3 and FOXO3 levels are tightly correlated in HCC patients. In mouse xenograft models, METTL3 depletion significantly enhances sorafenib resistance of HCC by abolishing the identified METTL3‐mediated FOXO3 mRNA stabilization, and overexpression of FOXO3 restores m6A‐dependent sorafenib sensitivity. Collectively, our work reveals a critical function for METTL3‐mediated m6A modification in the hypoxic tumor microenvironment and identifies FOXO3 as an important target of m6A modification in the resistance of HCC to sorafenib therapy.
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Affiliation(s)
- Ziyou Lin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yi Niu
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Arabella Wan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Dongshi Chen
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heng Liang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xijun Chen
- Department of Abdominal Surgery, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Lei Sun
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Siyue Zhan
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Liutao Chen
- School of Life Science, Sun Yat-Sen University, Guangzhou, China
| | - Chao Cheng
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaolei Zhang
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xianzhang Bu
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China.,Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Guohui Wan
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
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