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Hu Q, Yin J, Zhao S, Wang Y, Shi R, Yan K, Huang S. ZFHX3 acts as a tumor suppressor in prostate cancer by targeting FTO-mediated m 6A demethylation. Cell Death Discov 2024; 10:284. [PMID: 38871709 DOI: 10.1038/s41420-024-02060-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Zinc-finger homeobox 3 (ZFHX3, also known as ATBF1) suppresses prostatic tumorigenesis. ZFHX3 is frequently found to have numerous deletions in human prostate cancer (PCa). However, the underlying molecular function of ZFHX3 during prostatic tumorigenesis is not well understood. N6-methyladenosine (m6A) modification in RNA plays a critical role in the development of cancers; however, the relationship between ZFHX3 and m6A modification is largely unknown in PCa. In this study, we found that ZFHX3 knockdown decreased total m6A levels through enhancing the transcriptional activity of FTO in PCa cells. Importantly, FTO inhibition suppressed cell proliferation and rescued the promoting function of ZFHX3 knockdown on cell proliferation. In vivo, we verified that FTO was upregulated and ZFHX3 was decreased in PCa patients and that a high level of ZFHX3 is indispensable for low FTO expression and is correlated with better patient survival. Through transcriptome sequencing and MeRIP sequencing, we revealed that E2F2 and CDKN2C were the direct targets of FTO-mediated m6A modification and ZFXH3 was required for the regulation of FTO on E2F2 and CDKN2C expression. Unexpectedly, we uncovered that ZFHX3 expression was in return regulated by FTO in an m6A-dependent way. These findings establish a novel crosstalk mechanism between ZFHX3 and FTO in prostatic tumorigenesis.
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Affiliation(s)
- Qingxia Hu
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Hospital of Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Junling Yin
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Sijie Zhao
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yibo Wang
- Shandong Provincial Hospital of Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ruxue Shi
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Keqiang Yan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China.
| | - Shuhong Huang
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China.
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2
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Hodara E, Mades A, Swartz L, Iqbal M, Xu T, Bsteh D, Farnham P, Rhie S, Goldkorn A. m 6A epitranscriptome analysis reveals differentially methylated transcripts that drive early chemoresistance in bladder cancer. NAR Cancer 2023; 5:zcad054. [PMID: 38023731 PMCID: PMC10653028 DOI: 10.1093/narcan/zcad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
N 6-Methyladenosine (m6A) RNA modifications dynamically regulate messenger RNA processing, differentiation and cell fate. Given these functions, we hypothesized that m6A modifications play a role in the transition to chemoresistance. To test this, we took an agnostic discovery approach anchored directly to chemoresistance rather than to any particular m6A effector protein. Specifically, we used methyl-RNA immunoprecipitation followed by sequencing (MeRIP-seq) in parallel with RNA sequencing to identify gene transcripts that were both differentially methylated and differentially expressed between cisplatin-sensitive and cisplatin-resistant bladder cancer (BC) cells. We filtered and prioritized these genes using clinical and functional database tools, and then validated several of the top candidates via targeted quantitative polymerase chain reaction (qPCR) and MeRIP-PCR. In cisplatin-resistant cells, SLC7A11 transcripts had decreased methylation associated with decreased m6A reader YTHDF3 binding, prolonged RNA stability, and increased RNA and protein levels, leading to reduced ferroptosis and increased survival. Consistent with this, cisplatin-sensitive BC cell lines and patient-derived organoids exposed to cisplatin for as little as 48 h exhibited similar mechanisms of SLC7A11 upregulation and chemoresistance, trends that were also reflected in public cancer survival databases. Collectively, these findings highlight epitranscriptomic plasticity as a mechanism of rapid chemoresistance and a potential therapeutic target.
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Affiliation(s)
- Emmanuelle Hodara
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Aubree Mades
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Lisa Swartz
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Maheen Iqbal
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Tong Xu
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Daniel Bsteh
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Amir Goldkorn
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine of USC and Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
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3
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Wang Q, Fan X, Sheng Q, Yang M, Zhou P, Lu S, Gao Y, Kong Z, Shen N, Lv Z, Wang R. N6-methyladenosine methylation in kidney injury. Clin Epigenetics 2023; 15:170. [PMID: 37865763 PMCID: PMC10590532 DOI: 10.1186/s13148-023-01586-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023] Open
Abstract
Multiple mechanisms are involved in kidney damage, among which the role of epigenetic modifications in the occurrence and development of kidney diseases is constantly being revealed. However, N6-methyladenosine (M6A), a well-known post-transcriptional modification, has been regarded as the most prevalent epigenetic modifications in higher eukaryotic, which is involved in various biological processes of cells such as maintaining the stability of mRNA. The role of M6A modification in the mechanism of kidney damage has attracted widespread attention. In this review, we mainly summarize the role of M6A modification in the progression of kidney diseases from the following aspects: the regulatory pattern of N6-methyladenosine, the critical roles of N6-methyladenosine in chronic kidney disease, acute kidney injury and renal cell carcinoma, and then reveal its potential significance in the diagnosis and treatment of various kidney diseases. A better understanding of this field will be helpful for future research and clinical treatment of kidney diseases.
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Affiliation(s)
- Qimeng Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Xiaoting Fan
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Qinghao Sheng
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Meilin Yang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Ping Zhou
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Shangwei Lu
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Ying Gao
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Zhijuan Kong
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Ning Shen
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Zhimei Lv
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
| | - Rong Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Department of Nephrology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
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4
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Wang GC, Gan X, Zeng YQ, Chen X, Kang H, Huang SW, Hu WH. The Role of NCS1 in Immunotherapy and Prognosis of Human Cancer. Biomedicines 2023; 11:2765. [PMID: 37893139 PMCID: PMC10604305 DOI: 10.3390/biomedicines11102765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/01/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The Neural Calcium Sensor1 (NCS1) is a crucial protein that binds to Ca2+ and is believed to play a role in regulating tumor invasion and cell proliferation. However, the role of NCS1 in immune infiltration and cancer prognosis is still unknown. Our study aimed to explore the expression profile, immune infiltration pattern, prognostic value, biological function, and potential compounds targeting NCS1 using public databases. High expression of NCS1 was detected by immune histochemical staining in LIHC (Liver hepatocellular carcinoma), BRCA (Breast invasive carcinoma), KIRC (Kidney renal clear cell carcinoma), and SKCM (Skin Cutaneous Melanoma). The expression of NCS1 in cancer was determined by TCGA (The Cancer Genome Atlas Program), GTEx (The Genotype-Tissue Expression), the Kaplan-Meier plotter, GEO (Gene Expression Omnibus), GEPIA2.0 (Gene Expression Profiling Interactive Analysis 2.0), HPA (The Human Protein Atlas), UALCAN, TIMER2.0, TISIDB, Metascape, Drugbank, chEMBL, and ICSDB databases. NCS1 has genomic mutations as well as aberrant DNA methylation in multiple cancers compared to normal tissues. Also, NCS1 was significantly different in the immune microenvironment, tumor mutational burden (TMB), microsatellite instability (MSI), and immune infiltrate-associated cells in different cancers, which could be used for the typing of immune and molecular subtypes of cancer and the presence of immune checkpoint resistance in several cancers. Univariate regression analysis, multivariate regression analysis, and gene enrichment analysis to construct prognostic models revealed that NCS1 is involved in immune regulation and can be used as a prognostic biomarker for SKCM, LIHC, BRCA, COAD, and KIRC. These results provide clues from a bioinformatic perspective and highlight the importance of NCS1 in a variety of cancers.
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Affiliation(s)
- Gen-Chun Wang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Gan
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yun-Qian Zeng
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Chen
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hao Kang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuai-Wen Huang
- Department of General Practice, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei-Hua Hu
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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5
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Cuevas-Estrada B, Montalvo-Casimiro M, Munguia-Garza P, Ríos-Rodríguez JA, González-Barrios R, Herrera LA. Breaking the Mold: Epigenetics and Genomics Approaches Addressing Novel Treatments and Chemoresponse in TGCT Patients. Int J Mol Sci 2023; 24:ijms24097873. [PMID: 37175579 PMCID: PMC10178517 DOI: 10.3390/ijms24097873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
Testicular germ-cell tumors (TGCT) have been widely recognized for their outstanding survival rates, commonly attributed to their high sensitivity to cisplatin-based therapies. Despite this, a subset of patients develops cisplatin resistance, for whom additional therapeutic options are unsuccessful, and ~20% of them will die from disease progression at an early age. Several efforts have been made trying to find the molecular bases of cisplatin resistance. However, this phenomenon is still not fully understood, which has limited the development of efficient biomarkers and precision medicine approaches as an alternative that could improve the clinical outcomes of these patients. With the aim of providing an integrative landscape, we review the most recent genomic and epigenomic features attributed to chemoresponse in TGCT patients, highlighting how we can seek to combat cisplatin resistance through the same mechanisms by which TGCTs are particularly hypersensitive to therapy. In this regard, we explore ongoing treatment directions for resistant TGCT and novel targets to guide future clinical trials. Through our exploration of recent findings, we conclude that epidrugs are promising treatments that could help to restore cisplatin sensitivity in resistant tumors, shedding light on potential avenues for better prognosis for the benefit of the patients.
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Affiliation(s)
- Berenice Cuevas-Estrada
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico
| | - Michel Montalvo-Casimiro
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico
| | - Paulina Munguia-Garza
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico
| | - Juan Alberto Ríos-Rodríguez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City 14080, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Mexico
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6
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Li Y, Zhu S, Chen Y, Ma Q, Kan D, Yu W, Zhang B, Chen X, Wei W, Shao Y, Wang K, Zhang M, Deng S, Niu Y, Shang Z. Post-transcriptional modification of m 6A methylase METTL3 regulates ERK-induced androgen-deprived treatment resistance prostate cancer. Cell Death Dis 2023; 14:289. [PMID: 37095108 PMCID: PMC10126012 DOI: 10.1038/s41419-023-05773-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/14/2023] [Accepted: 03/23/2023] [Indexed: 04/26/2023]
Abstract
As the most common modification of RNA, N6-methyladenosin (m6A) has been confirmed to be involved in the occurrence and development of various cancers. However, the relationship between m6A and castration resistance prostate cancer (CRPC), has not been fully studied. By m6A-sequencing of patient cancer tissues, we identified that the overall level of m6A in CRPC was up-regulated than castration sensitive prostate cancer (CSPC). Based on the analysis of m6A-sequencing data, we found m6A modification level of HRas proto-oncogene, GTPase (HRAS) and mitogen-activated protein kinase kinase 2 (MEK2 or MAP2K2) were enhanced in CRPC. Specifically, tissue microarray analysis and molecular biology experiments confirmed that METTL3, an m6A "writer" up-regulated after castration, activated the ERK pathway to contribute to malignant phenotype including ADT resistance, cell proliferation and invasion. We revealed that METTL3-mediated ERK phosphorylation by stabilizing the transcription of HRAS and positively regulating the translation of MEK2. In the Enzalutamide-resistant (Enz-R) C4-2 and LNCap cell line (C4-2R, LNCapR) established in the current study, the ERK pathway was confirmed to be regulated by METTL3. We also found that applying antisense oligonucleotides (ASOs) to target the METTL3/ERK axis can restore Enzalutamide resistance in vitro and in vivo. In conclusion, METTL3 activated the ERK pathway and induced the resistance to Enzalutamide by regulating the m6A level of critical gene transcription in the ERK pathway.
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Affiliation(s)
- Yang Li
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shimiao Zhu
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yutong Chen
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Qianwang Ma
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Duo Kan
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Wenyue Yu
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Boya Zhang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Xuanrong Chen
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Wanqing Wei
- Lianshui People's Hospital of Kangda College affiliated with Nanjing Medical University, Huai'an, China
| | - Yi Shao
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Keruo Wang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Mingpeng Zhang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shu Deng
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuanjie Niu
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.
| | - Zhiqun Shang
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.
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7
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Amentoflavone and methyl hesperidin, novel lead molecules targeting epitranscriptomic modulator in acute myeloid leukemia: in silico drug screening and molecular dynamics simulation approach. J Mol Model 2023; 29:9. [DOI: 10.1007/s00894-022-05407-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
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8
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Li Z, Zheng C, Huang L, Yin X, Wang Z, Liu C, Li B. The landscape of m6A regulators in esophageal cancer: molecular characteristics, immuno-oncology features, and clinical relevance. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1347. [PMID: 36660671 PMCID: PMC9843396 DOI: 10.21037/atm-22-5895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022]
Abstract
Background Squamous cell carcinoma (SCC) and adenocarcinoma (AC) are the two main pathological types of esophageal cancer (EC), which differ in molecular features, genetic variation, and treatment sensitivity. However, as a key process in tumorigenesis and development, the role of N6-methyladenosine (m6A) regulators in esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) is not fully understood. Methods This study systematically compared the role of m6A regulators of ESCC and EAC in terms of molecular characteristics, immuno-oncology characteristics, and clinical relevance, and validated our findings in a long-term follow-up patient cohort. Results There were many differences in m6A regulators between ESCC and EAC in terms of expression patterns, genetic variation, association with tumor pathways, immune signatures, and immunotherapy sensitivity. Furthermore, VIRMA was identified as a factor with opposite functional and prognostic effects in ESCC and EAC. ESCC patients with high VIRMA expression and EAC patients with low VIRMA expression had a better prognosis. Single-center data showed that low expression of FTO may be associated with superior immunotherapy efficacy in ESCC patients. Conclusions The results herein provide novel ideas for understanding the tumor characteristics, occurrence, and development of ESCC and EAC, and suggest new targets for the treatment and intervention of EC.
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Affiliation(s)
- Zhe Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Chunyan Zheng
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Liquan Huang
- Department of Anesthesiology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaoyang Yin
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zhongtang Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Chengxin Liu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Baosheng Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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9
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Wu Z, Lin Y, Wei N. N6-methyladenosine-modified HOTAIRM1 promotes vasculogenic mimicry formation in glioma. Cancer Sci 2022; 114:129-141. [PMID: 36086906 PMCID: PMC9807531 DOI: 10.1111/cas.15578] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/22/2022] [Accepted: 09/06/2022] [Indexed: 01/07/2023] Open
Abstract
Vasculogenic mimicry (VM) has been reported to accelerate angiogenesis in malignant tumors, yet the mechanism underlying VM has not been fully elucidated. N6-methyladenosine (m6A) mainly modulates mRNA fate and affects multiple tumorigenesis. Here, we aimed to investigate m6A-modified HOXA transcript antisense RNA myeloid-specific 1 (HOTAIRM1) in the regulation of glioma-associated VM formation. Gene expression was analyzed by quantitative RT-PCR. Cell viability, metastases, and VM formation capacity were determined by CCK-8, migration and invasion, as well as tube formation assays, respectively. The function and mechanisms of m6A-modified HOTAIRM1 were defined through liquid chromatography-tandem mass spectrometry m6A quantification, methylated RNA immunoprecipitation sequencing, RNA stability assays, and RNA pull-down experiments. A glioma xenograft mouse model was further established for VM evaluation in vivo. The results showed that HOTAIRM1, methyltransferase-like 3 (METTL3), and insulin-like growth factor binding protein 2 (IGFBP2) were upregulated in glioma tissues and cell lines. HOTAIRM1 functions as an oncogene in glioma progression; however, knockdown of HOTAIRM1 significantly reduced cell viability, migration, invasion, and VM formation. Notably, METTL3-dependent m6A modification enhanced HOTAIRM1 mRNA stability, whereas knockdown of METTL3 deficiency significantly suppressed VM in glioma. Moreover, HOTAIRM1 was found to bind IGFBP2, and HOTAIRM1 deficiency blocked glioma progression and VM formation in vivo. Our results indicated that METTL3-dependent m6A-modified HOTAIRM1 promoted VM formation in glioma.
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Affiliation(s)
- Zhangyi Wu
- Department of NeurosurgeryZhejiang Provincial Tongde HospitalHangzhouChina
| | - Yihai Lin
- Department of NeurosurgeryZhejiang Provincial Tongde HospitalHangzhouChina
| | - Nan Wei
- Department of OncologyZhejiang HospitalHangzhouChina
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10
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Liu P, Fan B, Othmane B, Hu J, Li H, Cui Y, Ou Z, Chen J, Zu X. m 6A-induced lncDBET promotes the malignant progression of bladder cancer through FABP5-mediated lipid metabolism. Am J Cancer Res 2022; 12:6291-6307. [PMID: 36168624 PMCID: PMC9475447 DOI: 10.7150/thno.71456] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/13/2022] [Indexed: 12/23/2022] Open
Abstract
The limited effect of adjuvant therapy for advanced bladder cancer (BCa) leads to a poor prognosis. Increasing evidence has shown that RNA N6-methyladenosine (m6A) modification plays important functional roles in tumorigenesis. Nevertheless, the role and mechanism of m6A-modified noncoding RNAs (ncRNAs) in BCa remain largely unknown. Methods: RT-PCR, western blotting and ONCOMINE dataset were used to determine the dominant m6A-related enzyme in BCa. M6A-lncRNA epitranscriptomic microarray was used to screen candidate targets of METTL14. RT-PCR, MeRIP and TCGA dataset were carried out to confirm the downstream target of METTL14. CHIRP/MS was conducted to identify the candidate proteins binding to lncDBET. RT-PCR, western blotting, RIP and KEGG analysis were used to confirm the target of lncDBET. The levels of METTL14, lncDBET and FABP5 were tested in vitro and in vivo. CCK-8, EdU, transwell and flow cytometry assays were performed to determine the oncogenic function of METTL14, lncDBET and FABP5, and their regulatory networks. Results: We identified that the m6A level of total RNA was elevated and that METTL14 was the dominant m6A-related enzyme in BCa. m6A modification mediated by METTL14 promoted the malignant progression of BCa by promoting the expression of lncDBET. Upregulated lncDBET activated the PPAR signalling pathway to promote the lipid metabolism of cancer cells through direct interaction with FABP5, thus promoting the malignant progression of BCa in vitro and in vivo. Conclusions: Our study establishes METTL14/lncDBET/FABP5 as a critical oncogenic axis in BCa.
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Affiliation(s)
- Peihua Liu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Benyi Fan
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Belaydi Othmane
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Jiao Hu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Huihuang Li
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Yu Cui
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Zhenyu Ou
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
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11
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Wan H, Feng Y, Wu J, Zhu L, Mi Y. Functions and mechanisms of N6‑methyladenosine in prostate cancer (Review). Mol Med Rep 2022; 26:280. [PMID: 35856412 PMCID: PMC9364137 DOI: 10.3892/mmr.2022.12796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
Prostate cancer (PCa) has long been a major public health problem affecting men worldwide. Even with treatment, it can develop into castration-resistant PCa. With the continuous advancement in epigenetics, researchers have explored N6-methyladenosine (m6A) in search of a more effective and lasting treatment for PCa. m6A is widely distributed in mammalian cells and influences various aspects of mRNA metabolism. Recently, it has been associated with the development or suppression of various types of cancer, including PCa. This review summarizes the recent findings on m6A regulation and its functions and mechanisms in cells, focusing on the various functional proteins operating within m6A in PCa cells. Moreover, the potential clinical value of exploiting m6A modification as an early diagnostic marker in PCa diagnosis and therapeutics was discussed. m6A may also be used as an indicator to evaluate treatment outcome and prognosis.
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Affiliation(s)
- Hongyuan Wan
- Wuxi Medical College, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Yanyan Feng
- Wuxi Medical College, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Junjie Wu
- Department of Burns and Plastic Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Lijie Zhu
- Department of Urology, The Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Yuanyuan Mi
- Department of Urology, The Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
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12
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Luo G, Xu W, Chen X, Wang S, Wang J, Dong F, Hu DN, Reinach PS, Yan D. NSUN2-mediated RNA m 5C modification modulates uveal melanoma cell proliferation and migration. Epigenetics 2022; 17:922-933. [PMID: 35757999 DOI: 10.1080/15592294.2022.2088047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
RNA 5-methylcytosine (m5C) is a widespread post-transcriptional modification involved in diverse biological processes through controlling RNA metabolism. However, its roles in uveal melanoma (UM) remain unknown. Here, we describe the biological roles and regulatory mechanisms of RNA m5C in UM. Initially, we identified significantly elevated global RNA m5C levels in both UM cells and tissue specimens using ELISA assay and dot blot analysis. Meanwhile, NOP2/Sun RNA methyltransferase family member 2 (NSUN2) was upregulated in both types of these samples, whereas NSUN2 knockdown significantly decreased RNA m5C level. Such declines inhibited UM cell migration and suppressed cell proliferation through cell cycle G1 arrest. Furthermore, bioinformatic analyses, m5C-RIP-qPCR, and luciferase assay identified β-Catenin (CTNNB1) as a direct target of NSUN2-mediated m5C modification in UM cells. Additionally, overexpression of miR-124a in UM cells diminished NSUN2 expression levels indicating that it is an upstream regulator of this response. Our study suggests that NSUN2-mediated RNA m5C methylation provides a potential novel target to improve the therapeutic management of UM pathogenesis.
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Affiliation(s)
- Guangying Luo
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang, China
| | - Weiwei Xu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang, China
| | - Xiaoyan Chen
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang, China
| | - Siqi Wang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang, China
| | - Jiao Wang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang, China
| | - Feng Dong
- The First Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dan-Ning Hu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang, China.,Tissue Culture Center, The New York Eye and Ear Infirmary, New York Medical College, Valhalla, New York, USA
| | - Peter S Reinach
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang, China
| | - Dongsheng Yan
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, Zhejiang, China
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13
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Alagia A, Gullerova M. The Methylation Game: Epigenetic and Epitranscriptomic Dynamics of 5-Methylcytosine. Front Cell Dev Biol 2022; 10:915685. [PMID: 35721489 PMCID: PMC9204050 DOI: 10.3389/fcell.2022.915685] [Citation(s) in RCA: 8] [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: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA and RNA methylation dynamics have been linked to a variety of cellular processes such as development, differentiation, and the maintenance of genome integrity. The correct deposition and removal of methylated cytosine and its oxidized analogues is pivotal for cellular homeostasis, rapid responses to exogenous stimuli, and regulated gene expression. Uncoordinated expression of DNA/RNA methyltransferases and demethylase enzymes has been linked to genome instability and consequently to cancer progression. Furthermore, accumulating evidence indicates that post-transcriptional DNA/RNA modifications are important features in DNA/RNA function, regulating the timely recruitment of modification-specific reader proteins. Understanding the biological processes that lead to tumorigenesis or somatic reprogramming has attracted a lot of attention from the scientific community. This work has revealed extensive crosstalk between epigenetic and epitranscriptomic pathways, adding a new layer of complexity to our understanding of cellular programming and responses to environmental cues. One of the key modifications, m5C, has been identified as a contributor to regulation of the DNA damage response (DDR). However, the various mechanisms of dynamic m5C deposition and removal, and the role m5C plays within the cell, remains to be fully understood.
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Affiliation(s)
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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14
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Guimarães‐Teixeira C, Lobo J, Miranda‐Gonçalves V, Barros‐Silva D, Martins‐Lima C, Monteiro‐Reis S, Sequeira JP, Carneiro I, Correia MP, Henrique R, Jerónimo C. Downregulation of m 6 A writer complex member METTL14 in bladder urothelial carcinoma suppresses tumor aggressiveness. Mol Oncol 2022; 16:1841-1856. [PMID: 35048498 PMCID: PMC9067151 DOI: 10.1002/1878-0261.13181] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/06/2021] [Accepted: 01/17/2022] [Indexed: 11/08/2022] Open
Abstract
N6-methyladenosine (m6 A) and its regulatory proteins have been associated with tumorigenesis in several cancer types. However, knowledge on the mechanistic network related to m6 A in bladder cancer (BlCa) is rather limited, requiring further investigation of its functional role. We aimed to uncover the biological role of m6 A and related proteins in BlCa and understand how this influences tumor aggressiveness. N6-adenosine-methyltransferase catalytic subunit (METTL3), N6-adenosine-methyltransferase noncatalytic subunit (METTL14), protein virilizer homolog (VIRMA), and RNA demethylase ALKBH5 (ALKBH5) had significantly lower expression levels in BlCa compared to that in normal urothelium. METTL14 knockdown led to disruption of the remaining methyltransferase complex and a decrease in m6 A abundance, as well as overall reduced tumor aggressiveness (decreased cell invasion and migration capacity and increased apoptosis). Furthermore, in vivo, METTL14 knockdown caused tumor size reduction. Collectively, we propose methyltransferase METTL14 as a key component for m6 A RNA deposit and that it is closely related to BlCa progression, playing an important role in tumor aggressiveness. These data contribute to a better understanding of the m6 A writer complex, which might constitute an appealing therapeutic target.
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Affiliation(s)
- Catarina Guimarães‐Teixeira
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
- PhD Programme in Pathology & Molecular GeneticsSchool of Medicine & Biomedical Sciences–University of Porto (ICBAS‐UP)Portugal
| | - João Lobo
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
- PhD Programme in Pathology & Molecular GeneticsSchool of Medicine & Biomedical Sciences–University of Porto (ICBAS‐UP)Portugal
- Department of PathologyPortuguese Oncology Institute of Porto (IPOP)Portugal
- Department of Pathology and Molecular ImmunologySchool of Medicine & Biomedical Sciences–University of Porto (ICBAS‐UP)Portugal
| | - Vera Miranda‐Gonçalves
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
- Department of Pathology and Molecular ImmunologySchool of Medicine & Biomedical Sciences–University of Porto (ICBAS‐UP)Portugal
| | - Daniela Barros‐Silva
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
- PhD Programme in Pathology & Molecular GeneticsSchool of Medicine & Biomedical Sciences–University of Porto (ICBAS‐UP)Portugal
| | - Cláudia Martins‐Lima
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
| | - Sara Monteiro‐Reis
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
| | - José Pedro Sequeira
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
| | - Isa Carneiro
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
- Department of PathologyPortuguese Oncology Institute of Porto (IPOP)Portugal
| | - Margareta P. Correia
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
- Department of Pathology and Molecular ImmunologySchool of Medicine & Biomedical Sciences–University of Porto (ICBAS‐UP)Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
- Department of PathologyPortuguese Oncology Institute of Porto (IPOP)Portugal
- Department of Pathology and Molecular ImmunologySchool of Medicine & Biomedical Sciences–University of Porto (ICBAS‐UP)Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics GroupResearch Center of IPO Porto (CI‐IPOP)/RISE@CI‐IPOP (Health Research Network)Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC)Portugal
- Department of Pathology and Molecular ImmunologySchool of Medicine & Biomedical Sciences–University of Porto (ICBAS‐UP)Portugal
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15
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Gray JS, Wani SA, Campbell MJ. Epigenomic alterations in cancer: mechanisms and therapeutic potential. Clin Sci (Lond) 2022; 136:473-492. [PMID: 35383835 DOI: 10.1042/cs20210449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022]
Abstract
The human cell requires ways to specify its transcriptome without altering the essential sequence of DNA; this is achieved through mechanisms which govern the epigenetic state of DNA and epitranscriptomic state of RNA. These alterations can be found as modified histone proteins, cytosine DNA methylation, non-coding RNAs, and mRNA modifications, such as N6-methyladenosine (m6A). The different aspects of epigenomic and epitranscriptomic modifications require protein complexes to write, read, and erase these chemical alterations. Reflecting these important roles, many of these reader/writer/eraser proteins are either frequently mutated or differentially expressed in cancer. The disruption of epigenetic regulation in the cell can both contribute to cancer initiation and progression, and increase the likelihood of developing resistance to chemotherapies. Development of therapeutics to target proteins involved in epigenomic/epitranscriptomic modifications has been intensive, but further refinement is necessary to achieve ideal treatment outcomes without too many off-target effects for cancer patients. Therefore, further integration of clinical outcomes combined with large-scale genomic analyses is imperative for furthering understanding of epigenomic mechanisms in cancer.
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Affiliation(s)
- Jaimie S Gray
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Sajad A Wani
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Moray J Campbell
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
- Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43210, U.S.A
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16
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Cui J, Zhu Y, Liu X, Wang W, Jiang X, Xia Y, Zhou G, Chen S, Shi B. Comprehensive analysis of N 6-methyladenosine regulators with the tumor immune landscape and correlation between the insulin-like growth factor 2 mRNA-binding protein 3 and programmed death ligand 1 in bladder cancer. Cancer Cell Int 2022; 22:72. [PMID: 35148766 PMCID: PMC8840771 DOI: 10.1186/s12935-022-02456-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 01/04/2022] [Indexed: 12/17/2022] Open
Abstract
Background N6-methyladenosine (m6A) is one of the most abundant post-transcriptional modifications of RNA. However, there is limited information about the potential roles of m6A regulators in tumor immunity. Therefore, in this study, we aimed to testify the functions of m6A regulators in bladder cancer as well as their association with the tumor immune landscape. Methods We reported the variation and expression levels of m6A regulators in the TCGA database and GTEx database of bladder cancer. Clusters, risk score patterns, and nomograms were constructed to evaluate the function and prognostic value of m6A regulators. Furthermore, we constructed nomogram to evaluate the prognosis of the individual patients. The correlation between insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and programmed cell death ligand 1 (PD-L1) was evaluated both in vitro and in vivo. Results We found that the tumor grade and DNA damage pathways were strongly correlated with distinct clusters. Furthermore, two risk score groups with six m6A regulators were identified using the least absolute shrinkage and selection operator (LASSO) and multivariable Cox regression analysis, which could be regarded as independent prognostic markers in patients with bladder cancer. The risk score pattern was linked to the tumor immune landscape, indicating a correlation between immune checkpoints and m6A regulators. Moreover, an m6A regulator, IGF2BP3, was found to be highly expressed in the tumor samples, regulating both the total and membrane-bound PD-L1 expression levels. Conclusions The results of this study revealed that the m6A clusters and patterns play crucial roles in the regulation of tumor immunity, which may be used to develop comprehensive treatment strategies for the management of bladder cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02456-7.
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Affiliation(s)
- Jianfeng Cui
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Jinan, 250012, Shandong, China
| | - Yaofeng Zhu
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Jinan, 250012, Shandong, China
| | - Xiaochen Liu
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan, 250012, Shandong, China
| | - Wenfu Wang
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Jinan, 250012, Shandong, China
| | - Xuewen Jiang
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Jinan, 250012, Shandong, China
| | - Yangyang Xia
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Jinan, 250012, Shandong, China
| | - Guanwen Zhou
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Jinan, 250012, Shandong, China
| | - Shouzhen Chen
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China. .,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Jinan, 250012, Shandong, China.
| | - Benkang Shi
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China. .,Key Laboratory of Urinary Precision Diagnosis and Treatment in Universities of Shandong, Jinan, 250012, Shandong, China.
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17
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He W, Lin G, Pan C, Li W, Shen J, Liu Y, Li H, Wu D, Lin X. The Identification of Two RNA Modification Patterns and Tumor Microenvironment Infiltration Characterization of Lung Adenocarcinoma. Front Genet 2022; 13:761681. [PMID: 35154267 PMCID: PMC8831702 DOI: 10.3389/fgene.2022.761681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background: RNA modification plays an important role in many diseases. A comprehensive study of tumor microenvironment (TME) characteristics mediated by RNA modification regulators will improve the understanding of TME immune regulation. Methods: We selected 26 RNA modification “writers” of lung adenocarcinoma (LUAD) samples and performed unsupervised clustering analysis to explore RNA modification patterns in LUAD. Differentially expressed genes (DEGs) with RNA modification patterns were screened to develop a “writers” of RNA modification score (WM score) system. The infiltration ratio of TME cell subsets was analyzed by CIBERSORT. Results: We identified two RNA modification modes showing different characteristics of overall survival (OS) and TME cell infiltration. According to WM score, LUAD patients were divided into a high-WM score group and a low-WM score group. High-scored patients had a poor prognosis and higher tumor mutation burden (TMB), they were more sensitive to four LUAD therapies (erlotinib, XA V939, gefitinib, and KU-55933) and more clinically responsive to PD-L1 treatment. Those with a low WM score showed higher stromal scores, ESTIMATE scores, and survival chance. Conclusion: Our work revealed the potential role of RNA modification patterns in TME, genetic variation, targeted inhibitor therapy, and immunotherapy. Identifying RNA modification pattern of LUAD patients help understand the characteristics of TME and may promote the development of immunotherapy strategies.
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Affiliation(s)
- Wan He
- Department of Oncology, Shenzhen People’s Hospital, Shenzhen, China
- *Correspondence: Xuejia Lin, ; Wan He,
| | - Gengpeng Lin
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - Chaohu Pan
- Zhuhai Institute of Translational Medicine, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Jinan University, Zhuhai, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, China
- YuceBio Technology Co., Ltd., Shenzhen, China
| | - Wenwen Li
- Department of Oncology, Shenzhen People’s Hospital, Shenzhen, China
| | - Jing Shen
- Department of Oncology, Shenzhen People’s Hospital, Shenzhen, China
| | - Yangli Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - Hui Li
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dongfang Wu
- YuceBio Technology Co., Ltd., Shenzhen, China
| | - Xuejia Lin
- Zhuhai Institute of Translational Medicine, Zhuhai People’s Hospital (Zhuhai Hospital Affiliated With Jinan University), Jinan University, Zhuhai, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, China
- *Correspondence: Xuejia Lin, ; Wan He,
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18
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Ye S, Liu Q, Huang K, Jiang X, Zhang X. The comprehensive analysis based study of perfluorinated compounds-Environmental explanation of bladder cancer progression. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 229:113059. [PMID: 34894427 DOI: 10.1016/j.ecoenv.2021.113059] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 05/15/2023]
Abstract
Perfluorinated compounds are emerging organic pollutants widely used in building materials, textiles, and electric equipment. Herein, silico analysis was conducted using bioinformatics approach to assess the potential relationship between bladder cancer and perfluorinated compounds. Transcriptome profiles and data of perfluorinated compounds were obtained from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression and Comparative Toxicogenomics databases. Gene Ontology (GO9 and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that interactive genes were mainly enriched in bladder cancer (BC). Transcriptome profiles were used to verify the expression of m6A-related genes at the mRNA and protein levels. Most m6A-related genes predicted BC prognosis. Survival analysis and ROC curves demonstrated that the expression levels of m6A-related genes were associated with BC prognosis. Perfluorooctanoic acid (PFOA) significantly increased the cell proliferation ability and promoted cell invasion capacity. In addition, PFOA significantly increased the cell viability and cell invasion capacity of T24 and BIU-87 cell lines compared with the control group. Taken together, these results show that perfluorinated compounds could promote BC progression. DATA AVAILABILITY: Data and materials are available within the manuscript.
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Affiliation(s)
- Shaopei Ye
- Department of Urology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Qin Liu
- Department of Gastroenterology, Zhongshan Hospital Affiliated to Xiamen University, Fujian 361000, China
| | - Ke Huang
- Peoples Hosp Deyang City, Dept Clin Lab, Deyang, China
| | - Xinlu Jiang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 30001, China
| | - Xu Zhang
- Nanjing Medical University, Nanjing 210029, China.
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19
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Wang Y, Zhao X, Li J, Wang X, Hu W, Zhang X. Four m6A RNA Methylation Gene Signatures and Their Prognostic Values in Lung Adenocarcinoma. Technol Cancer Res Treat 2022; 21:15330338221085373. [PMID: 35343834 PMCID: PMC8966122 DOI: 10.1177/15330338221085373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Introduction: Evidence demonstrates that N6-methyladenosine (m6A) modification plays an increasingly important role in the development of tumors. The aim of this study is to explore the expression of m6A-related regulators in lung adenocarcinoma, identify the effect of altered key factors modified by m6A on the prognosis of patients with lung adenocarcinoma. Methods: A comprehensive analysis of m6A-related gene expressions in patients with lung adenocarcinoma based on The Cancer Genome Atlas database (TCGA) and the CBioPortal database. A prognostic risk score was established based on a linear combination of 4 key gene expression levels using the regression coefficients of the multivariate Cox regression models. Immunohistochemical staining analysis was performed to validate the relationship between the protein expression level of m6A regulators and the prognosis of patients retrospectively. The possible mechanism and prospective therapeutic targets of these key m6A molecules were explored by the M6A2Target database and the CMAP database. Results: Mutation pattern analysis revealed that 32% of 656 patients had genetic alterations. Four genes (writer: methyltransferase like 3 [METTL3] and three readers: insulin like growth factor 2 mRNA binding protein 2 [IGF2BP2], heterogeneous nuclear ribonucleoprotein C [HNRNPC], and heterogeneous nuclear ribonucleoprotein A2/B1 [HNRNPA2B1]) were selected to construct a survival risk prediction model and the results of immunohistochemical staining showed that the expression of these four m6A genes was significantly different between lung adenocarcinoma tissues and normal lung tissues (p < .01). The possible downstream genes and prospective therapeutic targets of these four m6A key molecules were discovered. Conclusion: These four m6A RNA methylation regulators may be effective prognostic and diagnostic factors which can provide auxiliary diagnosis and prognosis of lung adenocarcinoma.
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Affiliation(s)
- Yuzhu Wang
- Department of Radiation Oncology, The First Affiliated Hospital of 12480Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xu Zhao
- Department of Radiation Oncology, The First Affiliated Hospital of 12480Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jing Li
- Department of Radiation Oncology, The First Affiliated Hospital of 12480Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xuan Wang
- Department of Radiation Oncology, The First Affiliated Hospital of 12480Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - WeiBin Hu
- Department of Radiation Oncology, The First Affiliated Hospital of 12480Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaozhi Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of 12480Xi'an Jiaotong University, Xi'an, Shaanxi, China
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20
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Somasekharan SP, Saxena N, Zhang F, Beraldi E, Huang J, Gentle C, Fazli L, Thi M, Sorensen P, Gleave M. Regulation of AR mRNA translation in response to acute AR pathway inhibition. Nucleic Acids Res 2021; 50:1069-1091. [PMID: 34939643 PMCID: PMC8789049 DOI: 10.1093/nar/gkab1247] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
We report a new mechanism of androgen receptor (AR) mRNA regulation and cytoprotection in response to AR pathway inhibition (ARPI) stress in prostate cancer (PCA). AR mRNA translation is coordinately regulated by RNA binding proteins, YTHDF3 and G3BP1. Under ambient conditions m6A-modified AR mRNA is bound by YTHDF3 and translationally stimulated, while m6A-unmodified AR mRNA is bound by G3BP1 and translationally repressed. When AR-regulated PCA cell lines are subjected to ARPI stress, m6A-modified AR mRNA is recruited from actively translating polysomes (PSs) to RNA-protein stress granules (SGs), leading to reduced AR mRNA translation. After ARPI stress, m6A-modified AR mRNA liquid–liquid phase separated with YTHDF3, while m6A-unmodified AR mRNA phase separated with G3BP1. Accordingly, these AR mRNA messages form two distinct YTHDF3-enriched or G3BP1-enriched clusters in SGs. ARPI-induced SG formation is cell-protective, which when blocked by YTHDF3 or G3BP1 silencing increases PCA cell death in response to ARPI stress. Interestingly, AR mRNA silencing also delays ARPI stress-induced SG formation, highlighting its supportive role in triggering this stress response. Our results define a new mechanism for stress adaptive cell survival after ARPI stress involving SG-regulated translation of AR mRNA, mediated by m6A RNA modification and their respective regulatory proteins.
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Affiliation(s)
- Syam Prakash Somasekharan
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Neetu Saxena
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Fan Zhang
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Eliana Beraldi
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Jia Ni Huang
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Christina Gentle
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Ladan Fazli
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Marisa Thi
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
| | - Poul H Sorensen
- British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, British Columbia, Canada and Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Department of Urologic Sciences, University of British Columbia, Vancouver Prostate Centre, Vancouver, Canada
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21
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Comprehensive Analysis of m 5C RNA Methylation Regulator Genes in Clear Cell Renal Cell Carcinoma. Int J Genomics 2021; 2021:3803724. [PMID: 34631874 PMCID: PMC8497170 DOI: 10.1155/2021/3803724] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Background Recent research found that N5-methylcytosine (m5C) was involved in the development and occurrence of numerous cancers. However, the function and mechanism of m5C RNA methylation regulators in clear cell renal cell carcinoma (ccRCC) remains undiscovered. This study is aimed at investigating the predictive and clinical value of these m5C-related genes in ccRCC. Methods Based on The Cancer Genome Atlas (TCGA) database, the expression patterns of twelve m5C regulators and matched clinicopathological characteristics were downloaded and analyzed. To reveal the relationships between the expression levels of m5C-related genes and the prognosis value in ccRCC, consensus clustering analysis was carried out. By univariate Cox analysis and last absolute shrinkage and selection operator (LASSO) Cox regression algorithm, a m5C-related risk signature was constructed in the training group and further validated in the testing group and the entire cohort. Then, the predictive ability of survival of this m5C-related risk signature was analyzed by Cox regression analysis and nomogram. Functional annotation and single-sample Gene Set Enrichment Analysis (ssGSEA) were applied to further explore the biological function and potential signaling pathways. Furthermore, we performed qRT-PCR experiments and measured global m5C RNA methylation level to validate this signature in vitro and tissue samples. Results In the TCGA-KIRC cohort, we found significant differences in the expression of m5C RNA methylation-related genes between ccRCC tissues and normal kidney tissues. Consensus cluster analysis was conducted to separate patients into two m5C RNA methylation subtypes. Significantly better outcomes were observed in ccRCC patients in cluster 1 than in cluster 2. m5C RNA methylation-related risk score was calculated to evaluate the prognosis of ccRCC patients by seven screened m5C RNA methylation regulators (NOP2, NSUN2, NSUN3, NSUN4, NSUN5, TET2, and DNMT3B) in the training cohort. The AUC for the 1-, 2-, and 3-year survival in the training cohort were 0.792, 0.675, and 0.709, respectively, indicating that the risk signature had an excellent prognosis prediction in ccRCC. Additionally, univariate and multivariate Cox regression analyses revealed that the risk signature could be an independent prognostic factor in ccRCC. The results of ssGSEA suggested that the immune cells with different infiltration degrees between the high-risk and low-risk groups were T cells including follicular helper T cells, Th1_cells, Th2_cells, and CD8+_T_cells, and the main differences in immune-related functions between the two groups were the interferon response and T cell costimulation. In addition, qRT-PCR experiments confirmed our results in renal cell lines and tissue samples. Conclusions According to the seven selected regulatory factors of m5C RNA methylation, a risk signature associated with m5C methylation that can independently predict prognosis in patients with ccRCC was developed and further verified the predictive efficiency.
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22
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Zhu H, Jia X, Wang Y, Song Z, Wang N, Yang Y, Shi X. M6A Classification Combined With Tumor Microenvironment Immune Characteristics Analysis of Bladder Cancer. Front Oncol 2021; 11:714267. [PMID: 34604051 PMCID: PMC8479184 DOI: 10.3389/fonc.2021.714267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/25/2021] [Indexed: 01/12/2023] Open
Abstract
Background Studies have shown that N6-methyl adenosine (m6A) plays an important role in cancer progression; however, the underlying mechanism of m6A modification in tumor microenvironment (TME) cell infiltration of bladder cancer remains unclear. This study aimed to investigate the role of m6A modification in TME cell infiltration of bladder cancer. Methods The RNA expression profile and clinical data of bladder cancer were obtained from The Cancer Genome Atlas and Gene Expression Omnibus. We assessed the m6A modification patterns of 664 bladder cancer samples based on 20 m6A regulators through unsupervised clustering analysis and systematically linked m6A modification patterns to TME cell infiltration characteristics. Gene ontology and gene set variation analyses were conducted to analyze the underlying mechanism based on the assessment of m6A methylation regulators. Principal component analysis was used to construct the m6A score to quantify m6A modification patterns of bladder cancer. Results The genetic and expression alterations in m6A regulators were highly heterogeneous between normal and bladder tissues. Three m6A modification patterns were identified. The cell infiltration characteristics were highly consistent with the three immune phenotypes, including immune rejection, immune inflammation, and immune desert. The biological functions of three m6A modification patterns were different. Cox regression analyses revealed that the m6A score was an independent signature with patient prognosis (HR = 1.198, 95% CI: 1.031-1.390). Patients with a low-m6A score were characterized by increased tumor mutation burden, PD-L1 expression, and poorer survival. Patients in the low-m6A score group also showed significant immune responses and clinical benefits in the CTLA-4 immunotherapy cohort (p =0.0069). Conclusions The m6A methylation modification was related to the formation of TME heterogeneity and complexity. Assessing the m6A modification pattern of individual bladder cancer will improve the understanding of TME infiltration characteristics.
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Affiliation(s)
- Huili Zhu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaocan Jia
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yuping Wang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zhijuan Song
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Nana Wang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Yongli Yang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xuezhong Shi
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, China
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23
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Deregulation of N6-Methyladenosine RNA Modification and Its Erasers FTO/ALKBH5 among the Main Renal Cell Tumor Subtypes. J Pers Med 2021; 11:jpm11100996. [PMID: 34683137 PMCID: PMC8538585 DOI: 10.3390/jpm11100996] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/25/2021] [Accepted: 09/29/2021] [Indexed: 11/24/2022] Open
Abstract
(1) Background: Methylation of N6-adenosine (m6A) is the most abundant messenger RNA (mRNA) modification in eukaryotes. We assessed the expression profiles of m6A regulatory proteins in renal cell carcinoma (RCC) and their clinical relevance, namely, as potential biomarkers. (2) Methods: In silico analysis of The Cancer Genome Atlas (TCGA) dataset was use for evaluating the expression of the m6A regulatory proteins among RCC subtypes and select the most promising candidates for further validation. ALKBH5 and FTO transcript and protein expression were evaluated in a series of primary RCC (n = 120) and 40 oncocytomas selected at IPO Porto. (3) Results: In silico analysis of TCGA dataset disclosed altered expression of the major m6A demethylases among RCC subtypes, particularly FTO and ALKBH5. Furthermore, decreased FTO mRNA levels associated with poor prognosis in ccRCC and pRCC. In IPO Porto’s cohort, FTO and ALKBH5 transcript levels discriminated ccRCC from oncocytomas. Furthermore, FTO and ALKBH5 immunoexpression differed among RCC subtypes, with higher expression levels found in ccRCC comparatively to the other RCC subtypes and oncocytomas. (4) Conclusion: We conclude that altered expression of m6A RNA demethylases is common in RCC and seems to be subtype specific. Specifically, FTO and ALKBH5 might constitute new candidate biomarkers for RCC patient management, aiding in differential diagnosis of renal masses and prognostication.
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Liu C, Yang S, Zhang Y, Wang C, Du D, Wang X, Liu T, Liang G. Emerging Roles of N6-Methyladenosine Demethylases and Its Interaction with Environmental Toxicants in Digestive System Cancers. Cancer Manag Res 2021; 13:7101-7114. [PMID: 34526822 PMCID: PMC8437382 DOI: 10.2147/cmar.s328188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/19/2021] [Indexed: 01/02/2023] Open
Abstract
Digestive system cancers are common cancers with high cancer deaths worldwide. They have become a major threat to public health and economic burden. As one of the most universal RNA modifications in eukaryotes, the N6-methyladenosine (m6A) modification is involved in the occurrence, development, prognosis, and treatment response of various cancers, including digestive system cancers. M6A demethylases shape the m6A landscape dynamically, playing important roles in cancers. In addition, accumulating evidence reveal that many environmental toxicants are the established risk factors for digestive system cancers and associated with m6A modification. In this review, we summarize the multiple functions of M6A demethylases (fat mass and obesity-associated protein (FTO), AlkB homolog 5 (ALKBH5) and AlkB homolog 3 (ALKBH3)) in digestive system cancers, which are aberrantly expressed and affect cancer progression. We also discuss the potential roles of m6A demethylases in the assessment of environmental exposure, the signature for prevention and diagnosis of digestive system cancers.
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Affiliation(s)
- Caiping Liu
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Sheng Yang
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Yanqiu Zhang
- Department of Environmental Occupational Health, Taizhou Center for Disease Control and Prevention, Taizhou, 225300, Jiangsu, People's Republic of China
| | - Chuntao Wang
- Jiangsu Vocational College of Medicine, Yancheng, 224000, Jiangsu, People's Republic of China
| | - Dandan Du
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Xian Wang
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Tong Liu
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
| | - Geyu Liang
- School of Public Health, Key Laboratory of Environmental Medicine Engineering, Ministry of Education, Southeast University, Nanjing, 210009, Jiangsu, People's Republic of China
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25
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Wu XR, Chen Z, Liu Y, Chen ZZ, Tang F, Chen ZZ, Li JJ, Liao JL, Cao K, Chen X, Zhou J. Prognostic signature and immune efficacy of m 1 A-, m 5 C- and m 6 A-related regulators in cutaneous melanoma. J Cell Mol Med 2021; 25:8405-8418. [PMID: 34288419 PMCID: PMC8419166 DOI: 10.1111/jcmm.16800] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/18/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
Cutaneous melanoma (CM) is an aggressive cancer; given that initial and specific signs are lacking, diagnosis is often late and the prognosis is poor. RNA modification has been widely studied in tumour progression. Nevertheless, little progress has been made in the signature of N1 -methyladenosine (m1 A), 5-methylcytosine (m5 C), N6 -methyladenosine (m6 A)-related regulators and the tumour microenvironment (TME) cell infiltration in CM. Our study identified the characteristics of m1 A-, m5 C- and m6 A-related regulators based on 468 CM samples from the public database. Using univariate, multivariate and LASSO Cox regression analysis, a risk model of regulators was established and validated by a nomogram on independent prognostic factors. The gene set variation analysis (GSVA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) clarified the involved functional pathways. A combined single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT approach revealed TME of regulator-related prognostic signature. The nine-gene signature stratified the patients into distinct risk subgroups for personalized prognostic assessment. Additionally, functional enrichment, immune infiltration and immunotherapy response analysis indicated that the high-risk group was correlated with T-cell suppression, while the low-risk group was more sensitive to immunotherapy. The findings presented here contribute to our understanding of the TME molecular heterogeneity in CM. Nine m1 A-, m5 C- and m6 A-related regulators may also be promising biomarkers for future research.
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Affiliation(s)
- Xian rui Wu
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zheng Chen
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yang Liu
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zi zi Chen
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Fengjie Tang
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zhi zhao Chen
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Jing jing Li
- Department of Plastic Surgery of Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Jun lin Liao
- Departments of Medical CosmetologyThe First Affiliated HospitalUniversity of South ChinaHengyangHunanChina
| | - Ke Cao
- Department of Oncology of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xiang Chen
- Department of DermatologyThe Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Jianda Zhou
- Department of Plastic Surgery of Third Xiangya HospitalCentral South UniversityChangshaHunanChina
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26
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Miranda-Gonçalves V, Lobo J, Guimarães-Teixeira C, Barros-Silva D, Guimarães R, Cantante M, Braga I, Maurício J, Oing C, Honecker F, Nettersheim D, Looijenga LHJ, Henrique R, Jerónimo C. The component of the m 6A writer complex VIRMA is implicated in aggressive tumor phenotype, DNA damage response and cisplatin resistance in germ cell tumors. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:268. [PMID: 34446080 PMCID: PMC8390281 DOI: 10.1186/s13046-021-02072-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022]
Abstract
Background Germ cell tumors (GCTs) are developmental cancers, tightly linked to embryogenesis and germ cell development. The recent and expanding field of RNA modifications is being increasingly implicated in such molecular events, as well as in tumor progression and resistance to therapy, but still rarely explored in GCTs. In this work, and as a follow-up of our recent study on this topic in TGCT tissue samples, we aim to investigate the role of N6-methyladenosine (m6A), the most abundant of such modifications in mRNA, in in vitro and in vivo models representative of such tumors. Methods Four cell lines representative of GCTs (three testicular and one mediastinal), including an isogenic cisplatin resistant subline, were used. CRISPR/Cas9-mediated knockdown of VIRMA was established and the chorioallantoic membrane assay was used to study its phenotypic effect in vivo. Results We demonstrated the differential expression of the various m6A writers, readers and erasers in GCT cell lines representative of the major classes of these tumors, seminomas and non-seminomas, and we evidenced changes occurring upon differentiation with all-trans retinoic acid treatment. We showed differential expression also among cells sensitive and resistant to cisplatin treatment, implicating these players in acquisition of cisplatin resistant phenotype. Knockdown of VIRMA led to disruption of the remaining methyltransferase complex and decrease in m6A abundance, as well as overall reduced tumor aggressiveness (with decreased cell viability, tumor cell proliferation, migration, and invasion) and increased sensitivity to cisplatin treatment, both in vitro and confirmed in vivo. Enhanced response to cisplatin after VIRMA knockdown was related to significant increase in DNA damage (with higher γH2AX and GADD45B levels) and downregulation of XLF and MRE11. Conclusions VIRMA has an oncogenic role in GCTs confirming our previous tissue-based study and is further involved in response to cisplatin by interfering with DNA repair. These data contribute to our better understanding of the emergence of cisplatin resistance in GCTs and support recent attempts to therapeutically target elements of the m6A writer complex. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02072-9.
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Affiliation(s)
- Vera Miranda-Gonçalves
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584, CS, Utrecht, The Netherlands
| | - Catarina Guimarães-Teixeira
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rita Guimarães
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Mariana Cantante
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Isaac Braga
- Department of Urology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Joaquina Maurício
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Christoph Oing
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, Mildred Scheel Cancer Career Center HaTriCs4, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Friedemann Honecker
- Tumour and Breast Center ZeTuP St. Gallen, Rorschacher Strasse 150, 9006, St. Gallen, Switzerland
| | - Daniel Nettersheim
- Department of Urology, Urological Research Lab, Translational UroOncology, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Leendert H J Looijenga
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584, CS, Utrecht, The Netherlands
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal. .,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal.
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27
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Tao Z, Zhang E, Li L, Zheng J, Zhao Y, Chen X. A united risk model of 11 immune‑related gene pairs and clinical stage for prediction of overall survival in clear cell renal cell carcinoma patients. Bioengineered 2021; 12:4259-4277. [PMID: 34304692 PMCID: PMC8806637 DOI: 10.1080/21655979.2021.1955558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cancer. Currently, we lack effective risk models for the prognosis of ccRCC patients. Given the significant role of cancer immunity in ccRCC, we aimed to establish a novel united risk model including clinical stage and immune-related gene pairs (IRGPs) to assess the prognosis. The gene expression profile and clinical data of ccRCC patients from The Cancer Genome Atlas and Arrayexpress were divided into training cohort (n = 381), validation cohort 1 (n = 156), and validation cohort 2 (n = 101). Through univariate Cox regression analysis and Least Absolute Shrinkage and Selection Operator analysis, 11 IRGPs were obtained. After further analysis, it was found that clinical stage could be an independent prognostic factor; hence, we used it to construct a united prognostic model with 11 IRGPs. Based on this model, patients were divided into high-risk and low-risk groups. In Kaplan–Meier analysis, a significant difference was observed in overall survival (OS) among all three cohorts (p < 0.001). The calibration curve revealed that the signature model is in high accordance with the observed values of each data cohort. The 1-year, 3-year, and 5-year receiver operating characteristic curves of each data cohort showed better performance than only IRGP signatures. The results of immune infiltration analysis revealed significantly (p < 0.05) higher abundance of macrophages M0, T follicular helper cells, and other tumor infiltrating cells. In summary, we successfully established a united prognostic risk model, which can effectively assess the OS of ccRCC patients.
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Affiliation(s)
- Zijia Tao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Enchong Zhang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Lei Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Yiqiao Zhao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
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Hu J, Qiu D, Yu A, Hu J, Deng H, Li H, Yi Z, Chen J, Zu X. YTHDF1 Is a Potential Pan-Cancer Biomarker for Prognosis and Immunotherapy. Front Oncol 2021; 11:607224. [PMID: 34026603 PMCID: PMC8134747 DOI: 10.3389/fonc.2021.607224] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Background YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) has been indicated proven to participate in the cross-presentation of tumor antigens in dendritic cells and the cross-priming of CD8+ T cells. However, the role of YTHDF1 in prognosis and immunology in human cancers remains largely unknown. Methods All original data were downloaded from TCGA and GEO databases and integrated via R 3.2.2. YTHDF1 expression was explored with the Oncomine, TIMER, GEPIA, and BioGPS databases. The effect of YTHDF1 on prognosis was analyzed via GEPIA, Kaplan-Meier plotter, and the PrognoScan database. The TISIDB database was used to determine YTHDF1 expression in different immune and molecular subtypes of human cancers. The correlations between YTHDF1 expression and immune checkpoints (ICP), tumor mutational burden (TMB), microsatellite instability (MSI), and neoantigens in human cancers were analyzed via the SangerBox database. The relationships between YTHDF1 expression and tumor-infiltrated immune cells were analyzed via the TIMER and GEPIA databases. The relationships between YTHDF1 and marker genes of tumor-infiltrated immune cells in urogenital cancers were analyzed for confirmation. The genomic alterations of YTHDF1 were investigated with the c-BioPortal database. The differential expression of YTHDF1 in urogenital cancers with different clinical characteristics was analyzed with the UALCAN database. YTHDF1 coexpression networks were studied by the LinkedOmics database. Results In general, YTHDF1 expression was higher in tumors than in paired normal tissue in human cancers. YTHDF1 expression had strong relationships with prognosis, ICP, TMB, MSI, and neoantigens. YTHDF1 plays an essential role in the tumor microenvironment (TME) and participates in immune regulation. Furthermore, significant strong correlations between YTHDF1 expression and tumor immune-infiltrated cells (TILs) existed in human cancers, and marker genes of TILs were significantly related to YTHDF expression in urogenital cancers. TYHDF1 coexpression networks mostly participated in the regulation of immune response and antigen processing and presentation. Conclusion YTHDF1 may serve as a potential prognostic and immunological pan-cancer biomarker. Moreover, YTHDF1 could be a novel target for tumor immunotherapy.
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Affiliation(s)
- Jian Hu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Dongxu Qiu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Anze Yu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Jiao Hu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Huihuang Li
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenglin Yi
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
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Gundert L, Strick A, Hagen F, Schmidt D, Klümper N, Tolkach Y, Toma M, Kristiansen G, Ritter M, Ellinger J. Systematic expression analysis of m
6
A RNA methyltransferases in clear cell renal cell carcinoma. BJUI COMPASS 2021; 2:402-411. [PMID: 35474700 PMCID: PMC8988738 DOI: 10.1002/bco2.89] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 01/17/2023] Open
Abstract
Objectives To investigate the regulation of the N‐6‐methyladenosine (m6A) methyltransferases METTL3, METTL14, WTAP, KIAA1429, and METTL4, referred to as “m6A writers,” in clear cell renal cell carcinoma (ccRCC), and other RCC subtypes in respect of the potential prognostic value. Patients and methods Tissue samples were collected within the framework of the Biobank at the Center for Integrated Oncology Bonn. The expression of the methyltransferases was systematically determined in clear cell renal carcinoma (ccRCC) on the RNA (real‐time PCR) and protein level (immunohistochemistry). Additionally, protein expression of the m6A writers was further investigated in papillary RCC, chromophobe RCC, sarcomatoid RCC, oncocytoma, and normal renal tissue (immunohistochemistry). Results The expression of all m6A‐methyltransferases was significantly downregulated in ccRCC compared to benign renal tissue. Low m6A‐methyltransferase levels were correlated with higher histological grade, advanced pT‐stage, pN‐stage, and metastatic disease. Reduced m6A‐methyltransferase expression was associated with shorter overall survival. Conclusion In conclusion, m6A‐methyltransferases are dysregulated in ccRCC and might act as tumor suppressor genes, which could be of particular importance for future diagnostic and therapeutic options.
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Affiliation(s)
| | | | - Felix Hagen
- Department of Urology University Hospital Bonn Bonn Germany
| | - Doris Schmidt
- Department of Urology University Hospital Bonn Bonn Germany
| | - Niklas Klümper
- Department of Urology University Hospital Bonn Bonn Germany
| | - Yuri Tolkach
- Department of Pathology University Hospital Bonn Bonn Germany
- Department of Pathology University Hospital Cologne Cologne Germany
| | - Marieta Toma
- Department of Pathology University Hospital Bonn Bonn Germany
| | | | - Manuel Ritter
- Department of Urology University Hospital Bonn Bonn Germany
| | - Jörg Ellinger
- Department of Urology University Hospital Bonn Bonn Germany
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The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
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Chen H, Xiang Y, Yin Y, Peng J, Peng D, Li D, Kitazawa R, Tang Y, Yang J. The m6A methyltransferase METTL3 regulates autophagy and sensitivity to cisplatin by targeting ATG5 in seminoma. Transl Androl Urol 2021; 10:1711-1722. [PMID: 33968659 PMCID: PMC8100844 DOI: 10.21037/tau-20-1411] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background Our previous work shows Autophagy enhanced resistance to cisplatin in seminoma. The expression of the N6-methyladenosine (m6A) methyltransferases METTL3 was significantly increased in the cisplatin-resistant TCam-2 cell line of seminoma. We aimed to investigate the role of m6A methylation in autophagy and the chemosensitivity of seminoma cells. Methods Plasmid and siRNA were used to overexpress and knockdown METTL3. Autophagy was detected by western blot and immunofluorescence, respectively. The expression of downstream targets of METTL3 was detected by quantitative real-time PCR (qRT-PCR) and western blot, and the m6A level of them was detected by MeRIP-qPCR. Chemosensitivity of the TCam-2 cell line was identified through MTT assay. Results Upon METTL3 overexpression, autophagy of TCam-2 cell line was enhanced and its sensitivity to cisplatin was decreased. The use of autophagy inhibitors 3-methyladenine (3-MA) could reverse the protective effect of METTL3 on TCam-2 cells. We found that the up-regulation of METTL3 could increase the m6A modification level of ATG5 transcript, thus increased expression of ATG5. Moreover, knockdown of ATG5 reduced METTL3-induced autophagy, suggesting that ATG5 was a potential target for METTL3 to promote autophagy. Conclusions In summary, our research unveiled the unique mechanism by which m6A methylation regulates autophagy and chemosensitivity of the TCam-2 cell line and METTL3 was a potential target to overcome the cisplatin resistance of seminoma.
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Affiliation(s)
- Hanfei Chen
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yali Xiang
- Health Management Center, Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Yinghao Yin
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jingxuan Peng
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Dongyi Peng
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Dongjie Li
- Xiangya International Medical Center, Department of Geriatric Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Riko Kitazawa
- Department of Diagnostic Pathology, Ehime University Hospital, Toon, Japan
| | - Yuxin Tang
- Department of Urology, Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China.,Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Jianfu Yang
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha, China
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32
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Between a Rock and a Hard Place: An Epigenetic-Centric View of Testicular Germ Cell Tumors. Cancers (Basel) 2021; 13:cancers13071506. [PMID: 33805941 PMCID: PMC8036638 DOI: 10.3390/cancers13071506] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary This minireview focuses on the role of epigenetics in testicular cancer. A working model is developed that postulates that epigenetic features that drive testicular cancer malignancy also enable these tumors to be cured at a high rate with chemotherapy. Chemoresistance may occur by epigenetic uncoupling of malignancy and chemosensitivity, a scenario that may be amenable to epigenetic-based therapies. Abstract Compared to many common solid tumors, the main genetic drivers of most testicular germ cell tumors (TGCTs) are unknown. Decades of focus on genomic alterations in TGCTs including awareness of a near universal increase in copies of chromosome 12p have failed to uncover exceptional driver genes, especially in genes that can be targeted therapeutically. Thus far, TGCT patients have missed out on the benefits of targeted therapies available to treat most other malignancies. In the past decade there has been a greater appreciation that epigenetics may play an especially prominent role in TGCT etiology, progression, and hypersensitivity to conventional chemotherapy. While genetics undoubtedly plays a role in TGCT biology, this mini-review will focus on the epigenetic “states” or features of testicular cancer, with an emphasis on DNA methylation, histone modifications, and miRNAs associated with TGCT susceptibility, initiation, progression, and response to chemotherapy. In addition, we comment on the current status of epigenetic-based therapy and epigenetic biomarker development for TGCTs. Finally, we suggest a unifying “rock and a hard place” or “differentiate or die” model where the tumorigenicity and curability of TGCTs are both dependent on common but still ill-defined epigenetic states.
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33
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von Hagen F, Gundert L, Strick A, Klümper N, Schmidt D, Kristiansen G, Tolkach Y, Toma M, Ritter M, Ellinger J. N 6 -Methyladenosine (m 6 A) readers are dysregulated in renal cell carcinoma. Mol Carcinog 2021; 60:354-362. [PMID: 33755994 DOI: 10.1002/mc.23297] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 12/18/2022]
Abstract
N6 -Methyladenosine (m6 A) is the most common modification of messenger RNA (mRNA) in mammals. It critically influences RNA metabolism and plays an essential role in virtually all types of bioprocesses including gene expression, tissue development, self-renewal and differentiation of stem cells, stress response and circadian clock control. It plays a crucial role in carcinogenesis and could be used as a prognostic and a diagnostic tool and as a target for new anticancer therapies. m6 A modification is dynamically and reversibly regulated by three types of proteins. Methyltransferases, so-called "writers" add a methyl group to the adenosine, which can be removed by demethylases, also called "erasers." m6 A-specific RNA-binding proteins, from here on referred to as "readers," preferentially bind to the m6 A site and mediate biological functions, such as translation, splicing or decay of RNA. In this study, we examined the expression of the six m6 A readers HNRNPA2B1, HNRNPC, YTHDC1 and YTHDF1-3 in clear cell renal carcinoma (ccRCC). We show that on mRNA level the expression of all six m6 A readers is significantly downregulated compared to normal renal tissue and on protein level five out of six readers are dysregulated. Lower levels of some m6 A readers are correlated with advanced stage and grade as well as associated with a shorter overall, progression-free and cancer-specific survival. In summary, we could show that m6 A readers are dysregulated in ccRCC and might therefore act as a tumor marker, could give further information on the individual prognosis and be a target of innovative cancer therapy.
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Affiliation(s)
- Felix von Hagen
- Klinik und Poliklinik für Urologie und Kinderurologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Larissa Gundert
- Klinik und Poliklinik für Urologie und Kinderurologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Alexander Strick
- Klinik und Poliklinik für Urologie und Kinderurologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Niklas Klümper
- Klinik und Poliklinik für Urologie und Kinderurologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Doris Schmidt
- Klinik und Poliklinik für Urologie und Kinderurologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Glen Kristiansen
- Institut für Pathologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Yuri Tolkach
- Institut für Pathologie, Universitätsklinikum Bonn, Bonn, Germany.,Institut für Allgemeine Pathologie und Pathologische Anatomie, Universitätsklinikum Köln, Cologne, Germany
| | - Marieta Toma
- Institut für Pathologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Manuel Ritter
- Klinik und Poliklinik für Urologie und Kinderurologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Jörg Ellinger
- Klinik und Poliklinik für Urologie und Kinderurologie, Universitätsklinikum Bonn, Bonn, Germany
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34
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Zhu W, Wang JZ, Wei JF, Lu C. Role of m6A methyltransferase component VIRMA in multiple human cancers (Review). Cancer Cell Int 2021; 21:172. [PMID: 33731118 PMCID: PMC7968318 DOI: 10.1186/s12935-021-01868-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022] Open
Abstract
N6-Methyladenosine (m6A) modification is one of the most widely distributed RNA modifications in eukaryotes. It participates in various RNA functions and plays vital roles in tissue development, stem cell formation and differentiation, heat shock response control, and circadian clock controlling, particularly during tumor development. The reversible regulation of m6A modification is affected by the so-called ‘reader’, ‘writer’ and ‘eraser’. As a required component and the largest methyltransferase, vir-like m6A methyltransferase associated (VIRMA) can promote the progression of cancer and is associated with poor survival in multiple types of cancer. The present review investigated the role of VIRMA in various types of cancer. In an m6A-dependent or -independent manner, VIRMA can play an oncogenic role by regulating cancer cell proliferation, migration and invasion, metastasis, apoptosis resistance and tumor growth in different pathways by targeting stem factors, CCAT1/2, ID2, GATA3, CDK1, c-Jun, etc. VIRMA can also predict better prognosis in kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP) and papillary thyroid carcinoma by TCGA analysis. The obvious oncogenic roles of VIRMA observed in different types of cancer and the mechanisms of VIRMA promoting cancers provided the basis for potential therapeutic targeting for cancer treatments.
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Affiliation(s)
- Wei Zhu
- Precision Medicine Center, First Affiliated Hospital of Gannan Medical University, 128 Jinling Road, Ganzhou, 341000, China.,Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Jing-Zi Wang
- Department of Urology, Children's Hospital of Nanjing Medical University, 72 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Ji-Fu Wei
- Precision Medicine Center, First Affiliated Hospital of Gannan Medical University, 128 Jinling Road, Ganzhou, 341000, China. .,Research Division of Clinical Pharmacology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China.
| | - Chen Lu
- Precision Medicine Center, First Affiliated Hospital of Gannan Medical University, 128 Jinling Road, Ganzhou, 341000, China.
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35
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Fu Y, Sun S, Bi J, Kong C, Yin L. Expression patterns and prognostic value of m6A RNA methylation regulators in adrenocortical carcinoma. Medicine (Baltimore) 2021; 100:e25031. [PMID: 33725886 PMCID: PMC7969304 DOI: 10.1097/md.0000000000025031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 02/05/2021] [Indexed: 01/05/2023] Open
Abstract
Adrenocortical carcinoma (ACC) is considered a rare cancer with poor prognosis. We used public datasets from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases to assess the relationships between N6-methyladenosine (m6A)-related genes and ACC.We used the Wilcoxon signed-rank test to compare m6A-related gene expression in ACC tissues with that in normal tissues. Then, ACC patients were grouped based on a cluster analysis of m6A-related gene expression. m6A-related genes that were significantly associated with survival were incorporated into a risk signature, and 2 groups were divided according to median risk score. Fisher exact tests were utilized to analyze differences in clinical variables between groups. We compared the overall survival (OS) rates of the groups by means of Kaplan-Meier curves and Cox regression analyses.We found that RBM15, ZC3H3, YTDHF1, YTDHF2, and ALBH5 were overexpressed in ACC and that KIAA1429, YTHDC1, HNRNPC, WTAP, METTL3, and FTO were down regulated in ACC. In addition, membership in cluster 2 or the high-risk group was associated with advanced clinical factors and poor prognosis. The univariable and multivariable Cox regression analyses showed that risk score can be considered an independent prognostic factor for ACC.We found that the expression of m6A-related genes could be used as an independent prognostic factor in ACC. However, the current study has some limitations, and further studies of m6A-related genes in ACC are needed.
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Affiliation(s)
| | - Shanshan Sun
- Department of Pharmacy, The First Hospital of China Medical University, Shenyang, PR China
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36
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Liu K, Gao Y, Gan K, Wu Y, Xu B, Zhang L, Chen M. Prognostic Roles of N6-Methyladenosine METTL3 in Different Cancers: A System Review and Meta-Analysis. Cancer Control 2021; 28:1073274821997455. [PMID: 33631954 PMCID: PMC8482712 DOI: 10.1177/1073274821997455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Recent studies have shown that methyltransferase-like 3, a catalytic enzyme that is predominant in the N6-methyladenosine methyltransferase system, is abnormally expressed in various types of carcinoma and is correlated with poorer prognosis. However, the clinical functions of methyltransferase-like 3 in the prognosis of tumors are not fully understood. METHODS We identified studies by searching PubMed, Web of Science, and MedRvix for literature (up to June 30, 2020), and collected a total of 9 studies with 1257 patients for this meta-analysis. The cancer types included gastric cancer, breast cancer, non-small cell lung cancer, bladder cancer, colorectal cancer and ovarian. We further used The Cancer Genome Atlas dataset to validate the results. RESULTS High methyltransferase-like 3 expression clearly predicted a worse outcome (high vs. low methyltransferase-like 3 expression group; hazard ratio = 2.09, 95% confidence interval 1.53-2.89, P = 0.0001). Moreover, methyltransferase-like 3 expression was associated with differentiation (moderate + poor vs. well, pooled odds ratio = 1.76, 95% confidence interval 1.32-2.35, P = 0.0001), and gender (male vs. female, pooled odds ratio = 0.73, 95% confidence interval 0.55-0.97, P = 0.029). CONCLUSION Our results suggest that methyltransferase-like 3 upregulation is significantly associated with poor prognosis and could potentially function as a tumor biomarker in cancer prognosis.
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Affiliation(s)
- KuangZheng Liu
- Medical College of 12579Southeast University, Nanjing, Jiangsu, China
| | - Yue Gao
- Medical College of 12579Southeast University, Nanjing, Jiangsu, China
| | - Kai Gan
- Medical College of 12579Southeast University, Nanjing, Jiangsu, China
| | - YuQing Wu
- Medical College of 12579Southeast University, Nanjing, Jiangsu, China
| | - Bin Xu
- Department of Urology, 12579Southeast University Affiliated Zhongda Hospital, Nanjing, Jiangsu, China
| | - LiHua Zhang
- Department of Pathology, 12579Southeast University Affiliated Zhongda Hospital, Nanjing, Jiangsu, China
| | - Ming Chen
- Department of Urology, 12579Southeast University Affiliated Zhongda Hospital, Nanjing, Jiangsu, China
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Aberrant expression of m 6A mRNA methylation regulators in colorectal adenoma and adenocarcinoma. Life Sci 2021; 273:119258. [PMID: 33636176 DOI: 10.1016/j.lfs.2021.119258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/06/2021] [Accepted: 02/16/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND As the most prevalent post-transcriptional mRNA modification in eukaryotes, N6-Methyladenosine (m6A) is closely linked to the occurrence and development of colorectal cancer (CRC). However, there is no systematic evaluation of the expression of m6A regulatory genes in CRC. METHODS By analyzing the TCGA database, we identified METTL3, YTHDF1, IGF2BP1, IGF2BP3, EIF3B, HNRNPA2B1 as overexpressed m6A regulators in CRC. After verification by immunohistochemistry (IHC) in 10 CRC cases, YTHDF1, IGF2BP1, IGF2BP3, and EIF3B were identified as potential biomarkers in CRC. Further validation was done by IHC and qRT-PCR in two larger cohorts. RESULTS We identified 6 up-regulated m6A regulatory genes in CRC in TCGA analysis, and verified that YTHDF1, IGF2BP1, IGF2BP3, and EIFB3 were all significantly differentially expressed between CRC and normal tissues by IHC (p < 0.0001). In another larger cohort, we further validated the overexpression of those genes in CRC as compared to both normal tissues (p < 0.0001) and adenoma tissues (p < 0.05). Detailed analysis suggested that detection of one of the three genes, YTHDF1, IGF2BP1 and IGF2BP3, and combined detection of EIF3B gene could be a good strategy for early diagnosis of both CRC and precancerous lesions. Furthermore, we found that the mRNA levels of YTHDF1, IGF2BP1, and IGF2BP3 were also significantly up-regulated in CRC but not adenoma as compared to normal tissues. CONCLUSION We evaluted the abnormal expression of m6A regulatory genes during CRC carcinogenesis, and identified four m6A genes (YTHDF1, IGF2BP1, IGF2BP3, and EIF3B) as potential biomarkers of both CRC and adenoma.
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Epigenetic reprogramming during prostate cancer progression: A perspective from development. Semin Cancer Biol 2021; 83:136-151. [PMID: 33545340 DOI: 10.1016/j.semcancer.2021.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 12/15/2022]
Abstract
Conrad Waddington's theory of epigenetic landscape epitomize the process of cell fate and cellular decision-making during development. Wherein the epigenetic code maintains patterns of gene expression in pluripotent and differentiated cellular states during embryonic development and differentiation. Over the years disruption or reprogramming of the epigenetic landscape has been extensively studied in the course of cancer progression. Cellular dedifferentiation being a key hallmark of cancer allow us to take cues from the biological processes involved during development. Here, we discuss the role of epigenetic landscape and its modifiers in cell-fate determination, differentiation and prostate cancer progression. Lately, the emergence of RNA-modifications has also furthered our understanding of epigenetics in cancer. The overview of the epigenetic code regulating androgen signalling, and progression to aggressive neuroendocrine stage of PCa reinforces its gene regulatory functions during the development of prostate gland as well as cancer progression. Additionally, we also highlight the clinical implications of cancer cell epigenome, and discuss the recent advancements in the therapeutic strategies targeting the advanced stage disease.
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Huang J, Chen Z, Chen X, Chen J, Cheng Z, Wang Z. The role of RNA N 6-methyladenosine methyltransferase in cancers. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:887-896. [PMID: 33614237 PMCID: PMC7868687 DOI: 10.1016/j.omtn.2020.12.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Modification of eukaryotic RNA by methylation of adenosine residues to generate N6-methyladenosine (m6A) is a highly prevalent process. m6A is dynamically regulated during cell metabolism and embryo development, and it is mainly involved in various aspects of RNA metabolism, including RNA splicing, processing, transport from the nucleus, translation, and degradation. Accumulating evidence shows that dynamic changes to m6A are closely related to the occurrence and development of cancer and that methyltransferases, as key elements in the dynamic regulation of m6A, play a crucial role in these processes. Therefore, in this review, we describe the role of methyltransferases as m6A writers in cancer and summarize their potential molecular mechanisms of action.
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Affiliation(s)
- Jiali Huang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Zhenyao Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Jun Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China.,Department of Oncology, Suzhou Ninth People's Hospital, Suzhou, China
| | - Zhixiang Cheng
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
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40
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Wu Q, Xie X, Huang Y, Meng S, Li Y, Wang H, Hu Y. N6-methyladenosine RNA methylation regulators contribute to the progression of prostate cancer. J Cancer 2021; 12:682-692. [PMID: 33403026 PMCID: PMC7778550 DOI: 10.7150/jca.46379] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 11/03/2020] [Indexed: 01/12/2023] Open
Abstract
Prostate cancer (PCa) is one of the most common epithelial malignant tumors and the fifth leading cause of cancer death in men. An increasing number of studies have demonstrated that N6-methyladenosine (m6A) plays a crucial role in tumorigenesis and tumor development. However, little is known about the role and levels of common m6A regulators and m6A levels in PCa. In this study, we analyzed the characteristic expression of m6A regulators in PCa and castration-resistant prostate cancer (CRPC). UALCAN and cBioPortal were used to estimate the clinical value and genetic alterations of m6A regulators, respectively. The correlation between m6A regulators and androgen receptor (AR) was assessed using Gene Expression Profiling Interactive Analysis (GEPIA) by Pearson correlation statistics. Total m6A levels were detected in transgenic adenocarcinoma of the mouse prostate (TRAMP) mice and PCa cell lines. Results showed that the expression of methyltransferase-like 3 (METTL3) and YTH domain family members, namely, YTHDC2, YTHDF1, and YTHDF2 were generally upregulated in PCa, whereas those of fat mass and obesity-associated protein (FTO), AlkB homolog 5 (ALKBH5), and methyltransferase-like 14 (METTL14) were downregulated. The expression of METTL3, METTL14, Wilms' tumor 1-associating protein (WTAP), YTHDC2, YTHDF1, and YTHDF2 were remarkably higher in CRPC with lymph node metastasis than that in CRPC with bone metastasis, whereas ALKBH5, FTO, and YTHDF3 significantly decreased in CRPC with lymph node metastasis tissues. YTHDF1, YTHDF2, and YTHDC2 were positively correlated with the Gleason grades of PCa, and METTL14, FTO, and ALKBH5 were negatively associated with the Gleason classification. M6A regulators were positively correlated with AR. Patients with a genomic alteration of m6A were associated with poor disease-free survival (DFS). The total m6A levels in TRAMP mice increased dramatically compared with those in tumor-free mice, and m6A levels in LNCaP cell lines were higher than DU145 and PC3 cell lines. In summary, METTL3, METTL14, ALKBH5, FTO, YTHDC2, YTHDF1, and YTHDF2 were abnormally expressed in PCa and related to Gleason classification. Changes in m6A levels maybe contributed to the development and progression of PCa.
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Affiliation(s)
- Qunying Wu
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Xing Xie
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yiming Huang
- Center of Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Shanshan Meng
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Youcheng Li
- Department of Clinical Laboratory, Guigang City People's Hospital, The Eighth Affiliated Hospital of Guangxi Medical University, Guigang, Guangxi, 537100, China
| | - Huifeng Wang
- Department of Biochemistry and Molecular Biology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yanling Hu
- Center of Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
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41
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Sun Z, Jing C, Xiao C, Li T, Wang Y. Prognostic risk signature based on the expression of three m6A RNA methylation regulatory genes in kidney renal papillary cell carcinoma. Aging (Albany NY) 2020; 12:22078-22094. [PMID: 33177247 PMCID: PMC7695403 DOI: 10.18632/aging.104053] [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: 04/01/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
In this study, we investigated the prognostic significance of the expression of N6-methyladenosine (m6A) RNA methylation regulatory genes in kidney renal papillary cell carcinoma (KIRP). RNA-sequencing data analysis showed that 14 of 20 major m6A RNA methylation regulatory genes were differentially expressed in the KIRP tissues from The Cancer Genome Atlas (TCGA) database. We constructed a prognostic risk signature with three m6A RNA methylation regulatory genes, IGF2BP3, KIAA1429 and HNRNPC, based on the results from univariate and LASSO Cox regression analyses. Multivariate Cox regression analysis confirmed that the risk score based on the three-gene prognostic risk signature was an independent predictive factor in KIRP. The overall survival of high-risk KIRP patients was significantly shorter than the low-risk KIRP patients. Expression of the three prognostic risk-related genes correlated with the AJCC and TNM stages of KIRP patients from TCGA and GEPIA datasets. ROC curve analysis showed that the three-gene prognostic risk signature precisely predicted the 1-year, 3-year and 5-year survival of KIRP patients. These findings demonstrate that expression of three prognostic risk-related m6A RNA methylation regulatory genes accurately predicts survival outcomes in KIRP patients.
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Affiliation(s)
- Zhuolun Sun
- Department of Urology, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China
| | - Changying Jing
- Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan 250002, China
| | - Chutian Xiao
- Department of Urology, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China
| | - Tengcheng Li
- Department of Urology, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China
| | - Yu Wang
- Department of Urology, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China
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42
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Epitranscriptomics in Normal and Malignant Hematopoiesis. Int J Mol Sci 2020; 21:ijms21186578. [PMID: 32916783 PMCID: PMC7555315 DOI: 10.3390/ijms21186578] [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: 08/07/2020] [Revised: 09/05/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Epitranscriptomics analyze the biochemical modifications borne by RNA and their downstream influence. From this point of view, epitranscriptomics represent a new layer for the control of genetic information and can affect a variety of molecular processes including the cell cycle and the differentiation. In physiological conditions, hematopoiesis is a tightly regulated process that produces differentiated blood cells starting from hematopoietic stem cells. Alteration of this process can occur at different levels in the pathway that leads from the genetic information to the phenotypic manifestation producing malignant hematopoiesis. This review focuses on the role of epitranscriptomic events that are known to be implicated in normal and malignant hematopoiesis, opening a new pathophysiological and therapeutic scenario. Moreover, an evolutionary vision of this mechanism will be provided.
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43
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Cardoso AR, Lobo J, Miranda-Gonçalves V, Henrique R, Jerónimo C. Epigenetic alterations as therapeutic targets in Testicular Germ Cell Tumours : current and future application of 'epidrugs'. Epigenetics 2020; 16:353-372. [PMID: 32749176 DOI: 10.1080/15592294.2020.1805682] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Testicular germ cell tumours (TGCTs) are heterogeneous neoplasms mostly affecting young-adult men. Despite high survival rates, some patients with disseminated disease acquire cisplatin resistance, entailing the need for less toxic therapies. Epigenetic alterations constitute an important feature of TGCTs, which are also implicated in resistance mechanism(s). These alterations might be used as potential targets to design epigenetic drugs. To date, several compounds have been explored and evaluated regarding therapeutic efficacy, making use of pre-clinical studies with in vitro and in vivo models, and some have already been explored in clinical trials. This review summarizes the several epigenetic mechanisms at play in these neoplasms, the current challenges in the field of TGCTs and critically reviews available data on 'epidrugs' in those tumours.
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Affiliation(s)
- Ana Rita Cardoso
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072, Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-513, Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-513, Porto, Portugal
| | - Vera Miranda-Gonçalves
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-513, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-513, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-513, Porto, Portugal
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44
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Zhang Z, Wang Q, Zhang M, Zhang W, Zhao L, Yang C, Wang B, Jiang K, Ye Y, Shen Z, Wang S. Comprehensive analysis of the transcriptome-wide m6A methylome in colorectal cancer by MeRIP sequencing. Epigenetics 2020; 16:425-435. [PMID: 32749190 DOI: 10.1080/15592294.2020.1805684] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Accumulating evidence has demonstrated that N6-methyladenosine (m6A) plays important roles in various cancers, making it essential to profile m6A modifications at a transcriptome-wide scale in colorectal cancer (CRC). In the present study, we performed high-throughput sequencing to determine the m6A methylome in CRC. We obtained six pairs of CRC samples and tumour-adjacent normal tissues from Peking University People's Hospital. We used MeRIP-seq to determine that compared to the tumour-adjacent normal tissues, the CRC samples had 1343 dysregulated m6A peaks, and 625 m6A peaks were significantly upregulated and 718 m6A peaks were significantly downregulated. Genes with altered m6A peaks play critical roles in regulating glucose metabolism, RNA metabolism, and cancer stem cells. Furthermore, we identified 297 hypermethylated m6A peaks and 328 hypomethylated m6A peaks in mRNAs through conjoint analyses of MeRIP-seq and RNA-seq data. After analysing these genes with differentially methylated m6A peaks and synchronously differential expression, we identified four genes (WDR72, SPTBN2, MORC2, and PARM1) that were associated with prognosis of colorectal cancer patients by searching The Cancer Genome Atlas (TCGA). Our study suggests that m6A modifications play important roles in tumour progression and survival of CRC patients. The results also indicate that modulating m6A modifications may represent an alternative strategy to predict the survival of cancer patients and interfere with tumour progression in the future.
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Affiliation(s)
- Zhen Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Quan Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Mengmeng Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Wei Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Bo Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Kewei Jiang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
| | - Shan Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, China
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45
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Pi J, Wang W, Ji M, Wang X, Wei X, Jin J, Liu T, Qiang J, Qi Z, Li F, Liu Y, Ma Y, Si Y, Huo Y, Gao Y, Chen Y, Dong L, Su R, Chen J, Rao S, Yi P, Yu S, Wang F, Yu J. YTHDF1 Promotes Gastric Carcinogenesis by Controlling Translation of FZD7. Cancer Res 2020; 81:2651-2665. [PMID: 32788173 DOI: 10.1158/0008-5472.can-20-0066] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/08/2020] [Accepted: 08/06/2020] [Indexed: 11/16/2022]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal RNA modification in mammals that regulates homeostasis and function of modified RNA transcripts. Here, we aimed to investigate the role of YTH m6A RNA-binding protein 1 (YTHDF1), a key regulator of m6A methylation in gastric cancer tumorigenesis. Multiple bioinformatic analyses of different human cancer databases identified key m6A-associated genetic mutations that regulated gastric tumorigenesis. YTHDF1 was mutated in about 7% of patients with gastric cancer, and high expression of YTHDF1 was associated with more aggressive tumor progression and poor overall survival. Inhibition of YTHDF1 attenuated gastric cancer cell proliferation and tumorigenesis in vitro and in vivo. Mechanistically, YTHDF1 promoted the translation of a key Wnt receptor frizzled7 (FZD7) in an m6A-dependent manner, and mutated YTHDF1 enhanced expression of FZD7, leading to hyperactivation of the Wnt/β-catenin pathway and promotion of gastric carcinogenesis. Our results demonstrate the oncogenic role of YTHDF1 and its m6A-mediated regulation of Wnt/β-catenin signaling in gastric cancer, providing a novel approach of targeting such epigenetic regulators in this disease. SIGNIFICANCE: This study provides a rationale for controlling translation of key oncogenic drivers in cancer by manipulating epigenetic regulators, representing a novel and efficient strategy for anticancer treatment. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/10/2651/F1.large.jpg.
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Affiliation(s)
- Jingnan Pi
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Wen Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Ji
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoshuang Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Xueju Wei
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Jin
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Liu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiaqi Qiang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Qi
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Feng Li
- Department of Molecular Biology, Shanxi Cancer Hospital, Affiliated Cancer Hospital of Shanxi Medical University, Shanxi, China
| | - Yue Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanmin Si
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Yue Huo
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Yufeng Gao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Yiying Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Dong
- Department of Systems Biology and Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California
| | - Rui Su
- Department of Systems Biology and Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California
| | - Jianjun Chen
- Department of Systems Biology and Gehr Family Center for Leukemia Research, The Beckman Research Institute of City of Hope, Monrovia, California
| | - Shuan Rao
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ping Yi
- Department of Obstetrics and Gynecology, Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuyang Yu
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China. .,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China. .,The Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, China.,Medical Epigenetic Research Center, Chinese Academy of Medical Sciences, Beijing, China
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46
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Yang G, Sun Z, Zhang N. Reshaping the role of m6A modification in cancer transcriptome: a review. Cancer Cell Int 2020; 20:353. [PMID: 32760220 PMCID: PMC7391667 DOI: 10.1186/s12935-020-01445-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
N6-methyl-adenosine(m6A) modification emerges as an abundant and dynamic regulation throughout the Eukaryotic transcriptome. Dysregulation of the m6A regulators has increasingly been found in many neoplasms. It is reasonable to believe that m6A changes the fate of cancer cells and subsequently affected all aspects of cancer progression. In view of the context-dependent role of m6A modification, we emphasize a dual effect of m6A in a particular tumor model, that is, m6A plays a promoting role or a suppressing role in different stages of cancer. This novel sight is compared to the older view that a particular m6A regulator acts as a consistent role in cancer progression.
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Affiliation(s)
- Guanqun Yang
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250013 Shandong China
| | - Zhigang Sun
- Department of Thoracic Surgery, Jinan Central Hospital Affiliated to Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250013 Shandong China
| | - Nan Zhang
- Department of Oncology, Jinan Central Hospital Affiliated to Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250013 Shandong China
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47
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Tao Z, Zhao Y, Chen X. Role of methyltransferase-like enzyme 3 and methyltransferase-like enzyme 14 in urological cancers. PeerJ 2020; 8:e9589. [PMID: 32765970 PMCID: PMC7382367 DOI: 10.7717/peerj.9589] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) modifications can be found in eukaryotic messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA). Several studies have demonstrated a close relationship between m6A modifications and cancer cells. Methyltransferase-like enzyme 3 (METTL3) and methyltransferase-like enzyme 14 (METTL14) are two major enzymes involved in m6A modifications that play vital roles in various cancers. However, the roles and regulatory mechanisms of METTL3 and METTL14 in urological cancers are largely unknown. In this review, we summarize the current research results for METTL3 and METTL14 and identify potential pathways involving these enzymes in kidney, bladder, prostate, and testicular cancer. We found that METTL3 and METTL14 have different expression patterns in four types of urological cancers. METTL3 is highly expressed in bladder and prostate cancer and plays an oncogenic role on cancer cells; however, its expression and role are opposite in kidney cancer. METTL14 is expressed at low levels in kidney and bladder cancer, where it has a tumor suppressive role. Low METTL3 or METTL14 expression in cancer cells negatively regulates cell growth-related pathways (e.g., mTOR, EMT, and P2XR6) but positively regulates cell death-related pathways (e.g., P53, PTEN, and Notch1). When METTL3 is highly expressed, it positively regulates the NF-kB and SHH-GL1pathways but negatively regulates PTEN. These results suggest that although METTL3 and METTL14 have different expression levels and regulatory mechanisms in urological cancers, they control cancer cell fate via cell growth- and cell death-related pathways. These findings suggest that m6A modification may be a potential new therapeutic target in urological cancer.
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Affiliation(s)
- Zijia Tao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yiqiao Zhao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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48
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Zhang QJ, Luan JC, Song LB, Cong R, Ji CJ, Zhou X, Xia JD, Song NH. m6A RNA methylation regulators correlate with malignant progression and have potential predictive values in clear cell renal cell carcinoma. Exp Cell Res 2020; 392:112015. [PMID: 32333907 DOI: 10.1016/j.yexcr.2020.112015] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023]
Abstract
N6-methyladenosine (m6A) has been reported to be involved in several biological processes in tumors. In this study, we found that most of the m6A RNA methylation regulators were not only differentially expressed between clear cell renal cell carcinoma (ccRCC) and normal but also among ccRCC stratified by different clinicopathologic characters. Two ccRCC subgroups, cluster 1 and 2, were identified using consensus clustering based on the expression of m6A methylation regulators. Although no obvious differences were observed between two subgroups regarding clinicopathologic characters, except gender, patients in cluster 1 had a relatively more favorable survival rate than cluster 2. Moreover, we established a risk signature with two m6A methylation regulators, METTL3 and METTL14, which was not only of great value for prognosis prediction but also closely associated with clinicopathological features. In conclusion, m6A RNA methylation regulators play an important role in ccRCC progression and are potentially favorable for prognostic stratification.
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MESH Headings
- Adenosine/metabolism
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/diagnosis
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cohort Studies
- Disease Progression
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Kidney Neoplasms/diagnosis
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Male
- Methylation/drug effects
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Middle Aged
- Predictive Value of Tests
- Prognosis
- RNA Processing, Post-Transcriptional/drug effects
- RNA Processing, Post-Transcriptional/physiology
- Survival Analysis
- Transcriptome
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Affiliation(s)
- Qi-Jie Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiao-Chen Luan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Le-Bin Song
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Cong
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chen-Jian Ji
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jia-Dong Xia
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Ning-Hong Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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VIRMA-Dependent N6-Methyladenosine Modifications Regulate the Expression of Long Non-Coding RNAs CCAT1 and CCAT2 in Prostate Cancer. Cancers (Basel) 2020; 12:cancers12040771. [PMID: 32218194 PMCID: PMC7226055 DOI: 10.3390/cancers12040771] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 01/26/2023] Open
Abstract
RNA methylation at position N6 in adenosine (m6A) and its associated methyltransferase complex (MTC) are involved in tumorigenesis. We aimed to explore m6A biological function for long non-coding RNAs (lncRNAs) in prostate cancer (PCa) and its clinical significance. m6A and MTC levels in PCa cells were characterized by ELISA and western blot. Putative m6A-regulated lncRNAs were identified and validated by lncRNA profiler qPCR array and bioinformatics analysis, followed by m6A/RNA co-immunoprecipitation. Impact of m6A depletion on RNA stability was assessed by Actinomycin D assay. The association of m6A-levels with PCa prognosis was examined in clinical samples. Higher m6A-levels and VIRMA overexpression were detected in metastatic castration-resistant PCa (mCRPC) cells (p < 0.05). VIRMA knockdown in PC-3 cells significantly decreased m6A-levels (p = 0.0317), attenuated malignant phenotype and suppressed the expression of oncogenic lncRNAs CCAT1 and CCAT2 (p < 0.00001). VIRMA depletion and m6A reduction decreased the stability and abundance of CCAT1/2 transcripts. Higher expression of VIRMA, CCAT1, and CCAT2 as a group variable was an independent predictor of poor prognosis (HR = 9.083, CI95% 1.911–43.183, p = 0.006). VIRMA is a critical factor sustaining m6A-levels in PCa cells. VIRMA downregulation attenuates the aggressive phenotype of PCa by overall reduction of m6A-levels decreasing stability and abundance of oncogenic lncRNAs.
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Zhao Y, Tao Z, Chen X. Identification of a three-m6A related gene risk score model as a potential prognostic biomarker in clear cell renal cell carcinoma. PeerJ 2020; 8:e8827. [PMID: 32219036 PMCID: PMC7085294 DOI: 10.7717/peerj.8827] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/28/2020] [Indexed: 12/14/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent malignancies worldwide, N6-methyladenosine (m6A) has been shown to play important roles in regulating gene expression and phenotypes in both health and disease. Here, our purpose is to construct a m6A-regulrator-based risk score (RS) for prediction of the prognosis of ccRCC. Methods We used clinical and expression data of m6A related genes from The Cancer Genome Atlas (TCGA) dataset and the Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis to develop an RS to predict survival of patients with ccRCC, and analyzed correlations between RS and other clinical indicators such as age, grade and stage. Validation of this RS was then engaged in another cohort, E-MTAB-1980 from the ArrayExpress dataset. Finally, we used quantitative real-time PCR to analyze the expression profile of genes consists of the RS. Results A three-gene RS including METTL3, METTL14 and HNRNPA2B1 which can predict overall survival (OS) of ccRCC patients from TCGA. After applying this RS into the validation cohort from Arrayexpress, we found that it successfully reproduced the result; furthermore, the results of PCR validation were in line with our analysis. Conclusion To sum up, our study has identified an RS composed of m6A related genes that may predict the prognosis of ccRCC patients, which might be helpful for future therapeutic strategies. Our results call for further experimental studies for validations.
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Affiliation(s)
- Yiqiao Zhao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zijia Tao
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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