1
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Seigel GM, Onwumere O, Sauane M, Lopez S, Shang E, Habiba H, Redenti S, Grossniklaus HE, Gharbaran R. ALYREF/THOC4 expression and cell growth modulation in retinoblastoma. Pathol Res Pract 2024; 260:155392. [PMID: 38880039 DOI: 10.1016/j.prp.2024.155392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/17/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024]
Abstract
In this study, we tested the hypothesis that ALYREF/THOC4, a poor prognostic factor in different cancer types, has potential as a drug target and prognostic biomarker for retinoblastoma (RB). Immunostaining (IHC), Western blot, and RT-qPCR analyses detected overexpression of ALYREF in the RB cell lines Y79, RB143, WERI-RB1, and RB116. IHC analysis on RB tumor array showed that 11/14 of RB tumors were ALYREF+ to varying degrees, with eight tumors at maximum 3+ intensity. The IHC analysis also detected ALYREF+ cells in normal retina, mainly in the inner nuclear and ganglion cell layer, while some tumor-bearing human eyes were ALYREF+ in the optic nerve suggesting a role in optic invasion/tumor invasion. The expression of ALYREF within the tumor itself, in the optic nerve, as well as in adjacent "normal" retina, suggest that this pattern of expression may lead to ALYREF being a potentially useful prognostic indicator for RB, as it is for other tumors. siRNA knockdown of ALYREF resulted in a 40 % decrease in cell growth in both WERI-RB1 and Y79 cells (p<0.05) and this was associated with decreased expression of mRNAs for the cell proliferation markers Ki67 and PCNA (p<0.005). These results suggest a role for ALYREF in RB cell growth regulation and its potential as both a target and a biomarker for tumor growth inhibition by anti-cancer therapies.
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Affiliation(s)
- Gail M Seigel
- Department of Communicative Disorders and Sciences, University at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA
| | - Onyekwere Onwumere
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA; Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY 10016 USA, USA
| | - Moira Sauane
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA; Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY 10016 USA, USA
| | - Sual Lopez
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA
| | - Enyuan Shang
- Department of Biological Sciences, Bronx Community College/City University of New York, 2155 University Avenue, Bronx, NY 10453, USA
| | - Habiba Habiba
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA
| | - Stephen Redenti
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA; Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY 10016 USA, USA
| | | | - Rajendra Gharbaran
- Department of Biological Sciences, Lehman College/City University of New York, Bronx, NY, USA; Department of Biological Sciences, Bronx Community College/City University of New York, 2155 University Avenue, Bronx, NY 10453, USA.
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2
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Li F, Li W. Readers of RNA Modification in Cancer and Their Anticancer Inhibitors. Biomolecules 2024; 14:881. [PMID: 39062595 PMCID: PMC11275166 DOI: 10.3390/biom14070881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024] Open
Abstract
Cancer treatment has always been a challenge for humanity. The inadequacies of current technologies underscore the limitations of our efforts against this disease. Nevertheless, the advent of targeted therapy has introduced a promising avenue, furnishing us with more efficacious tools. Consequently, researchers have turned their attention toward epigenetics, offering a novel perspective in this realm. The investigation of epigenetics has brought RNA readers to the forefront, as they play pivotal roles in recognizing and regulating RNA functions. Recently, the development of inhibitors targeting these RNA readers has emerged as a focal point in research and holds promise for further strides in targeted therapy. In this review, we comprehensively summarize various types of inhibitors targeting RNA readers, including non-coding RNA (ncRNA) inhibitors, small-molecule inhibitors, and other potential inhibitors. We systematically elucidate their mechanisms in suppressing cancer progression by inhibiting readers, aiming to present inhibitors of readers at the current stage and provide more insights into the development of anticancer drugs.
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Affiliation(s)
| | - Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China;
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3
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Zhang TH, Jo S, Zhang M, Wang K, Gao SJ, Huang Y. Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg. Brief Bioinform 2024; 25:bbae170. [PMID: 38622358 PMCID: PMC11018547 DOI: 10.1093/bib/bbae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/05/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024] Open
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation and splicing. Furthermore, it plays a critical role in the regulation of RNA degradation by primarily recruiting the YTHDF2 reader protein. However, the selective regulation of mRNA decay of the m6A-methylated mRNA through YTHDF2 binding is poorly understood. To improve our understanding, we developed m6A-BERT-Deg, a BERT model adapted for predicting YTHDF2-mediated degradation of m6A-methylated mRNAs. We meticulously assembled a high-quality training dataset by integrating multiple data sources for the HeLa cell line. To overcome the limitation of small training samples, we employed a pre-training-fine-tuning strategy by first performing a self-supervised pre-training of the model on 427 760 unlabeled m6A site sequences. The test results demonstrated the importance of this pre-training strategy in enabling m6A-BERT-Deg to outperform other benchmark models. We further conducted a comprehensive model interpretation and revealed a surprising finding that the presence of co-factors in proximity to m6A sites may disrupt YTHDF2-mediated mRNA degradation, subsequently enhancing mRNA stability. We also extended our analyses to the HEK293 cell line, shedding light on the context-dependent YTHDF2-mediated mRNA degradation.
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Affiliation(s)
- Ting-He Zhang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA,15261, USA
| | - Sumin Jo
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Michelle Zhang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA,15261, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
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4
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YE XING, TUO ZHOUTING, CHEN KAI, WU RUICHENG, WANG JIE, YU QINGXIN, YE LUXIA, MIYAMOTO AKIRA, YOO KOOHAN, ZHANG CHI, WEI WURAN, LI DENGXIONG, FENG DECHAO. Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF). Oncol Res 2024; 32:503-515. [PMID: 38361753 PMCID: PMC10865740 DOI: 10.32604/or.2024.045050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/01/2023] [Indexed: 02/17/2024] Open
Abstract
The increasing interest in RNA modifications has significantly advanced epigenomic and epitranscriptomic technologies. This study focuses on the immuno-oncological impact of ALYREF in human cancer through a pan-cancer analysis, enhancing understanding of this gene's role in cancer. We observed differential ALYREF expression between tumor and normal samples, correlating strongly with prognosis in various cancers, particularly kidney renal papillary cell carcinoma (KIRP) and liver hepatocellular carcinoma (LIHC). ALYREF showed a negative correlation with most tumor-infiltrating cells in lung squamous cell carcinoma (LUSC) and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), while positive correlations were noted in LIHC, kidney chromophobe (KICH), mesothelioma (MESO), KIRP, pheochromocytoma and paraganglioma (PARD), and glioma (GBMLGG). Additionally, ALYREF expression was closely associated with tumor heterogeneity, stemness indices, and a high mutation rate in TP53 across these cancers. In conclusion, ALYREF may serve as an oncogenic biomarker in numerous cancers, meriting further research attention.
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Affiliation(s)
- XING YE
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - ZHOUTING TUO
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - KAI CHEN
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - RUICHENG WU
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - JIE WANG
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - QINGXIN YU
- Department of Pathology, Ningbo Diagnostic Pathology Center, Ningbo, 315021, China
| | - LUXIA YE
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, 317000, China
| | - AKIRA MIYAMOTO
- Department of Rehabilitation, West Kyushu University, Kanzaki-shi, 842-8585, Japan
| | - KOO HAN YOO
- Department of Urology, Kyung Hee University, Seoul, 446 701, South Korea
| | - CHI ZHANG
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - WURAN WEI
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - DENGXIONG LI
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - DECHAO FENG
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
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5
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Goswami N, Singh A, Bharadwaj S, Sahoo AK, Singh IK. Targeting neuroblastoma by small-molecule inhibitors of human ALYREF protein: mechanistic insights using molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:1352-1367. [PMID: 37158061 DOI: 10.1080/07391102.2023.2204376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
Neuroblastoma is a tumour of the sympathetic nervous system mainly prevalent in children. Many strategies have been employed to target several drug-targetable proteins for the clinical management of neuroblastoma. However, the heterogeneous nature of neuroblastoma presents serious challenges in drug development for its treatment. Albeit numerous medications have been developed to target various signalling pathways in neuroblastoma, the redundant nature of the tumour pathways makes its suppression unsuccessful. Recently, the quest for neuroblastoma therapy resulted in the identification of human ALYREF, a nuclear protein that plays an essential role in tumour growth and progression. Therefore, this study used the structure-based drug discovery method to identify the putative inhibitors targeting ALYREF for the Neuroblastoma treatment. Herein, a library of 119 blood-brain barrier crossing small molecules from the ChEMBL database was downloaded and docked against the predicted binding pocket of the human ALYREF protein. Based on docking scores, the top four compounds were considered for intermolecular interactions and molecular dynamics simulation analysis, which revealed CHEMBL3752986 and CHEMBL3753744 with substantial affinity and stability with the ALYREF. These results were further supported by binding free energies and essential dynamics analysis of the respective complexes. Hence, this study advocates the sorted compounds targeting ALYREF for further in vitro and in vivo assessment to develop a drug against neuroblastoma.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nidhi Goswami
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
- Neuropharmacology and Drug Delivery Laboratory, Department of Zoology, Daulat Ram College, University of Delhi, Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
- Delhi School of Public Health, Institute of Eminence, University of Delhi, Delhi, India
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6
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Zhao Y, Xing C, Peng H. ALYREF (Aly/REF export factor): A potential biomarker for predicting cancer occurrence and therapeutic efficacy. Life Sci 2024; 338:122372. [PMID: 38135116 DOI: 10.1016/j.lfs.2023.122372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
5-Methylcytosine (m5C) methylation is present in almost all types of RNA as an essential epigenetic modification. It is dynamically modulated by its associated enzymes, including m5C methyltransferases (NSUN, DNMT and TRDMT family members), demethylases (TET family and ALKBH1) and binding proteins (YTHDF2, ALYREF and YBX1). Among them, aberrant expression of the RNA-binding protein ALYREF can facilitate a variety of malignant phenotypes such as maintenance of proliferation, malignant heterogeneity, metastasis, and drug resistance to cell death through different regulatory mechanisms, including pre-mRNA processing, mRNA stability, and nuclear-cytoplasmic shuttling. The induction of these cellular processes by ALYREF results in treatment resistance and poor outcomes for patients. However, there are currently few reports of clinical applications or drug trials related to ALYREF. In addition, the looming observations on the role of ALYREF in the mechanisms of carcinogenesis and disease prognosis have triggered considerable interest, but critical evidence is not available. For example, animal experiments and ALYREF small molecule inhibitor trials. In this review, we, therefore, revisit the literature on ALYREF and highlight its importance as a prognostic biomarker for early prevention and as a therapeutic target.
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Affiliation(s)
- Yan Zhao
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Cheng Xing
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Changsha, Hunan 410011, China; Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan 410011, China.
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7
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Zhang TH, Jo S, Zhang M, Wang K, Gao SJ, Huang Y. Understanding YTHDF2-mediated mRNA Degradation By m 6A-BERT-Deg. ARXIV 2024:arXiv:2401.08004v1. [PMID: 38292306 PMCID: PMC10827231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation, and splicing. Furthermore, it plays a critical role in the regulation of RNA degradation by primarily recruiting the YTHDF2 reader protein. However, the selective regulation of mRNA decay of the m6A-methylated mRNA through YTHDF2 binding is poorly understood. To improve our understanding, we developed m6A-BERT-Deg, a BERT model adapted for predicting YTHDF2-mediated degradation of m6A-methylated mRNAs. We meticulously assembled a high-quality training dataset by integrating multiple data sources for the HeLa cell line. To overcome the limitation of small training samples, we employed a pre-training-fine-tuning strategy by first performing a self-supervised pre-training of the model on 427,760 unlabeled m6A site sequences. The test results demonstrated the importance of this pre-training strategy in enabling m6A-BERT-Deg to outperform other benchmark models. We further conducted a comprehensive model interpretation and revealed a surprising finding that the presence of co-factors in proximity to m6A sites may disrupt YTHDF2-mediated mRNA degradation, subsequently enhancing mRNA stability. We also extended our analyses to the HEK293 cell line, shedding light on the context-dependent YTHDF2-mediated mRNA degradation.
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Affiliation(s)
- Ting-He Zhang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sumin Jo
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelle Zhang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
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8
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Nulali J, Zhang K, Long M, Wan Y, Liu Y, Zhang Q, Yang L, Hao J, Yang L, Song H. ALYREF-mediated RNA 5-Methylcytosine modification Promotes Hepatocellular Carcinoma Progression Via Stabilizing EGFR mRNA and pSTAT3 activation. Int J Biol Sci 2024; 20:331-346. [PMID: 38164181 PMCID: PMC10750289 DOI: 10.7150/ijbs.82316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/23/2023] [Indexed: 01/03/2024] Open
Abstract
5-Methylcytosine (m5C) is one of the most ubiquitous modifications of mRNA and contributes to cancer pathogenesis. Aly/REF export factor (ALYREF), an m5C reader, is associated with the prognosis of liver hepatocellular carcinoma (LIHC). However, the effects of ALYREF on the progression of LIHC and the underlying molecular mechanisms remains elusive. Through an analysis of an online database and 3 independent LIHC cohorts, we found that ALYREF was markedly elevated in human liver cancer tissues and was significantly correlated with LIHC clinicopathological parameters, including Ki67+ cell rate, high-grade TNM stage, and poor prognosis. Several experiments were conducted to investigate the molecular basis and functional role of ALYREF-related progression in this study. ALYREF could enhance LIHC cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in vitro and tumor formation in vivo. Mechanistically, ALYREF promoted the progression of human LIHC through EGFR pathways. Furthermore, ALYREF could directly bind to the m5C modification site of EGFR 3' untranslated region (3' UTR) to stabilize EGFR mRNA. Collectively, ALYREF played a crucial oncogenic role in LIHC via the stabilization of EGFR mRNA and subsequent activation of the STAT3 signaling pathway. Our results may help to elucidate the potential mechanisms of ALYREF-induced m5C modification in the progression of human LIHC.
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Affiliation(s)
- Jiayida Nulali
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Kaiwen Zhang
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Manmei Long
- Department of Pathology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yueyue Wan
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yu Liu
- Department of Respiration, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qianyue Zhang
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Liu Yang
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Jun Hao
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Linhua Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Huaidong Song
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
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9
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Yang Q, Wang M, Xu J, Yu D, Li Y, Chen Y, Zhang X, Zhang J, Gu J, Zhang X. LINC02159 promotes non-small cell lung cancer progression via ALYREF/YAP1 signaling. Mol Cancer 2023; 22:122. [PMID: 37537569 PMCID: PMC10401734 DOI: 10.1186/s12943-023-01814-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/25/2023] [Indexed: 08/05/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Long non-coding RNAs (lncRNAs) have emerged as key regulators of cancer development and progression, and as promising biomarkers for the diagnosis and prognosis of cancer. In this study, we identified a new lncRNA (LINC02159) that was upregulated in the tumor tissues and serum of non-small cell lung cancer (NSCLC) patients. We demonstrated that knockdown of LINC02159 inhibited NSCLC cell proliferation, migration, and invasion, but induced cell apoptosis and cell cycle arrest in vitro and retarded tumor growth in vivo, while overexpression of LINC02159 led to the opposite effect. We discovered that LINC02159 was highly correlated with cancer growth and metastasis-related pathways by using transcriptomic analysis and that YAP1 was a potential target gene of LINC02159. Mechanistically, LINC02159 bound to the Aly/REF export factor (ALYREF) to enhance the stability of YAP1 messenger RNA (mRNA) via m5C modification, which led to the overexpression of YAP1 and the activation of the Hippo and β-catenin signaling pathways in NSCLC cells. Rescue experiments showed that LINC01259 promoted NSCLC progression in a YAP1- and ALYREF-dependent manner. In conclusion, LINC02159 plays an oncogenic role in NSCLC progression by regulating ALYREF/YAP1 signaling, and it has the potential to be utilized as a diagnostic marker and therapeutic target for NSCLC.
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Affiliation(s)
- Qiurong Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Maoye Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jing Xu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Dan Yu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Yixin Li
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Yanke Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaoxin Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jiahui Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jianmei Gu
- Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, 226300, China.
| | - Xu Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
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10
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Gu X, Ma X, Chen C, Guan J, Wang J, Wu S, Zhu H. Vital roles of m 5C RNA modification in cancer and immune cell biology. Front Immunol 2023; 14:1207371. [PMID: 37325635 PMCID: PMC10264696 DOI: 10.3389/fimmu.2023.1207371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
RNA modification plays an important role in epigenetics at the posttranscriptional level, and 5-methylcytosine (m5C) has attracted increasing attention in recent years due to the improvement in RNA m5C site detection methods. By influencing transcription, transportation and translation, m5C modification of mRNA, tRNA, rRNA, lncRNA and other RNAs has been proven to affect gene expression and metabolism and is associated with a wide range of diseases, including malignant cancers. RNA m5C modifications also substantially impact the tumor microenvironment (TME) by targeting different groups of immune cells, including B cells, T cells, macrophages, granulocytes, NK cells, dendritic cells and mast cells. Alterations in immune cell expression, infiltration and activation are highly linked to tumor malignancy and patient prognosis. This review provides a novel and holistic examination of m5C-mediated cancer development by examining the exact mechanisms underlying the oncogenicity of m5C RNA modification and summarizing the biological effects of m5C RNA modification on tumor cells as well as immune cells. Understanding methylation-related tumorigenesis can provide useful insights for the diagnosis as well as the treatment of cancer.
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Affiliation(s)
- Xinyu Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao Ma
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Guan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shanshan Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haihong Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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11
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The "Superoncogene" Myc at the Crossroad between Metabolism and Gene Expression in Glioblastoma Multiforme. Int J Mol Sci 2023; 24:ijms24044217. [PMID: 36835628 PMCID: PMC9966483 DOI: 10.3390/ijms24044217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The concept of the Myc (c-myc, n-myc, l-myc) oncogene as a canonical, DNA-bound transcription factor has consistently changed over the past few years. Indeed, Myc controls gene expression programs at multiple levels: directly binding chromatin and recruiting transcriptional coregulators; modulating the activity of RNA polymerases (RNAPs); and drawing chromatin topology. Therefore, it is evident that Myc deregulation in cancer is a dramatic event. Glioblastoma multiforme (GBM) is the most lethal, still incurable, brain cancer in adults, and it is characterized in most cases by Myc deregulation. Metabolic rewiring typically occurs in cancer cells, and GBM undergoes profound metabolic changes to supply increased energy demand. In nontransformed cells, Myc tightly controls metabolic pathways to maintain cellular homeostasis. Consistently, in Myc-overexpressing cancer cells, including GBM cells, these highly controlled metabolic routes are affected by enhanced Myc activity and show substantial alterations. On the other hand, deregulated cancer metabolism impacts Myc expression and function, placing Myc at the intersection between metabolic pathway activation and gene expression. In this review paper, we summarize the available information on GBM metabolism with a specific focus on the control of the Myc oncogene that, in turn, rules the activation of metabolic signals, ensuring GBM growth.
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Zhang T, Gu J, Wang X, Luo J, Yan J, Cai K, Li H, Nie Y, Chen X, Wang J. RNA methylation regulators contribute to poor prognosis of hepatocellular carcinoma associated with the suppression of bile acid metabolism: a multi-omics analysis. Am J Cancer Res 2022; 12:2989-3013. [PMID: 35968321 PMCID: PMC9360234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023] Open
Abstract
RNA methylation has been known to promote the initiation and progression of many types of cancer, including hepatocellular carcinoma (HCC). To fully understand the importance of this post-transcriptional modification in HCC, a thorough investigation that combines different patterns of RNA methylation is urgently needed. In this study, we investigated the regulators of the three most common types of RNA methylation: m6A, N1-methyladenosine (m1A) and 5-methylcytosine (m5C). Based on the genomic and proteomic data, we constructed a classifier consisting of seven RNA methylation regulators. This classifier performed well and robustly predicted the prognosis of HCC patients. By analysis using this classifier, we found that the primary bile acid biosynthesis pathway was mostly downregulated in high-risk HCC patients. Furthermore, we found that the gene expression patterns regulated by several bile acids were similar to those regulated by some well-defined anti-tumor compounds, indicating that bile acid metabolism plays a crucial role in the progression of HCC, and the related metabolites can be used as the potential agents for HCC treatments. Moreover, our study revealed a crosstalk between RNA methylation and bile acid regulators, demonstrating a novel mechanism of the downregulation of bile acid metabolism in HCC and providing new insights into how RNA methylation regulators affect the oncogenesis of HCC.
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Affiliation(s)
- Tao Zhang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Jian Gu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Xinyi Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Jiajia Luo
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Jing Yan
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Kailin Cai
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Huili Li
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Yingli Nie
- Department of Dermatology, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430014, China
| | - Xiangdong Chen
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Jiliang Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
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13
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Klec C, Knutsen E, Schwarzenbacher D, Jonas K, Pasculli B, Heitzer E, Rinner B, Krajina K, Prinz F, Gottschalk B, Ulz P, Deutsch A, Prokesch A, Jahn SW, Lellahi SM, Perander M, Barbano R, Graier WF, Parrella P, Calin GA, Pichler M. ALYREF, a novel factor involved in breast carcinogenesis, acts through transcriptional and post-transcriptional mechanisms selectively regulating the short NEAT1 isoform. Cell Mol Life Sci 2022; 79:391. [PMID: 35776213 PMCID: PMC9249705 DOI: 10.1007/s00018-022-04402-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 12/15/2022]
Abstract
The RNA-binding protein ALYREF (THOC4) is involved in transcriptional regulation and nuclear mRNA export, though its role and molecular mode of action in breast carcinogenesis are completely unknown. Here, we identified high ALYREF expression as a factor for poor survival in breast cancer patients. ALYREF significantly influenced cellular growth, apoptosis and mitochondrial energy metabolism in breast cancer cells as well as breast tumorigenesis in orthotopic mouse models. Transcriptional profiling, phenocopy and rescue experiments identified the short isoform of the lncRNA NEAT1 as a molecular trigger for ALYREF effects in breast cancer. Mechanistically, we found that ALYREF binds to the NEAT1 promoter region to enhance the global NEAT1 transcriptional activity. Importantly, by stabilizing CPSF6, a protein that selectively activates the post-transcriptional generation of the short isoform of NEAT1, as well as by direct binding and stabilization of the short isoform of NEAT1, ALYREF selectively fine-tunes the expression of the short NEAT1 isoform. Overall, our study describes ALYREF as a novel factor contributing to breast carcinogenesis and identifies novel molecular mechanisms of regulation the two isoforms of NEAT1.
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Affiliation(s)
- Christiane Klec
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Medical Biology, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsö, Norway
| | - Daniela Schwarzenbacher
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Katharina Jonas
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Barbara Pasculli
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz (MUG), Graz, Austria
| | - Beate Rinner
- Biomedical Research, Medical University of Graz (MUG), Graz, Austria
| | - Katarina Krajina
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Felix Prinz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria
| | - Benjamin Gottschalk
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cellular Signaling, Metabolism and Aging, Medical University of Graz (MUG), Graz, Austria
| | - Peter Ulz
- Institute of Human Genetics, Medical University of Graz (MUG), Graz, Austria
| | - Alexander Deutsch
- Division of Hematology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Andreas Prokesch
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | - Stephan W Jahn
- Institute of Pathology, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - S Mohammad Lellahi
- Department of Medical Biology, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsö, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, UiT-the Arctic University of Norway, Tromsö, Norway
| | - Raffaela Barbano
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - Wolfgang F Graier
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cellular Signaling, Metabolism and Aging, Medical University of Graz (MUG), Graz, Austria
| | - Paola Parrella
- Fondazione IRCCS Casa Sollievo della Sofferenza Laboratorio di Oncologia, San Giovanni Rotondo, FG, Italy
| | - George Adrian Calin
- Department of Translational Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Augenbruggerplatz 15, 8010, Graz, Austria.
- Research Unit for Non-Coding RNAs and Genome Editing, Medical University of Graz (MUG), Graz, Austria.
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14
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Wang ZZ, Meng T, Yang MY, Wang W, Zhang Y, Liu Y, Han AQ, Wu J, Wang HX, Qian B, Zhu LX. ALYREF associated with immune infiltration is a prognostic biomarker in hepatocellular carcinoma. Transl Oncol 2022; 21:101441. [PMID: 35523010 PMCID: PMC9079359 DOI: 10.1016/j.tranon.2022.101441] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/07/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022] Open
Abstract
ALYREF is a potential prognostic marker for hepatocellular carcinoma. ALYREF affects the biological function of hepatocellular carcinoma cells. ALYREF is associated with immune infiltration in hepatocellular carcinoma. The model constructed based on ALYREF-related immune genes provides a reference for the evaluation of immunotherapy.
Background Although ALYREF has been demonstrated to have a role in a number of malignancies, its role in hepatocellular carcinoma (HCC) has received little attention. Our objective was to research at the prognostic value, biological role and relevance of ALYREF to the immune system in HCC. Methods The expression of ALYREF and its relationship with clinical parameters of HCC patients were analyzed by liver cancer cohort (LIHC) of The Cancer Genome Atlas. The expression and prognosis were verified by immunohistochemistry experiments. Gene transfection, CCK-8, scratch healing, transwell invasion and flow cytometry were used to assess the molecular function of ALYREF in vitro. The TIMER and TISIDB online data portals were used to assess the relevance of ALYREF to immunization. Stepwise regression analysis of ALYREF-related immune genes in the LIHC training set was used to construct a prognostic risk prediction model. Also, construct a nomogram to predict patient survival. The testing set for internal verification. Results Knockdown of ALYREF changed the biological phenotypes of HCC cells, such as proliferation, apoptosis, and invasion. In addition, the expression of ALYREF in HCC affected the level of immune cell infiltration and correlated with the overall survival time of patients. The constructed immune prognostic model allows for a valid assessment of patients. Conclusion ALYREF is increased in HCC, has an impact on cellular function and the immune system, and might be used as a prognostic marker.
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Affiliation(s)
- Zhen-Zhen Wang
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Tao Meng
- Department of General Surgery, The First People's Hospital of Hefei, Hefei 230000, China
| | - Ming-Ya Yang
- Department of Haematology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Wei Wang
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Yan Zhang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Yu Liu
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - An-Qi Han
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Jin Wu
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Hui-Xiao Wang
- Department of Medicine, The Second People's Hospital of Anhui Province, Hefei 230000, China.
| | - Bo Qian
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230022, China.
| | - Li-Xin Zhu
- Department of General Surgery, Central Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China.
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15
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Chen Y, Lei J, He S. m 6A Modification Mediates Mucosal Immune Microenvironment and Therapeutic Response in Inflammatory Bowel Disease. Front Cell Dev Biol 2021; 9:692160. [PMID: 34422815 PMCID: PMC8378837 DOI: 10.3389/fcell.2021.692160] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Accumulating evidence links m6A modification with immune infiltration. However, the correlation and mechanism by which m6A modification promotes intestinal immune infiltration in inflammatory bowel disease (IBD) is unknown. Here, genomic information from IBD tissues was integrated to evaluate disease-related m6A modification, and the correlation between the m6A modification pattern and the immune microenvironment in the intestinal mucosa was explored. Next, we identified hub genes from the key modules of the m6Acluster and analyzed the correlation among the hub genes, immune infiltration, and therapy. We found that IGF2BP1 and IGF2BP2 expression was decreased in Crohn's disease (CD) tissues and that IGF2BP2 was decreased in ulcerative colitis (UC) tissues compared with normal tissues (P < 0.05). m6Acluster2, containing higher expressions of IL15, IL16, and IL18, was enriched in M0 macrophage, M1 macrophage, native B cells, memory B cells, and m6Acluster1 with high expression of IL8 and was enriched in resting dendritic and plasma cells (P < 0.05). Furthermore, we reveal that expression of m6A phenotype-related hub genes (i.e., NUP37, SNRPG, H2AFZ) was increased with a high abundance of M1 macrophages, M0 macrophages, and naive B cells in IBD (P < 0.01). Immune checkpoint expression in the genecluster1 with higher expression of hub genes was increased. The anti-TNF therapeutic response of patients in genecluster1 was more significant, and the therapeutic effect of CD was better than that of UC. These findings indicate that m6A modification may affect immune infiltration and therapeutic response in IBD. Assessing the expression of m6A phenotype-related hub genes might guide the choice of IBD drugs and improve the prediction of therapeutic response to anti-TNF therapy.
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Affiliation(s)
- Yongyu Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Lei
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Song He
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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