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Xu Q, Yang C, Wang L, Zhou J. Unveiling the role of RNA methylation in glioma: Mechanisms, prognostic biomarkers, and therapeutic targets. Cell Signal 2024:111380. [PMID: 39236835 DOI: 10.1016/j.cellsig.2024.111380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/30/2024] [Accepted: 09/01/2024] [Indexed: 09/07/2024]
Abstract
Gliomas, the most prevalent malignant brain tumors in the central nervous system, are marked by rapid growth, high recurrence rates, and poor prognosis. Glioblastoma (GBM) stands out as the most aggressive subtype, characterized by significant heterogeneity. The etiology of gliomas remains elusive. RNA modifications, particularly reversible methylation, play a crucial role in regulating transcription and translation throughout the RNA lifecycle. Increasing evidence highlights the prevalence of RNA methylation in primary central nervous system malignancies, underscoring its pivotal role in glioma pathogenesis. This review focuses on recent findings regarding changes in RNA methylation expression and their effects on glioma development and progression, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N7-methylguanosine (m7G). Given the extensive roles of RNA methylation in gliomas, the potential of RNA methylation-related regulators as prognostic markers and therapeutic targets was also explored, aiming to enhance clinical management and improve patient outcomes.
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Affiliation(s)
- Qichen Xu
- Department of Neurosurgery, Shengzhou People's Hospital (the First Affiliated Hospital of Zhejiang University Shengzhou Branch), Zhejiang, China
| | - Chunsong Yang
- Department of Neurosurgery, Shengzhou People's Hospital (the First Affiliated Hospital of Zhejiang University Shengzhou Branch), Zhejiang, China
| | - Liyun Wang
- Department of Neurosurgery, Shengzhou People's Hospital (the First Affiliated Hospital of Zhejiang University Shengzhou Branch), Zhejiang, China
| | - Jing Zhou
- Department of Neurosurgery, Shengzhou People's Hospital (the First Affiliated Hospital of Zhejiang University Shengzhou Branch), Zhejiang, China.
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2
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Han X, Zhu Y, Ke J, Zhai Y, Huang M, Zhang X, He H, Zhang X, Zhao X, Guo K, Li X, Han Z, Zhang Y. Progression of m 6A in the tumor microenvironment: hypoxia, immune and metabolic reprogramming. Cell Death Discov 2024; 10:331. [PMID: 39033180 PMCID: PMC11271487 DOI: 10.1038/s41420-024-02092-2] [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: 12/24/2023] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024] Open
Abstract
Recently, N6-methyladenosine (m6A) has aroused widespread discussion in the scientific community as a mode of RNA modification. m6A comprises writers, erasers, and readers, which regulates RNA production, nuclear export, and translation and is very important for human health. A large number of studies have found that the regulation of m6A is closely related to the occurrence and invasion of tumors, while the homeostasis and function of the tumor microenvironment (TME) determine the occurrence and development of tumors to some extent. TME is composed of a variety of immune cells (T cells, B cells, etc.) and nonimmune cells (tumor-associated mesenchymal stem cells (TA-MSCs), cancer-associated fibroblasts (CAFs), etc.). Current studies suggest that m6A is involved in regulating the function of various cells in the TME, thereby affecting tumor progression. In this manuscript, we present the composition of m6A and TME, the relationship between m6A methylation and characteristic changes in TME, the role of m6A methylation in TME, and potential therapeutic strategies to provide new perspectives for better treatment of tumors in clinical work.
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Affiliation(s)
- Xuan Han
- First Clinical College of Changzhi Medical College, Changzhi, China
| | - Yu Zhu
- Linfen Central Hospital, Linfen, China
| | - Juan Ke
- Linfen Central Hospital, Linfen, China
| | | | - Min Huang
- Linfen Central Hospital, Linfen, China
| | - Xin Zhang
- Linfen Central Hospital, Linfen, China
| | | | | | | | | | | | - Zhongyu Han
- School of Medicine and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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3
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Bai B, An X, Qu Q, Liu X, Liu Y, Wei L. The clinical features and prognostic implications of the co-mutated TP53 gene in advanced non-small cell lung cancer. Clin Transl Oncol 2024:10.1007/s12094-024-03533-1. [PMID: 38872053 DOI: 10.1007/s12094-024-03533-1] [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: 01/09/2024] [Accepted: 05/18/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND TP53 is a frequently mutated oncogene within non-small cell lung cancer (NSCLC). However, the clinical and prognostic significance of co-mutations in TP53 in patients with advanced NSCLC has not been fully elucidated. METHODS A total of 174 patients with advanced NSCLC were enrolled in this study. All patients were subjected to sequencing analysis of tumor-related genes and information such as PD-L1 expression, TMB, and co-mutation changes were collected. Patients were categorized into TP53 mutant and TP53 wild-type groups according to their TP53 mutation status and then statistically analyzed. RESULTS TP53 mutations were the most common among all patients, accounting for 56.32%, followed by epidermal growth factor receptor mutations at 48.27%. The most common mutation sites in the TP53 mutation group were exons 5-8.TP53 mutations were significantly associated with PD-L1 and TMB levels. Univariate Cox analysis showed that gender and EGFR mutation affected the prognosis of TP53-mutated NSCLC patients, and multivariate Cox regression analysis identified EGFR mutation as an independent risk factor. The OS of NSCLC patients in the TP53 mutation group was significantly shorter than that of the TP53wt group. Survival curves in the TP53/EGFR combined mutation group showed that patients with combined EGFR mutation had a lower survival rate. DISCUSSION TP53 mutations are associated with different clinical indicators and have important implications in clinical treatment. TP53 is a poor prognostic factor for NSCLC patients, and TP53/EGFR co-mutation will affect the survival time of patients. TP53/EGFR co-mutation may be a new prognostic marker for NSCLC.
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Affiliation(s)
- Bing Bai
- Tai'an City Central Hospital (Tai'an Central Hospital Affiliated to Qingdao University, Mount Taishan Medical Center), Tai'an, 271000, Shandong, China
| | - Xia An
- Department of Respiratory Medicine, The Second Affiliated Hospital of Shandong First Medical University, No. 336 Taishan Street, Taishan District, Tai'an, 271000, Shandong, China
| | - Qinghui Qu
- Yutai County People's Hospital, Jining, 272300, Shandong, China
| | - Xin Liu
- Department of Respiratory Medicine, The Second Affiliated Hospital of Shandong First Medical University, No. 336 Taishan Street, Taishan District, Tai'an, 271000, Shandong, China.
| | - Yuanyuan Liu
- Department of Respiratory Medicine, The Second Affiliated Hospital of Shandong First Medical University, No. 336 Taishan Street, Taishan District, Tai'an, 271000, Shandong, China
| | - Li Wei
- Department of Respiratory Medicine, The Second Affiliated Hospital of Shandong First Medical University, No. 336 Taishan Street, Taishan District, Tai'an, 271000, Shandong, China
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4
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Guo H, Han Q, Guan X, Li Z, Wang Y, He L, Guo Y, Zhao L, Xue X, Liu H, Zhang C. M6A reader YTHDF1 promotes malignant progression of laryngeal squamous carcinoma through activating the EMT pathway by EIF4A3. Cell Signal 2024; 114:111002. [PMID: 38048860 DOI: 10.1016/j.cellsig.2023.111002] [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: 09/27/2023] [Revised: 11/09/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Laryngeal squamous cell carcinoma (LSCC) is one of the common malignant tumors in the head and neck region, and its high migration and invasion seriously threaten the survival and health of patients. In cancer development, m6A RNA modification plays a crucial role in regulating gene expression and signaling. This study delved into the function and mechanism of the m6A reading protein YTHDF1 in LSCC. It was found that YTHDF1 was highly expressed in the GEO database and LSCC tissues. Cell function experiments confirmed that the downregulation of YTHDF1 significantly inhibited the proliferation, migration, and invasion ability of LSCC cells. Further studies revealed that EIF4A3 was a downstream target gene of YTHDF1, and knockdown of EIF4A3 similarly significantly inhibited the malignant progression of LSCC in both in vivo and in vitro experiments. The molecular mechanism studies suggested that YTHDF1-EIF4A3 may promote the malignant development of LSCC by activating the EMT signaling pathway. This study provides important clues for an in-depth understanding of the pathogenesis of LSCC and is a solid foundation for the discovery of new therapeutic targets and approaches.
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Affiliation(s)
- Huina Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Qi Han
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Xiaoya Guan
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Zhongxun Li
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Ying Wang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Long He
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Yujia Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Liting Zhao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Xuting Xue
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Hongliang Liu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Department of Cell Biology and Genetics, the Basic Medical School of Shanxi Medical University, Taiyuan 030001, Shanxi, China.
| | - Chunming Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, China.
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Rong H, Wang D, Wang Y, Dong C, Wang G. YTHDF1 in Tumor Cell Metabolism: An Updated Review. Molecules 2023; 29:140. [PMID: 38202722 PMCID: PMC10779796 DOI: 10.3390/molecules29010140] [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: 11/22/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
With the advancement of research on m6A-related mechanisms in recent years, the YTHDF protein family within m6A readers has garnered significant attention. Among them, YTHDF1 serves as a pivotal member, playing a crucial role in protein translation, tumor proliferation, metabolic reprogramming of various tumor cells, and immune evasion. In addition, YTHDF1 also exerts regulatory effects on tumors through multiple signaling pathways, and numerous studies have confirmed its ability to assist in the reprogramming of the tumor cell-related metabolic processes. The focus of research on YTHDF1 has shifted in recent years from its m6A-recognition and -modification function to the molecular mechanisms by which it regulates tumor progression, particularly by exploring the regulatory factors that interact with YTHDF1 upstream and downstream. In this review, we elucidate the latest signaling pathway mechanisms of YTHDF1 in various tumor cells, with a special emphasis on its distinctive characteristics in tumor cell metabolic reprogramming. Furthermore, we summarize the latest pathological and physiological processes involving YTHDF1 in tumor cells, and analyze potential therapeutic approaches that utilize YTHDF1. We believe that YTHDF1 represents a highly promising target for future tumor treatments and a novel tumor biomarker.
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Affiliation(s)
| | | | | | | | - Guiling Wang
- Key Laboratory of Cell Biology, Department of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China; (H.R.); (D.W.); (Y.W.); (C.D.)
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6
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Huang J, Chen P, Jia L, Li T, Yang X, Liang Q, Zeng Y, Liu J, Wu T, Hu W, Kee K, Zeng H, Liang X, Zhou C. Multi-Omics Analysis Reveals Translational Landscapes and Regulations in Mouse and Human Oocyte Aging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301538. [PMID: 37401155 PMCID: PMC10502832 DOI: 10.1002/advs.202301538] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/28/2023] [Indexed: 07/05/2023]
Abstract
Abnormal resumption of meiosis and decreased oocyte quality are hallmarks of maternal aging. Transcriptional silencing makes translational control an urgent task during meiosis resumption in maternal aging. However, insights into aging-related translational characteristics and underlying mechanisms are limited. Here, using multi-omics analysis of oocytes, it is found that translatomics during aging is related to changes in the proteome and reveals decreased translational efficiency with aging phenotypes in mouse oocytes. Translational efficiency decrease is associated with the N6-methyladenosine (m6A) modification of transcripts. It is further clarified that m6A reader YTHDF3 is significantly decreased in aged oocytes, inhibiting oocyte meiotic maturation. YTHDF3 intervention perturbs the translatome of oocytes and suppress the translational efficiency of aging-associated maternal factors, such as Hells, to affect the oocyte maturation. Moreover, the translational landscape is profiled in human oocyte aging, and the similar translational changes of epigenetic modifications regulators between human and mice oocyte aging are observed. In particular, due to the translational silence of YTHDF3 in human oocytes, translation activity is not associated with m6A modification, but alternative splicing factor SRSF6. Together, the findings profile the specific translational landscapes during oocyte aging in mice and humans, and uncover non-conservative regulators on translation control in meiosis resumption and maternal aging.
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Affiliation(s)
- Jiana Huang
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Peigen Chen
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Lei Jia
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Tingting Li
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Xing Yang
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Qiqi Liang
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Yanyan Zeng
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Jiawen Liu
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Taibao Wu
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Wenqi Hu
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of MedicineTsinghua UniversityBeijing100084China
| | - Kehkooi Kee
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of MedicineTsinghua UniversityBeijing100084China
| | - Haitao Zeng
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Xiaoyan Liang
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
| | - Chuanchuan Zhou
- Reproductive Medicine CenterThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510655China
- Guangdong Engineering Technology Research Center of Fertility PreservationGuangzhou510610China
- Biomedical Innovation CenterThe Sixth Affiliated Hospital, Sun Yat‐sen UniversityGuangzhou510655China
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Zhang J, Bai S, Yan Y, Kang H, Li G, Feng Z, Ma W, Wang X, Ren J. Construction of lncRNA-m6A gene-mRNA regulatory network to identify m6A-related lncRNAs associated with the progression of lung adenocarcinoma. BMC Pulm Med 2023; 23:284. [PMID: 37537521 PMCID: PMC10401877 DOI: 10.1186/s12890-023-02545-x] [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: 01/03/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND We evaluated the prognostic value of m6A-related long noncoding RNAs (lncRNAs) in lung adenocarcinoma (LUAD). METHODS The expression levels of lncRNAs and mRNAs in LUAD and normal adjacent tissues from The Cancer Genome Atlas dataset were analyzed using the limma package. m6A enzyme-related differentially expressed lncRNAs and mRNAs were identified and used to construct a regulatory network. Survival analysis was performed and the correlation between lncRNAs, m6A regulators, and mRNAs was analyzed; followed by functional enrichment analysis. RESULTS A comparison of LUAD samples and normal tissues identified numerous differentially expressed lncRNAs and mRNAs, demonstrating that a comprehensive network was established. Two lncRNAs and six mRNAs were selected as prognosis related factors including SH3PXD2A-AS1, MAD2L1, CCNA2, and CDC25C. The pathological stage and recurrence status were identified as independent clinical factors (P < 0.05). The expression levels of these RNAs in the different clinical groups were consistent with those in the different risk groups. The interactions of m6A proteins, two lncRNAs, and six mRNAs were predicted, and functional analysis showed that m6A target mRNAs were involved in the cell cycle, progesterone-mediated oocyte maturation, and oocyte meiosis pathways. CONCLUSIONS These m6A target lncRNAs and mRNAs may be promising biomarkers for predicting clinical prognosis, and the lncRNA-m6A regulator-mRNA regulatory network could improve our understanding of m6A modification in LUAD progression.
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Affiliation(s)
- Jiangzhou Zhang
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, Shaanxi Province, 710061, China
- Department of Oncology, The Eighth Hospital of Wuhan, No. 1241 Zhongshan Avenue, Jiang'an District, Wuhan, Hubei Province, 430010, China
| | - Shuheng Bai
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, Shaanxi Province, 710061, China
| | - Yanli Yan
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, Shaanxi Province, 710061, China
| | - Haojing Kang
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, Shaanxi Province, 710061, China
| | - Guangzu Li
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, Shaanxi Province, 710061, China
| | - Zhaode Feng
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, Shaanxi Province, 710061, China
| | - Wen Ma
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, Shaanxi Province, 710061, China
| | - Xuan Wang
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, Shaanxi Province, 710061, China
| | - Juan Ren
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Yanta District, Xi'an, Shaanxi Province, 710061, China.
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8
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Diao MN, Zhang XJ, Zhang YF. The critical roles of m6A RNA methylation in lung cancer: from mechanism to prognosis and therapy. Br J Cancer 2023; 129:8-23. [PMID: 36997662 PMCID: PMC10307841 DOI: 10.1038/s41416-023-02246-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/05/2023] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
Lung cancer, a highly malignant disease, greatly affects patients' quality of life. N6-methyladenosine (m6A) is one of the most common posttranscriptional modifications of various RNAs, including mRNAs and ncRNAs. Emerging studies have demonstrated that m6A participates in normal physiological processes and that its dysregulation is involved in many diseases, especially pulmonary tumorigenesis and progression. Among these, regulators including m6A writers, readers and erasers mediate m6A modification of lung cancer-related molecular RNAs to regulate their expression. Furthermore, the imbalance of this regulatory effect adversely affects signalling pathways related to lung cancer cell proliferation, invasion, metastasis and other biological behaviours. Based on the close association between m6A and lung cancer, various prognostic risk models have been established and novel drugs have been developed. Overall, this review comprehensively elaborates the mechanism of m6A regulation in the development of lung cancer, suggesting its potential for clinical application in the therapy and prognostic assessment of lung cancer.
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Affiliation(s)
- Mei-Ning Diao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Xiao-Jing Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.
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9
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Tian L, Wang Y, Tian J, Song W, Li L, Che G. Prognostic Value and Genome Signature of m6A/m5C Regulated Genes in Early-Stage Lung Adenocarcinoma. Int J Mol Sci 2023; 24:ijms24076520. [PMID: 37047493 PMCID: PMC10095361 DOI: 10.3390/ijms24076520] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/19/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
RNA modifications implicate pathological and prognosis significance in cancer development and progression, of which, m6A and m5C are representative regulators. These RNA modifications could produce effects on the function of other RNA by regulating gene expression. Thus, in this study, we aimed to explore the correlation between m6A/m5C regulators and early-stage lung adenocarcinoma (LUAD). Only the early-stage LUAD samples were included in this investigation, and the RNA-seq dataset of The Cancer Genome Atlas (TCGA) cohort was utilized to evaluate the expression of 37 m6A/m5C regulated genes. Based on the expression level of these 37 genes, early-stage LUAD patients were divided into 2 clusters, which were performed by consensus clustering, and the m6A/m5C subtypes had significantly different prognostic outcomes (p < 0.001). Cluster1, which has a better prognosis, was characterized by the C3 (inflammatory) immune subtype, low immune infiltration, chemokine expression, major histocompatibility complex (MHC) expression, and immune checkpoint molecule expression. Furthermore, compared with cluster1, cluster2 showed a T cell exhaustion state, characterized by a high expression of immune checkpoint genes, and immune cells, such as T cells, CD8+ T cells, cytotoxic lymphocytes, NK cells, and so on. In addition, patients in cluster2 were with high tumor mutational burden (TMB) and numerous significant mutated oncogene and tumor suppressor genes, such as WNT10B, ERBB4, SMARCA4, TP53, and CDKN2A (p < 0.001). A total of 19 genes were mostly related to the prognosis of LUAD and were upregulated in cluster2 (p < 0.05), showing a positive correlation with the mRNA expression of 37 m6A/m5C regulated genes. The predictive risk model was constructed using Cox and LASSO (least absolute shrinkage and selection operator) regression analysis. Finally, a seven-gene m6A/m5C risk model, comprising of METTL3, NPLOC4, RBM15, YTHDF1, IGF2BP1, NSUN3, and NSUN7, was constructed to stratify the prognosis of early-stage LUAD (p = 0.0049, AUC = 0.791). The high-risk score was associated with a poorer prognosis. This model was also validated using two additional GEO datasets: GSE72094 (p = 0.011, AUC = 0.736) and GSE50081 (p = 0.012, AUC = 0.628). In summary, it was established that the m6A/m5C-regulated genes performed a crosstalk function in the mRNA expression of early-stage LUAD. By interacting with other mRNA genes, m6A/m5C modification disturbs DNA replication and the tumor immune microenvironment (TIME). The seven-gene risk model may be a critical tool for the prognostic assessment of early-stage LUAD.
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Affiliation(s)
- Long Tian
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yan Wang
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jie Tian
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenpeng Song
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lu Li
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence: (L.L.); (G.C.)
| | - Guowei Che
- Lung Cancer Center, Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence: (L.L.); (G.C.)
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10
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Chen L, Gao Y, Xu S, Yuan J, Wang M, Li T, Gong J. N6-methyladenosine reader YTHDF family in biological processes: Structures, roles, and mechanisms. Front Immunol 2023; 14:1162607. [PMID: 36999016 PMCID: PMC10043241 DOI: 10.3389/fimmu.2023.1162607] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
As the most abundant and conserved internal modification in eukaryote RNAs, N6-methyladenosine (m6A) is involved in a wide range of physiological and pathological processes. The YT521-B homology (YTH) domain-containing family proteins (YTHDFs), including YTHDF1, YTHDF2, and YTHDF3, are a class of cytoplasmic m6A-binding proteins defined by the vertebrate YTH domain, and exert extensive functions in regulating RNA destiny. Distinct expression patterns of the YTHDF family in specific cell types or developmental stages result in prominent differences in multiple biological processes, such as embryonic development, stem cell fate, fat metabolism, neuromodulation, cardiovascular effect, infection, immunity, and tumorigenesis. The YTHDF family mediates tumor proliferation, metastasis, metabolism, drug resistance, and immunity, and possesses the potential of predictive and therapeutic biomarkers. Here, we mainly summary the structures, roles, and mechanisms of the YTHDF family in physiological and pathological processes, especially in multiple cancers, as well as their current limitations and future considerations. This will provide novel angles for deciphering m6A regulation in a biological system.
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Affiliation(s)
- Lin Chen
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Gao
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Simiao Xu
- Division of Endocrinology, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Branch of National Clinical Research Center for Metabolic Disease, Wuhan, China
| | - Jinxiong Yuan
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Wang
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tianyu Li
- Trauma Center/Department of Emergency and Traumatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Gong
- Department of Biliary-Pancreatic Surgery, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jun Gong,
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11
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HNRNPA2B1-Mediated MicroRNA-92a Upregulation and Section Acts as a Promising Noninvasive Diagnostic Biomarker in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15051367. [PMID: 36831695 PMCID: PMC9954252 DOI: 10.3390/cancers15051367] [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: 12/23/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
MicroRNA-92a (miR-92a) may serve as a novel promising biomarker in multiple cancers, including colorectal cancer (CRC); however, the diagnostic accuracy and the underlying molecular mechanism of miR-92a in CRC is poorly understood. We first carried out meta-analysis and found that serum/plasma miR-92a yield better diagnostic efficacy when compared to stool samples and CRC tissues, and this finding was validated by our independent study through stool sample. Multiple bioinformatics assay indicated that miR-92a expression was positively correlated with heterogeneous nuclear ribonucleoproteins A2/B1 (HNRNPA2B1) expression and closely related with the clinical characteristics of CRC. Experimental evidence showed that knockdown of HNRNPA2B1 could significantly decrease miR-92a expression and secretion in RKO cells. HNRNPA2B1 mediated miR-92a via m6A RNA modification. These findings indicate that HNRNPA2B1-m6A RNA modification-derived MicroRNA-92a upregulation and section from the local CRC acts a candidate noninvasive serum biomarker in colorectal cancer. Our study provides a novel insight into miR-92a mechanisms in relation to both expression and secretion for CRC diagnosis.
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12
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Roles of RNA Methylations in Cancer Progression, Autophagy, and Anticancer Drug Resistance. Int J Mol Sci 2023; 24:ijms24044225. [PMID: 36835633 PMCID: PMC9959100 DOI: 10.3390/ijms24044225] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
RNA methylations play critical roles in RNA processes, including RNA splicing, nuclear export, nonsense-mediated RNA decay, and translation. Regulators of RNA methylations have been shown to be differentially expressed between tumor tissues/cancer cells and adjacent tissues/normal cells. N6-methyladenosine (m6A) is the most prevalent internal modification of RNAs in eukaryotes. m6A regulators include m6A writers, m6A demethylases, and m6A binding proteins. Since m6A regulators play important roles in regulating the expression of oncogenes and tumor suppressor genes, targeting m6A regulators can be a strategy for developing anticancer drugs. Anticancer drugs targeting m6A regulators are in clinical trials. m6A regulator-targeting drugs could enhance the anticancer effects of current chemotherapy drugs. This review summarizes the roles of m6A regulators in cancer initiation and progression, autophagy, and anticancer drug resistance. The review also discusses the relationship between autophagy and anticancer drug resistance, the effect of high levels of m6A on autophagy and the potential values of m6A regulators as diagnostic markers and anticancer therapeutic targets.
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Zhu Y, Li J, Yang H, Yang X, Zhang Y, Yu X, Li Y, Chen G, Yang Z. The potential role of m6A reader YTHDF1 as diagnostic biomarker and the signaling pathways in tumorigenesis and metastasis in pan-cancer. Cell Death Dis 2023; 9:34. [PMID: 36707507 PMCID: PMC9883452 DOI: 10.1038/s41420-023-01321-4] [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: 11/26/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/29/2023]
Abstract
m6A is an important RNA methylation in progression of various human cancers. As the m6A reader protein, YTHDF1 is reported to accelerate m6A-modified mRNAs translation in cytoplasm. It is highly expressed in various human cancers and contributes to the progression and metastasis of cancers. YTHDF1 was closely associated with poor prognosis and also used as a molecular marker for clinical diagnosis or therapy in human cancers. It has been reported to promote chemoresistance to Adriamycin, Cisplatin and Olaparib by increasing mRNA stability of its target molecule. Moreover, it contributes to CSC-like characteristic of tumor cells and inducing the antitumor immune microenvironment. Here, we reviewed the clinical diagnostic and prognostic values of YTHDF1, as well as the molecular mechanisms of YTHDF1 in progression and metastasis of human cancers.
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Affiliation(s)
- Yanan Zhu
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Jing Li
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Hang Yang
- grid.415444.40000 0004 1800 0367Department of Rehabilitation Medicine, The Second Affiliated Hospital of Kunming Medical University, 650106 Kunming, Yunnan China
| | - Xinyi Yang
- grid.413458.f0000 0000 9330 9891Guizhou Medical University, 550004 Guiyang, Guizhou China
| | - Ya Zhang
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Xinchao Yu
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Ying Li
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Gangxian Chen
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
| | - Zuozhang Yang
- grid.452826.fBone and Soft Tissue Tumors Research Centre of Yunnan Province, Department of Orthopaedics, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), 650118 Kunming, Yunnan China
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14
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Identification of Potential Key Genes and Prognostic Biomarkers of Lung Cancer Based on Bioinformatics. BIOMED RESEARCH INTERNATIONAL 2023; 2023:2152432. [PMID: 36714024 PMCID: PMC9876670 DOI: 10.1155/2023/2152432] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/31/2022] [Accepted: 11/17/2022] [Indexed: 01/19/2023]
Abstract
Objective To analyze and identify the core genes related to the expression and prognosis of lung cancer including lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) by bioinformatics technology, with the aim of providing a reference for clinical treatment. Methods Five sets of gene chips, GSE7670, GSE151102, GSE33532, GSE43458, and GSE19804, were obtained from the Gene Expression Omnibus (GEO) database. After using GEO2R to analyze the differentially expressed genes (DEGs) between lung cancer and normal tissues online, the common DEGs of the five sets of chips were obtained using a Venn online tool and imported into the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database for Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The protein-protein interaction (PPI) network was constructed by STRING online software for further study, and the core genes were determined by Cytoscape software and KEGG pathway enrichment analysis. The clustering heat map was drawn by Excel software to verify its accuracy. In addition, we used the University of Alabama at Birmingham Cancer (UALCAN) website to analyze the expression of core genes in P53 mutation status, confirmed the expression of crucial core genes in lung cancer tissues with Gene Expression Profiling Interactive Analysis (GEPIA) and GEPIA2 online software, and evaluated their prognostic value in lung cancer patients with the Kaplan-Meier online plotter tool. Results CHEK1, CCNB1, CCNB2, and CDK1 were selected. The expression levels of these four genes in lung cancer tissues were significantly higher than those in normal tissues. Their increased expression was negatively correlated with lung cancer patients (including LUAD and LUSC) prognosis and survival rate. Conclusion CHEK1, CCNB1, CCNB2, and CDK1 are the critical core genes of lung cancer and are highly expressed in lung cancer. They are negatively correlated with the prognosis of lung cancer patients (including LUAD and LUSC) and closely related to the formation and prediction of lung cancer. They are valuable predictors and may be predictive biomarkers of lung cancer.
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15
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Verghese M, Wilkinson E, He YY. Recent Advances in RNA m 6A Modification in Solid Tumors and Tumor Immunity. Cancer Treat Res 2023; 190:95-142. [PMID: 38113000 DOI: 10.1007/978-3-031-45654-1_4] [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] [Indexed: 12/21/2023]
Abstract
An analogous field to epigenetics is referred to as epitranscriptomics, which focuses on the study of post-transcriptional chemical modifications in RNA. RNA molecules, including mRNA, tRNA, rRNA, and other non-coding RNA molecules, can be edited with numerous modifications. The most prevalent modification in eukaryotic mRNA is N6-methyladenosine (m6A), which is a reversible modification found in over 7000 human genes. Recent technological advances have accelerated the characterization of these modifications, and they have been shown to play important roles in many biological processes, including pathogenic processes such as cancer. In this chapter, we discuss the role of m6A mRNA modification in cancer with a focus on solid tumor biology and immunity. m6A RNA methylation and its regulatory proteins can play context-dependent roles in solid tumor development and progression by modulating RNA metabolism to drive oncogenic or tumor-suppressive cellular pathways. m6A RNA methylation also plays dynamic roles within both immune cells and tumor cells to mediate the anti-tumor immune response. Finally, an emerging area of research within epitranscriptomics studies the role of m6A RNA methylation in promoting sensitivity or resistance to cancer therapies, including chemotherapy, targeted therapy, and immunotherapy. Overall, our understanding of m6A RNA methylation in solid tumors has advanced significantly, and continued research is needed both to fill gaps in knowledge and to identify potential areas of focus for therapeutic development.
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Affiliation(s)
- Michelle Verghese
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA
- Pritzker School of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Emma Wilkinson
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA
- Committee on Cancer Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, 60637, USA.
- Committee on Cancer Biology, University of Chicago, Chicago, IL, 60637, USA.
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16
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Nag S, Goswami B, Das Mandal S, Ray PS. Cooperation and competition by RNA-binding proteins in cancer. Semin Cancer Biol 2022; 86:286-297. [PMID: 35248729 DOI: 10.1016/j.semcancer.2022.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023]
Abstract
Post-transcriptional regulation of gene expression plays a major role in determining the cellular proteome in health and disease. Post-transcriptional control mechanisms are disrupted in many cancers, contributing to multiple processes of tumorigenesis. RNA-binding proteins (RBPs), the main post-transcriptional regulators, often show altered expression and activity in cancer cells. Dysregulation of RBPs contributes to many cancer phenotypes, functioning in complex regulatory networks with other cellular players such as non-coding RNAs, signaling mediators and transcription factors to alter the expression of oncogenes and tumor suppressor genes. RBPs often function combinatorially, based on their binding to target sequences/structures on shared mRNA targets, to regulate the expression of cancer-related genes. This gives rise to cooperativity and competition between RBPs in mRNA binding and resultant functional outcomes in post-transcriptional processes such as mRNA splicing, stability, export and translation. Cooperation and competition is also observed in the case of interaction of RBPs and microRNAs with mRNA targets. RNA structural change is a common mechanism mediating the cooperative/competitive interplay between RBPs and between RBPs and microRNAs. RNA modifications, leading to changes in RNA structure, add a new dimension to cooperative/competitive binding of RBPs to mRNAs, further expanding the RBP regulatory landscape. Therefore, cooperative/competitive interplay between RBPs is a major determinant of the RBP interactome and post-transcriptional regulation of gene expression in cancer cells.
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Affiliation(s)
- Sharanya Nag
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Binita Goswami
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Sukhen Das Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India.
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17
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Shi Q, Han S, Liu X, Wang S, Ma H. Integrated single-cell and transcriptome sequencing analyses determines a chromatin regulator-based signature for evaluating prognosis in lung adenocarcinoma. Front Oncol 2022; 12:1031728. [PMID: 36324565 PMCID: PMC9618736 DOI: 10.3389/fonc.2022.1031728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/28/2022] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Accumulating evidence has highlighted the significance of chromatin regulator (CR) in pathogenesis and progression of cancer. However, the prognostic role of CRs in LUAD remains obscure. We aim to detect the prognostic value of CRs in LUAD and create favorable signature for assessing prognosis and clinical value of LUAD patients. METHODS The mRNA sequencing data and clinical information were obtained from TCGA and GEO databases. Gene consensus clustering analysis was utilized to determine the molecular subtype of LUAD. Cox regression methods were employed to set up the CRs-based signature (CRBS) for evaluating survival rate in LUAD. Biological function and signaling pathways were identified by KEGG and GSEA analyses. In addition, we calculated the infiltration level of immunocyte by CIBERSORT algorithm. The expressions of model hub genes were detected in LUAD cell lines by real-time polymerase chain reaction (PCR). RESULTS KEGG analysis suggested the CRs were mainly involved in histone modification, nuclear division and DNA modification. Consensus clustering analysis identified a novel CRs-associated subtype which divided the combined LUAD cohort into two clusters (C1 = 217 and C2 = 296). We noticed that a remarkable discrepancy in survival rate among two clusters. Then, a total of 120 differentially expressed CRs were enrolled into stepwise Cox analyses. Four hub CRs (CBX7, HMGA2, NPAS2 and PRC1) were selected to create a risk signature which could accurately forecast patient outcomes and differentiate patient risk. GSEA unearthed that mTORC1 pathway, PI3K/Akt/mTOR and p53 pathway were greatly enriched in CRBS-high cohort. Moreover, the infiltration percentages of macrophage M0, macrophage M2, resting NK cells, memory B cells, dendritic cells and mast cells were statistically significantly different in the two groups. PCR assay confirmed the differential expression of four model biomarkers. CONCLUSIONS Altogether, our project developed a robust risk signature based on CRs and offered novel insights into individualized treatment for LUAD cases.
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Affiliation(s)
- Qingtong Shi
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Thoracic Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Song Han
- Department of Thoracic Surgery, Suzhou Science and Technology Town Hospital, Suzhou, China
| | - Xiong Liu
- Department of Thoracic Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
- Graduate School of Dalian Medical University, Dalian, China
| | - Saijian Wang
- Department of Thoracic Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
- Graduate School of Dalian Medical University, Dalian, China
| | - Haitao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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18
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Abstract
Pyroptosis, as a proinflammatory form of regulated cell death, plays an important role in multiple cancers. However, the diagnostic and prognostic values of pyroptosis and its interaction with tumor immunity in pan-cancer are still unclear. Here, we show an elevated general expression of 17 pyroptosis-associated genes of tumor patients with high-immune-activity and a reduced pyroptosis in low-immune-activity tumors. Moreover, pyroptosis is positively correlated with immune infiltration and immune-related signatures across 30 types of cancer. Furthermore, our experimental data suggest that pyroptosis directly modulate the expression of immune checkpoint molecules and cytokines. We generate a pyroptosis score model as a potential independent prognostic indicator in melanoma patients. Interestingly, 3 of pyroptosis-associated genes including CASP1, CASP4 and PYCARD, can predict the effectiveness of anti-PD-1 immunotherapy for patients with melanoma. Our study demonstrates that pyroptosis correlates with tumor immunity and prognosis, might be used as a potential target for immune therapy. A pan-cancer analysis demonstrates that pyroptosis is involved in tumor development, prognosis and immunotherapy through the promotion of tumor immunity.
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19
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Lu X, Li R, Ying Y, Zhang W, Wang W. Gene signatures, immune infiltration, and drug sensitivity based on a comprehensive analysis of m6a RNA methylation regulators in cervical cancer. J Transl Med 2022; 20:385. [PMID: 36058934 PMCID: PMC9441061 DOI: 10.1186/s12967-022-03600-7] [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: 04/19/2022] [Accepted: 08/18/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Cervical cancer is the fourth most common cancer in women. N6-dimethyladenosine (m6A) mRNA methylation is closely associated with cervical cancer. METHODS Using TCGA database, we studied the expression and mutation of m6A-related genes in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) and obtained genetic characteristics based on an m6A risk model and prognostic value of m6A. We studied the effects of the m6A risk score on immune features and genomic changes of patients with CESC, evaluated the sensitivity of patients with CESC to different small-molecule drugs based on the m6A risk score, and established a clinical prediction model. RESULTS Ten m6A-related genes were differentially expressed between CESC and normal tissues. High-risk patients had a low overall survival (OS) and significantly low immune scores but showed no significantly altered stromal scores. The tumor mutation burden (TMB) and tumor neoantigen levels significantly differed between the high- and low-risk groups. In the high-risk group, copy number variation (CNV) changes mainly led to gene amplification, while in the low-risk group, CNV changes primarily manifested as gene copy number deletions. ZC3H13 expression was low in CESC tissues. ZC3H13 knockdown promoted CESC cell proliferation, migration, and invasion, reducing the RNA methylation levels. Rapamycin suppressed the CESC cell proliferation, migration, and invasion abilities, increasing the m6A levels. CONCLUSION m6A mRNA methylation is closely related to the occurrence, development, immune invasion, drug sensitivity, and prognosis of cervical cancer. The prognostic m6A feature model of m6A signature genes can accurately predict the OS of patients with CESC. Drugs targeting factors regulating m6A mRNA methylation might offer a good prospect for treating cervical cancer.
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Affiliation(s)
- Xiaoqin Lu
- grid.452842.d0000 0004 8512 7544Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Zhengzhou University, 2nd, Jingba RoadHenan Province, Zhengzhou, 450053 China
| | - Rui Li
- grid.452842.d0000 0004 8512 7544Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Zhengzhou University, 2nd, Jingba RoadHenan Province, Zhengzhou, 450053 China
| | - Yanqi Ying
- grid.452842.d0000 0004 8512 7544Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Zhengzhou University, 2nd, Jingba RoadHenan Province, Zhengzhou, 450053 China
| | - Wenyi Zhang
- grid.452842.d0000 0004 8512 7544Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Zhengzhou University, 2nd, Jingba RoadHenan Province, Zhengzhou, 450053 China
| | - Wuliang Wang
- grid.452842.d0000 0004 8512 7544Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Zhengzhou University, 2nd, Jingba RoadHenan Province, Zhengzhou, 450053 China
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20
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Multiple Roles of m6A RNA Modification in Translational Regulation in Cancer. Int J Mol Sci 2022; 23:ijms23168971. [PMID: 36012237 PMCID: PMC9408962 DOI: 10.3390/ijms23168971] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Despite its discovery in the early 1970s, m6A modification within mRNA molecules has only powerfully entered the oncology field in recent years. This chemical modification can control all aspects of the maturation of mRNAs, both in the nucleus and in the cytoplasm. Thus, the alteration in expression levels of writers, erasers, and readers may significantly contribute to the alteration of gene expression observed in cancer. In particular, the activation of oncogenic pathways can lead to an alteration of the global rate of mRNA translation or the selective translation of specific mRNAs. In both cases, m6A can play an important role. In this review, we highlight the role of m6A in the regulation of translation by focusing on regulatory mechanisms and cancer-related functions of this novel but still controversial field.
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21
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Fang Z, Mei W, Qu C, Lu J, Shang L, Cao F, Li F. Role of m6A writers, erasers and readers in cancer. Exp Hematol Oncol 2022; 11:45. [PMID: 35945641 PMCID: PMC9361621 DOI: 10.1186/s40164-022-00298-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/04/2022] [Indexed: 02/06/2023] Open
Abstract
The N(6)-methyladenosine (m6A) modification is the most pervasive modification of human RNAs. In recent years, an increasing number of studies have suggested that m6A likely plays important roles in cancers. Many studies have demonstrated that m6A is involved in the biological functions of cancer cells, such as proliferation, invasion, metastasis, and drug resistance. In addition, m6A is closely related to the prognosis of cancer patients. In this review, we highlight recent advances in understanding the function of m6A in various cancers. We emphasize the importance of m6A to cancer progression and look forward to describe future research directions.
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Affiliation(s)
- Zhen Fang
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Wentong Mei
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Chang Qu
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jiongdi Lu
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
| | - Feng Cao
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China.
| | - Fei Li
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China.
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22
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Yang L, Xiong H, Li X, Li Y, Zhou H, Lin X, Chan TF, Li R, Lai KP, Chen X. Network Pharmacology and Comparative Transcriptome Reveals Biotargets and Mechanisms of Curcumol Treating Lung Adenocarcinoma Patients With COVID-19. Front Nutr 2022; 9:870370. [PMID: 35520289 PMCID: PMC9063984 DOI: 10.3389/fnut.2022.870370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/16/2022] [Indexed: 12/31/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has led to 4,255,892 deaths worldwide. Although COVID-19 vaccines are available, mutant forms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have reduced the effectiveness of vaccines. Patients with cancer are more vulnerable to COVID-19 than patients without cancer. Identification of new drugs to treat COVID-19 could reduce mortality rate, and traditional Chinese Medicine(TCM) has shown potential in COVID-19 treatment. In this study, we focused on lung adenocarcinoma (LUAD) patients with COVID-19. We aimed to investigate the use of curcumol, a TCM, to treat LUAD patients with COVID-19, using network pharmacology and systematic bioinformatics analysis. The results showed that LUAD and patients with COVID-19 share a cluster of common deregulated targets. The network pharmacology analysis identified seven core targets (namely, AURKA, CDK1, CCNB1, CCNB2, CCNE1, CCNE2, and TTK) of curcumol in patients with COVID-19 and LUAD. Clinicopathological analysis of these targets demonstrated that the expression of these targets is associated with poor patient survival rates. The bioinformatics analysis further highlighted the involvement of this target cluster in DNA damage response, chromosome stability, and pathogenesis of LUAD. More importantly, these targets influence cell-signaling associated with the Warburg effect, which supports SARS-CoV-2 replication and inflammatory response. Comparative transcriptomic analysis on in vitro LUAD cell further validated the effect of curcumol for treating LUAD through the control of cell cycle and DNA damage response. This study supports the earlier findings that curcumol is a potential treatment for patients with LUAD and COVID-19.
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Affiliation(s)
- Lu Yang
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Hao Xiong
- Guilin Center for Disease Control and Prevention, Guilin, China
| | - Xin Li
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
| | - Yu Li
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Huanhuan Zhou
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Xiao Lin
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ting Fung Chan
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Rong Li
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
- *Correspondence: Rong Li
| | - Keng Po Lai
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
- Keng Po Lai
| | - Xu Chen
- Department of Pharmacy, Guilin Medical University, Guilin, China
- Xu Chen ;
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23
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Xiao X, Rui B, Rui H, Ju M, Hongtao L. MEOX1 suppresses the progression of lung cancer cells by inhibiting the cell-cycle checkpoint gene CCNB1. ENVIRONMENTAL TOXICOLOGY 2022; 37:504-513. [PMID: 34837450 DOI: 10.1002/tox.23416] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/04/2021] [Accepted: 11/14/2021] [Indexed: 05/12/2023]
Abstract
The previous study has shown that transcriptional factor MEOX1 could promote proliferation and sphere formation ability of non-small cell lung cancer (NSCLC) cells, however, we found that MEOX1 mRNA was lowly expressed in lung cancer tissues compared to that in normal adjacent tissues, and MEOX1 mRNA expression was positively correlated with the survival of lung cancer patients, especially in lung adenocarcinoma patients. Functional experiments using in vitro and in vivo experiments revealed that stable overexpression of MEOX1 significantly suppressed the proliferation ability, promoted cell cycle arrest in G2 phase, and apoptotic ability of NSCLC cells. Additionally, it was identified that MEOX1 and CCNB1 mRNA expression exhibited a negative correlation in different lung cancer tissues. Mechanistically, we indicated that MEOX1 bound to the transcriptional initiation site of CCNB1 and thus suppressed CCNB1 expression. Notably, CCNB1 overexpression rescued the inhibition of MEOX1 overexpression on NSCLC progression. This study deciphers a novel MEOX1/CCNB1 axis suppressing NSCLC progression.
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Affiliation(s)
- Xie Xiao
- Department of Cardio-thoracic Surgery, Xinhua Hospital Chongming Branch, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bi Rui
- Department of Cardio-thoracic Surgery, Xinhua Hospital Chongming Branch, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hu Rui
- Department of Cardio-thoracic Surgery, Xinhua Hospital Chongming Branch, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mei Ju
- Department of Cardio-thoracic Surgery, Xinhua Hospital Chongming Branch, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liu Hongtao
- Department of Cardio-thoracic Surgery, Xinhua Hospital Chongming Branch, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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24
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Liu X, Zuo X, Ma L, Wang Q, Zhu L, Li L, Zhao X. Integrated Analysis of the m6A-Related lncRNA Identified lncRNA ABALON/miR-139-3p/ NOB1 Axis Was Involved in the Occurrence of Lung Cancer. Cancer Manag Res 2021; 13:8707-8722. [PMID: 34849026 PMCID: PMC8627251 DOI: 10.2147/cmar.s339032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/15/2021] [Indexed: 12/30/2022] Open
Abstract
Background Lung cancer has the characteristics of early metastasis, high recurrence, and high mortality rate despite emerging advances in diagnostic. Early diagnosis can significantly improve the patient’s chances of cure and survival. Purpose This study aimed to identify and assess a prognostic lncRNA/miRNA/gene signature in patients with lung cancer. Methods Pearson correlation analysis, univariate Cox analysis and LASSO Cox analysis were used to construct a lung cancer prognostic risk model based on m6A-related lncRNA. The interaction between lncRNA-miRNA-gene was verified by luciferase reporter gene experiment. Results The Pearson correlation analysis determined that 1655 lncRNAs significantly correlated with the expression of m6A genes. A lung cancer prognostic risk model, including 14 m6A-related lncRNAs, was constructed through univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox analysis. ABALON was identified as the key lncRNA through cluster analysis and gene expression difference analysis. Conclusion It was experimentally verified that ABALON acted as a competing endogenous RNA by sponging miR-139-3p and indirectly regulated the expression of NOB1. This study provided a new biological target for the early diagnosis of lung cancer and a new direction for studying the mechanism of lung cancer.
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Affiliation(s)
- Xinhong Liu
- College of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China
| | - Xin Zuo
- Department of Gastroenterology, The Sixth People's Hospital of Chongqing, Chongqing, People's Republic of China
| | - Lijun Ma
- College of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China
| | - Qin Wang
- College of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China
| | - Lilan Zhu
- College of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China
| | - Li Li
- College of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China
| | - Xin Zhao
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China.,Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, People's Republic of China
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