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Peng R, Jiang S, Jin Z. The potential mechanism of WT1-associated protein-induced N-6-methyladenosine modification of colony-stimulating factor 2 in the progression of oral squamous cell carcinoma by JAK/STAT3 pathway regulation. Eur J Oral Sci 2024; 132:e13001. [PMID: 38831514 DOI: 10.1111/eos.13001] [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: 12/07/2023] [Revised: 05/11/2024] [Accepted: 05/19/2024] [Indexed: 06/05/2024]
Abstract
Colony-stimulating factor 2 (CSF2) plays a regulatory role in numerous cancers. However, there is needed to investigate the role of CSF2 in oral squamous cell carcinoma (OSCC) malignant phenotype and the specific mechanisms of CSF2 N-6-methyladenosine (m6A) modification. Therefore, we investigated the regulatory mechanism of m6A-modified CSF2 by WT1-associated protein (WTAP) in OSCC via qRT-PCR, western blot, WTAP and CSF2 overexpression in OSCC. In a panel of OSCCs, Kaplan-Meier plot analysis indicated that high expression of CSF2 was associated with poorer prognosis. Cell functional experiments revealed that enrichment of CSF2 promoted the proliferation and migration of OSCC cells by activating the JAK/STAT3 pathway, whereas the reduced expression of CSF2 resulted in the malignant decline of OSCC cells by blocking the JAK/STAT3 pathway. This study also confirmed that WTAP enhanced the m6A level of CSF2 and facilitated the expression of CSF2 and that CSF2 silencing blocked the invasive phenotype of OSCC cells and reversed the malignancy induced by WTAP overexpression. Overall, this study demonstrated that WTAP mediates the m6A modification of CSF2 and the JAK/STAT3 pathway, which plays an oncogenic role in the development of OSCC and can be a target for the treatment of patients with OSCC.
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Affiliation(s)
- Ruobing Peng
- Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Shengjun Jiang
- Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhongzhi Jin
- Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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2
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Wang Y, Seliger B. Identification of RNA-binding protein hnRNP C targeting the 3'UTR of the TAP-associated glycoprotein tapasin in melanoma. Oncoimmunology 2024; 13:2370928. [PMID: 38948930 PMCID: PMC11212565 DOI: 10.1080/2162402x.2024.2370928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024] Open
Abstract
Deregulation or loss of the human leukocyte antigen class I (HLA-I) molecules on tumor cells leading to inhibition of CD8+ T cell recognition is an important tumor immune escape strategy, which could be caused by a posttranscriptional control of molecules in the HLA-I pathway mediated by RNA-binding proteins (RBPs). So far, there exists only limited information about the interaction of RBPs with HLA-I-associated molecules, but own work demonstrated a binding of the heterogeneous ribonucleoprotein C (hnRNP C) to the 3' untranslated region (UTR) of the TAP-associated glycoprotein tapasin (tpn). In this study, in silico analysis of pan-cancer TCGA datasets revealed that hnRNP C is higher expressed in tumor specimens compared to corresponding normal tissues, which is negatively correlated to tpn expression, T cell infiltration and the overall survival of tumor patients. Functional analysis demonstrated an upregulation of tpn expression upon siRNA-mediated downregulation of hnRNP C, which is accompanied by an increased HLA-I surface expression. Thus, hnRNP C has been identified to target tpn and its inhibition could improve the HLA-I surface expression on melanoma cells suggesting its use as a possible biomarker for T-cell-based tumor immunotherapies.
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Affiliation(s)
- Yuan Wang
- Institute for Medical Immunology, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Barbara Seliger
- Institute for Medical Immunology, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
- Institute of Translational Immunology, Medical School “Theodor Fontane”, Brandenburg an der Havel, Germany
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Liu Y, Shen L, Li Y, Sun X, Liang L, Jiang S, Zhang Z, Tang X, Tao Y, Xie L, Jiang Y, Cong L. ETS1-mediated Regulation of SOAT1 Enhances the Malignant Phenotype of Oral Squamous Cell Carcinoma and Induces Tumor-associated Macrophages M2-like Polarization. Int J Biol Sci 2024; 20:3372-3392. [PMID: 38993570 PMCID: PMC11234219 DOI: 10.7150/ijbs.93815] [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: 01/02/2024] [Accepted: 05/22/2024] [Indexed: 07/13/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) is an aggressive cancer that poses a substantial threat to human life and quality of life globally. Lipid metabolism reprogramming significantly influences tumor development, affecting not only tumor cells but also tumor-associated macrophages (TAMs) infiltration. SOAT1, a critical enzyme in lipid metabolism, holds high prognostic value in various cancers. This study revealed that SOAT1 is highly expressed in OSCC tissues and positively correlated with M2 TAMs infiltration. Increased SOAT1 expression enhanced the capabilities of cell proliferation, tumor sphere formation, migration, and invasion in OSCC cells, upregulated the SREBP1-regulated adipogenic pathway, activated the PI3K/AKT/mTOR pathway and promoted M2-like polarization of TAMs, thereby contributing to OSCC growth both in vitro and in vivo. Additionally, we explored the upstream transcription factors that regulate SOAT1 and discovered that ETS1 positively regulates SOAT1 expression levels. Knockdown of ETS1 effectively inhibited the malignant phenotype of OSCC cells, whereas restoring SOAT1 expression significantly mitigated this suppression. Based on these findings, we suggest that SOAT1 is regulated by ETS1 and plays a pivotal role in the development of OSCC by facilitating lipid metabolism and M2-like polarization of TAMs. We propose that SOAT1 is a promising target for OSCC therapy with tremendous potential.
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Affiliation(s)
- Yueying Liu
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
| | - Li Shen
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
| | - Yi Li
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
| | - Xiaoyan Sun
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
| | - Lu Liang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
| | - Shiyao Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
| | - Ziyun Zhang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
| | - Xingjie Tang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
| | - Yongguang Tao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, School of Basic Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Li Xie
- Department of Head and Neck Surgery, Hunan Cancer Hospital, Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Yiqun Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
| | - Li Cong
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013 Hunan, China
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Duan K, Fang K, Sui C. TFAIP6 facilitates hepatocellular carcinoma cell glycolysis through upregulating c-myc/PKM2 axis. Heliyon 2024; 10:e30959. [PMID: 38813227 PMCID: PMC11133704 DOI: 10.1016/j.heliyon.2024.e30959] [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: 10/23/2023] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most prevalent liver cancer. Despite of the improvement of therapies, the durable response rate and survival benefit are still limited for HCC patients. It's urgent to clarify the molecular mechanisms and find therapeutic strategies to improve the clinical outcome. TNFα-stimulated gene-6 (TNFAIP6) plays a critical role in the prognosis of various tumors, but its roles in HCC are still unclear. Methods Quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC) analysis were employed to evaluate the clinical relevance of TNFAIP6 expressions in HCC patients. Cell counting kit-8 (CCK-8), Edu assay, and transwell assay were performed to evaluate the malignancy of HCC cells. Glucose uptake, lactate production, ATP production, extracellular acidification rate (ECAR) by Seahorse XF analyzer were employed to evaluate the role of TNFAIP6 in the regulation of aerobic glycolysis. The expressions of key proteins involved in glycolysis were examined by Western blot. Co-immunoprecipitation (Co-IP) and chromatin immunoprecipitation (ChIP) were used for protein-protein interactions or protein-RNA interactions respectively. Knockdown and overexpression of TNFAIP6 in HCC cells were employed for analyzing the functions of TNFAIP6 in HCC. Results TNFAIP6 was significantly upregulated in HCC and predicted a poor clinical prognosis. Knockdown of TNFAIP6 inhibited in vitro cell proliferation, invasion, migration, as well as glycolysis in HCC cells. Mechanistically, we clarified that TNFAIP6 interacted with heterogeneous nuclear ribonucleoprotein C (HNRNPC), stabilized c-Myc mRNA and upregulated pyruvate kinase M2 (PKM2) to promote glycolysis. Conclusions Our study reveals a molecular mechanism by which TNFAIP6 promotes aerobic glycolysis, which is beneficial for malignance of HCC and provides a potential clinical therapy for disease management.
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Affiliation(s)
- Kecai Duan
- Department of Special Medical Services, Third Affiliated Hospital of Naval Medical University (Shanghai Eastern Hepatobiliary Surgery Hospital), China
| | - Kunpeng Fang
- Department of Special Medical Services, Third Affiliated Hospital of Naval Medical University (Shanghai Eastern Hepatobiliary Surgery Hospital), China
| | - Chengjun Sui
- Department of Special Medical Services, Third Affiliated Hospital of Naval Medical University (Shanghai Eastern Hepatobiliary Surgery Hospital), China
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Zhou Q, Song W, Li X, Lin J, Zhu C, Cao L, Li W, Lin S. N6-Methyladenosine reader HNRNPC-mediated downregulation of circITCH prevents miR-224-3p sequestering and contributes to tumorigenesis in nasopharyngeal carcinoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:2893-2907. [PMID: 38299319 DOI: 10.1002/tox.24139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/20/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024]
Abstract
BACKGROUND N6-Methyladenosine (m6A) RNA methylation modulators are implicated in nasopharyngeal carcinoma (NPC). Circular RNAs (circRNAs) stimulate/inhibit the development of NPC by sponging microRNAs (miRNAs). Herein, m6A modifications affecting the circRNA/miRNA axis in NPC were explored. METHODS Twenty prognostic m6A RNA methylation regulators were identified from 504 head/neck squamous cell carcinoma and 44 normal samples from The Cancer Genome Atlas (TCGA). Differentially expressed miRNAs were screened from the TCGA and Gene Expression Omnibus (GEO) databases. RNA-binding protein (RBP)-circRNA and circRNA-miRNA interactive pairs were verified using RBPmap and RNAhybrid, respectively. The RBP/circRNA/miRNA network was constructed using Cytoscape. Furthermore, CircITCH (hsa_circ_00059948), HNRNPC, and miR-224-3p expressions were detected by western blotting and quantitative polymerase chain reaction. The role of circITCH in NPC was examined using apoptosis, scratch wound healing, transwell invasion, and cell counting kit-8 assays. Finally, CircITCH-miR-224-3p and circITCH-HNRNPC interactions were assessed by dual-luciferase reporter and RNA-immunoprecipitation (RIP) assays, respectively. RESULTS Bioinformatics analysis revealed that high pathological grade, late-stage tumors, and low survival were associated with increased HNRNPC expression. MiR-224-3p was upregulated in NPC and sequestered by circITCH. Construction of the RBP/circRNA/miRNA network highlighted the HNRNPC/circITCH/miR-224-3p axis. In vitro experiments demonstrated decreased circITCH expression and increased HNRNPC and miR-224-3p expressions in NPC. In NPC cells overexpressing circITCH, HNRNPC and miR-224-3p expressions were significantly decreased. Dual-luciferase assays demonstrated a targeting relationship between circITCH and miR-224-3p, and RIP assays demonstrated interaction of HNRNPC targets with circITCH. CONCLUSION CircITCH overexpression inhibited NPC progression by sequestering miR-224-3p, and HNRNPC reduced circITCH expression through direct interaction.
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Affiliation(s)
- Qiang Zhou
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Wei Song
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Xianhui Li
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Jinyan Lin
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Chuansai Zhu
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Longhe Cao
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Wanqing Li
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Sen Lin
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
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Chen C, Huang F, Li X, Liu L, Zhang J, Zhao J, Zhang W, Li H, Xu W, Qi Y, Wang Y. Identification of splicing factors signature predicting prognosis risk and the mechanistic roles of novel oncogenes in HNSCC. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167115. [PMID: 38458543 DOI: 10.1016/j.bbadis.2024.167115] [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: 09/21/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the most frequent subtype of head and neck cancer, generally with a poor prognosis and limited therapeutic options due to its highly heterogeneous malignancy. In this study, we screened functional splicing regulatory RNA binding proteins (RBPs) that were closely related with the prognosis of HNSCC patients and showed significant expression differences between HNSCC tumors and normal tissues. Based on this finding, we chose six candidate genes (HNRNPC, ZCRB1, RBM12B, SF3A2, SF3B3, and SRSF11) to generate a prognostic prediction model and validated the accuracy of the prognostic model for predicting patient survival outcomes. We found that the risk score predicted by our model can serve as an independent prognostic predictor. Notably, HNSCC tumors showing higher expression of SF3B3, HNRNPC, or ZCRB1 possessed higher risk scores in the discovered prediction model. The investigation of the underlying mechanism validated that knockdown of SF3B3, HNRNPC, and ZCRB1 separately induced a substantial impairment of HNSCC cell survival. Conversely, overexpression of each of the three genes promoted tumor cellular proliferation. High throughput RNA sequencing analysis revealed that changes in the expression of SF3B3 and HNRNPC remarkably affected alternative splicing of genes related to cell cycle regulation, whereas the depletion of ZCRB1 contributed to aberrant splicing events involving in DNA damage response. In addition, the prognostic prediction model's risk score was demonstrated to be related with the immune infiltration score. Particularly, SF3B3 has a negative correlation with CD8A expression. Therefore, our findings provide promising prognosis predictors and potential therapeutic targets for better treatment efficacy of HNSCC.
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Affiliation(s)
- Chaoqun Chen
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116023, China
| | - Fang Huang
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116023, China
| | - Xiaojie Li
- Department of Prosthodontics, College of Stomatology, Dalian Medical University, Dalian 116044, China
| | - Lin Liu
- Department of Otolaryngology Head and Neck Surgery, Dalian Friendship Hospital, Dalian 116001, China
| | - Jinrui Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Huizheng Li
- Department of Otolaryngology Head and Neck Surgery, Dalian Friendship Hospital, Dalian 116001, China.
| | - Wei Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China.
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China; Soochow University Cancer Institute, Suzhou, China.
| | - Yang Wang
- Sino-US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116023, China.
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Yu YM, Hu Y. The m6A reader HNRNPC predicts adverse prognosis and promotes the progression of colorectal cancer. Technol Health Care 2024; 32:1445-1453. [PMID: 37661903 DOI: 10.3233/thc-230429] [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: 09/05/2023]
Abstract
BACKGROUND As a critical m6A RNA methylation regulator, HNRNPC has been revealed to serve as potential biomarkers in various human cancers. The specific expression and significance of HNRNPC in colorectal cancer remain unknown. OBJECTIVE This study aimed to confirm HNRNPC expression level and evaluate its function in colorectal cancer progression. METHODS 101 paired tissue samples were collected from colorectal cancer patients. HNRNPC levels in colorectal cancer were detected using PCR. CCK8 and transwell assays were conducted to estimate the effect of HNRNPC on cell growth and metastasis with the regulation of HNRNPC by cell transfection. RESULTS Upregulated HNRNPC was observed in colorectal cancer compared with normal tissues and cells. The higher HNRNPC levels in tumor tissues were associated with the advanced TNM stage and positive lymph node metastasis. Meanwhile, HNRNPC upregulation could indicate adverse outcomes of colorectal cancer patients. In vitro, the knockdown of HNRNPC significantly suppressed the proliferation, migration, and invasion of colorectal cancer cells. CONCLUSIONS Upregulated HNRNPC served as a biomarker for the prognosis and development of colorectal cancer, which provides a novel therapeutic target for colorectal cancer.
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Affiliation(s)
- Yong Ming Yu
- Department of Gastroenterology, Jiangxi Province Hospital of Integrated Chinese and Western Medicine, Nanchang, Jiangxi, China
| | - Yang Hu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Wang X, Li X, Zong Y, Yu J, Chen Y, Zhao M, Wu D, Liao Y, Jiang C, Zhu H. Identification and Validation of Genes Related to RNA Methylation Modification in Diabetic Retinopathy. Curr Eye Res 2023; 48:1034-1049. [PMID: 37529844 DOI: 10.1080/02713683.2023.2238144] [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: 05/11/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
PURPOSE To identify and validate the differentially expressed genes related to RNA methylation modification in diabetic retinopathy. METHODS The data sets GSE12610 and GSE111465 related to diabetic retinopathy in the Gene Expression Omnibus were selected. The R software package was used to identify differentially expressed genes related to RNA methylation modification in diabetic retinopathy. Protein-protein interaction network was constructed to explore the interactions between proteins and predict proteins. Then, Gene Ontology annotation analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were used to analyze the potential enrichment pathways and clarify the biological functions of these genes. In addition, the correlation between them and immune cells was visualized, and receiver operating characteristic curves were drawn to evaluate the diagnostic performance of each one of them for diabetic retinopathy. To verify the differentially expressed genes, the mRNA expression of rat retinal vascular endothelial cells cultured in low and high glucose medium separately were detected by RT-qPCR. RESULTS The expression of Lrpprc, Nsun4, Nsun6 and Trdmt1 were significantly up-regulated in diabetic retinopathy samples, while the expression of Cbll1, Hnrnpc, Mettl3 and Wtap were significantly down-regulated. Differentially expressed genes were mainly enriched in the RNA-methylation-medication pathways and biological function. The results of immune infiltration analysis proved that eosinophils aggregated more in diabetic group, while T cells follicular helper aggregated more in normal samples. These genes of Cbll1 (AUC = 0.986), Hnrnpc (AUC = 0.819), Lrpprc (AUC = 0.806), Mettl3 (AUC = 0.917), Nsun4 (AUC = 0.819), Nsun6 (AUC = 0.819), Trdmt1 (AUC = 0.972) and Wtap (AUC = 0.972) were respectively used as the diagnostic basis of diabetic retinopathy. According to the RT-qPCR results, the expression of Mettl3 was significantly down-regulated (p < 0.0005) in cells cultured in high glucose, while Trdmt1 (p < 0.05), Nsun4 (p < 0.05) and Nsun6 (p < 0.05) were significantly up-regulated. CONCLUSION Differentially expressed genes such as Mettl3, Nsun4, Nsun6, and Trdmt1 should be conducted to explore, and the role of RNA methylation in the process of diabetic retinopathy would be revealed in-depth.
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Affiliation(s)
- Xue Wang
- Department of Ophthalmology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Xiaomei Li
- Department of Ophthalmology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Yuan Zong
- Department of Ophthalmology, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Jian Yu
- Department of Ophthalmology, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Yan Chen
- Department of Ophthalmology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Minghui Zhao
- Department of Ophthalmology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Danping Wu
- Department of Ophthalmology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Yujie Liao
- Department of Ophthalmology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Chunhui Jiang
- Department of Ophthalmology, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Haohao Zhu
- Department of Ophthalmology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
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Liang J, Cai H, Hou C, Song F, Jiang Y, Wang Z, Qiu D, Zhu Y, Wang F, Yu D, Hou J. METTL14 inhibits malignant progression of oral squamous cell carcinoma by targeting the autophagy-related gene RB1CC1 in an m6A-IGF2BP2-dependent manner. Clin Sci (Lond) 2023; 137:1373-1389. [PMID: 37615536 PMCID: PMC10500204 DOI: 10.1042/cs20230219] [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: 03/08/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 08/25/2023]
Abstract
N6-methyladenosine (m6A) plays crucial roles in tumorigenesis and autophagy. However, the underlying mechanisms mediated by m6A and autophagy in the malignant progression of oral squamous cell carcinoma (OSCC) remain unclear. In the present study, we revealed that down-regulated expression of METTL14 was correlated with advanced clinicopathological characteristics and poor prognosis in OSCC. METTL14 knockdown significantly inhibited autophagy and facilitated malignant progression in vitro, and promoted tumor growth and metastasis in vivo. A cell model of rapamycin-induced autophagy was established to identify RB1CC1 as a potential target gene involved in m6A-regulated autophagy in OSCC, through RNA sequencing and methylated RNA immunoprecipitation sequencing (meRIP-seq) analysis. Mechanistically, we confirmed that METTL14 posttranscriptionally enhanced RB1CC1 expression in an m6A-IGF2BP2-dependent manner, thereby affecting autophagy and progression in OSCC, through methylated RNA immunoprecipitation qRT-PCR (meRIP-qPCR), RNA stability assays, mutagenesis assays and dual-luciferase reporter. Collectively, our findings demonstrated that METTL14 serves as an OSCC suppressor by regulating the autophagy-related gene RB1CC1 through m6A modification, which may provide a new insight for the diagnosis and therapy of OSCC.
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Affiliation(s)
- Jianfeng Liang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Hongshi Cai
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Chen Hou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Fan Song
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yaoqi Jiang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Ziyi Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Danqi Qiu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Yue Zhu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Fang Wang
- Department of Oral Surgery, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Dongsheng Yu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Jinsong Hou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
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Dai Y, Wu Z, Chen Y, Ye X, Wang C, Zhu H. OCT4's role and mechanism underlying oral squamous cell carcinoma. J Zhejiang Univ Sci B 2023; 24:796-806. [PMID: 37701956 PMCID: PMC10500100 DOI: 10.1631/jzus.b2200602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/06/2023] [Indexed: 09/14/2023]
Abstract
Oral squamous cell carcinoma (OSCC), a common malignancy of the head and neck, ranks sixth worldwide in terms of cancers with the most negative impact, owing to tumor relapse rates, cervical lymphnode metastasis, and the lack of an efficacious systemic therapy. Its prognosis is poor, and its mortality rate is high. Octamer-binding transcription factor 4 (OCT4) is a member of the Pit-Oct-Unc (POU) family and is a key reprogramming factor that produces a marked effect in preserving the pluripotency and self-renewal state of embryonic stem cells (ESCs). According to recent studies, OCT4 participates in retaining the survival of OSCC cancer stem cells (CSCs), which has far-reaching implications for the occurrence, recurrence, metastasis, and prognosis of oral carcinogenesis. Therefore, we summarize the structure, subtypes, and function of OCT4 as well as its role in the occurrence, progression, and prognosis of OSCC.
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Affiliation(s)
- Yuwei Dai
- Department of Oral and Maxillofacial Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
- School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ziqiong Wu
- School of Stomatology, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Yitong Chen
- School of Stomatology, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xinjian Ye
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Clinical Research Center for Oral Disease of Zhejiang Province, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, China
| | - Chaowei Wang
- Department of Oral and Maxillofacial Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Huiyong Zhu
- Department of Oral and Maxillofacial Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
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Sun X, Fu S, Yuan X, Pu X, Wang R, Wang X, Lu H. RNA N6-methyladenosine (m6A) modification in HNSCC: molecular mechanism and therapeutic potential. Cancer Gene Ther 2023; 30:1209-1214. [PMID: 37221404 DOI: 10.1038/s41417-023-00628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/12/2023] [Indexed: 05/25/2023]
Abstract
Head and neck squamous cell carcinoma ranks seventh in incidence of malignant tumours in the world. Although there are treatments including surgery, radiotherapy and chemotherapy, targeted therapy and immunotherapy, drug resistance to treatment is caused by various reasons, and the survival rate of patients remains frustrating. To overcome the bottleneck of treatment at this stage, it is urgent to identify possible diagnostic and prognostic markers. N6-methyladenosine is a methylation modification on the sixth N atom of adenine which is the most abundant epitope transcriptome modification in mammalian genes. N6-methyladenosine modification is reversible and results from the interaction among writers, erasers and readers. A large number of studies have proven that N6-methyladenosine modification has important significance in promoting the progression and treatment of tumours and have made great progress in research. In this review, we introduce how N6-methyladenosine modification promotes the occurrence and development of tumours, the mechanism of drug resistance, and new findings of N6-methyladenosine modification in radiotherapy and chemotherapy, immunotherapy, and targeted therapy. N6-methyladenosine modification provides more possibilities for improving the overall survival rate and prognosis of patients.
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Affiliation(s)
- Xinyu Sun
- Department of Otorhinolaryngology, Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Department of Radiation Oncology, Cancer Institute Of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Shengqiao Fu
- Department of Radiation Oncology, Cancer Institute Of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xiao Yuan
- Department of Radiation Oncology, Cancer Institute Of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xi Pu
- Department of Radiation Oncology, Cancer Institute Of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - RunKun Wang
- Department of Otorhinolaryngology, Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xu Wang
- Department of Radiation Oncology, Cancer Institute Of Jiangsu University, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Hanqiang Lu
- Department of Otorhinolaryngology, Affiliated Hospital, Jiangsu University, Zhenjiang, Jiangsu Province, China.
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Jia R, Che X, Jia J, Guo J. FOXM1a Isoform of Oncogene FOXM1 Is a Tumor Suppressor Suppressed by hnRNP C in Oral Squamous Cell Carcinoma. Biomolecules 2023; 13:1331. [PMID: 37759731 PMCID: PMC10526205 DOI: 10.3390/biom13091331] [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: 07/18/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
FOXM1 is an oncogenic transcriptional factor and includes several isoforms generated by alternative splicing. Inclusion of alternative exon 9 produces FOXM1a, a transcriptionally inactive isoform. However, the role of FOXM1a in tumorigenesis remains unknown. In addition, the regulatory mechanisms of exon 9 splicing are also unclear. In the present study, we found that overexpression of FOXM1a significantly reduced cell proliferation and colony formation of oral squamous cell carcinoma (OSCC) cell proliferation in vitro. Importantly, OSCC cells with FOXM1a overexpression showed significantly slower tumor formation in nude mice. Moreover, we identified a U-rich exonic splicing suppressor (ESS) which is responsible for exon 9 skipping. Splicing factor heterogeneous nuclear ribonucleoprotein C (hnRNP C) can bind to the ESS and suppress exon 9 inclusion and FOXM1a expression. Silence of hnRNP C also significantly suppresses OSCC cell proliferation. HnRNP C is significantly co-expressed with FOXM1 in cancers. Our study uncovered a novel regulatory mechanism of oncogene FOXM1 expression in OSCC.
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Affiliation(s)
- Rong Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
| | - Xiaoxuan Che
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
| | - Jun Jia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China
| | - Jihua Guo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China; (R.J.); (X.C.)
- Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan 430072, China
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Shi Y, Wang Y, Zhang W, Niu K, Mao X, Feng K, Zhang Y. N6-methyladenosine with immune infiltration and PD-L1 in hepatocellular carcinoma: novel perspective to personalized diagnosis and treatment. Front Endocrinol (Lausanne) 2023; 14:1153802. [PMID: 37469973 PMCID: PMC10352105 DOI: 10.3389/fendo.2023.1153802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/02/2023] [Indexed: 07/21/2023] Open
Abstract
Background Increasing evidence elucidated N6-methyladenosine (m6A) dysregulation participated in regulating RNA maturation, stability, and translation. This study aimed to demystify the crosstalk between m6A regulators and the immune microenvironment, providing a potential therapeutic target for patients with hepatocellular carcinoma (HCC). Methods Totals of 371 HCC and 50 normal patients were included in this study. GSE121248 and GSE40367 datasets were used to validate the expression of HNRNPC. The R package "ConsensusClusterPlus" was performed to screen consensus clustering types based on the expression of m6A regulators in HCC. The R package "pheatmap", "immunedeconv", "survival", "survminer" and "RMS" were applied to investigate the expression, immunity, overall survival, and clinical application in different clusters and expression groups. Comprehensive analysis of HNRNPC in pan-cancer was conducted by TIMER2 database. Besides, HNRNPC mRNA and protein expression were verified by qRT-PCR and immunohistochemistry analysis. Results Most of m6A regulators were over-expressed excerpt for ZC3H13 in HCC. Three independent clusters were screened based on m6A regulators expression, and the cluster 2 had a favorable prognosis in HCC. Then, the cluster 2 was positively expression in macrophage, hematopoietic stem cell, endothelial cell, and stroma score, while negatively in T cell CD4+ memory and mast cell. We identified HNRNPC was an independent prognostic factor in HCC, and nomogram performed superior application value for clinical decision making. Moreover, PD-L1 was significantly up-regulated in HCC tissues, cluster 1, and cluster 3, and we found PD-L1 expression was positively correlated with HNRNPC. Patients with HCC in high-expression groups was associated with tumor-promoting cells. Besides, HNRNPC was correlated with prognosis, TMB, and immune checkpoints in cancers. Particularly, the experiments confirmed that HNRNPC was positively expression in HCC cells and tissues. Conclusion The m6A regulators play irreplaceable roles in prognosis and immune infiltration in HCC, and the relationship of HNRNPC and PD-L1 possesses a promising direction for therapeutic targets of immunotherapy response. Exploration of m6A regulators pattern could be build the prognostic stratification of individual patients and move toward to personalized treatment.
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Zhao Y, Che Y, Liu Q, Zhou S, Xiao Y. Analyses of m6A regulatory genes and subtype classification in atrial fibrillation. Front Cell Neurosci 2023; 17:1073538. [PMID: 37435047 PMCID: PMC10330950 DOI: 10.3389/fncel.2023.1073538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/08/2023] [Indexed: 07/13/2023] Open
Abstract
Objective To explore the role of m6A regulatory genes in atrial fibrillation (AF), we classified atrial fibrillation patients into subtypes by two genotyping methods associated with m6A regulatory genes and explored their clinical significance. Methods We downloaded datasets from the Gene Expression Omnibus (GEO) database. The m6A regulatory gene expression levels were extracted. We constructed and compared random forest (RF) and support vector machine (SVM) models. Feature genes were selected to develop a nomogram model with the superior model. We identified m6A subtypes based on significantly differentially expressed m6A regulatory genes and identified m6A gene subtypes based on m6A-related differentially expressed genes (DEGs). Comprehensive evaluation of the two m6A modification patterns was performed. Results The data of 107 samples from three datasets, GSE115574, GSE14975 and GSE41177, were acquired from the GEO database for training models, comprising 65 AF samples and 42 sinus rhythm (SR) samples. The data of 26 samples from dataset GSE79768 comprising 14 AF samples and 12 SR samples were acquired from the GEO database for external validation. The expression levels of 23 regulatory genes of m6A were extracted. There were correlations among the m6A readers, erasers, and writers. Five feature m6A regulatory genes, ZC3H13, YTHDF1, HNRNPA2B1, IGFBP2, and IGFBP3, were determined (p < 0.05) to establish a nomogram model that can predict the incidence of atrial fibrillation with the RF model. We identified two m6A subtypes based on the five significant m6A regulatory genes (p < 0.05). Cluster B had a lower immune infiltration of immature dendritic cells than cluster A (p < 0.05). On the basis of six m6A-related DEGs between m6A subtypes (p < 0.05), two m6A gene subtypes were identified. Both cluster A and gene cluster A scored higher than the other clusters in terms of m6A score computed by principal component analysis (PCA) algorithms (p < 0.05). The m6A subtypes and m6A gene subtypes were highly consistent. Conclusion The m6A regulatory genes play non-negligible roles in atrial fibrillation. A nomogram model developed by five feature m6A regulatory genes could be used to predict the incidence of atrial fibrillation. Two m6A modification patterns were identified and evaluated comprehensively, which may provide insights into the classification of atrial fibrillation patients and guide treatment.
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Affiliation(s)
- Yingliang Zhao
- Department of Cardiovascular Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yanyun Che
- Department of Cardiovascular Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Qiming Liu
- Department of Cardiovascular Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shenghua Zhou
- Department of Cardiovascular Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yichao Xiao
- Department of Cardiovascular Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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15
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Qiao X, Zhu L, Song R, Shang C, Guo Y. METTL3/14 and IL-17 signaling contribute to CEBPA-DT enhanced oral cancer cisplatin resistance. Oral Dis 2023; 29:942-956. [PMID: 34807506 DOI: 10.1111/odi.14083] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Oral squamous cell carcinoma (OSCC) is the most common head and neck cancer. Chemotherapy has been recognized as an optional combination treatment, which enhance the overall survival of OSCC patients. However, the majority of patients would suffer therapeutic resistance, which led to the treatment failure and poor prognosis. MATERIALS AND METHODS To explore the mechanism of chemoresistance in OSCC, we first constructed two chemoresistant cell lines using Cal27 and HSC4. Then MeRIP sequencing together with bioinformatics analysis and a series of in vitro experiments were used to assess the possible regulation manner of RNA methylation on OSCC chemoresistance. Finally, xenograft models were constructed to confirm the relationship among OSCC chemoresistance. RESULTS METTL3/METTL14 upregulation could enhance OSCC chemoresistance. CEBPA-DT overexpression could regulate METTL3/METTL14 expression and further activate downstream BHLHB9. CEBPA-DT overexpression could inhibit the activity of IL-17 signaling, resulting in the homeostasis breakdown of immune infiltration and cytokine release. CEBPA-DT overexpression could significantly enhance chemoresistance through METTL3/METTL14/BHLHB9 in vivo, which accelerated the tumor growth. CONCLUSIONS Our results suggest that CEBPA-DT might regulate OSCC chemoresistance through BHLHB9 gene manipulated by METTL3/METTL14 as well as through IL-17 signaling inhibition, which may contribute to the assessment of potential therapeutic targets in OSCC chemoresistance.
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Affiliation(s)
- Xue Qiao
- Department of Central Laboratory, School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Disease, China Medical University, Shenyang, China
- Department of Oral Biology, School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Disease, China Medical University, Shenyang, China
| | - Li Zhu
- Department of Central Laboratory, School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Disease, China Medical University, Shenyang, China
| | - Rongbo Song
- Department of Central Laboratory, School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Disease, China Medical University, Shenyang, China
| | - Chao Shang
- Department of Neurobiology, China Medical University, Shenyang, China
| | - Yan Guo
- Department of Central Laboratory, School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Disease, China Medical University, Shenyang, China
- Department of Oral Biology, School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Disease, China Medical University, Shenyang, China
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Zhao F, Zhao P, Chang J, Sun X, Ma X, Shi B, Yin M, Wang Y, Yang Y. Identification and vitro verification of the potential drug targets of active ingredients of Chonglou in the treatment of lung adenocarcinoma based on EMT-related genes. Front Genet 2023; 14:1112671. [PMID: 36824434 PMCID: PMC9942681 DOI: 10.3389/fgene.2023.1112671] [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: 11/30/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the main histological type of lung cancer with an unfavorable survival rate. Metastasis is the leading LUAD-related death with Epithelial-Mesenchymal Transition (EMT) playing an essential role. The anticancer efficacies of the active ingredients in Chonglou have been widely reported in various cancers. However, the potential therapeutic targets of the Chonglou active ingredients in LUAD patients remain unknown. Here, the network pharmacology and bioinformatics were performed to analyze the associations of the clinical characteristics, immune infiltration factors and m6A-related genes with the EMT-related genes associated with LUAD (EMT-LUAD related genes), and the molecular docking, STRING, GO, and KEGG enrichment for the drug targets of Chonglou active ingredients associated with EMT (EMT-LUAD-Chonglou related genes). And, cell viability analysis and cell invasion and infiltration analysis were used to confirm the theoretical basis of this study. A total of 166 EMT-LUAD related genes were identified and a multivariate Cox proportional hazards regression model with a favorable predictive accuracy was constructed. Meanwhile, the immune cell infiltration, immune cell subsets, checkpoint inhibitors and the expression of m6A-related genes were significantly associated with the risk scores for EMT-LUAD related genes with independent significant prognostic value of all included LUAD patients. Furthermore, 12 EMT-LUAD-Chonglou related genes with five core drug targets were identified, which participated in LUAD development through extracellular matrix disassembly, collagen metabolic process, collagen catabolic process, extracellular matrix organization, extracellular structure organization and inflammatory response. Moreover, we found that the active ingredients of Chonglou could indeed inhibit the progression of lung adenocarcinoma cells. These results are oriented towards EMT-related genes to achieve a better understanding of the role of Chonglou and its targets in osteosarcoma development and metastasis, thus guiding future preclinical studies and facilitating clinical translation of LUAD treatment.
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Affiliation(s)
- Fulai Zhao
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Peng Zhao
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Junli Chang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Xingyuan Sun
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Xiaoping Ma
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Binhao Shi
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Mengchen Yin
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China
| | - Yongjun Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China,*Correspondence: Yongjun Wang, ; Yanping Yang,
| | - Yanping Yang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Key Laboratory of Theory and Therapy of Muscles and Bones, Ministry of Education, Shanghai, China,*Correspondence: Yongjun Wang, ; Yanping Yang,
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Huang G, Chen S, Washio J, Paka Lubamba G, Takahashi N, Li C. Glycolysis-Related Gene Analyses Indicate That DEPDC1 Promotes the Malignant Progression of Oral Squamous Cell Carcinoma via the WNT/β-Catenin Signaling Pathway. Int J Mol Sci 2023; 24:ijms24031992. [PMID: 36768316 PMCID: PMC9916831 DOI: 10.3390/ijms24031992] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Increasing evidence suggests that aerobic glycolysis is related to the progression of oral squamous cell carcinoma (OSCC). Hence, we focused on glycolysis-related gene sets to screen for potential therapeutic targets for OSCC. The expression profiles of OSCC samples and normal controls were obtained from The Cancer Genome Atlas (TCGA). Then, the differentially expressed gene sets were selected from the official GSEA website following extraction of the differentially expressed core genes (DECGs). Subsequently, we tried to build a risk model on the basis of DECGs to predict the prognosis of OSCC patients via Cox regression analysis. Furthermore, crucial glycolysis-related genes were selected to explore their biological roles in OSCC. Two active glycolysis-related pathways were acquired and 66 DECGs were identified. Univariate Cox regression analysis showed that six genes, including HMMR, STC2, DDIT4, DEPDC1, SLC16A3, and AURKA, might be potential prognostic factors. Subsequently, a risk formula consisting of DEPDC1, DDIT4, and SLC16A3 was established on basis of the six molecules. Furthermore, DEPDC1 was proven to be related to advanced stage cancer and lymph node metastasis. Moreover, functional experiments suggested that DEPDC1 promoted the aerobic glycolysis, migration, and invasion of OSCC via the WNT/β-catenin pathway. The risk score according to glycolysis-related gene expression might be an independent prognostic factor in OSCC. In addition, DEPDC1 was identified as playing a carcinogenic role in OSCC progression, suggesting that DEPDC1 might be a novel biomarker and therapeutic target for OSCC.
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Affiliation(s)
- Guangzhao Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610044, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu 610044, China
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Su Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610044, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu 610044, China
| | - Jumpei Washio
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Grace Paka Lubamba
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610044, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu 610044, China
| | - Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Chunjie Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610044, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu 610044, China
- Correspondence:
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Shang QX, Kong WL, Huang WH, Xiao X, Hu WP, Yang YS, Zhang H, Yang L, Yuan Y, Chen LQ. Identification of m6a-related signature genes in esophageal squamous cell carcinoma by machine learning method. Front Genet 2023; 14:1079795. [PMID: 36733344 PMCID: PMC9886874 DOI: 10.3389/fgene.2023.1079795] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Background: We aimed to construct and validate the esophageal squamous cell carcinoma (ESCC)-related m6A regulators by means of machine leaning. Methods: We used ESCC RNA-seq data of 66 pairs of ESCC from West China Hospital of Sichuan University and the transcriptome data extracted from The Cancer Genome Atlas (TCGA)-ESCA database to find out the ESCC-related m6A regulators, during which, two machine learning approaches: RF (Random Forest) and SVM (Support Vector Machine) were employed to construct the model of ESCC-related m6A regulators. Calibration curves, clinical decision curves, and clinical impact curves (CIC) were used to evaluate the predictive ability and best-effort ability of the model. Finally, western blot and immunohistochemistry staining were used to assess the expression of prognostic ESCC-related m6A regulators. Results: 2 m6A regulators (YTHDF1 and HNRNPC) were found to be significantly increased in ESCC tissues after screening out through RF machine learning methods from our RNA-seq data and TCGA-ESCA database, respectively, and overlapping the results of the two clusters. A prognostic signature, consisting of YTHDF1 and HNRNPC, was constructed based on our RNA-seq data and validated on TCGA-ESCA database, which can serve as an independent prognostic predictor. Experimental validation including the western and immunohistochemistry staining were further successfully confirmed the results of bioinformatics analysis. Conclusion: We constructed prognostic ESCC-related m6A regulators and validated the model in clinical ESCC cohort as well as in ESCC tissues, which provides reasonable evidence and valuable resources for prognostic stratification and the study of potential targets for ESCC.
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Abstract
To investigate the impact of lactate metabolism genes, lactate metabolism-related genes (LMRG), and immune infiltrating cells on the prognosis of breast cancer. LMRG was identified via single-cell sequencing. Immune cell infiltration was obtained by the CIBERSORT method. The prognostic genes were chosen by cox regression and the least absolute selection operator approach. lactate metabolism-associated immune-infiltrating cells was determined by difference analysis. The GSE20685 dataset was used as an external validation cohort. The model's prognostic usefulness was evaluated utilizing survival, immunological microenvironment, and drug sensitivity assessments. NDUFAF6 was most associated with breast cancer prognosis. We obtained a total of 450 LMRG. SUSD3, IL18, MAL2, and CDKN1C comprised the Model2. NK cell activation was most relevant to lactate metabolism. The combined prognostic model outperformed the individual model, with the area under the curve ranging from 0.7 to 0.8 in all three cohorts. The lactate metabolism-related combination model assisted in evaluating breast cancer prognosis, providing new insights for treatment, particularly immunotherapy.
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Affiliation(s)
- Na Lu
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Xiao Guan
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Wei Bao
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zongyao Fan
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianping Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
- * Correspondence: Jianping Zhang, Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, No. 121, Jiangjiayuan Road, Nanjing, Jiangsu Province 210011, China (e-mail: )
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Liu M, Guo J, Jia R. Emerging roles of alternative RNA splicing in oral squamous cell carcinoma. Front Oncol 2022; 12:1019750. [PMID: 36505770 PMCID: PMC9732560 DOI: 10.3389/fonc.2022.1019750] [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: 08/15/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Alternative RNA splicing (ARS) is an essential and tightly regulated cellular process of post-transcriptional regulation of pre-mRNA. It produces multiple isoforms and may encode proteins with different or even opposite functions. The dysregulated ARS of pre-mRNA contributes to the development of many cancer types, including oral squamous cell carcinoma (OSCC), and may serve as a biomarker for the diagnosis and prognosis of OSCC and an attractive therapeutic target. ARS is mainly regulated by splicing factors, whose expression is also often dysregulated in OSCC and involved in tumorigenesis. This review focuses on the expression and roles of splicing factors in OSCC, the alternative RNA splicing events associated with OSCC, and recent advances in therapeutic approaches that target ARS.
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Affiliation(s)
- Miaomiao Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China,Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China,*Correspondence: Jihua Guo, ; Rong Jia,
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China,RNA Institute, Wuhan University, Wuhan, China,*Correspondence: Jihua Guo, ; Rong Jia,
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Yin L, Feng S, Sun Y, Jiang Y, Tang C, Sun D. Identification of a five m6A-relevant mRNAs signature and risk score for the prognostication of gastric cancer. J Gastrointest Oncol 2022; 13:2234-2248. [PMID: 36388685 PMCID: PMC9660063 DOI: 10.21037/jgo-22-962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is the most abundant form of methylation modification in eukaryotic cell messenger RNA (mRNA). However, the role of m6A in gastric cancer (GC), which is one of the most common gastrointestinal malignancies, is unclear. In this study, m6A-relevant mRNA signatures and risk scores were determined to predict the prognosis of GC. METHODS The expression profiles and clinical information of 367 patients were downloaded from The Cancer Genome Atlas (TCGA). Cluster analysis and univariate Cox analysis were performed to identify the regulatory factors of RNA methylation associated with GC prognosis. A co-expression network was constructed using the WGCNA package in R. The correlations between module eigengenes and clinical traits were then calculated to identify the relevant modules. We used univariate Cox analysis to screen for genes that are significantly associated with prognosis in the module. We identified hub genes by least absolute shrinkage and selection operator (LASSO) and multivariate analysis and developed a Cox prognostic model. Finally, the hub gene expression values weighted by the coefficients from the LASSO regression were applied to generate a risk score for each patient, and receiver operating characteristic (ROC) and Kaplan-Meier curves were used to assess the prognostic capacity of the risk scores. The asporin (ASPN) gene in GC cell lines was verified via quantitative polymerase chain reaction (qPCR) and Western blot. Moreover, 5-ethynyl-2'-deoxyuridine (EdU) and transwell assays were applied to evaluate the effects of the proliferation, migration, and invasion abilities in GC cells after ASPN knockdown. Western blot verified the effects of ASPN on the phosphoinositide 3-kinase (PI3K)/serine/threonine kinase (AKT)/mechanistic target of rapamycin kinase (mTOR) pathway and epithelial-mesenchymal transition (EMT) pathway-related gene expression. RESULTS Our results indicated that AARD, ASPN, SLAMF9, MIR3117 and DUSP1 were hub genes affecting the prognosis of GC patients. Besides, we found that ASPN expression was upregulated in GC cells. The knockdown of ASPN expression suppressed GC cell proliferation, migration, and invasion by deactivating the PI3K/AKT/mTOR and EMT pathways, respectively. CONCLUSIONS Our findings indicated that ASPN participates in the biological process of GC as an oncogene and may be a promising biomarker in GC.
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Affiliation(s)
- Lei Yin
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Shichun Feng
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Yongqiang Sun
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Yasu Jiang
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Chong Tang
- Department of General Surgery, Affiliated Hospital 2 of Nantong University, Nantong, China
| | - Dongwei Sun
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People’s Hospital, Yangzhou, China
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Chen X, Chen L, Tang Y, He Y, Pan K, Yuan L, Xie W, Chen S, Zhao W, Yu D. Transcriptome-wide m6A methylome analysis uncovered the changes of m6A modification in oral pre-malignant cells compared with normal oral epithelial cells. Front Oncol 2022; 12:939449. [PMID: 36249071 PMCID: PMC9554554 DOI: 10.3389/fonc.2022.939449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
As the most common post-transcriptional RNA modification, m6A methylation extensively regulates the structure and function of RNA. The dynamic and reversible modification of m6A is coordinated by m6A writers and erasers. m6A reader proteins recognize m6A modification on RNA, mediating different downstream biological functions. mRNA m6A modification and its corresponding regulators play an important role in cancers, but its characteristics in the precancerous stage are still unclear. In this study, we used oral precancerous DOK cells as a model to explore the characteristics of transcriptome-wide m6A modification and major m6A regulator expression in the precancerous stage compared with normal oral epithelial cell HOEC and oral cancer cell SCC-9 through MeRIP-seq and RT-PCR. Compared with HOEC cells, we found 1180 hyper-methylated and 1606 hypo-methylated m6A peaks and 354 differentially expressed mRNAs with differential m6A peaks in DOK cells. Although the change of m6A modification in DOK cells was less than that in SCC-9 cells, mRNAs with differential m6A in both cell lines were enriched into many identical GO terms and KEGG pathways. Among the 20 known m6A regulatory genes, FTO, ALKBH5, METTL3 and VIRMA were upregulated or downregulated in DOK cells, and the expression levels of 10 genes such as METTL14/16, FTO and IGF2BP2/3 were significantly changed in SCC-9 cells. Our data suggest that precancerous cells showed, to some extent, changes of m6A modification. Identifying some key m6A targets and corresponding regulators in precancerous stage may provide potential intervention targets for the prevention of cancer development through epigenetic modification in the future.
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Affiliation(s)
- Xun Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Liutao Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory for Biocontrol, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuquan Tang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yi He
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Kuangwu Pan
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Linyu Yuan
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Weihong Xie
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Shangwu Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory for Biocontrol, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Zhao
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Wei Zhao, ; Dongsheng Yu,
| | - Dongsheng Yu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Wei Zhao, ; Dongsheng Yu,
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Guan X, Lu N, Zhang J. Construction of a prognostic model related to copper dependence in breast cancer by single-cell sequencing analysis. Front Genet 2022; 13:949852. [PMID: 36082002 PMCID: PMC9445252 DOI: 10.3389/fgene.2022.949852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose: To explore the clinical significance of copper-dependent-related genes (CDRG) in female breast cancer (BC). Methods: CDRG were obtained by single-cell analysis of the GSE168410 dataset in the Gene Expression Omnibus (GEO) database. According to a 1:1 ratio, the Cancer Genome Atlas (TCGA) cohort was separated into a training and a test cohort randomly. Based on the training cohort, the prognostic model was built using COX and Lasso regression. The test cohort was used to validate the model. The GSE20685 dataset and GSE20711 dataset were used as two external validation cohorts to further validate the prognostic model. According to the median risk score, patients were classified as high-risk or low-risk. Survival analysis, immune microenvironment analysis, drug sensitivity analysis, and nomogram analysis were used to evaluate the clinical importance of this prognostic model. Results: 384 CDRG were obtained by single-cell analysis. According to the prognostic model, patients were classified as high-risk or low-risk in both cohorts. The high-risk group had a significantly worse prognosis. The area under the curve (AUC) of the model was around 0.7 in the four cohorts. The immunological microenvironment was examined for a possible link between risk score and immune cell infiltration. Veliparib, Selumetinib, Entinostat, and Palbociclib were found to be more sensitive medications for the high-risk group after drug sensitivity analysis. Conclusion: Our CDRG-based prognostic model can aid in the prediction of prognosis and treatment of BC patients.
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Wang X, Yu Q, Yu H, Wang Y, Sun L, Yu L, Cui H, Yang H. The prognostic value and multiomic features of m6A-related risk signature in lung adenocarcinoma. Am J Transl Res 2022; 14:5379-5393. [PMID: 36105012 PMCID: PMC9452311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVES N6-methyladenosine (m6A), a predominant RNA modification, has been recently linked to messenger RNA splicing, stability and expression, and its dysregulation may be important in the initiation as well as development of human cancers. The current study was proposed to investigate the clinico-pathological value and multiomic characteristics of m6A-linked genes in the diagnosis and prognosis of lung adenocarcinoma (LUAD). METHODS The expression levels and mutation types of 21 previously identified m6A regulators were analyzed using the TCGA (The Cancer Genome Atlas) database. The patients were categorized into two groups, a training group (n=392) and a testing group (n=98). Next, the prognostic score of m6A regulators was determined by the Cox survival analysis and a regression model of LASSO to develop a risk profile for patients with LUAD. Moreover, features of risk signature, including chemosensitivity, tumor immune microenvironment and genetic mutation, were also explored. RESULTS In total, 18 of 21 m6A regulators showed significantly differential expression in LUAD (P<0.05). Among them, 6 genes were observed to be associated with the Overall Survival (OS) of patients with LUAD. Three genes (IGF2BP1 and 2, and HNRNPC) were further evaluated as a prognostic signature in LUAD. Patients, grouped as high risk based on the median of risk score, had poorer OS in comparison with those in low-risk group (P<0.05). The accuracy of our prognostic signatures was high: the AUC were 0.67, 0.59, 0.64 (training set), and 0.65, 0.69, 0.64 (testing set) at survival of 1- , 3- and 5-year, respectively. The prognostic performance of IGF2BP1, IGF2BP2 and HNRNPC was successfully validated in two independent external cohorts. High-risk score was an indicator of chemoresistance, TP53 mutation and increased infiltration of immune cells, and in vitro assessment of the cellular function of HNRNPC confirmed that the gene is involved in cell proliferation and invasion. CONCLUSION The prognostic signature based on m6A regulators might provide novel insights into prognostic assessment and individualized treatment for patients with LUAD.
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Affiliation(s)
- Xiangcheng Wang
- Department of Nuclear Medicine, Shenzhen People’s HospitalShenzhen 518020, Guangdong, China
| | - Qin Yu
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
| | - Hongfang Yu
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
| | - Yuzhe Wang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
| | - Liping Sun
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
| | - Lei Yu
- Department of Pharmacy, Traditional Chinese Medicine Hospital of Inner Mongolia Autonomous RegionHohhot 010020, Inner Mongolia Autonomous Region, China
| | - Hongwei Cui
- Scientific Research Department, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- Clinical Research Center, The Affiliated Hospital of Inner Mongolia Medical UniversityHuhhot 010050, Inner Mongolia Autonomous Region, China
| | - Hao Yang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People’s Hospital of Inner Mongolia Medical UniversityHuhhot 010020, Inner Mongolia Autonomous Region, China
- The Laboratory of Radiation Physics and Biology, Affiliated People’s Hospital of Inner Mongolia Medical University & Inner Mongolia Cancer HospitalHuhhot 010020, Inner Mongolia Autonomous Region, China
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Xu L, Yu C, Du XJ. Prognostic Evaluation for Oral Squamous Cell Carcinoma: A Novel Method Based on m6A Methylation Regulators. Curr Med Sci 2022; 42:841-846. [DOI: 10.1007/s11596-022-2611-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/15/2021] [Indexed: 12/24/2022]
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Chen Y, Feng Y, Yan F, Zhao Y, Zhao H, Guo Y. A Novel Immune-Related Gene Signature to Identify the Tumor Microenvironment and Prognose Disease Among Patients With Oral Squamous Cell Carcinoma Patients Using ssGSEA: A Bioinformatics and Biological Validation Study. Front Immunol 2022; 13:922195. [PMID: 35935989 PMCID: PMC9351622 DOI: 10.3389/fimmu.2022.922195] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most invasive oral malignancy in adults and is associated with a poor prognosis. Accurate prognostic models are urgently needed, however, knowledge of the probable mechanisms behind OSCC tumorigenesis and prognosis remain limited. The clinical importance of the interplay between the immune system and tumor microenvironment has become increasingly evident. This study explored immune-related alterations at the multi-omics level to extract accurate prognostic markers linked to the immune response and presents a more accurate landscape of the immune genomic map during OSCC. The Cancer Genome Atlas (TCGA) OSCC cohort (n = 329) was used to detect the immune infiltration pattern of OSCC and categorize patients into two immunity groups using single-sample gene set enrichment analysis (ssGSEA) and hierarchical clustering analysis. Multiple strategies, including lasso regression (LASSO), Cox proportional hazards regression, and principal component analysis (PCA) were used to screen clinically significant signatures and identify an incorporated prognosis model with robust discriminative power on the survival status of both the training and testing set. We identified two OSCC subtypes based on immunological characteristics: Immunity-high and immunity low, and verified that the categorization was accurate and repeatable. Immunity_ high cluster with a higher immunological and stromal score. 1047 differential genes (DEGs) integrate with immune genes to obtain 319 immue-related DEGs. A robust model with five signatures for OSCC patient prognosis was established. The GEO cohort (n = 97) were used to validate the risk model’s predictive value. The low-risk group had a better overall survival (OS) than the high-risk group. Significant prognostic potential for OSCC patients was found using ROC analysis and immune checkpoint gene expression was lower in the low-risk group. We also investigated at the therapeutic sensitivity of a number of frequently used chemotherapeutic drugs in patients with various risk factors. The underlying biological behavior of the OSCC cell line was preliminarily validated. This study characterizes a reliable marker of OSCC disease progression and provides a new potential target for immunotherapy against this disease.
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Affiliation(s)
- Yun Chen
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yunzhi Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Fei Yan
- Hunan Key Laboratory of Oral Health Research, Hunan 3D Printing Engineering Research Center of Oral Care, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, China
| | - Yaqiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Han Zhao
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai, China
- Laboratory of Myopia, National Health Commission (NHC) Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- *Correspondence: Han Zhao, ; Yue Guo,
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Han Zhao, ; Yue Guo,
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N 6-methyladenosine (m 6A) reader IGF2BP2 stabilizes HK2 stability to accelerate the Warburg effect of oral squamous cell carcinoma progression. J Cancer Res Clin Oncol 2022; 148:3375-3384. [PMID: 35763110 DOI: 10.1007/s00432-022-04093-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
PURPOSE The N6-methyladenosine (m6A) has been involved in the regulation of cell proliferation and metastasis in multiple cancers. However, the biological significance of m6A reader IGF2BP2 in oral squamous cell carcinoma (OSCC) and the mechanism of IGF2BP2 itself have not been fully investigated. METHODS The cellular phenotypes of OSCC cells were determined by CCK-8 and transwell migration assays. The energy metabolism was detected using glucose uptake/lactate production assay and extracellular acidification rate analysis. The molecular interaction was tested by RNA immunoprecipitation assay. RESULTS Here, results indicated that IGF2BP2 was up-regulated in OSCC and that it acted as a predictor of poor prognosis. IGF2BP2 promoted the proliferation, migration and Warburg effect of OSCC cells in vitro. Mechanistical assays illustrated that IGF2BP2 directly interacted with HK2 mRNA by binding the 3'-UTR m6A site. Moreover, IGF2BP2 positively promoted the stability of HK2 mRNA and thus the protein level of HK2 increased upon IGF2BP2 overexpression. CONCLUSIONS In conclusion, the IGF2BP2/m6A/HK2 axis accelerated the abnormal energy metabolism of OSCC. Taken together, these findings revealed a novel mechanism by which IGF2BP2 functions in OSCC progression, which may provide new therapy options for OSCC patients.
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FCGBP Is a Promising Prognostic Biomarker and Correlates with Immunotherapy Efficacy in Oral Squamous Cell Carcinoma. J Immunol Res 2022; 2022:8443392. [PMID: 35733916 PMCID: PMC9207623 DOI: 10.1155/2022/8443392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 12/03/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most common malignancies of the head and neck. In OSCC patients, the prognosis was dramatically different. In this research, we aimed to study the expressions and prognostic values of IgG Fc binding protein (FCGBP) in OSCC patients. The expression of FCGBP was analyzed using TCGA datasets and GEO datasets. FCGBP was evaluated for its predictive significance in OSCC patients by the use of a Kaplan-Meier and Cox regression model. Enrichment analysis for the GO and KEGG databases were conducted. CIBERSORT used TCGA datasets to show immune cell infiltration. In addition, researchers looked into the relationships between FCGBP and immune cells. The levels of FCGBP in OSCC cells was examined through the use of RT-PCR. FCGBP overexpression was tested for its effects on OSCC cell proliferation and invasion using CCK-8 and Transwell assays. We observed that FCGBP expressions were distinctly downregulated in OSCC specimens compared with nontumor tissues in both TCGA and GEO datasets, which was further confirmed by RT-PCR. OSCC patients with advanced clinical stages and poor prognoses had lower levels of FCGBP expression. Many immune-related biological activities and signaling pathways were found to be considerably abundant in KEGG tests and GO analysis results. The correlation analysis indicated that FCGBP was associated with a number of immune cells in a positive way. We found that FCGBP expressions were strongly and distinctly linked to the expressions of known immunological checkpoints, and FCGBP expression had significant positive connections with tumor mutational burden. FCGBP upregulation distinctly slowed the growth and invasion of OSCC cells in functional experiments. FCGBP has the potential to be a therapeutic target for OSCC and a biomarker for OSCC patients' prognosis.
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Xiang Z, Lv Q, Zhang Y, Chen X, Guo R, Liu S, Peng X. Long non-coding RNA DDX11-AS1 promotes the proliferation and migration of glioma cells by combining with HNRNPC. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:601-612. [PMID: 35614994 PMCID: PMC9109126 DOI: 10.1016/j.omtn.2022.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/23/2022] [Indexed: 12/11/2022]
Abstract
Glioma is a malignant tumor of the central nervous system with complex pathogenesis, difficult operation, and a high postoperative recurrence rate. At present, there is still a lack of effective treatment. Long non-coding RNA DDX11 antisense RNA 1 (DDX11-AS1) has been shown to promote tumor development, such as hepatocellular carcinoma, esophageal cancer, etc. However, its molecular mechanism in glioma is poorly understood. In this study, we found that the expression of DDX11-AS1 was elevated in glioma tissues, and patients with high expression of DDX11-AS1 had poor prognosis. DDX11-AS1 was a potential prognostic marker. Functionally, DDX11-AS1 promoted glioma cell proliferation and migration. Mechanistically, DDX11-AS1 interacted with RNA-binding protein heterogeneous nuclear ribonucleoprotein C (HNRNPC) to promote Wnt/β-catenin and AKT pathways and the epithelial-mesenchymal transition process. In summary, our study manifests that the DDX11-AS1/HNRNPC axis may play a vital part in the occurrence and development of glioma, which provides new ideas and therapeutic targets for the diagnosis, treatment, and prognosis of glioma.
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Affiliation(s)
- Zijin Xiang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Qiaoli Lv
- Jiangxi Key Laboratory of Translational Cancer Research, Department of Head and Neck Surgery, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Yujun Zhang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Xueru Chen
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Ren Guo
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Shikun Liu
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Xiangdong Peng
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
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[Comprehensive Analysis of the Relationship between m6A Methylation Patterns and Immune Microenvironment in Lung Adenocarcinoma]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2022; 25:311-322. [PMID: 35599007 PMCID: PMC9127756 DOI: 10.3779/j.issn.1009-3419.2022.103.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND m6A RNA methylation modification plays an important role in the occurrence and progression of lung cancer and regulates tumor immunity. Current studies mostly focus on the differential expression of some specific m6A effectors and infiltrating immune cell. m6A methylation modification is the result of mutual adjustment and balance between effectors, and changes in the expression of one or two effectors are far from enough to reflect the panorama of m6A methylation. The role of m6A in the immune microenvironment of lung adenocarcinoma (LUAD) is still poorly understood. The aim of this study is to investigate the effect of different m6A modification patterns in immune microenvironment of LUAD. METHODS LUAD data was obtained from The Cancer Genome Atlas (TCGA), University of California Santa Cruz Xena (UCSC Xena) and Gene Expression Omnibus (GEO) databases. Gene mutation, differential expression and survival analysis were performed for 24 m6A effectors. The m6A modification pattern was constructed by unsupervised clustering method, and the m6A clusters survival analysis, gene set variation analysis, immune score and immune cell infiltration analysis were performed. The association between LRPPRC protein expression levels and infiltration of CD8+ cytotoxic T lymphocytes and CD68+ macrophages in the tumor microenvironment was validated by immunohistochemistry in LUAD tissue microarray with 68 cases. RESULTS The mutations of m6A effector were found in 150 of 567 LUAD cases with a frequency of 26.46%. 6 readers and 3 writers were significantly up regulated in LUAD tissues compared with normal tissues. IGF2BP1 and HNRNPC are the independent risk factors for prognosis of LUAD. Abundant cross-talks among writers, erasers and readers were demonstrated. Three m6A modification patterns with different immune cell infiltration characteristics and clinical prognosis were established. Among m6A effectors, LRPPRC was found to be inversely associated with the infiltration of CD8+ cytotoxic T lymphocytes and CD68+ macrophages, and was validated in 68 LUAD tissues. CONCLUSIONS m6A modification patterns play non-negligible roles in regulating the immune microenvironment. LRPPRC has potential to be a new biomarker for checkpoint inhibitor immunotherapy.
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Metabolism-Related Bioinformatics Analysis Reveals That HPRT1 Facilitates the Progression of Oral Squamous Cell Carcinoma In Vitro. JOURNAL OF ONCOLOGY 2022; 2022:7453185. [PMID: 35586208 PMCID: PMC9110220 DOI: 10.1155/2022/7453185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022]
Abstract
Objectives Many studies have shown that dysregulation of metabolism contributes to oncogenesis. However, the exact roles of metabolism-related genes (MRGs) in oral squamous cell carcinoma (OSCC) remain unclear. Thus, we aimed to identify a prognostic signature related to MRGs in OSCC. Methods The gene sequencing data of OSCC samples and the MRG set were downloaded from The Cancer Genome Atlas (TCGA) and the Molecular Signatures Database (MSigDB). The Wilcoxon rank-sum test was used to identify differentially expressed MRGs. Then, a prognostic signature was established by multivariate Cox regression analysis. Finally, prognosis-related MRGs were selected and further validated in OSCC tissues and cell lines. Results A prognostic signature that included 8 MRGs was constructed. Multiple survival analysis revealed that only HPRT1 might be an independent biomarker and indicator of poor overall survival in OSCC patients. The expression of HPRT1 was then found to be upregulated in OSCC tissues and cell lines, and suppression of HPRT1 gene expression by siRNA inhibited the proliferation, migration, and invasion of OSCC cells in vitro. Conclusions MRGs play an important role in the development of OSCC. Furthermore, HPRT1 might be an independent biomarker of OSCC and enhance OSCC proliferation, migration, and invasion in vitro; these results emphasize the potential utility of HPRT1 in OSCC therapy.
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Mo L, Meng L, Huang Z, Yi L, Yang N, Li G. An analysis of the role of HnRNP C dysregulation in cancers. Biomark Res 2022; 10:19. [PMID: 35395937 PMCID: PMC8994388 DOI: 10.1186/s40364-022-00366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/20/2022] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins C (HnRNP C) is part of the hnRNP family of RNA-binding proteins. The relationship between hnRNP C and cancers has been extensively studied, and dysregulation of hnRNP C has been found in many cancers. According to existing public data, hnRNP C could promote the maturation of new heterogeneous nuclear RNAs (hnRNA s, also referred to as pre-mRNAs) into mRNAs and could stabilize mRNAs, controlling their translation. This paper reviews the regulation and dysregulation of hnRNP C in cancers. It interacts with some cancer genes and other biological molecules, such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and double-stranded RNAs (dsRNAs). Even directly binds to them. The effects of hnRNP C on biological processes such as alternative cleavage and polyadenylation (APA) and N6-methyladenosine (m6A) modification differ among cancers. Its main function is regulating stability and level of translation of cancer genes, and the hnRNP C is regarded as a candidate biomarker and might be valuable for prognosis evaluation.
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Affiliation(s)
- Liyi Mo
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lijuan Meng
- Department of Ultrasonography, Second Affiliated Hospital, University of South China, Hengyang, 421001, Hunan, China
| | - Zhicheng Huang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lan Yi
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Nanyang Yang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
| | - Guoqing Li
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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Yang Q, Cheng C, Zhu R, Guo F, Lai R, Liu X, Li M. A N6-methyladenosine-related long noncoding RNAs model for predicting prognosis in oral squamous cell carcinoma: Association with immune cell infiltration and tumor metastasis. Oral Oncol 2022; 127:105771. [DOI: 10.1016/j.oraloncology.2022.105771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/28/2022] [Accepted: 02/11/2022] [Indexed: 02/09/2023]
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Zhao X, Li X, Li X. Multiple roles of m6A methylation in epithelial–mesenchymal transition. Mol Biol Rep 2022; 49:8895-8906. [DOI: 10.1007/s11033-022-07368-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/11/2022] [Indexed: 01/17/2023]
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35
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Huo XX, Wang SJ, Song H, Li MD, Yu H, Wang M, Gong HX, Qiu XT, Zhu YF, Zhang JY. Roles of Major RNA Adenosine Modifications in Head and Neck Squamous Cell Carcinoma. Front Pharmacol 2021; 12:779779. [PMID: 34899345 PMCID: PMC8657411 DOI: 10.3389/fphar.2021.779779] [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: 09/19/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer malignancy worldwide and is known to have poor prognosis. The pathogenesis behind the development of HNSCC is not fully understood. Modifications on RNA are involved in many pathophysiological processes, such as tumor development and inflammation. Adenosine-related RNA modifications have shown to be linked to cancer and may play a role in cancer occurrence and development. To date, there are at least 170 different chemical RNA modifications that modify coding and non-coding RNAs (ncRNAs). These modifications affect RNA stability and transcription efficiency. In this review, we focus on the current understanding of the four major RNA adenosine modifications (N6-Methyladenosine, N1-Methyladenosine, Alternative Polyadenylation Modification and A-to-I RNA editing) and their potential molecular mechanisms related to HNSCC development and progression. We also touch on how these RNA modifications affect treatment of HNSCCs.
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Affiliation(s)
- Xing-Xing Huo
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Shu-Jie Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hang Song
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Ming-de Li
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Hua Yu
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao, China
| | - Meng Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hong-Xiao Gong
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Xiao-Ting Qiu
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Yong-Fu Zhu
- Experimental Center of Clinical Research, Scientific Research Department, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Jian-Ye Zhang
- Key Laboratory of Molecular Target and Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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Du A, Wu X, Gao Y, Jiang B, Wang J, Zhang P, Zhao Q. m6A Regulator-Mediated Methylation Modification Patterns and Tumor Microenvironment Infiltration Characterization in Acute Myeloid Leukemia. Front Immunol 2021; 12:789914. [PMID: 34887874 PMCID: PMC8650218 DOI: 10.3389/fimmu.2021.789914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/02/2021] [Indexed: 01/10/2023] Open
Abstract
Recent studies have demonstrated epigenetic regulation of immune responses. Nevertheless, the underlying effect of RNA N6-methyladenosine (m6A) modifications on tumor microenvironment cell infiltration remains elusive. In this study, we thoroughly assessed m6A modification patterns of 255 myeloid leukemia specimens based on 23 m6A regulators. Consensus clustering of the 23 m6A regulators was performed to determine three distinct m6A modification patterns that were remarkably consistent with three immunophenotypes of tumors: immunorejection, immune activation, and immune inertness. Further evaluation and prognostic analysis of the m6A modification patterns of individual tumors revealed that low m6A score was characterized by increased mutational burden, immune activation, and survival rates, whereas high m6A score was characterized by poorer survival rates and the absence of effective immune infiltration. In addition, this study investigated the association between m6A regulators and antitumor immune responses and discovered higher expression of the immune regulators PD-L1, PD-L2, MRP1, and MRP2 in low m6A scores. Generally, the expression pattern of m6A regulators was remarkably associated with prognostic results and antitumor immune responses in acute myeloid leukemia and may be an underlying target and biological marker for immune therapies.
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Affiliation(s)
- Ashuai Du
- Department of Infectious Diseases, Third Xiangya Hospital, Central South University, Changsha, China.,Department of Infectious Diseases, Guizhou Provincial People's Hospital, Guizhou, China
| | - Xin Wu
- Department of Orthopedics, Third Xiangya Hospital, Central South University, Changsha, China
| | - Yunmei Gao
- Department of Hematology, The Qinghai Provincial People's Hospital, Xining, China
| | - Baili Jiang
- Department of Medical Oncology, The Xiayi County Traditional Chinese Medicine Hospital, Shangqiu, China
| | - Jianlong Wang
- Department of Orthopedics, Third Xiangya Hospital, Central South University, Changsha, China
| | - Pan Zhang
- Department of Infectious Diseases, Third Xiangya Hospital, Central South University, Changsha, China
| | - Qiangqiang Zhao
- Department of Hematology, The Qinghai Provincial People's Hospital, Xining, China.,Department of Blood Transfusion, The Third Xiangya Hospital, Central South University, Changsha, China
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Li C, Chen X, Ren X, Chen JL, Chen H, Yu JJ, Ran QC, Kang S, Chen XM, Zhao ZJ. Identification of Hypoxia-Related Molecular Classification and Associated Gene Signature in Oral Squamous Cell Carcinoma. Front Oncol 2021; 11:709865. [PMID: 34888229 PMCID: PMC8649955 DOI: 10.3389/fonc.2021.709865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/29/2021] [Indexed: 12/24/2022] Open
Abstract
The high heterogeneity of oral squamous cell carcinoma (OSCC) is the main obstacle for individualized treatment. Recognizing the characteristics of different subtypes and investigating the promising strategies for each subclass are of great significance in precise treatment. In this study, we systematically evaluated hypoxia-mediated patterns together with immune characteristics of 309 OSCC patients in the TCGA training set and 97 patients in the GSE41613 testing set. We further identified two different hypoxia subtypes with distinct immune microenvironment traits and provided treatment programs for the two subclasses. In order to assess hypoxia level individually, we finally constructed a hypoxia-related risk score, which could predict the clinical outcome and immunotherapy response of OSCC patients. In summary, the recognition of different hypoxia patterns and the establishment of hypoxia-related risk score might enhance our understanding of the tumor microenvironment of OSCC and provide more personalized treatment strategies in the future.
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Affiliation(s)
- Chen Li
- Department of Orthodontics, The First Clinic of Stomatological Hospital of China Medical University, Shenyang, China
| | - Xin Chen
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Xiaolin Ren
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China.,Department of Neurosurgery, Shenyang Red Cross Hospital, Shenyang, China
| | - Jia-Lin Chen
- Department of Orthodontics, The First Clinic of Stomatological Hospital of China Medical University, Shenyang, China
| | - Hao Chen
- Department of Orthodontics, The First Clinic of Stomatological Hospital of China Medical University, Shenyang, China
| | - Jing-Jia Yu
- Department of Orthodontics, The First Clinic of Stomatological Hospital of China Medical University, Shenyang, China
| | - Qiu-Chi Ran
- Department of Orthodontics, The First Clinic of Stomatological Hospital of China Medical University, Shenyang, China
| | - Shuang Kang
- Department of Orthodontics, The First Clinic of Stomatological Hospital of China Medical University, Shenyang, China
| | - Xi-Meng Chen
- Department of Orthodontics, The First Clinic of Stomatological Hospital of China Medical University, Shenyang, China
| | - Zhen-Jin Zhao
- Department of Orthodontics, The First Clinic of Stomatological Hospital of China Medical University, Shenyang, China
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Zhu XL, Li Q, Shen J, Shan L, Zuo ED, Cheng X. Use of 6 m6A-relevant lncRNA genes as prognostic markers of primary liver hepatocellular carcinoma based on TCGA database. Transl Cancer Res 2021; 10:5337-5351. [PMID: 35116381 PMCID: PMC8797289 DOI: 10.21037/tcr-21-2440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is diagnosed at the middle and advanced stages, negating radical treatment. Identifying specific and effective prognostic HCC biomarkers is important and can facilitate the discovery of potential therapeutic targets. N6-methyladenosine (m6A) and long non-coding RNAs (lncRNAs) are associated with the development of multiple tumors. The role of m6A-relevant lncRNAs in the initiation and progression of HCC is unclear. The aim of the present study was to investigate the expression of m6A-relevant lncRNAs in HCC and to identify new prognostic markers of the disease. METHODS Gene expression and clinical data were retrieved from The Cancer Genome Atlas database. m6A-relevant lncRNAs were identified by co-expression analysis and were screened by univariate Cox regression analysis. Different HCC patient clusters were established via consensus clustering. Gene set enrichment analysis (GSEA) was used to determine the cluster enrichment pathways. A risk score model was constructed, and Kaplan-Meier analysis of the overall survival (OS) between cluster 1 (high risk) and cluster 2 (low risk) was performed. Relationships between the clusters, risk scores, and clinicopathological characteristics were clarified. RESULTS Of the 1,852 m6A-relevant lncRNAs identified, 68 had prognostic relevance. The pathological grade, American Joint Committee on Cancer stage, and T stage of cluster 1 were significantly more advanced than those of cluster 2. Based on GSEA, mitotic spindle, G2M_CHECKPOINT, glycolysis, the phosphoinositide 3-kinase (PI3K) protein kinase B (AKT) mammalian target of rapamycin (mTOR) pathway, and DNA repair were more enriched in cluster 1. Six key m6A-relevant lncRNAs were selected to build a risk score model predicting the prognosis of HCC. The OS of patients in the high-risk group was shorter than that of patients in the low-risk group. Risk score was an independent prognostic factor of HCC patients. CONCLUSIONS The findings indicated that m6A-relevant lncRNAs may be important in the progression of HCC. The risk score model based on the 6 key m6A-relevant lncRNAs can accurately predict the prognosis of patients with HCC.
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Affiliation(s)
- Xiao-Li Zhu
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
| | - Qing Li
- Department of Gastroenterology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
| | - Jie Shen
- Department of Administrative Office, Jiangsu University Affiliated Kunshan Hospital (The First People’s Hospital of Kunshan), Kunshan, China
| | - Li Shan
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
| | - Er-Dong Zuo
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
| | - Xu Cheng
- Department of Hematology and Oncology, Soochow University Affiliated Taicang Hospital (The First People’s Hospital of Taicang), Taicang, China
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Zhou Y, Yang J, Tian Z, Zeng J, Shen W. Research progress concerning m 6A methylation and cancer. Oncol Lett 2021; 22:775. [PMID: 34589154 PMCID: PMC8442141 DOI: 10.3892/ol.2021.13036] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A) methylation is a type of methylation modification on RNA molecules, which was first discovered in 1974, and has become a hot topic in life science in recent years. m6A modification is an epigenetic regulation similar to DNA and histone modification and is dynamically reversible in mammalian cells. This chemical marker of RNA is produced by m6A 'writers' (methylase) and can be degraded by m6A 'erasers' (demethylase). Methylated reading protein is the 'reader', that can recognize the mRNA containing m6A and regulate the expression of downstream genes accordingly. m6A methylation is involved in all stages of the RNA life cycle, including RNA processing, nuclear export, translation and regulation of RNA degradation, indicating that m6A plays a crucial role in RNA metabolism. Recent studies have shown that m6A modification is a complicated regulatory network in different cell lines, tissues and spatio-temporal models, and m6A methylation is associated with the occurrence and development of tumors. The present review describes the regulatory mechanism and physiological functions of m6A methylation, and its research progress in several types of human tumor, to provide novel approaches for early diagnosis and targeted treatment of cancer.
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Affiliation(s)
- Yang Zhou
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Jie Yang
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Zheng Tian
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Jing Zeng
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Weigan Shen
- Department of Cell Biology, School of Medicine of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
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Wang S, Xu G, Chao F, Zhang C, Han D, Chen G. HNRNPC Promotes Proliferation, Metastasis and Predicts Prognosis in Prostate Cancer. Cancer Manag Res 2021; 13:7263-7276. [PMID: 34584453 PMCID: PMC8464311 DOI: 10.2147/cmar.s330713] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/13/2021] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION The incidence of prostate cancer remains high worldwide, while exploring new therapeutic targets for prostate cancer is essential. Heterogeneous nuclear ribonucleoproteins have been proved to regulate tumorigeneses in various cancers. This study aimed to explore the role of HNRNPC in prostate cancer progression. METHODS HNRNPC expression and its correlation with clinical features and immune infiltration were analyzed by bioinformatics analysis. The effects of HNRNPC on prostate cell proliferation, migration, and invasion were accessed by EdU, colony formation, transwell, and wound-healing assays. RESULTS The expression level of HNRNPC was significantly increased in prostate cancer tissues and was correlated with the T stage, N stage, Gleason score, PSA level, residual tumors, overall survival, disease-specific survival, and progression-free interval of prostate cancer patients. Silencing HNRNPC inhibited the proliferation and metastasis of prostate cancer cells. The expression of HNRNPC was negatively correlated with the infiltration level of most immune cells in prostate cancer. Mechanistically, HNRNPC may function through regulating gene expression at the posttranscriptional level. CONCLUSION HNRNPC could be a potential marker for the treatment and prognosis prediction of prostate cancer.
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Affiliation(s)
- Shiyu Wang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Guoxiong Xu
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
| | - Fan Chao
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Cong Zhang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Dunsheng Han
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
| | - Gang Chen
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, 201508, People’s Republic of China
- Department of Surgery, Shanghai Medical College, Fudan University, Shanghai, 200032, People’s Republic of China
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METTL3 Intensifies the Progress of Oral Squamous Cell Carcinoma via Modulating the m6A Amount of PRMT5 and PD-L1. J Immunol Res 2021; 2021:6149558. [PMID: 34476262 PMCID: PMC8408004 DOI: 10.1155/2021/6149558] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 12/19/2022] Open
Abstract
N6-Methyladenosine (m6A) modification is one of the commonest chemical modifications in eukaryotic mRNAs, which has essential effects on mRNA translation, splicing, and stability. Currently, there is a rising concern on the regulatory role of m6A in tumorigenesis. As a known component in the m6A methyltransferase complex, METTL3 (methyltransferase-like 3) plays an essential role in m6A methylation. Till now, the functions of METTL3 in oral squamous cell carcinoma (OSCC) and its relative mechanism remain to be explored. In this research, through the GEPIA database, we found that high METTL3 expression has a correlation with poor prognosis of squamous cell carcinoma of head and neck. qRT-PCR displayed that METTL3 was highly expressed in OSCC cells. Functionally, METTL3 knockdown reduced the invasion, migration, and proliferation competence of OSCC cells and attenuated the activation of CD8+ T cells. In contrast, METTL3 overexpression resulted in opposite results. GEPIA, UALCAN, and SRAMP databases, PCR, western blot, and m6A RNA methylation assay confirmed the m6A modification of PRMT5 and PD-L1 mediated by METTL3. In conclusion, our results displayed that METTL3 intensified the metastasis and proliferation of OSCC by modulating the m6A amounts of PRMT5 and PD-L1, suggesting that METTL3 may be a therapeutic target for OSCC patients.
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Herzner AM, Khan Z, Van Nostrand EL, Chan S, Cuellar T, Chen R, Pechuan-Jorge X, Komuves L, Solon M, Modrusan Z, Haley B, Yeo GW, Behrens TW, Albert ML. ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses. J Exp Med 2021; 218:212507. [PMID: 34297039 PMCID: PMC8313407 DOI: 10.1084/jem.20201833] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/11/2020] [Accepted: 06/24/2021] [Indexed: 01/26/2023] Open
Abstract
Cytosolic double-stranded RNA (dsRNA) initiates type I IFN responses. Endogenous retroelements, notably Alu elements, constitute a source of dsRNA. Adenosine-to-inosine (A-to-I) editing by ADAR induces mismatches in dsRNA and prevents recognition by MDA5 and autoinflammation. To identify additional endogenous dsRNA checkpoints, we conducted a candidate screen in THP-1 monocytes and found that hnRNPC and ADAR deficiency resulted in synergistic induction of MDA5-dependent IFN responses. RNA-seq analysis demonstrated dysregulation of Alu-containing introns in hnRNPC-deficient cells via utilization of unmasked cryptic splice sites, including introns containing ADAR-dependent A-to-I editing clusters. These putative MDA5 ligands showed reduced editing in the absence of ADAR, providing a plausible mechanism for the combined effects of hnRNPC and ADAR. This study contributes to our understanding of the control of repetitive element-induced autoinflammation and suggests that patients with hnRNPC-mutated tumors might maximally benefit from ADAR inhibition-based immunotherapy.
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Affiliation(s)
| | - Zia Khan
- Department of Human Genetics, Genentech, South San Francisco, CA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, Stem Cell Program and the Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA
| | - Sara Chan
- Department of Pathology, Genentech, South San Francisco, CA
| | - Trinna Cuellar
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Ronald Chen
- Department of Human Genetics, Genentech, South San Francisco, CA
| | | | - Laszlo Komuves
- Department of Pathology, Genentech, South San Francisco, CA
| | - Margaret Solon
- Department of Pathology, Genentech, South San Francisco, CA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics & Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, South San Francisco, CA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program and the Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA
| | | | - Matthew L Albert
- Department of Cancer Immunology, Genentech, South San Francisco, CA
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Vallina C, López-Pintor RM, González-Serrano J, de Vicente JC, Hernández G, Lorz C. Genes involved in the epithelial-mesenchymal transition in oral cancer: A systematic review. Oral Oncol 2021; 117:105310. [PMID: 33901766 DOI: 10.1016/j.oraloncology.2021.105310] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Epithelial-mesenchymal transition (EMT) is considered the initial step in the invasion-metastasis cascade. The aim of this systematic review was to study the signature of genes involved in the EMT process in oral cancer (OC) confirmed by protein expression and its possible relationship with oral squamous cell carcinoma (OSCC) prognostic variables. MATERIALS AND METHODS A search of the scientific literature was carried out with no start date restriction until 17 September 2020 in the electronic databases Pubmed/MEDLINE, Web of Science, Cochrane Library and Scopus, following specific eligibility criteria. The methodological quality of the included studies was assessed using the Newcastle-Ottawa tool. RESULTS A total of 8 retrospective cohort studies were included, all of them performed in China and with low risk of bias. Overexpression of the genes HNRNPC, ITGA5, HMGA2 and SRSF3, and low expression of ALDH3A1 and ARID2 promote EMT in OC. The more advanced clinical stages of the TNM classification were significantly associated with overexpression of HNRNPC, ITGA5, HMGA2 and SRSF3, and low expression of ARID2. CONCLUSIONS HNRNPC, ITGA5, HMGA2, SRSF3, ALDH3A1 and ARID2 genes were associated with EMT process. Over- or under-expression of these genes is associated with worse stages of OSCC and/or worse prognosis of the tumor. Further studies on this topic are needed in different countries to be able to confirm these results, since the detection of these genes can help to know which tumors have a worse prognosis.
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Affiliation(s)
- Carmen Vallina
- School of Medicine and Dentistry, Oviedo University, Julián clavería s/n, 33006 Oviedo, Spain
| | - Rosa María López-Pintor
- ORALMED Research Group, Department of Dental Clinical Specialties, School of Dentistry, Complutense University, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain.
| | - José González-Serrano
- ORALMED Research Group, Department of Dental Clinical Specialties, School of Dentistry, Complutense University, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain.
| | - Juan Carlos de Vicente
- ORALMED Research Group, Department of Oral and Maxillofacial Surgery, Hospital Central Universitario de Asturias (HUCA), Carretera de Rubín s/n, 33011 Oviedo, Asturias, Spain.
| | - Gonzalo Hernández
- ORALMED Research Group, Department of Dental Clinical Specialties, School of Dentistry, Complutense University, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain.
| | - Corina Lorz
- Molecular Oncology Unit, Environmental and Technological Energy Research Center (CIEMAT), Avd. Complutense 40, 28040, Spain; Research Institute 12 de Octubre i+12, University Hospital 12 de Octubre, Ave Córdoba s/n, 28041, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Ave Monforte de Lemos 3-5, 28029 Madrid, Spain.
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Liu H, Qin G, Ji Y, Wang X, Bao H, Guan X, Wei A, Cai Z. Potential role of m6A RNA methylation regulators in osteosarcoma and its clinical prognostic value. J Orthop Surg Res 2021; 16:294. [PMID: 33952279 PMCID: PMC8097785 DOI: 10.1186/s13018-021-02422-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Osteosarcoma is a disease with high mortality in children and adolescents, and metastasis is one of the important clinical features of osteosarcoma. N6-Methyladenosine (m6A) is the most abundant methylation modification in mRNA, which is regulated by m6A regulators. It is reported that it is related to the occurrence and development of tumors. However, the mechanism of its action in osteosarcoma is rarely known. The purpose of this study was to identify the potential role of m6A regulatory factor in osteosarcoma and its clinical prognostic value. METHODS Here, we used The Cancer Genome Atlas (TCGA) to comprehensively analyze the relationship between m6A regulatory factors and osteosarcoma (metastasis group and non-metastasis group). We analyzed their survival relationship and analyzed all the m6A regulatory factors in TCGA tumor data set by using the univariate Cox proportional hazard regression model. Finally, we selected two survival-related methylation regulators (FTO and IGF2BP2) as risk gene signature. RESULTS According to the median risk, patients were divided into low-risk group and high-risk group. Multivariate Cox regression analysis showed that these two risk genes were considered to be the key factors independently predicting the prognosis of patients with osteosarcoma. In addition, we verified their characteristics with gene expression omnibus (GEO) DataSets and confirmed that they are related to tumor and immune-related signaling pathways through gene set enrichment analysis (GESA) and immune infiltration analysis. CONCLUSIONS In conclusion, m6A regulators might play an important role in the metastasis of osteosarcoma and have potential important value for the prognosis and treatment strategy of osteosarcoma patients.
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Affiliation(s)
- Hua Liu
- Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, 55 Ninghai Middle Road, Haian, Nantong, Jiangsu Province, 226600, People's Republic of China
| | - Guangzhen Qin
- Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, 55 Ninghai Middle Road, Haian, Nantong, Jiangsu Province, 226600, People's Republic of China
| | - Yanan Ji
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Nantong University, Nantong, Jiangsu Province, 226001, People's Republic of China
| | - Xiaojian Wang
- Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, 55 Ninghai Middle Road, Haian, Nantong, Jiangsu Province, 226600, People's Republic of China
| | - Hailin Bao
- Clinical Laboratory, Haian Hospital of Traditional Chinese Medicine, Haian, Nantong, Jiangsu Province, 226600, People's Republic of China
| | - Xiaojun Guan
- Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, 55 Ninghai Middle Road, Haian, Nantong, Jiangsu Province, 226600, People's Republic of China
| | - Aichun Wei
- Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, 55 Ninghai Middle Road, Haian, Nantong, Jiangsu Province, 226600, People's Republic of China
| | - Zhigang Cai
- Department of Orthopedics, Haian Hospital of Traditional Chinese Medicine, 55 Ninghai Middle Road, Haian, Nantong, Jiangsu Province, 226600, People's Republic of China.
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Chen L, Hu B, Song X, Wang L, Ju M, Li Z, Zhou C, Zhang M, Wei Q, Guan Q, Jiang L, Chen T, Wei M, Zhao L. m 6A RNA Methylation Regulators Impact Prognosis and Tumor Microenvironment in Renal Papillary Cell Carcinoma. Front Oncol 2021; 11:598017. [PMID: 33796449 PMCID: PMC8008109 DOI: 10.3389/fonc.2021.598017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/02/2021] [Indexed: 12/24/2022] Open
Abstract
Accumulating evidence has proven that N6-methyladenosine (m6A) RNA methylation plays an essential role in tumorigenesis. However, the significance of m6A RNA methylation modulators in the malignant progression of papillary renal cell carcinoma (PRCC) and their impact on prognosis has not been fully analyzed. The present research set out to explore the roles of 17 m6A RNA methylation regulators in tumor microenvironment (TME) of PRCC and identify the prognostic values of m6A RNA methylation regulators in patients afflicted by PRCC. We investigated the different expression patterns of the m6A RNA methylation regulators between PRCC tumor samples and normal tissues, and systematically explored the association of the expression patterns of these genes with TME cell-infiltrating characteristics. Additionally, we used LASSO regression to construct a risk signature based upon the m6A RNA methylation modulators. Two-gene prognostic risk model including IGF2BP3 and HNRNPC was constructed and could predict overall survival (OS) of PRCC patients from the Cancer Genome Atlas (TCGA) dataset. The prognostic signature-based risk score was identified as an independent prognostic indicator in Cox regression analysis. Moreover, we predicted the three most significant small molecule drugs that potentially inhibit PRCC. Taken together, our study revealed that m6A RNA methylation regulators might play a significant role in the initiation and progression of PRCC. The results might provide novel insight into exploration of m6A RNA modification in PRCC and provide essential guidance for therapeutic strategies.
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Affiliation(s)
- Lianze Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Baohui Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Xinyue Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Lin Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Mingyi Ju
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Zinan Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Chenyi Zhou
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Ming Zhang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Qian Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Qiutong Guan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Longyang Jiang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Ting Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Liaoning Medical Diagnosis and Treatment Center, Shenyang, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
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46
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Zhao H, Xu Y, Xie Y, Zhang L, Gao M, Li S, Wang F. m6A Regulators Is Differently Expressed and Correlated With Immune Response of Esophageal Cancer. Front Cell Dev Biol 2021; 9:650023. [PMID: 33748145 PMCID: PMC7970005 DOI: 10.3389/fcell.2021.650023] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
N6 methyladenosine (m6A) RNA methylation regulators play an important role in the development of tumors. However, their function in esophageal cancer (EC) has not been fully elucidated. Here, we analyzed the gene expression data of 24 major m6A RNA methylation regulators from 775 patients with EC from TCGA dataset. The present study showed the aberrations of m6A regulators in genome were correlated to prognosis in human ECs. Meanwhile, 17 m6A regulators showed increased expression in EC samples, including YTHDC1, IGF2BP2, FTO, METTL14, YTHDF3, RBM15, WTAP, HNRNPA2B1, HNRNPC, ALKBH5, YTHDF2, METTL16, IGF2BP3, VIRMA, RBM15B, YTHDF1, KIAA1429, HAKAI, and ZC3H13. Among them, we found HNRNPC, YTHDC2, WTAP, VIRMA, IGF2BP3, and HNRNPA2B1 were significantly correlated to worse outcomes and advanced stage in EC. Furthermore, we showed levels of m6A regulators is correlated with the expression of Immuno-regulators (Immunoinhibitors, Immunostimulators, and MHC molecules) and immune infiltration levels in EC. Bioinformatics further confirm m6A regulators were involved in regulating RNA splicing, RNA stability, and cell proliferation. Our study showed m6A regulators are promising targets and biomarkers for cancer immunotherapy in EC.
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Affiliation(s)
- Huaying Zhao
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yue Xu
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Yilin Xie
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Lan Zhang
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ming Gao
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shenglei Li
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Feng Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Huang GZ, Wu QQ, Zheng ZN, Shao TR, Li F, Lu XY, Ye HY, Chen GX, Song YX, Zeng WS, Ai YL, Lv XZ. Bioinformatics Analyses Indicate That Cathepsin G (CTSG) is a Potential Immune-Related Biomarker in Oral Squamous Cell Carcinoma (OSCC). Onco Targets Ther 2021; 14:1275-1289. [PMID: 33658795 PMCID: PMC7920606 DOI: 10.2147/ott.s293148] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose Plenty of studies showed that the immune system was associated with cancer initiation and progression. This study aimed to explore the prognostic biomarkers from immune-related genes (IRGs) in oral squamous cell carcinoma (OSCC). Materials and Methods RNA-seq data were downloaded from The Cancer Genome Atlas (TCGA) and IRGs and transcription factors (TFs) were extracted. Then, the co-expression network between IRGs and TFs was constructed using the "WGCNA" package in R software. Furthermore, a gene expression signature according to IRGs was constructed to predict OSCC prognosis and its accuracy was validated by survival analysis. Subsequently, correlation analyses between risk-score and immune cells level and clinical parameters were performed. Finally, immune-related biomarkers were selected and further investigated using gain-of-function assays in vitro. Results A total of 32 normal cases and 317 OSCC cases were selected in our study. Differentially-expressed analysis indicated that there were 381 differentially-expressed IRGs and 62 TFs in OSCC. Among them, 25 TFs and 21 IRGs were enrolled in the co-expression network. Furthermore, we found that gene expression signature on the basis of 10 IRGs could predict the prognosis accurately and a high-risk score based on gene expression signature meant a high T classification, terminal clinical stage, and low immune cells level in OSCC. Finally, cathepsin G (CTSG) was identified as a potential immune-related biomarker and therapeutic target in OSCC. Conclusion In conclusion, IRGs were directly involved in the development and progression of OSCC. Furthermore, CTSG was identified as a potential independent biomarker and might be an immunotherapeutic target in OSCC treatment.
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Affiliation(s)
- Guang-Zhao Huang
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Qing-Qing Wu
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Ze-Nan Zheng
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Ting-Ru Shao
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Fei Li
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Xin-Yan Lu
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Heng-Yu Ye
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Gao-Xiang Chen
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Yu-Xing Song
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Wei-Sen Zeng
- Department of Cell Biology, School of Basic Medical Science, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Yi-Long Ai
- Foshan Stomatological Hospital, School of Stomatology and Medicine, Foshan University, Foshan, Guangdong Province, People's Republic of China
| | - Xiao-Zhi Lv
- Department of Oral & Maxillofacial Surgery, NanFang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China
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48
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Li H, Wu H, Wang Q, Ning S, Xu S, Pang D. Dual effects of N 6-methyladenosine on cancer progression and immunotherapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 24:25-39. [PMID: 33738136 PMCID: PMC7933696 DOI: 10.1016/j.omtn.2021.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
According to the latest global cancer statistics, cancer has become a major threat to human health, but cancer treatment has encountered many bottlenecks. As an emerging topic in epigenetics, N6-methyladenosine (m6A) is the most common internal modification on eukaryotic mRNA, which has attracted increasing attention in recent years. Accumulating studies have shown that aberrant m6A modifications have profound effects on the characteristics of tumors, which undoubtedly led to a significant breakthrough in cancer treatment. Although m6A function as an oncogene or tumor suppressor is not fully revealed, determining its precise function in the development and evolution of malignant tumors is crucial in improving clinical decisions involving targeted therapies. In this review, we briefly introduce the composition of the m6A methylation machinery and mainly summarize the biological mechanism of m6A in cancer cell death, angiogenesis, epithelial-mesenchymal transition (EMT), and therapeutic resistance. Subsequently, we present the exogenous regulatory factors of m6A and highlight the role of m6A on immune cells and cancer immunotherapy. The potential therapeutic strategies of m6A in human cancer are also discussed, considering research gaps and future applications.
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Affiliation(s)
- Hui Li
- Harbin Medical University, 157 Baojian Road, Harbin 150086, China.,Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150081, China.,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin 150086, China
| | - Hao Wu
- Harbin Medical University, 157 Baojian Road, Harbin 150086, China.,Sino-Russian Medical Research Center, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150081, China.,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin 150086, China
| | - Qin Wang
- Harbin Medical University, 157 Baojian Road, Harbin 150086, China.,Sino-Russian Medical Research Center, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150081, China.,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin 150086, China
| | - Shipeng Ning
- Harbin Medical University, 157 Baojian Road, Harbin 150086, China.,Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150081, China.,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin 150086, China
| | - Shouping Xu
- Harbin Medical University, 157 Baojian Road, Harbin 150086, China.,Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150081, China.,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin 150086, China
| | - Da Pang
- Harbin Medical University, 157 Baojian Road, Harbin 150086, China.,Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150081, China.,Sino-Russian Medical Research Center, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150081, China.,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin 150086, China
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49
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Yang L, Wu S, Ma C, Song S, Jin F, Niu Y, Tong WM. RNA m 6A Methylation Regulators Subclassify Luminal Subtype in Breast Cancer. Front Oncol 2021; 10:611191. [PMID: 33585234 PMCID: PMC7878528 DOI: 10.3389/fonc.2020.611191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
RNA N6-methyladenosine (m6A) methylation is the most prevalent epitranscriptomic modification in mammals, with a complex and fine-tuning regulatory system. Recent studies have illuminated the potential of m6A regulators in clinical applications including diagnosis, therapeutics, and prognosis. Based on six datasets of breast cancer in The Cancer Genome Atlas (TCGA) database and two additional proteomic datasets, we provide a comprehensive view of all the known m6A regulators in their gene expression, copy number variations (CNVs), DNA methylation status, and protein levels in breast tumors and their association with prognosis. Among four breast cancer subtypes, basal-like subtype exhibits distinct expression and genomic alteration in m6A regulators from other subtypes. Accordingly, four representative regulators (IGF2BP2, IGF2BP3, YTHDC2, and RBM15) are identified as basal-like subtype-featured genes. Notably, luminal A/B samples are subclassified into two clusters based on the methylation status of those four genes. In line with its similarity to basal-like subtype, cluster1 shows upregulation in immune-related genes and cell adhesion molecules, as well as an increased number of tumor-infiltrating lymphocytes. Besides, cluster1 has worse disease-free and progression-free survival, especially among patients diagnosed with stage II and luminal B subtype. Together, this study highlights the potential functions of m6A regulators in the occurrence and malignancy progression of breast cancer. Given the heterogeneity within luminal subtype and high risk of recurrence and metastasis in a portion of patients, the prognostic stratification of luminal A/B subtypes utilizing basal-featured m6A regulators may help to improve the accuracy of diagnosis and therapeutics of breast cancer.
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Affiliation(s)
- Lin Yang
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.,School of Basic Medicine, Peking Union Medical College, Beijing, China.,Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuangling Wu
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Chunhui Ma
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.,School of Basic Medicine, Peking Union Medical College, Beijing, China.,Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuhui Song
- China National Center for Bioinformation, Beijing, China.,National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Feng Jin
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.,School of Basic Medicine, Peking Union Medical College, Beijing, China.,Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei-Min Tong
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.,School of Basic Medicine, Peking Union Medical College, Beijing, China.,Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
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50
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Zhou J, Guo Y, Huo Z, Xing Y, Fang J, Ma G, Han Q, Wang M, Xu Q. Identification of therapeutic targets and prognostic biomarkers from the hnRNP family in invasive breast carcinoma. Aging (Albany NY) 2021; 13:4503-4521. [PMID: 33495416 PMCID: PMC7906176 DOI: 10.18632/aging.202411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/13/2020] [Indexed: 04/12/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are RNA-binding proteins that are reported to play a crucial role in the pathogenic process of multiple malignancies. However, their expression patterns, clinical application significance and prognostic values in invasive breast carcinoma (BRCA) remain unknown. In this study, we investigated hnRNP family members in BRCA using accumulated data from Oncomine 4.5, UALCAN Web portal and other available databases. We explored the expression and prognostic value level of hnRNPs in BRCA. We further analyzed their association with the clinicopathological features of BRCA patients. Subsequently, we calculated the alteration frequency of hnRNPs, constructed the interaction network of hnRNPs, and examined the potential coexpression genes of hnRNPs, revealing that HNRNPU and SYNCRIP are the core molecular genes requiring further investigation for BRCA. We validated the immunohistochemistry (IHC) pattern to simulate clinical applications based on pathology. Cell function experiments conducted in vitro indicated that HNRNPU can promote epithelial-mesenchymal transition, functionally stimulating the invasion capacity and inhibiting the viability of invasive BRCA cells. In summary, our systematic analysis demonstrated that HNRNPU was the key molecule that played a fundamental role in BRCA metastasis, which may facilitate the development of new diagnostic and prognostic markers for the analysis of BRCA progression.
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MESH Headings
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/pathology
- Cell Line, Tumor
- Databases, Genetic
- Epithelial-Mesenchymal Transition/genetics
- Female
- Heterogeneous-Nuclear Ribonucleoprotein U/genetics
- Heterogeneous-Nuclear Ribonucleoproteins/genetics
- Humans
- In Vitro Techniques
- MCF-7 Cells
- Molecular Targeted Therapy
- Neoplasm Invasiveness
- Neoplasm Staging
- Prognosis
- RNA, Messenger/metabolism
- RNA, Small Interfering
- Transcriptome
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Affiliation(s)
- Jiawei Zhou
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, NanYang 473000, China
- School of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, NanYang 473000, China
| | - Yugang Guo
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, NanYang 473000, China
| | - Zheng Huo
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, NanYang 473000, China
| | - Yuxin Xing
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, NanYang 473000, China
- School of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, NanYang 473000, China
| | - Jintao Fang
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, NanYang 473000, China
| | - Guohui Ma
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, NanYang 473000, China
| | - Qinghui Han
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, NanYang 473000, China
- School of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, NanYang 473000, China
| | - Mengzhen Wang
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, NanYang 473000, China
- School of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, NanYang 473000, China
| | - Qian Xu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, NanYang 473000, China
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