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Yang M, Deng Y, Ma Y, Song C, Wu Z, Yibulayin X, Sun X, Guo Y, He D. Comprehensive pan-cancer analysis reveals that C5orf34 regulates the proliferation and mortality of lung cancer. Funct Integr Genomics 2024; 24:119. [PMID: 38951221 DOI: 10.1007/s10142-024-01397-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]
Abstract
The gene C5orf34 exhibits evolutionary conservation among mammals, and emerging evidence suggests its potential involvement in tumor development; however, comprehensive investigations of this gene are lacking. This study aims to elucidate the functional attributes and underlying mechanisms of C5orf34 in cancer. To evaluate its clinical predictive value, we conducted an analysis of the pan-cancerous expression, clinical data, mutation, and methylation data of C5orf34. Additionally, we investigated the correlation between C5orf34 and tumor mutant load (TMB), immune cell infiltration, and microsatellite instability (MSI) through relevant analyses. Furthermore, immunohistochemical (IHC) staining was employed to validate clinical samples, while knockdown and overexpression experiments and transcriptome RNA sequencing were utilized to examine the impact of C5orf34 on LUAD cells. According to our study, C5orf34 exhibits high expression levels in the majority of malignant tumors. The upregulation of C5orf34 is governed by DNA copy number alterations and methylation patterns, and it is closely associated with patients' survival prognosis and immune characteristics, thereby holding significant clinical implications. Furthermore, IHC staining analysis, cellular experiments, and transcriptome RNA sequencing have provided evidence supporting the role of C5orf34 in modulating the cell cycle to promote LUAD proliferation, migration, and invasion. This highlights its potential as a promising therapeutic target. The findings of this investigation suggest that C5orf34 may serve as a valuable biomarker for various tumor types and represent a potential target for immunotherapy, particularly in relation to the proliferation, migration, and apoptosis of LUAD cells.
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Affiliation(s)
- Meng Yang
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China.
| | - Yuhan Deng
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Yu Ma
- Department of Clinical Laboratory, The Fourth People' Hospital of Urumqi, Urumqi, 830011, China
| | - Chunli Song
- Department of Pharmacy, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Zhenhua Wu
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Xiayimaierdan Yibulayin
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Xiaohong Sun
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Yunquan Guo
- Department of Pathology, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China
| | - Dan He
- Thoracic Surgery, Cancer Hospital Affiliated to Xinjiang Medical University, Urumqi, 830011, China.
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Li H, Ma H, Ma J, Qin F, Fan S, Kong S, Zhao S, Ma J. Unveiling the role of RAC3 in the growth and invasion of cisplatin-resistant bladder cancer cells. J Cell Mol Med 2024; 28:e18473. [PMID: 38847477 PMCID: PMC11157678 DOI: 10.1111/jcmm.18473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024] Open
Abstract
Bladder cancer is one of the most prevalent cancers worldwide, and its morbidity and mortality rates have been increasing over the years. However, how RAC family small GTPase 3 (RAC3) affects the proliferation, migration and invasion of cisplatin-resistant bladder cancer cells remains unclear. Bioinformatics techniques were used to investigate the expression of RAC3 in bladder cancer tissues. Influences of RAC3 in the grade, stage, distant metastasis, and survival rate of bladder cancer were also examined. Analysis of the relationship between RAC3 expression and the immune microenvironment (TIME), genomic mutations, and stemness index. In normal bladder cancer cells (T24, 5637, and BIU-87) and cisplatin-resistant bladder cancer cells (BIU-87-DDP), the expression of RAC3 was detected separately with Western blotting. Plasmid transfection was used to overexpress or silence the expression of RAC3 in bladder cancer cells resistant to cisplatin (BIU-87-DDP). By adding activators and inhibitors, the activities of the JNK/MAPK signalling pathway were altered. Cell viability, invasion, and its level of apoptosis were measured in vitro using CCK-8, transwell, and flow cytometry. The bioinformatics analyses found RAC3 levels were elevated in bladder cancer tissues and were associated with a poor prognosis in bladder cancer. RAC3 in BIU-87-DDP cells expressed a higher level than normal bladder cancer cells. RAC3 overexpression promoted BIU-87-DDP proliferation. The growth of BIU-87-DDP cells slowed after the knockdown of RAC3, and RAC3 may have had an impact on the activation of the JNK/MAPK pathway.
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Affiliation(s)
- Haodong Li
- Department of UrologyHebei Medical University Third HospitalShijiazhuangChina
| | - Hongxuan Ma
- Faculty of Health and Behavioural SciencesThe University of QueenslandQueenslandAustralia
| | - JianHua Ma
- Geriatrics DepartmentHebei Chengde Central HospitalChengdeChina
| | - Fei Qin
- Department of UrologyHebei Medical University Third HospitalShijiazhuangChina
| | - Siqi Fan
- Department of UrologyHebei Medical University Third HospitalShijiazhuangChina
| | - Shaopeng Kong
- Department of UrologyHebei Medical University Third HospitalShijiazhuangChina
| | - Sitao Zhao
- Department of UrologyHebei Medical University Third HospitalShijiazhuangChina
| | - Jianguo Ma
- Department of UrologyHebei Medical University Third HospitalShijiazhuangChina
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3
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Huang F, Jin L, Zhang X, Wang M, Zhou C. Integrated pan-cancer analysis reveals the immunological and prognostic potential of RBFOX2 in human tumors. Front Pharmacol 2024; 15:1302134. [PMID: 38881877 PMCID: PMC11176534 DOI: 10.3389/fphar.2024.1302134] [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: 09/26/2023] [Accepted: 05/08/2024] [Indexed: 06/18/2024] Open
Abstract
Background The role of RNA-binding fox one homolog 2 (RBFOX2) in the progression of multiple tumors is increasingly supported by evidence. However, the unclearness pertaining to the expression of RBFOX2, its prognostic potential, and its correlation with the tumor microenvironment (TME) in pan-cancer persists. This study aims to comprehensively investigate the immunological prognostic value of RBFOX2. Methods The Cancer Genome Atlas Gene Expression Omnibus Genotype-Tissue Expression (GTEx), TIMER2.0, Kaplan-Meier (K-M) Plotter, University of Alabama at Birmingham Cancer data analysis Portal (UALCAN), cbioportal, and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) were utilized for a systematic analysis of RBFOX2. This analysis included studying its expression, prognostic value, DNA methylation, enrichment analysis, immune infiltration cells, and immune-related genes. Additionally, qRT-PCR, CCK-8, colony formation, transwell assays, and immunohistochemistry were employed to analyze the expression and biological function of RBFOX2 in liver cancer. Results Variations in RBFOX2 expression have been observed across diverse tumors and have been identified as indicators of unfavorable prognosis. It is closely linked to immune infiltration cells, immune checkpoints, chemokines, and chemokine receptors in the TME. Higher levels of RBFOX2 have been significantly associated with low response and poor prognosis in patients with non-small cell lung cancer (NSCLC) and melanoma who receive immunotherapy. Furthermore, the DNA methylation of RBFOX2 varies across different types of cancer and has shown better prognosis in patients with BLCA, BRCA, CESC, COAD, DLBC, HNSC, LAML, LGG, LUAD, PAAD, SKCM and THYM. Interestingly, RBFOX2 expression was found to be lower in hepatocellular carcinoma (HCC) patients' tumor tissues compared to their paired adjacent tissues. In vitro studies have shown that knockdown of RBFOX2 significantly promotes the growth and metastasis of liver cancer cells. Conclusion This study investigates the correlation between DNA methylation, prognostic value, and immune cell infiltration with the expression of RBFOX2 in pan-cancer and indicates its potential role to inhibit metastasis of liver cancer.
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Affiliation(s)
- Fengxian Huang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Long Jin
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Xinyue Zhang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Min Wang
- Department of Science and Education, Xi'an Children's Hospital Affiliated of Xi'an Jiaotong University, Xi'an, China
| | - Congya Zhou
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
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4
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Wang J, Zhao E, Geng B, Zhang W, Li Z, Liu Q, Liu W, Zhang W, Hou W, Zhang N, Liu Z, You B, Wu P, Li X. Downregulation of UBB potentiates SP1/VEGFA-dependent angiogenesis in clear cell renal cell carcinoma. Oncogene 2024; 43:1386-1396. [PMID: 38467852 PMCID: PMC11065696 DOI: 10.1038/s41388-024-03003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) presents a unique profile characterized by high levels of angiogenesis and robust vascularization. Understanding the underlying mechanisms driving this heterogeneity is essential for developing effective therapeutic strategies. This study revealed that ubiquitin B (UBB) is downregulated in ccRCC, which adversely affects the survival of ccRCC patients. UBB exerts regulatory control over vascular endothelial growth factor A (VEGFA) by directly interacting with specificity protein 1 (SP1), consequently exerting significant influence on angiogenic processes. Subsequently, we validated that DNA methyltransferase 3 alpha (DNMT3A) is located in the promoter of UBB to epigenetically inhibit UBB transcription. Additionally, we found that an unharmonious UBB/VEGFA ratio mediates pazopanib resistance in ccRCC. These findings underscore the critical involvement of UBB in antiangiogenic therapy and unveil a novel therapeutic strategy for ccRCC.
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MESH Headings
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/blood supply
- Carcinoma, Renal Cell/drug therapy
- Humans
- Kidney Neoplasms/pathology
- Kidney Neoplasms/genetics
- Kidney Neoplasms/blood supply
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/drug therapy
- Sp1 Transcription Factor/metabolism
- Sp1 Transcription Factor/genetics
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/pathology
- Vascular Endothelial Growth Factor A/metabolism
- Vascular Endothelial Growth Factor A/genetics
- Down-Regulation
- Gene Expression Regulation, Neoplastic
- Cell Line, Tumor
- Animals
- Pyrimidines/pharmacology
- Pyrimidines/therapeutic use
- Indazoles/pharmacology
- Indazoles/therapeutic use
- DNA Methyltransferase 3A/metabolism
- Sulfonamides/pharmacology
- Mice
- Ubiquitin/metabolism
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA (Cytosine-5-)-Methyltransferases/genetics
- Drug Resistance, Neoplasm/genetics
- Promoter Regions, Genetic
- Female
- Male
- Angiogenesis
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Affiliation(s)
- Jinpeng Wang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Enyang Zhao
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Bo Geng
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wei Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Zhuolun Li
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Qing Liu
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Department of Radiation Oncology, Urology, and Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Weiyang Liu
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wenfu Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wenbin Hou
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Nan Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Zhiming Liu
- Department of Urology, Shanghai Fengxian District Central Hospital, Shanghai, 200233, China
| | - Bosen You
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Pengfei Wu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Anhui Province Key Laboratory of Brain Function and Brain Disease, Hefei, Anhui, 230001, China.
- Anhui Provincial Stereotactic Neurosurgical Institute, Hefei, Anhui, 230001, China.
- Anhui Provincial Clinical Research Center for Neurosurgical Disease, Hefei, Anhui, 230001, China.
- Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui, 233030, China.
| | - Xuedong Li
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
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Zhao L, Guo J, Xu S, Duan M, Liu B, Zhao H, Wang Y, Liu H, Yang Z, Yuan H, Jiang X, Jiang X. Abnormal changes in metabolites caused by m 6A methylation modification: The leading factors that induce the formation of immunosuppressive tumor microenvironment and their promising potential for clinical application. J Adv Res 2024:S2090-1232(24)00159-0. [PMID: 38677545 DOI: 10.1016/j.jare.2024.04.016] [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: 02/18/2024] [Revised: 04/14/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) RNA methylation modifications have been widely implicated in the metabolic reprogramming of various cell types within the tumor microenvironment (TME) and are essential for meeting the demands of cellular growth and maintaining tissue homeostasis, enabling cells to adapt to the specific conditions of the TME. An increasing number of research studies have focused on the role of m6A modifications in glucose, amino acid and lipid metabolism, revealing their capacity to induce aberrant changes in metabolite levels. These changes may in turn trigger oncogenic signaling pathways, leading to substantial alterations within the TME. Notably, certain metabolites, including lactate, succinate, fumarate, 2-hydroxyglutarate (2-HG), glutamate, glutamine, methionine, S-adenosylmethionine, fatty acids and cholesterol, exhibit pronounced deviations from normal levels. These deviations not only foster tumorigenesis, proliferation and angiogenesis but also give rise to an immunosuppressive TME, thereby facilitating immune evasion by the tumor. AIM OF REVIEW The primary objective of this review is to comprehensively discuss the regulatory role of m6A modifications in the aforementioned metabolites and their potential impact on the development of an immunosuppressive TME through metabolic alterations. KEY SCIENTIFIC CONCEPTS OF REVIEW This review aims to elaborate on the intricate networks governed by the m6A-metabolite-TME axis and underscores its pivotal role in tumor progression. Furthermore, we delve into the potential implications of the m6A-metabolite-TME axis for the development of novel and targeted therapeutic strategies in cancer research.
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Affiliation(s)
- Liang Zhao
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; Department of Colorectal Anal Surgery, Shenyang Coloproctology Hospital, Shenyang 110002, China.
| | - Junchen Guo
- Department of Radiology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Shasha Xu
- Department of Gastroendoscopy, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Meiqi Duan
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Baiming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - He Zhao
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Yihan Wang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Haiyang Liu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Zhi Yang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
| | - Hexue Yuan
- Department of Colorectal Anal Surgery, Shenyang Coloproctology Hospital, Shenyang 110002, China.
| | - Xiaodi Jiang
- Department of Infectious Disease, Shengjing Hospital of China Medical University, Shenyang 110020, China.
| | - Xiaofeng Jiang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China.
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6
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Zhang FB, Gan L, Zhu TH, Ding HQ, Wu CH, Guan YT, Chen XQ. Pan-cancer analyses reveal genomics and clinical outcome association of the fatty acid oxidation regulators in cancer. Heliyon 2024; 10:e28441. [PMID: 38590909 PMCID: PMC10999922 DOI: 10.1016/j.heliyon.2024.e28441] [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: 06/05/2023] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Background Fatty acid oxidation (FAO) is considered to play a vital part in tumor metabolic reprogramming. But the comprehensive description of FAO dysregulation in tumors has not been unknown. Methods We obtained FAO genes, RNA-seq data and clinical information from the Msigdb, TCGA and GTEx databases. We assessed their prognosis value using univariate cox analysis, survival analysis and Kaplan-Meier curve. We determined the function of FAO genes using gene set variation analysis. The correlation analysis was calculated by corrplot R package. Immunotherapy response was assessed through TIDE scores. The protein expression levels of FAO genes were validated using immunohistochemistry (IHC). Results The FAO scores were highest in COAD but lowest in PCPG. FAO scores were significantly associated with the prognosis of some cancers in OS, DSS, DFI and PFI. Besides, gene set variation analysis identified that FAO scores were related to immune-related pathways, and immune infiltration analysis showed FAO scores were positively related to cancer-associated fibroblasts and various immune-related genes. TIDE scores were significantly decreased in ACC, CHOL, ESCA, GBM, LAML, SARC, SKCM and THCA compared with normal samples, while it was significantly increased in BLCA, LUAD, LUSC, PCPG, PRAD and STAD. Besides, most FAO genes were downregulated in pan-cancer compared with normal samples. Moreover, we found copy number variation (CNV) of FAO genes played a positive role in their mRNA expression, while methylation was negative. We determined FAO genes were closely related to some drugs in pan-cancer. Conclusions FAO score is a novel and promising factor for predicting outcomes.
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Affiliation(s)
- Fu-bin Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China
| | - Lei Gan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China
| | - Tian-hong Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China
| | - Hui-qing Ding
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China
| | - Cheng-hao Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji University School of Medicine, No.389 Xincun Road, Shanghai, 200065, China
| | - Yu-tao Guan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China
| | - Xue-qin Chen
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China
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7
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Huang L, Irshad S, Sultana U, Ali S, Jamil A, Zubair A, Sultan R, Abdel-Maksoud MA, Mubarak A, Almunqedhi BM, Almanaa TN, Malik A, Alamri A, Kodous AS, Mares M, Zaky MY, Saba Sajjad S, Hameed Y. Pan-cancer analysis of HS6ST2: associations with prognosis, tumor immunity, and drug resistance. Am J Transl Res 2024; 16:873-888. [PMID: 38586106 PMCID: PMC10994782 DOI: 10.62347/ncph5416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/08/2024] [Indexed: 04/09/2024]
Abstract
OBJECTIVES In this comprehensive study spanning 33 malignancies, we explored the differential expression and prognostic significance of Heparan sulfate 6-O-sulfotransferase 2 (HS6ST2). METHODS TIMER2, UALCAN, and GEPIA2 were used for the expression analysis. cBioPortal was used for mutational analysis. CancerSEA, STRING, and DAVID, were employed for the single cell sequencing data analysis, protein-protein interaction network development, and gene enrichment analyses, respectively. GSCAlite and RT-qPCR were used for drug sensitivity and expression validation analysis. RESULTS HS6ST2 exhibited significant (P < 0.05) overexpression in multiple cancers. Prognostically, elevated HS6ST2 expression was significantly associated with poor overall survival (OS) in patients with cervical squamous cell carcinoma (CESC), kidney chromophobe (KICH), lung adenocarcinoma (LUAD), and stomach adenocarcinoma (STAD), emphasizing its potential as a prognostic indicator in these cancers. Moreover, HS6ST2 expression correlated with pathological stages in CESC, KICH, LUAD, and STAD patients. Exploration of genetic alterations using cBioPortal unveiled distinct mutational landscapes, with low mutation frequencies in CESC, KICH, LUAD, and STAD. Additionally, reduced DNA methylation in CESC, KICH, LUAD, and STAD suggested a potential link between hypomethylation and heightened HS6ST2 expression. Analysis of immune cell infiltration revealed a positive correlation between HS6ST2 expression and the infiltration of CD8+ T and CD4+ T cells in CESC, KICH, LUAD, and STAD, highlighting its involvement in the tumor immunology processes. Single-cell functional states analysis demonstrated associations between HS6ST2 and diverse cellular processes. Moreover, gene enrichment analysis revealed the involvement HS6ST2 in crucial cellular activities. GSCAlite analysis underscored the potential of HS6ST2 as a therapeutic target, showing associations with drug sensitivity. Finally, experimental validation through reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry in LUAD tissues confirmed elevated HS6ST2 expression. CONCLUSION Overall, this study provides a comprehensive understanding of HS6ST2 in CESC, KICH, LUAD, and STAD, emphasizing its potential as a prognostic biomarker and therapeutic target.
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Affiliation(s)
- Luxin Huang
- Department of Gynecology, Jinan Maternity and Child Care Hospital Affiliated to Shandong First Medical UniversityJinan 250000, Shandong, China
| | - Sidra Irshad
- Department of Pharmacology, Muhammad College of MedicinePeshawar 25000, Pakistan
| | - Ulfat Sultana
- Department of Pharmacology, Muhammad College of MedicinePeshawar 25000, Pakistan
| | - Saqib Ali
- Department of Computer Science, University of AgricultureFaisalabad 38000, Pakistan
| | - Ayesha Jamil
- Department of Pharmacology, Khyber Girls Medical CollegePeshawar 25000, Pakistan
| | - Ayesha Zubair
- CMH Lahore Medical College and Institute of DentistryLahore 54000, Pakistan
| | - Rizwana Sultan
- Department of Pathology, Faculty of Veterinary and Animal Sciences, Cholistan University of Veterinary and Animal SciencesBahawalpur 63100, Pakistan
| | - Mostafa A Abdel-Maksoud
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Bandar M Almunqedhi
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud UniversityP.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud UniversitySaudi Arabia
| | - Abdulaziz Alamri
- Department of Biochemistry, College of Science King Saud UniversitySaudi Arabia
| | - Ahmad S Kodous
- Department of Molecular Oncology, Cancer Institute (WIA)38, Sardar Patel Road, Chennai, P.O. Box 600036, Tamilnadu, India
- Department of Radiation Biology, National Center for Radiation Research & Technology (NCRRT), Egyptian Atomic-Energy Authority (EAEA)Egypt
| | - Mohammed Mares
- Department of Zoology, College of Science King Saud UniversitySaudi Arabia
| | - Mohamed Y Zaky
- UPMC Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of PittsburghPittsburgh, PA 15213, USA
| | | | - Yasir Hameed
- Department of Biotechnology, Institute of Biochemistry Biotechnology, and Bioinformatics, The Islamia University of BahawalpurBahawalpur 63100, Pakistan
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8
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Huang H, Gu J, Kuang X, Yu Y, Rao B, Fang S, Lu J, Qiu F. An integrative pan-cancer analysis of WWC family genes and functional validation in lung cancer. Cell Signal 2024; 115:111034. [PMID: 38190957 DOI: 10.1016/j.cellsig.2024.111034] [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: 09/16/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/10/2024]
Abstract
The WW and C2 domain containing (WWC) protein family functions as scaffolds regulating cell proliferation and organ growth control through the Hippo signaling pathway. However, their pan-cancer dysregulation and mechanistic roles in signaling transduction have remained unclear. We performed integrated pan-cancer analyses of WWC family gene expression using data from The Cancer Genome Atlas (TCGA) across 33 different cancer types. Prognostic relevance was evaluated by survival analyses. WWC genetic alterations, DNA methylation, pathway activities, drug response, and tumor immunology were analyzed using online databases. Furthermore, we examined the functional roles of WWCs in lung cancer cells. We observed aberrant WWC expression in various cancers, which associated with patient prognosis. WWC hypermethylation occurred in many cancers and exhibited negative correlation with expression, alongside mutations linked to poor outcomes. Pathway analysis implicated WWCs as Hippo pathway scaffolds, while drug sensitivity analysis suggested associations with diverse chemotherapies. Additionally, pan-cancer analyses elucidated vital immunomodulatory roles for WWC through heterogeneous correlations with immune cell infiltrates, checkpoint molecules, tumor mutation burden, microsatellite instability, and chemokine pathways across cancers. Experimentally, WWCs suppressed lung cancer cell proliferation, migration, and invasion while enhancing apoptosis and paclitaxel chemosensitivity. Mechanistically, WWCs bound large tumor suppressor 1 and 2 (LATS1/2) kinases to stimulate phosphorylation cascades, thereby inhibiting nuclear translocation of the Yes-associated protein (YAP) oncoprotein. Taken together, our multi-omics characterization provides comprehensive evidence for WWCs as putative tumor suppressors across cancers via Hippo pathway modulation. WWCs may serve as prognostic markers and therapeutic targets in lung cancer.
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Affiliation(s)
- Hongmei Huang
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Jiaji Gu
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Xinjie Kuang
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Yonghui Yu
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Boqi Rao
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Shenying Fang
- The fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510799, PR China
| | - Jiachun Lu
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China
| | - Fuman Qiu
- State Key Lab of Respiratory Disease, Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, 1 Xinzao Road, Panyu District, Guangzhou 511436, PR China.
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Zhang Y, Sun J, Li M, Hou L, Wang Z, Dong H, Xu W, Jiang R, Geng Y, Guan C, Zhu Z, Wang H, Gong Q, Zhang G. Identification and validation of a disulfidptosis-related genes prognostic signature in lung adenocarcinoma. Heliyon 2024; 10:e23502. [PMID: 38223725 PMCID: PMC10784160 DOI: 10.1016/j.heliyon.2023.e23502] [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: 06/17/2023] [Revised: 10/26/2023] [Accepted: 12/05/2023] [Indexed: 01/16/2024] Open
Abstract
Disulfidptosis, a newly revealed form of cell death, regulated by numerous genes that has been recently identified. The exact role of disulfidptosis in lung adenocarcinoma (LUAD) still uncertain. Objective of this study was to explore potential prognostic markers among disulfidptosis genes in LUAD. By combining transcriptomic information from Gene Expression Omnibus databases and The Cancer Genome Atlas, we identified differentially expressed and prognostic disulfidptosis genes. By conducting least absolute shrinkage and selection operator with multivariate Cox regression, four disulfidptosis genes were selected to create the prognostic signature. The implementation of the signature separated the training and validation cohorts into groups with high- and low-risk. Subsequently, the model was verified by conducting an independent analysis of receiver operating characteristic (ROC) curves. Further comparisons were made between the two risk-divided groups with regards the tumor microenvironment, immune cell infiltration, immunotherapy response, and drug sensitivity. The signature was constructed using four disulfidptosis-related genes: SLC7A11, SLC3A2, NCKAP1, and GYS1. According to ROC curves, the signature was effective for predicting LUAD prognosis. In addition, the prognostic signature correlated with sensitivity to chemotherapeutic agents and the efficacy of immunotherapy in LUAD. Finally, through external validation, we showed that NCKAP1 are correlated with tumor migration, proliferation, and invasion of LUAD cells. GYS1 affects immune cell, especially M2 macrophage infiltration in the tumor microenvironment. The disulfidptosis four-gene model can reliably predict the prognosis of patients diagnosed with LUAD, thereby providing valuable information for clinical applications and immunotherapy.
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Affiliation(s)
- Yanpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingyang Sun
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- Department of Thoracic Surgery, Gansu Central Hospital, Lanzhou, China
| | - Meng Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Liren Hou
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhiyu Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huanhuan Dong
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wenjun Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rongxuan Jiang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuhan Geng
- Department of Thoracic Surgery, Gansu Central Hospital, Lanzhou, China
| | - Chungen Guan
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Thoracic Surgery, Gansu Central Hospital, Lanzhou, China
| | - Zijiang Zhu
- Department of Thoracic Surgery, Gansu Central Hospital, Lanzhou, China
| | - Hongyi Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qiuyu Gong
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Guangjian Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Mukherjee O, Paul S, Das S, Rakshit S, Shanmugam G, George M, Sarkar K. Doxorubicin induced epigenetic regulation of dendritic cell maturation in association with T cell activation facilitates tumor protective immune response in non-small cell lung cancer (NSCLC). Pathol Res Pract 2024; 253:155004. [PMID: 38086291 DOI: 10.1016/j.prp.2023.155004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024]
Abstract
BACKGROUND NSCLC is one of the leading causes of death and is often diagnosed at late stages with no alternative therapeutic approach. DCs are professional antigen-presenting cells and DC-based immunotherapy has been under the spotlight for its anti-cancer properties. Epigenetic modifications including DNA methylation and histone modification in DCs play a crucial role in regulating their functions such as maturation and activation,innate immune responses, T cell priming, antigen presentation, and cytokine production. In the current study, we investigated the anti-cancer properties of Doxorubicin at a noncytotoxic concentration that could be extrapolated as an epigenetic regulator for DC maturation to elicit anti-tumor activity. METHODOLOGIES PBMCs from normal and NSCLC blood samples were isolated and treated with growth factors. DCs were matured with low dose Doxorubicin and the DC maturation markers were checked by using flow-cytometry. Further, ELISA was performed and low dose Doxorubicin-induced DCs were pulsed with LCA (Lung Cancer Antigen) and primed with CD4 +T helper (Th) cells for cytotoxicity assessment. Further, epigenetic markers of T: DC conjugation were immunofluorescently visualized under a microscope. ChIP-qPCR and Invitro assays such as histone methylation, DNA methylation, and m6A methylation were performed to study the epigenetic changes under low dose Dox treatment. IL-12 neutralization assay was performed to check for the IL-12 dependency of DCs and their effect under Dox at low dose treatment. This was further followed by a Western Blotting analysis for histone and non-histone proteins. RESULTS Low dose Doxorubicin induces epigenetic changes in DCs to elicit an anti-tumor response in NSCLC through the generation of CTLs with a concomitant increase in the extracellular secretions of anti-inflammatory cytokines. We also found that low dosage of Doxorubicin matured DCs when pulsed with LCA and primed with CD4 +T helper cells, secrete IFN-γ which is important in orchestrating adaptive immunity by activating CD8 + cytotoxic T-lymphocytes. Also, the secretions of IL-12 help us infer that protective immunity is also induced via Th1 response which triggered selectively the translocation of PKCθ to immunological synapse in between DC and Th. Further, methylation and acetylation markers H3K4me3 and H3K14Ac respectively upregulated whereas levels of STAT5, NFkB, NOTCH1, and DNAPKcs were downregulated. DNA and RNA methylation assays then lead to confirmations about the epigenetic changes caused by low dose Dox treatment. DNA methylation was reduced which resulted in the activation of tumor suppressor gene p53 and Th1-associated transcription factor TBX21. On the other hand, both absolute and relative RNA methylation quantification increased in the presence of Dox at a low dose. CONCLUSION From this study, we understand that non-cytotoxic concentration of Doxorubicin increases the Ag-presenting ability of DCs via an IL-12-dependent mechanism and causes epigenetic modifications in NSCLC.
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Affiliation(s)
- Oishi Mukherjee
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Sambuddha Paul
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Sumana Das
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Sudeshna Rakshit
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Geetha Shanmugam
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Melvin George
- Department of Clinical Pharmacology, SRM Medical College Hospital and Research Centre, Kattankulathur, Chennai, Tamil Nadu 603203, India
| | - Koustav Sarkar
- Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu 603203, India.
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Yao L, Wang Q, Ma W. Navigating the Immune Maze: Pioneering Strategies for Unshackling Cancer Immunotherapy Resistance. Cancers (Basel) 2023; 15:5857. [PMID: 38136402 PMCID: PMC10742031 DOI: 10.3390/cancers15245857] [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: 11/04/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Cancer immunotherapy has ushered in a transformative era in oncology, offering unprecedented promise and opportunities. Despite its remarkable breakthroughs, the field continues to grapple with the persistent challenge of treatment resistance. This resistance not only undermines the widespread efficacy of these pioneering treatments, but also underscores the pressing need for further research. Our exploration into the intricate realm of cancer immunotherapy resistance reveals various mechanisms at play, from primary and secondary resistance to the significant impact of genetic and epigenetic factors, as well as the crucial role of the tumor microenvironment (TME). Furthermore, we stress the importance of devising innovative strategies to counteract this resistance, such as employing combination therapies, tailoring immune checkpoints, and implementing real-time monitoring. By championing these state-of-the-art methods, we anticipate a paradigm that blends personalized healthcare with improved treatment options and is firmly committed to patient welfare. Through a comprehensive and multifaceted approach, we strive to tackle the challenges of resistance, aspiring to elevate cancer immunotherapy as a beacon of hope for patients around the world.
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Affiliation(s)
- Liqin Yao
- Key Laboratory for Translational Medicine, The First Affiliated Hospital, Huzhou University, Huzhou 313000, China
| | - Qingqing Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Wenxue Ma
- Department of Medicine, Moores Cancer Center, Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA 92093, USA
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Ghosh A, Himaja A, Biswas S, Kulkarni O, Ghosh B. Advances in the Delivery and Development of Epigenetic Therapeutics for the Treatment of Cancer. Mol Pharm 2023; 20:5981-6009. [PMID: 37899551 DOI: 10.1021/acs.molpharmaceut.3c00610] [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: 10/31/2023]
Abstract
Gene expression at the transcriptional level is altered by epigenetic modifications such as DNA methylation, histone methylation, and acetylation, which can upregulate, downregulate, or entirely silence genes. Pathological dysregulation of epigenetic processes can result in the development of cancer, neurological problems, metabolic disorders, and cardiovascular diseases. It is of promising therapeutic interest to find medications that target these epigenetic alterations. Despite the enormous amount of work that has been done in this area, very few molecules have been approved for clinical purposes. This article provides a comprehensive review of recent advances in epigenetic therapeutics for cancer, with a specific focus on emerging delivery and development strategies. Various delivery systems, including pro-drugs, conjugated molecules, nanoparticles (NPs), and liposomes, as well as remedial strategies such as combination therapies, and epigenetic editing, are being investigated to improve the efficacy and specificity of epigenetic drugs (epi-drugs). Furthermore, the challenges associated with available epi-drugs and the limitations of their translation into clinics have been discussed. Target selection, isoform selectivity, physiochemical properties of synthesized molecules, drug screening, and scalability of epi-drugs from preclinical to clinical fields are the major shortcomings that are addressed. This Review discusses novel strategies for the identification of new biomarkers, exploration of the medicinal chemistry of epigenetic modifiers, optimization of the dosage regimen, and design of proper clinical trials that will lead to better utilization of epigenetic modifiers over conventional therapies. The integration of these approaches holds great potential for improving the efficacy and precision of epigenetic treatments, ultimately benefiting cancer patients.
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Affiliation(s)
- Aparajita Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
- Pharmacology Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
| | - Ambati Himaja
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
| | - Swati Biswas
- Nanomedicine Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
| | - Onkar Kulkarni
- Pharmacology Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science- Pilani, Hyderabad Campus, Jawahar Nagar, Medchal, Hyderabad 500078, Telangana, India
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13
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Tian B, Pang Y, Gao Y, Meng Q, Xin L, Sun C, Tang X, Wang Y, Li Z, Lin H, Wang L. A pan-cancer analysis of the oncogenic role of Golgi transport 1B in human tumors. J Transl Int Med 2023; 11:433-448. [PMID: 38130634 PMCID: PMC10732491 DOI: 10.2478/jtim-2023-0002] [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] [Indexed: 12/23/2023] Open
Abstract
Background Owing to the aggressiveness and treatment-refractory nature of cancer, ideal candidates for early diagnosis and treatment are needed. Golgi transport 1B (GOLT1B) has been associated with cellular malignant behaviors and immune responses in colorectal and lung cancer, but a systematic pan-cancer analysis on GOLT1B has not been conducted. Methods The expression status and clinical association of GOLT1B in The Cancer Genome Atlas (TCGA) were analyzed. Genetic and methylation alterations in GOLT1B were explored. The relationship between GOLT1B and immune cell infiltration was also investigated. Genes related to GOLT1B expression were selected and analyzed. Results GOLT1B was highly expressed in most tumors, and there was a positive correlation between GOLT1B expression and clinical pathological parameters. High expression levels of GOLT1B have been associated with poor prognosis of most cancers. Copy number amplification was the primary type of GOLT1B genetic alterations, which was related to the prognosis of pan-cancer cases. There were different levels of GOLT1B promoter methylation across cancer types. The methylation level of the probe cg07371838 and cg25816357 was closely associated with prognosis in diverse cancers. There was also a positive correlation between GOLT1B genetic alterations and CD4+ T lymphocytes, especially the Th2 subset, as well as between GOLT1B expression and the estimated infiltration value of cancer-associated fibroblasts. Serine/threonine kinase receptor-associated protein (STRAP), integrator complex subunit 13 (INTS13), and ethanolamine kinase 1 (ETNK1) were the most relevant genes for GOLT1B expression, and their interactions with GOLT1B were involved in regulating the transforming growth factor (TGF)-β receptor signaling pathway and epithelial-mesenchymal transition (EMT). Conclusions This pan-cancer analysis provided a comprehensive understanding of the oncogenic role of GOLT1B, highlighting a potential mechanism whereby GOLT1B influences the tumor microenvironment, as well as cancer immunotherapy.
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Affiliation(s)
- Bo Tian
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Yanan Pang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
- Shanghai Institute of Pancreatic Diseases, Shanghai200433, China
| | - Ye Gao
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Qianqian Meng
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Lei Xin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Chang Sun
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Xin Tang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Yilin Wang
- Georgetown Preparatory School, North Bethesda20852, MD, USA
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Han Lin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
| | - Luowei Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai200433, China
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Guo J, Huang M, Deng S, Wang H, Wang Z, Yan B. Highly expressed RPLP2 inhibits ferroptosis to promote hepatocellular carcinoma progression and predicts poor prognosis. Cancer Cell Int 2023; 23:278. [PMID: 37980521 PMCID: PMC10656893 DOI: 10.1186/s12935-023-03140-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/12/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND RPLP2, an integral part of ribosomal stalk, plays an important role in the tumorigenesis of various cancers. However, its specific effect on HCC remains elusive. METHODS TCGA, GTEx, HCCDB, HPA, UALCAN, MethSurv, TISIDB, K-M plotter, FerrDb, RNAactDrug, STRING, Cytoscape and R studio were conducted for bioinformatics analysis. RPLP2 expression level in HCC was verified by IHC and western blot. IHC was used to demonstrate the immune cell infiltration. Functional experiments including CCK8, transwell and colony formation assays, and nude mice xenograft model were performed for in vitro and in vivo validation. Western blot, IHC, CCK8 assay and detection of GSH and lipid ROS were adopted to determine the effect of RPLP2 on the ferroptosis of HCC cells. RESULTS Here, we demonstrate that elevated level of RPLP2 is strongly associated with advanced clinicopathologic features, and predicts poor prognosis of HCC patients. Additionally, DNA methylation level of RPLP2 decreases in HCC, and significantly correlates with patients outcome. Moreover, high RPLP2 expression level is linked closely to the unfavorable immune infiltration. Most importantly, RPLP2 positively associates with ferroptosis suppressor GPX4, and inhibition of RPLP2 could lead to the acceleration of ferroptosis to suppress tumor progression of HCC. Last, drug sensitivity analysis predicts many drugs that potentially target RPLP2. CONCLUSION Together, our study reveals previous unrecognized role of RPLP2 in HCC, and provides new regulatory mechanism of ferroptosis, indicating RPLP2 may be a novel therapeutic target for HCC.
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Affiliation(s)
- Jiaxing Guo
- Department of Hematology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Meiyuan Huang
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Shuang Deng
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Haiyan Wang
- Academy of Biomedical Engineering, Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Zuli Wang
- Center for Tissue Engineering and Stem Cell Research, Guizhou Medical University, Guiyang, 550025, Guizhou, China
| | - Bokang Yan
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China.
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15
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Zheng D, Long S, Xi M. A comprehensive pan-cancer analysis identifies a novel glycolysis score and its hub genes as prognostic and immunological biomarkers. Transl Cancer Res 2023; 12:2852-2874. [PMID: 37969385 PMCID: PMC10643978 DOI: 10.21037/tcr-23-325] [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: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 11/17/2023]
Abstract
Background Glycolysis plays significant roles in tumor progression and immune response. However, the exact role of glycolysis in prognosis and immune regulation has not been explored in all cancer types. This study first calculated a novel glycolysis score and screened out 12 glycolytic hub genes, and comprehensively analyzed molecular expression, clinical implications, and immune features of glycolysis among pan-cancer. Methods The glycolysis score was derived by the single sample gene set enrichment analysis (ssGSEA) algorithm. The correlations of glycolysis with clinical parameters were analyzed using "limma" package. Downstream pathways of glycolysis were identified by Gene Set Enrichment Analysis (GSEA). The immune cell infiltration was explored and validated by three databases. The association between glycolysis and some immunotherapy biomarkers was explored by Pearson correlation analysis. Single-nucleotide variation (SNV), copy number variation (CNV), DNA methylation, and drug sensitivity analyses of 12 glycolytic hub genes were investigated. IMvigor210 and GSE91061 immunotherapeutic cohorts were retrieved to assess the ability of glycolysis score to predict immunotherapy efficacy. The expression of glycolysis key genes was detected in normal and endometrial cancer cell lines. Results We found that glycolysis score was generally higher in tumor tissues compared to normal tissues and a high glycolysis score predominated as a risk prognostic factor. A high glycolysis score was associated with decreased immunostimulatory natural killer (NK) cells and CD8+ T cells infiltration, well increased immunosuppressive M2-tumor-associated macrophages (M2-TAM) cells infiltration. Tumor mutational burden (TMB), microsatellite instability (MSI), and immune checkpoints (ICPs) all closely interacted with glycolysis score and the frequency of gene mutation was confirmed to be higher in colon adenocarcinoma (COAD) patients with higher glycolysis score. The SNV, CNV, and DNA methylation of 12 glycolysis key genes occurred at different frequencies and showed different impacts on survival outcomes. The predictive and prognostic value of glycolysis score for immunotherapy outcomes was validated in two immunotherapy cohorts. The expression levels of key genes differ in normal endometrial and three endometrial cancer cell lines. Conclusions This work indicated that glycolysis score and 12 glycolytic hub genes were correlated with an immunosuppressive microenvironment. They could be served as promising biomarkers aiding diagnosis, predicting prognosis and immunotherapy response for some tumor patients.
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Affiliation(s)
- Danxi Zheng
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Siyu Long
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Mingrong Xi
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, China
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16
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Yao Y, Lai J, Yang Y, Wang G, Lv J. An integrative analysis reveals the prognostic value and potential functions of MTMR2 in hepatocellular carcinoma. Sci Rep 2023; 13:18701. [PMID: 37907649 PMCID: PMC10618242 DOI: 10.1038/s41598-023-46089-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023] Open
Abstract
Abnormal expression of myotubularin-related protein 2 (MTMR2) has been identified in certain types of cancer, leading to varying effects on tumor genesis and progression. However, the various biological significances of MTMR2 in hepatocellular carcinoma (HCC) have not been systematically and comprehensively studied. The aim of this study was to explore the role of MTMR2 in HCC. We obtained the raw data from Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Afterward, we analyzed the data using R and cBioPortal. We investigated the connection between MTMR2 and its expression, prognosis, clinical significance, methylation, genetic alterations, tumor microenvironment (TME), tumor mutation burden (TMB), and drug reactivity in HCC patients. MTMR2 expression levels in HCC cells were validated through western blotting and RT-qPCR. MTMR2 exhibits high levels of expression across a wide range of cancer types, including HCC. MTMR2 is diagnostically valuable in detecting HCC, with its up-regulated expression often being indicative of poor prognosis among HCC patients. The in vitro experiments confirmed elevated MTMR2 expression in HepG2, HUH-7, and MHCC-97H cells. Univariate and multivariate Cox analysis demonstrated that MTMR2 was an independent prognostic factor in HCC patients. The cg20195272 site has the highest degree of methylation in MTMR2, and it is positively correlated with MTMR2 expression. Patients with high levels of methylation at the cg20195272 site show poor prognosis. Analysis of the TME indicates that high expression of MTMR2 is associated with elevated ESTIMATE score and that MTMR2 expression correlates positively with infiltration by resting memory CD4 T cells, activated dendritic cells, as well as several immune checkpoints. There is a negative correlation between MTMR2 expression and TMB, and drug sensitivity analyses have shown that higher MTMR2 expression is associated with lower IC50 values. This study indicates that increased expression of MTMR2 may play a crucial role in the occurrence, progression, diagnosis, prognostic prediction and drug therapy of HCC.
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Affiliation(s)
- Yuanqian Yao
- Guangxi University of Chinese Medicine, Nanning, 530000, China
| | - Jiawen Lai
- Guangxi University of Chinese Medicine, Nanning, 530000, China
| | - Yuwen Yang
- Guangxi University of Chinese Medicine, Nanning, 530000, China
| | - Guangyao Wang
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, 530000, China
| | - Jianlin Lv
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, 530000, China.
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Ding N, Li M, Zhao X. PHF5A is a potential diagnostic, prognostic, and immunological biomarker in pan-cancer. Sci Rep 2023; 13:17521. [PMID: 37845358 PMCID: PMC10579340 DOI: 10.1038/s41598-023-44899-6] [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: 08/21/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023] Open
Abstract
Studying the molecular mechanisms and regulatory functions of genes is crucial for exploring new approaches and tactics in cancer therapy. Studies have shown that the aberrant expression of PHF5A in tumors is linked to the origin and advancement of multiple cancers. However, its role in diagnosis, prognosis, and immunological prediction has not been comprehensively investigated in a pan-cancer analysis. Using several bioinformatic tools, we conducted a systematic examination of the potential carcinogenesis of PHF5A in various tumors from multiple aspects. Our analysis indicated that PHF5A expression varied between normal and tumor tissues and was linked to clinical diagnosis and prognosis in various cancers. The results confirmed a notable variation in the levels of PHF5A promoter methylation among several types of primary tumor and normal tissues and methylation of the PHF5A promoter played a guiding role in prognosis in some cancers. According to our findings, PHF5A played a critical role in tumor immunity and it might be an excellent target for anticancer immunotherapy. To sum up, PHF5A can be used in pan-cancer diagnostics, prognostics, and immunotherapy.
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Affiliation(s)
- Na Ding
- Department of Pathology, Shaoxing Maternity and Child Health Care Hospital, Shaoxing, 312000, Zhejiang, People's Republic of China
| | - Meiping Li
- Department of Pathology, Shaoxing Maternity and Child Health Care Hospital, Shaoxing, 312000, Zhejiang, People's Republic of China
| | - Xiaokun Zhao
- School of Medicine, Shaoxing University, Shaoxing, 312000, Zhejiang, People's Republic of China.
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Gao X, Bu H, Gao X, Wang Y, Wang L, Zhang Z. Pan-cancer analysis: SPAG5 is an immunological and prognostic biomarker for multiple cancers. FASEB J 2023; 37:e23159. [PMID: 37650687 DOI: 10.1096/fj.202300626r] [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: 04/02/2023] [Revised: 06/30/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023]
Abstract
Sperm-associated antigen 5 (SPAG5) is a mitotic spindle protein that regulates the separation of sister chromatids into daughter cells. Recent studies have discovered its overexpression in various cancers, suggesting its oncogenic characteristics and functions. However, a comprehensive analysis of SPAG5 regarding its diagnostic, prognostic, and immune-related effects across different cancer types is lacking. In this study, we employed bioinformatics methods and integrated multiple public databases to explore the potential oncogenic role of SPAG5. We analyzed its expression, prognosis, related chemicals, enriched pathways, immune infiltration, and its impact on different tumor genetic alterations. The results revealed that SPAG5 is highly expressed in most cancers and significantly correlates with poor patient prognosis. Additionally, SPAG5 expression showed potential for early cancer diagnosis in 15 different cancer types. In terms of tumor immunity, high expression of SPAG5 was associated with an immunosuppressive tumor microenvironment and immune therapy efficacy indicators. SPAG5 expression exhibited a negative correlation with most immune cell infiltrates but demonstrated a significant positive correlation with Th2 cells and MDSC cells. Multicolor fluorescence immunohistochemistry demonstrated that SPAG5 activates immune cell populations within tumors, indicating its significant role in the tumor microenvironment. Enrichment analysis indicated that SPAG5-related genes are mainly involved in cell cycle, cellular senescence, P53 signaling pathway, and FoxO signaling pathway. Furthermore, we confirmed the high expression of SPAG5 in cancer cells and observed that its knockdown upregulated the expression of the p53 protein. In conclusion, SPAG5 holds value as a diagnostic, prognostic, and immune biomarker in various cancers and may provide a novel target for tumor immunotherapy.
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Affiliation(s)
- Xiaofeng Gao
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, People's Republic of China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, People's Republic of China
| | - Huitong Bu
- College of Biology, Hunan University, Changsha, People's Republic of China
| | - Xuzheng Gao
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, People's Republic of China
| | - Ying Wang
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, People's Republic of China
| | - Long Wang
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, People's Republic of China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, People's Republic of China
- School of Stomatology and Ophthalmology, Xianning Medical College, Hubei University of Science and Technology, Xianning, People's Republic of China
| | - Zhenwang Zhang
- Medicine Research Institute/Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, People's Republic of China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, People's Republic of China
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19
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Huang Q, Lv Q, Tang W, Pan Y, Xing Y, He M, Wu H, Huang J, Huang C, Lan H, Chen J, Xiao G. A comprehensively prognostic and immunological analysis of chloride intracellular channel protein 5 (CLIC5) in pan-cancer and identification in ovarian cancer. J Cancer Res Clin Oncol 2023; 149:10561-10583. [PMID: 37286734 DOI: 10.1007/s00432-023-04927-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]
Abstract
CLIC5 encoded protein associates with actin-based cytoskeletal and is increasingly thought to play significant roles in human cancers. We use TCGA and GEO to explore CLIC5 expression differences, mutation and DNA methylation, TMB, MSI, and immune cell infiltration. We verified the mRNA expression of CLIC5 in human ovarian cancer cells by real-time PCR and detected the expression of CLIC5 as well as immune marker genes in ovarian cancer by immunohistochemistry. The pan-cancer analysis showed that CLIC5 is highly expressed in several malignant tumors. In some cancers, CLIC5 expression in tumor samples is associated with poorer overall survival. For example, patients with ovarian cancer with high expression of CLIC5 have a poor prognosis. CLIC5 mutation frequency increased in all tumor types. The CLIC5 promoter is hypomethylated in most tumors. CLIC5 was associated with tumor immunity and different immune cells of different tumor types, such as CD8 + T cells, tumor-associated fibroblasts, macrophages, etc. CLIC5 was positively correlated with various immune checkpoints, and TMB and MSI were correlated with dysregulation of CLIC5 in tumors. The expression of CLIC5 in ovarian cancer was detected by qPCR and IHC, and the results were consistent with the bioinformatics results. There were a strong positive correlation between CLIC5 expression and M2 macrophage (CD163) infiltration and a negative correlation with CD8 + T-cell infiltration. In conclusions, our first pan-cancer analysis offered a detailed grasp of the cancerogenic functions of CLIC5 in a variety of malignancies. CLIC5 participated in immunomodulation and performed a crucial function in the tumor microenvironment.
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Affiliation(s)
- Qiaoling Huang
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
- Central Laboratory, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Quankun Lv
- Emergency Department, the Sixth Affiliated Hospital, South China University of Technology, Foshan, 528000, Guangdong, People's Republic of China
| | - Waner Tang
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
- Central Laboratory, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Yuhua Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Yue Xing
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, 510120, Guangdong, People's Republic of China
| | - Min He
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Huiyi Wu
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Jiamin Huang
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Che Huang
- Hubei University of Medicine, Shiyan, 442000, China
| | - Haifeng Lan
- Department of Orthopaedic Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, People's Republic of China
| | - Jingqi Chen
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China.
- Oncology Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China.
| | - Guohong Xiao
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China.
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20
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Tsuji Y, Hara T, Meng S, Sato H, Arao Y, Ofusa K, Ishii H. Role of RNA methylation in the regulation of pancreatic cancer stem cells (Review). Oncol Lett 2023; 26:336. [PMID: 37427348 PMCID: PMC10326658 DOI: 10.3892/ol.2023.13922] [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: 02/02/2023] [Accepted: 04/21/2023] [Indexed: 07/11/2023] Open
Abstract
Pancreatic cancer stem cells (CSCs) play a key role in the initiation and progression of pancreatic adenocarcinoma (PDAC). CSCs are responsible for resistance to chemotherapy and radiation, and for cancer metastasis. Recent studies have indicated that RNA methylation, a type of RNA modification, predominantly occurring as m6A methylation, plays an important role in controlling the stemness of cancer cells, therapeutic resistance against chemotherapy and radiation therapy, and their overall relevance to a patient's prognosis. CSCs regulate various behaviors of cancer through cell-cell communication by secreting factors, through their receptors, and through signal transduction. Recent studies have shown that RNA methylation is involved in the biology of the heterogeneity of PDAC. The present review provides an update on the current understanding of RNA modification-based therapeutic targets against deleterious PDAC. Several key pathways and agents that can specifically target CSCs have been identified, thus providing novel insights into the early diagnosis and efficient treatment of PDAC.
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Affiliation(s)
- Yoshiko Tsuji
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Tomoaki Hara
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Sikun Meng
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Hiromichi Sato
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Department of Gastrointestinal Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yasuko Arao
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Ken Ofusa
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
- Prophoenix Division, Food and Life-Science Laboratory, IDEA Consultants, Inc., Osaka, Osaka 559-8519, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
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21
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Lu J, Liang K, Zou R, Peng Y, Wang H, Huang R, Zeng Z, Feng Z, Fan Y, Zhang S, Ji Y, Pang X, Wang Y, Zhang H, Wang Z. Comprehensive analysis of the prognostic and immunological signature of eight Tripartitemotif (TRIM) family molecules in human gliomas. Aging (Albany NY) 2023; 15:5798-5825. [PMID: 37367937 PMCID: PMC10333093 DOI: 10.18632/aging.204841] [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: 02/13/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND TRIM family molecules have been identified as being involved in the tumor progression of various cancer types. Increasingly, experimental evidence indicates that some of TRIM family molecules are implicated in glioma tumorigenesis. However, the diverse genomic changes, prognostic values and immunological landscapes of TRIM family of molecules have yet to be fully determined in glioma. METHODS In our study, employing the comprehensive bioinformatics tools, we evaluated the unique functions of 8 TRIM members including TRIM5/17/21/22/24/28/34/47 in gliomas. RESULTS The expression levels of 7 TRIM members (TRIM5/21/22/24/28/34/47) were higher in glioma as well as its diverse cancer subtypes than in normal tissues, whereas the expression level of TRIM17 was the opposite, lower in the former than in the latter. In addition, survival analysis revealed that the high expression profiles of TRIM5/21/22/24/28/34/47 were associated with poor overall survival (OS), disease-specific survival (DSS) and progress-free interval (PFI) in glioma patients, whereas TRIM17 displayed adverse outcomes. Moreover, the 8 TRIM molecules expression as well as methylation profiles remarkably correlated with different WHO grades. And genetic alterations, including mutations and copy number alterations (CNAs), in the TRIM family were correlated with longer OS, DSS and progress-free survival (PFS) in glioma patients. Furthermore, through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results of these 8 molecules and their related genes, we found that these molecules may change the immune infiltration of the tumor microenvironment and regulate the expression of immune checkpoint molecules (ICMs), affecting the occurrence and development of gliomas. The correlation analyses between the 8 TRIM molecules and TMB (tumor mutational burden)/MSI (microsatellite instability)/ICMs discovered that as the expression level of TRIM5/21/22/24/28/34/47 increased, the TMB score also increased significantly, while TRIM17 showed an opposite outcome. Further, a 6-gene signature (TRIM 5/17/21/28/34/47) for predicting overall survival (OS) in gliomas was built by using the least absolute shrinkage and selection operator (LASSO) regression, and the survival and time-dependent ROC analyses all were found to perform well in testing and validation cohorts. Results of multivariate COX regression analysis showed that TRIM5/28 are both expected to become independent risk predictors to guide clinical treatment. CONCLUSION In general, the results indicate that TRIM5/17/21/22/24/28/34/47 might exert a crucial influence on gliomas tumorigenesis and might be putative prognostic markers and therapeutic targets for glioma patients.
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Affiliation(s)
- Jiajie Lu
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Kairong Liang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Renheng Zou
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yuecheng Peng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Haojian Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Rihong Huang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Zhaorong Zeng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Zejia Feng
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Yongyang Fan
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou 510182, China
| | - Shizhen Zhang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yunxiang Ji
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Xiao Pang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Yezhong Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Hongri Zhang
- Department of Neurosurgery, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, China
| | - Zhaotao Wang
- Institute of Neuroscience, Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
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22
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Yan B, Guo J, Deng S, Chen D, Huang M. A pan-cancer analysis of the role of USP5 in human cancers. Sci Rep 2023; 13:8972. [PMID: 37268697 DOI: 10.1038/s41598-023-35793-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023] Open
Abstract
Posttranslational modifications (PTM) such as acetylation, deubiquitination, and phosphorylation of proteins, play important roles in various kinds of cancer progression. Ubiquitin-specific proteinase 5 (USP5), a unique member of deubiquitinating enzymes (DUBs) which recognizes unanchored polyubiquitin specifically, could regulate the stability of many tumorigenesis-associated proteins to influence cancer initiation and progression. However, the diverse biological significance of USP5 in pan-cancer has not been systematically and comprehensively studied. Here, we explored the role of USP5 in pan-cancer using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database, and we also acquired and analyzed data via various software and web platforms such as R, GEPIA2.0, HPA, TISIDB, cBioPortal, UALCAN, TIMER 2.0, CancerSEA and BioGRID. USP5 expression was high in most cancers and differed significantly in different molecular and immune subtypes of cancers. In addition, USP5 had certain diagnostic value in multiple cancers, and high expression of USP5 generally predicted poor prognosis for cancer patients. We also found that the most frequent genetic alterations type of USP5 was mutation, and the DNA methylation level of USP5 decreased in various cancers. Furthermore, USP5 expression correlated with cancer-associated fibroblasts (CAFs), endothelial cells (EC) and genetic markers of immunodulators in cancers. Moreover, the result from single cell sequencing showed that USP5 could regulate several tumor biological behaviors such as apoptosis, DNA damage and metastasis. Gene enrichment analysis indicated "spliceosome" and "RNA splicing" may be the critical mechanism for USP5 to involve in cancer. Taken together, our study elucidates the biological significance of USP5 in the diagnosis, prognosis and immune in human pan-cancer.
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Affiliation(s)
- Bokang Yan
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Jiaxing Guo
- Department of Hematology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Shuang Deng
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China
| | - Dongliang Chen
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China.
| | - Meiyuan Huang
- Department of Pathology, Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, 412007, Hunan, China.
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23
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Wang Y, Yuan H, Yue G, Zhao L, Xia Y, Zhang N, Li H, Liu D, Su Y, Wang H, Gao Y. Pan-cancer analysis reveals IGFL2 as a potential target for cancer prognosis and immunotherapy. Sci Rep 2023; 13:6034. [PMID: 37055418 PMCID: PMC10101991 DOI: 10.1038/s41598-023-27602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/04/2023] [Indexed: 04/15/2023] Open
Abstract
Insulin-like growth factor like family member 2 (IGFL2) is a gene in the IGFL family, located on chromosome 19, whose role in cancer is unclear, and the aim of this study was to investigate the relevance of IGFL2 expression, prognosis, immunity, and mutation in pan-cancer. Obtaining information from The Cancer Genome Atlas and The Genotype-Tissue Expression Project (GTEx) databases for expression analysis and combining with The Gene Expression Profile Interaction Analysis database for prognostic aspects. Analysis of immune cell infiltration by TIMER and CIBERSORT algorithms. Calculation of correlation of immune-related genes with IGFL2 expression and tumor mutational burden and microsatellite instability. Mutations and DNA methylation were analyzed using the cBioPortal database and the UALCAN database, and functional enrichment was performed using Gene set enrichment analysis (GSEA). IGFL2 expression is significantly elevated in tumor tissue and high expression has a worse prognosis in most cancers. In immune correlation analysis, it was associated with most immune cells and immune-related genes. In most cancers, IGFL2 methylation is lower and the group with mutations in IGFL2 has a worse prognosis than the normal group. The GSEA analysis showed that IGFL2 was significantly enriched in signaling and metabolism. IGFL2 may be involved in the development of many types of cancer, influencing the course of cancer with different biological functions. It may also be a biomarker for tumor immunotherapy.
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Affiliation(s)
- Yuqi Wang
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
| | - Hongwei Yuan
- Department of Pathology, School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Genquan Yue
- Department of Urology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Lingyan Zhao
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
- Key Laboratory of Molecular Epidemiology of Chronic Diseases, Inner Mongolia Medical University, Hohhot, China
| | - Yuan Xia
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
- Key Laboratory of Molecular Epidemiology of Chronic Diseases, Inner Mongolia Medical University, Hohhot, China
| | - Nan Zhang
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
- Key Laboratory of Molecular Epidemiology of Chronic Diseases, Inner Mongolia Medical University, Hohhot, China
| | - Hailing Li
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
- Key Laboratory of Molecular Epidemiology of Chronic Diseases, Inner Mongolia Medical University, Hohhot, China
| | - Dongyang Liu
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
| | - Yubo Su
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
| | - Haisheng Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China.
| | - Yumin Gao
- School of Public Health, Inner Mongolia Medical University, Hohhot, China.
- Key Laboratory of Molecular Epidemiology of Chronic Diseases, Inner Mongolia Medical University, Hohhot, China.
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24
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Bi C, Wang Z, Xiao Y, Zhao Y, Guo R, Xiong L, Ji Z, Li Y, Li Q, Qin C. I kappa B kinase interacting protein as a promising biomarker in pan-cancer: A multi-omics analysis. Front Genet 2023; 14:1138137. [PMID: 36999060 PMCID: PMC10047260 DOI: 10.3389/fgene.2023.1138137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023] Open
Abstract
Background: Human chromosome 12 contains I kappa B kinase interacting protein (IKBIP) is also commonly known as IKIP. The involvement of IKBIP in the growth of tumors has only been discussed in a small number of publications.Purpose: To explore the role that IKBIP plays in the development of a wide variety of neoplasms, as well as the tumor immunological microenvironment.Methods: UALCAN, HPA, Genotype Tissue Expression, Cancer Genome Maps, and other datasets were used to analyze IKBIP expression. We thoroughly investigated the predictive importance of IKBIP in pan-cancer, clinical traits, and genetic anomalies. We studied whether there is a link between IKBIP and immune-related genes, microsatellite instability (MSI), and the incidence of tumor mutational burden (TMB). The link between immune cell infiltration and IKBIP expression was examined using data on immune cell infiltration from ImmuCellAI, TIMER2, and earlier studies. Finally, gene set enrichment analysis (GSEA) was performed to determine the signaling pathways associated with IKBIP.Results: IKBIP is highly expressed in most cancers and is negatively associated with the prognosis of several major cancer types. Furthermore, IKBIP expression was linked to TMB in 13 cancers and MSI in seven cancers. Additionally, IKBIP is associated with numerous immunological and cancer-promoting pathways. Simultaneously, various cancer types have unique tumor-infiltrating immune cell profiles.Conclusion: IKBIP has the potential to act as a pan-cancer oncogene and is crucial for both carcinogenesis and cancer immunity. Elevated IKBIP expression implies an immunosuppressive environment and may be used as a prognostic biomarker and therapeutic target.
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25
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Tang C, Lv Y, Ding K, Cao Y, Ma Z, Yang L, Zhang Q, Zhou H, Wang Y, Liu Z, Cao X. Comprehensive Pan-Cancer Analysis of MTF2 Effects on Human Tumors. Curr Probl Cancer 2023; 47:100957. [PMID: 37027952 DOI: 10.1016/j.currproblcancer.2023.100957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 04/03/2023]
Abstract
Understanding oncogenic processes and underlying mechanisms to advance research into human tumors is critical for effective treatment. Studies have shown that Metal regulatory transcription factor 2(MTF2) drives malignant progression in liver cancer and glioma. However, no systematic pan-cancer analysis of MTF2 has been performed. Here, we use University of California Santa Cruz, Cancer Genome Atlas , Genotype-Tissue Expression data, Tumor Immune Estimation Resource, and Clinical Proteomic Tumor Analysis Consortium bioinformatics tools to explore differential expression of MTF2 across different tumor types. MTF2 was found to be highly expressed in the cancer lines that were available through the respective databases included in the study, and overexpression of MTF2 may lead to a poor prognosis in tumor patients such as glioblastoma multiforme, brain lower grade glioma, KIPAN, LIHC, adrenocortical carcinoma, etc. We also validated MTF2 mutations in cancer, compared MTF2 methylation levels in normal and primary tumor tissues, analyzed the association of MTF2 with the immune microenvironment, and validated the functional role of MTF2 in glioma U87 and U251 and breast cancer MDA-MB-231 cell lines by cytometry. This also indicates that MTF2 has a promising application prospect in cancer treatment.
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26
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Gholami H, Chmiel JA, Burton JP, Maleki Vareki S. The Role of Microbiota-Derived Vitamins in Immune Homeostasis and Enhancing Cancer Immunotherapy. Cancers (Basel) 2023; 15:cancers15041300. [PMID: 36831641 PMCID: PMC9954268 DOI: 10.3390/cancers15041300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Not all cancer patients who receive immunotherapy respond positively and emerging evidence suggests that the gut microbiota may be linked to treatment efficacy. Though mechanisms of microbial contributions to the immune response have been postulated, one likely function is the supply of basic co-factors to the host including selected vitamins. Bacteria, fungi, and plants can produce their own vitamins, whereas humans primarily obtain vitamins from exogenous sources, yet despite the significance of microbial-derived vitamins as crucial immune system modulators, the microbiota is an overlooked source of these nutrients in humans. Microbial-derived vitamins are often shared by gut bacteria, stabilizing bioenergetic pathways amongst microbial communities. Compositional changes in gut microbiota can affect metabolic pathways that alter immune function. Similarly, the immune system plays a pivotal role in maintaining the gut microbiota, which parenthetically affects vitamin biosynthesis. Here we elucidate the immune-interactive mechanisms underlying the effects of these microbially derived vitamins and how they can potentially enhance the activity of immunotherapies in cancer.
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Affiliation(s)
- Hasti Gholami
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - John A. Chmiel
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
- Canadian Research and Development Centre for Probiotics, Lawson Research Health Research Institute, London, ON N6A 5W9, Canada
| | - Jeremy P. Burton
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
- Canadian Research and Development Centre for Probiotics, Lawson Research Health Research Institute, London, ON N6A 5W9, Canada
- Division of Urology, Department of Surgery, Western University, London, ON N6A 3K7, Canada
- Correspondence: (J.P.B.); (S.M.V.); Tel.: +1-519-685-8500 (ext. 55769) (S.M.V.)
| | - Saman Maleki Vareki
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6A 5W9, Canada
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, Western University, London, ON N6A 3K7, Canada
- Correspondence: (J.P.B.); (S.M.V.); Tel.: +1-519-685-8500 (ext. 55769) (S.M.V.)
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Mehdi A, Attias M, Arakelian A, Szyf M, Piccirillo CA, Rabbani SA. S-adenosylmethionine blocks tumorigenesis and with immune checkpoint inhibitor enhances anti-cancer efficacy against BRAF mutant and wildtype melanomas. Neoplasia 2023; 36:100874. [PMID: 36638586 PMCID: PMC9840362 DOI: 10.1016/j.neo.2022.100874] [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: 11/01/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023]
Abstract
Despite marked success in treatment with immune checkpoint inhibitor (CPI), only a third of patients are responsive. Thus, melanoma still has one of the highest prevalence and mortality rates; which has led to a search for novel combination therapies that might complement CPI. Aberrant methylomes are one of the mechanisms of resistance to CPI therapy. S-adenosylmethionine (SAM), methyl donor of important epigenetic processes, has significant anti-cancer effects in several malignancies; however, SAM's effect has never been extensively investigated in melanoma. We demonstrate that SAM modulates phenotype switching of melanoma cells and directs the cells towards differentiation indicated by increased melanogenesis (melanin and melanosome synthesis), melanocyte-like morphology, elevated Mitf and Mitf activators' expression, increased antigen expression, reduced proliferation, and reduced stemness genes' expression. Consistently, providing SAM orally, reduced tumor growth and progression, and metastasis of syngeneic BRAF mutant and wild-type (WT) melanoma mouse models. Of note, SAM and anti-PD-1 antibody combination treatment had enhanced anti-cancer efficacy compared to monotherapies, showed significant reduction in tumor growth and progression, and increased survival. Furthermore, SAM and anti-PD-1 antibody combination triggered significantly higher immune cell infiltration, higher CD8+ T cells infiltration and effector functions, and polyfunctionality of CD8+ T cells in YUMMER1.7 tumors. Therefore, SAM combined with CPI provides a novel therapeutic strategy against BRAF mutant and WT melanomas and provides potential to be translated into clinic.
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Affiliation(s)
- A Mehdi
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada; Program in Metabolic Disorders and Complications (MeDiC), Research Institute of the McGill University Health Centre, 1001 Décarie Blvd. (Glen site), Room EM1.3232, Montréal, QC H4A 3J1, Canada
| | - M Attias
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Program in Infectious Diseases and Immunology in Global Health, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Centre of Excellence in Translational Immunology (CETI), Montréal, QC H4A 3J1, Canada
| | - A Arakelian
- Program in Metabolic Disorders and Complications (MeDiC), Research Institute of the McGill University Health Centre, 1001 Décarie Blvd. (Glen site), Room EM1.3232, Montréal, QC H4A 3J1, Canada
| | - M Szyf
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3A 2B4, Canada
| | - C A Piccirillo
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Program in Infectious Diseases and Immunology in Global Health, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada; Centre of Excellence in Translational Immunology (CETI), Montréal, QC H4A 3J1, Canada
| | - S A Rabbani
- Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 2B4, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H3A 2B4, Canada; Department of Oncology, McGill University, Montreal, QC H3A 2B4, Canada; Program in Metabolic Disorders and Complications (MeDiC), Research Institute of the McGill University Health Centre, 1001 Décarie Blvd. (Glen site), Room EM1.3232, Montréal, QC H4A 3J1, Canada.
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Wang X, Zhu W, Long Q, Chen E, Sun H, Li X, Xu H, Li W, Dong P, He L, Chen M, Deng W. The prognostic value and immune correlation of IL18 expression and promoter methylation in renal cell carcinoma. Clin Epigenetics 2023; 15:14. [PMID: 36707882 PMCID: PMC9883904 DOI: 10.1186/s13148-023-01426-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/12/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is not sensitive to immunotherapy and has poor prognosis. DNA methylation regulates gene expression, and its abnormal changes are related to many human diseases. Recently, DNA methylation has been found to participate in immune infiltration in various cancers. However, its pattern in RCC remains poorly understood. RESULTS We found that IL18 was significantly over-expressed in RCC tumor tissues compared to normal adjacent tissues The IL18 promoter region was hypomethylated, which was strongly correlated with elevated IL18 mRNA expression, and predicted advanced clinicopathological characteristics and shorter overall survival. Furthermore, we found that IL18 promoter methylation was significantly related to the down-regulation of immune checkpoint molecules and increase of CD8 + T cell infiltration in RCC tumor tissues. CONCLUSIONS We have identified the important role of IL18 promoter methylation and expression, which are associated with clinicopathological characteristics, overall survival, immune cell infiltration and expression of immune checkpoint molecules in RCC. We present the rationale for IL18 promoter methylation as a molecular biomarker for predicting the response of RCC to immune checkpoint inhibitors.
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Affiliation(s)
- Xiaonan Wang
- grid.488530.20000 0004 1803 6191Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China ,grid.12981.330000 0001 2360 039XZhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Wancui Zhu
- grid.488530.20000 0004 1803 6191Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Qian Long
- grid.452708.c0000 0004 1803 0208Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Enni Chen
- grid.488530.20000 0004 1803 6191Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Haohui Sun
- grid.488530.20000 0004 1803 6191Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Xiaodi Li
- grid.488530.20000 0004 1803 6191Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Hailin Xu
- grid.412615.50000 0004 1803 6239The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Weizhao Li
- grid.511083.e0000 0004 7671 2506The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Pei Dong
- grid.488530.20000 0004 1803 6191Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Liru He
- grid.488530.20000 0004 1803 6191Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Miao Chen
- grid.488530.20000 0004 1803 6191Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Wuguo Deng
- grid.488530.20000 0004 1803 6191Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
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Co-Targeting Luminal B Breast Cancer with S-Adenosylmethionine and Immune Checkpoint Inhibitor Reduces Primary Tumor Growth and Progression, and Metastasis to Lungs and Bone. Cancers (Basel) 2022; 15:cancers15010048. [PMID: 36612044 PMCID: PMC9818024 DOI: 10.3390/cancers15010048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BCa) is the most prevalent cancer in females and has a high rate of mortality, especially due to increased metastasis to skeletal and non-skeletal sites. Despite the marked clinical accomplishment of immune checkpoint inhibitor (CPI) therapy in patients with several cancers, it has had limited success in luminal subtypes of BCa. Accordingly, recent efforts have focused on combination therapy with CPI, including epigenetic modulators, to increase response rates of CPI in luminal BCa. We have previously shown that S-adenosylmethionine (SAM), the ubiquitous methyl donor, has strong anti-cancer effects in various cancers, including all subtypes of BCa. In the current study, we took a novel approach and examined the effect of CPI alone and in combination with SAM on tumor growth and metastasis in a syngeneic mouse model of luminal B BCa. We showed that SAM decreases cell proliferation, colony-formation (survival), and invasion of luminal B BCa cell lines (Eo771, R221A) in vitro. In in vivo studies, in Eo771 tumor-bearing mice, either SAM or anti-PD-1 antibody treatment alone significantly reduced tumor growth and progression, while the SAM+anti-PD-1 combination treatment had the highest anti-cancer efficacy of all groups. The SAM+anti-PD-1 combination reduced the percentage of animals with lung metastasis, as well as total metastatic lesion area, compared to control. Additionally, the SAM+anti-PD-1 combination significantly reduced the skeletal lesion area and protected tibial integrity to a greater extent than the monotherapies in an Eo771 bone metastasis model. Transcriptome analysis of Eo771 primary tumors revealed significant downregulation of pro-metastatic genes, including Matrix metalloproteinases (MMPs) and related pathways. On the other hand, CD8+ T cell infiltration, CD8+ T cell cytotoxicity (elevated granzymes), and immunostimulatory genes and pathways were significantly upregulated by the combination treatment. The results presented point to a combination of SAM with CPI as a possible treatment for luminal B BCa that should be tested in clinical studies.
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Mehranzadeh E, Crende O, Badiola I, Garcia-Gallastegi P. What Are the Roles of Proprotein Convertases in the Immune Escape of Tumors? Biomedicines 2022; 10:biomedicines10123292. [PMID: 36552048 PMCID: PMC9776400 DOI: 10.3390/biomedicines10123292] [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: 10/27/2022] [Revised: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Protein convertases (PCs) play a significant role in post-translational procedures by transforming inactive precursor proteins into their active forms. The role of PCs is crucial for cellular homeostasis because they are involved in cell signaling. They have also been described in many diseases such as Alzheimer's and cancer. Cancer cells are secretory cells that send signals to the tumor microenvironment (TME), remodeling the surrounding space for their own benefits. One of the most important components of the TME is the immune system of the tumor. In this review, we describe recent discoveries that link PCs to the immune escape of tumors. Among PCs, many findings have determined the role of Furin (PC3) as a paramount enzyme causing the TME to induce tumor immune evasion. The overexpression of various cytokines and proteins, for instance, IL10 and TGF-B, moves the TME towards the presence of Tregs and, consequently, immune tolerance. Furthermore, Furin is implicated in the regulation of macrophage activity that contributes to the increased impairment of DCs (dendritic cells) and T effector cells. Moreover, Furin interferes in the MHC Class_1 proteolytic cleavage in the trans-Golgi network. In tumors, the T cytotoxic lymphocytes (CTLs) response is impeded by the PD1 receptor (PD1-R) located on CTLs and its ligand, PDL1, located on cancer cells. The inhibition of Furin is a subtle means of enhancing the antitumor response by repressing PD-1 expression in tumors or macrophage cells. The impacts of other PCs in tumor immune escape have not yet been clarified to the extent that Furin has. Accordingly, the influence of other types of PCs in tumor immune escape is a promising topic for further consideration.
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Affiliation(s)
- Elham Mehranzadeh
- Cell Biology and Histology Department, Faculty of Medicine and Nursery, University of the Basque Country (UPV/EHU), Barrio Sarriena, sn., 48940 Leioa, Spain
| | - Olatz Crende
- Cell Biology and Histology Department, Faculty of Medicine and Nursery, University of the Basque Country (UPV/EHU), Barrio Sarriena, sn., 48940 Leioa, Spain
| | - Iker Badiola
- Cell Biology and Histology Department, Faculty of Medicine and Nursery, University of the Basque Country (UPV/EHU), Barrio Sarriena, sn., 48940 Leioa, Spain
- Nanokide Therapeutics SL, Ed. ZITEK, Barrio Sarriena, sn., 48940 Leioa, Spain
| | - Patricia Garcia-Gallastegi
- Physiology Department, Faculty of Medicine and Nursery, University of the Basque Country (UPV/EHU), Barrio Sarriena, sn., 48940 Leioa, Spain
- Correspondence:
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Wang YQ, Chen WJ, Li WY, Pan XW, Cui X. Impact of interaction networks of B cells with other cells on tumorigenesis, progression and response to immunotherapy of renal cell carcinoma: A review. Front Oncol 2022; 12:995519. [PMID: 36465392 PMCID: PMC9712799 DOI: 10.3389/fonc.2022.995519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 10/31/2022] [Indexed: 08/06/2023] Open
Abstract
Ample evidence indicates that the development and progression of renal cell carcinoma (RCC) are complex pathological processes involving interactions between tumor cells, immune cells and stromal components. Tumor infiltrated immune cells determine whether tumor advancement is promoted or inhibited. Among them, infiltrated B lymphocytes are present in all stages of RCC, playing a major role in determining tumor formation and advancement, as an essential part in the tumor microenvironment (TME). Although the advent of targeted and immune therapies has remarkably improved the survival of patients with advanced RCC, few cases can achieve complete response due to drug resistance. In this review article, we intend to summary the recent studies that outline the interaction networks of B cells with other cells, discuss the role of B cells in RCC development and progression, and assess their impact on RCC immunotherapy.
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Affiliation(s)
- Yu-qi Wang
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Wen-jin Chen
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, China
| | - Wen-yan Li
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xiu-wu Pan
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xin−gang Cui
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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Kim D, Kim J, Lee J, Han SK, Lee K, Kong J, Kim YJ, Lee WY, Yun SH, Kim HC, Hong HK, Cho YB, Park D, Kim S. Deconvolution of bulk tumors into distinct immune cell states predicts colorectal cancer recurrence. iScience 2022; 25:105392. [PMID: 36345336 PMCID: PMC9636036 DOI: 10.1016/j.isci.2022.105392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/26/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Predicting colorectal cancer recurrence after tumor resection is crucial because it promotes the administration of proper subsequent treatment or management to improve the clinical outcomes of patients. Several clinical or molecular factors, including tumor stage, metastasis, and microsatellite instability status, have been used to assess the risk of recurrence, although their predictive ability is limited. Here, we predicted colorectal cancer recurrence based on cellular deconvolution of bulk tumors into two distinct immune cell states: cancer-associated (tumor-infiltrating immune cell-like) and noncancer-associated (peripheral blood mononuclear cell-like). Prediction model performed significantly better when immune cells were deconvoluted into two states rather than a single state, suggesting that the difference in cancer recurrence was better explained by distinct states of immune cells. It indicates the importance of distinguishing immune cell states using cellular deconvolution to improve the prediction of colorectal cancer recurrence. Distinct immune cell states predict colorectal cancer recurrence Methylation patterns of immune cells altered after tumor infiltration Combining immune cell states and clinical factors improves recurrence prediction The proportion of TIIC-like DCs is a crucial factor for the recurrence prediction
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Glycolysis-Related SLC2A1 Is a Potential Pan-Cancer Biomarker for Prognosis and Immunotherapy. Cancers (Basel) 2022; 14:cancers14215344. [PMID: 36358765 PMCID: PMC9657346 DOI: 10.3390/cancers14215344] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022] Open
Abstract
SLC2A1 plays a pivotal role in cancer glycometabolism. SLC2A1 has been proposed as a putative driver gene in various cancers. However, a pan-cancer analysis of SLC2A1 has not yet been performed. In this study, we explored the expression and prognosis of SLC2A1 in pan-cancer across multiple databases. We conducted genetic alteration, epigenetic, and functional enrichment analyses of SLC2A. We calculated the correlation between SLC2A1 and tumor microenvironment using the TCGA pan-cancer dataset. We observed high expression levels of SLC2A1 with poor prognosis in most cancers. The overall genetic alteration frequency of SLC2A1 was 1.8% in pan-cancer, and the SLC2A1 promoter was hypomethylation in several cancers. Most m6A-methylation-related genes positively correlated with the expression of SLC2A1 in 33 TCGA cancers. Moreover, SLC2A1 was mainly related to the functions including epithelial-mesenchymal transition, glycolysis, hypoxia, cell-cycle regulation, and DNA repair. Finally, SLC2A1 positively associated with neutrophils and cancer-associated fibroblasts in the tumor microenvironment of most cancers and significantly correlated with TMB and MSI in various cancers. Notably, SLC2A1 was remarkably positively correlated with PD-L1 and CTLA4 in most cancers. SLC2A1 might serve as an attractive pan-cancer biomarker for providing new insights into cancer therapeutics.
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The Oncogenic and Immunological Roles of Apoptosis Antagonistic Transcription Factors in Human Tumors: A Pan-Cancer Analysis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3355365. [PMID: 36275893 PMCID: PMC9581705 DOI: 10.1155/2022/3355365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/23/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022]
Abstract
Background Apoptosis-antagonizing transcription factor (AATF) participates in tumor progression in multiple cancer types. However, its role across cancers is not well understood. Methods Data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and Human Protein Atlas (HPA) were used to analyze the multiomic roles of AATF in 33 tumor types, including gene and protein expression, survival prognosis, gene mutation, DNA methylation, protein phosphorylation, AATF coexpressed genes and their enrichment analysis, and immunological analysis. Results In TCGA and GTEx databases, 31 tumors and their corresponding normal tissues had AATF expression data, and it was differentially expressed in 29 of them. AATF was elevated in 27 tumors, decreased in 2 tumors, and was a risk factor for overall survival (OS) in 8 tumors and a risk factor for disease-free survival (DFS) in 4 tumors. AATF expression levels in various cancer types were significantly correlated with the infiltration levels of cancer-associated fibroblasts, endothelial cells, CD4+ T cells, B cells, myeloid dendritic cells, eosinophils, and macrophages. The immune checkpoints PD-1, PD-L1, and CTLA4 were positively correlated with AATF expression in bladder urothelial carcinoma (BLCA), kidney chromophobe (KICH), and prostate adenocarcinoma (PRAD). Conclusion In cancer, AATF expression is generally higher than that in normal tissue, and it is also associated with immunomodulation-related genes. AATF may be a risk factor for poor prognosis across cancers.
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Pancancer Analysis of the Oncogenic and Prognostic Role of NOL7: A Potential Target for Carcinogenesis and Survival. Int J Mol Sci 2022; 23:ijms23179611. [PMID: 36077008 PMCID: PMC9455868 DOI: 10.3390/ijms23179611] [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: 07/24/2022] [Revised: 08/16/2022] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
Despite growing evidence suggesting the critical function of NOL7 in cancer initiation and development, a systematic pancancer analysis of NOL7 is lacking. Herein, we present a comprehensive study of NOL7 which aimed to explore its potential role and detailed mechanisms across 33 human tumors based on The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CATPAC) databases. As a result, both gene and protein levels of NOL7 were found to be increased in various tumor tissues, including breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), and head and neck squamous cell carcinoma (HNSC) as compared with corresponding normal tissues. Meanwhile, dysregulated NOL7 expression was found to be closely related to pathological stage and prognosis in several cancers, including LIHC, ovarian serous cystadenocarcinoma (OV), and bladder urothelial carcinoma (BLCA). The DNA methylation level of NOL7 was found to be decreased in most cancers and to be negatively associated with NOL7 expression. Furthermore, NOL7 expression was determined to be significantly associated with levels of infiltrating cells and immune checkpoint genes, including HMGB1. Analysis of NOL7-related genes revealed that RNA metabolism pathways, including “ribosome biogenesis”, “spliceosome”, and “RNA transport”, were mainly involved in the functional mechanism of NOL7 in human cancers. In summary, this pancancer study characterized the relationship between NOL7 expression and clinicopathologic features in multiple cancer types and further showed its potential regulatory network in human cancers. It represents a systemic analysis for further functional and therapeutic studies of NOL7 and highlights its predictive value with respect to the carcinogenesis and prognosis of various cancers, especially LIHC.
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Li Z, Wang W, Wu J, Ye X. Identification of N7-methylguanosine related signature for prognosis and immunotherapy efficacy prediction in lung adenocarcinoma. Front Med (Lausanne) 2022; 9:962972. [PMID: 36091687 PMCID: PMC9449120 DOI: 10.3389/fmed.2022.962972] [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: 06/14/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundLung adenocarcinoma (LUAD) is one of the most frequent causes of tumor-related mortality worldwide. Recently, the role of N7-methylguanosine (m7G) in tumors has begun to receive attention, but no investigation on the impact of m7G on LUAD. This study aims to elucidate the significance of m7G on the prognosis and immunotherapy in LUAD.MethodsConsensus clustering was employed to determine the molecular subtype according to m7G-related regulators extracted from The Cancer Genome Atlas (TCGA) database. Survival, clinicopathological features and tumor mutational burden (TMB) analysis were applied to research molecular characteristics of each subtype. Subsequently, “limma” package was used to screen differentially expressed genes (DEGs) between subtypes. In the TCGA train cohort (n = 245), a prognostic signature was established by univariate Cox regression, lasso regression and multivariate Cox regression analysis according to DEGs and survival analysis was employed to assess the prognosis. Then the prognostic value of the signature was verified by TCGA test cohort (n = 245), TCGA entire cohort (n = 490) and GSE31210 cohort (n = 226). Moreover, the association among immune infiltration, clinical features and the signature was investigated. The immune checkpoints, TMB and tumor immune dysfunction and exclusion (TIDE) were applied to predict the immunotherapy response.ResultsTwo novel molecular subtypes (C1 and C2) of LUAD were identified. Compared to C2 subtype, C1 subtype had poorer prognosis and higher TMB. Subsequently, the signature (called the “m7G score”) was constructed according to four key genes (E2F7, FAM83A, PITX3, and HOXA13). The distribution of m7G score were significantly different between two molecular subtypes. The patients with lower m7G score had better prognosis in TCGA train cohort and three verification cohort. The m7G score was intensively related to immune infiltration. Compared with the lower score, the higher m7G score was related to remarkable upregulation of the PD-1 and PD-L1, the higher TMB and the lower TIDE score.ConclusionThis study established a m7G-related signature for predicting prognosis and immunotherapy in LUAD, which may contribute to the development of new therapeutic strategies for LUAD.
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Chen Y, He J, Chen R, Wang Z, Dai Z, Liang X, Wu W, Luo P, Zhang J, Peng Y, Zhang N, Liu Z, Zhang L, Zhang H, Cheng Q. Pan-Cancer Analysis of the Immunological Role of PDIA5: A Potential Target for Immunotherapy. Front Immunol 2022; 13:881722. [PMID: 36003400 PMCID: PMC9393377 DOI: 10.3389/fimmu.2022.881722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/23/2022] [Indexed: 01/27/2023] Open
Abstract
The aberrant protein disulfide isomerase A5 (PDIA5) expression was relevant to the poor prognosis of patients with human cancers. However, its relationship with the epigenetic and genetic alterations and its effect on tumor immunity is still lacking. In the present study, we comprehensively analyzed the immune infiltration role of PDIA5 in human cancers based on large-scale bioinformatics analyses and in vitro experiments. Obvious DNA methylation and moderate alteration frequency of PDIA5 were observed in human cancers. The expression level of PDIA5 was significantly correlated with infiltrated immune cells, immune pathways, and other immune signatures. We found that cancer cells and macrophages exhibited high PDIA5 expression in human cancers using the single-cell RNA sequencing analysis. We also demonstrated the interaction between PDIA5 and immune cells in glioblastoma multiforme (GBM). Multiplex immunofluorescence staining showed the upregulated expression level of PDIA5 and the increased number of M2 macrophage markers-CD163 positive cells in pan-cancer samples. Notably, PDIA5 silencing resulted in upregulated expression of PD-L1 and SPP1 in U251 cells. Silencing of PDIA5 in hepG2 cells, U251 cells, and PC3 cells contributed to a decline in their ability of proliferation, clone formation, and invasion and inhibited the migration of cocultured M2 macrophages. Additionally, PDIA5 also displayed predictive value in the immunotherapy response of both murine and human cancer cohorts. Overall, our findings indicated that PDIA5 might be a potential target for immunotherapies in cancers.
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Affiliation(s)
- Yu Chen
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jialin He
- Department of Neurology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Rui Chen
- Department of Neurosurgery, Affiliated Nanhua Hospital, University of South China, Changsha, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xisong Liang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wantao Wu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Oncology, Xiangya Hospital, Central South University, Guangzhou, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Changsha, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Changsha, China
| | - Yun Peng
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
- Teaching and Research Section of Clinical Nursing, Xiangya Hospital of Central South University, Changsha, China
| | - Nan Zhang
- One-third Lab, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou, Changsha, China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Quan Cheng, ; Hao Zhang, ; Liyang Zhang,
| | - Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Quan Cheng, ; Hao Zhang, ; Liyang Zhang,
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Quan Cheng, ; Hao Zhang, ; Liyang Zhang,
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AURKA is a prognostic potential therapeutic target in skin cutaneous melanoma modulating the tumor microenvironment, apoptosis, and hypoxia. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04164-1. [DOI: 10.1007/s00432-022-04164-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/20/2022] [Indexed: 10/16/2022]
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Zhang P, Gao H, Ye C, Yan R, Yu L, Xia C, Yang D. Large-Scale Transcriptome Data Analysis Identifies KIF2C as a Potential Therapeutic Target Associated With Immune Infiltration in Prostate Cancer. Front Immunol 2022; 13:905259. [PMID: 35720323 PMCID: PMC9203693 DOI: 10.3389/fimmu.2022.905259] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/06/2022] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers of the urinary system. In previous research, Kinesin family member 2C (KIF2C), as an oncogene, has been demonstrated to have a key role in the incidence and progression of different cancers. However, KIF2C has not been reported in PCa. We combined data from different databases, including The Cancer Genome Atlas, the Cancer Cell Line Encyclopedia, Genotype Tissue-Expression, cBioPortal, and the Genomics of Drug Sensitivity in Cancer database, to explore the potential oncogenic role of KIF2C in PCa through a series of bioinformatics approaches, including analysis of the association between KIF2C and prognosis, clinicopathological features, gene mutations, DNA methylation, immune cell infiltration, and drug resistance. The results showed that KIF2C was significantly up-regulated in PCa. High KIF2C expression was associated with age, pathological stage, lymph node metastases, prostate-specific antigen (PSA), and Gleason score and significantly predicted an unfavorable prognosis in PCa patients. Results from Gene Set Enrichment Analysis (GSEA) suggested that KIF2C was involved in the cell cycle and immune response. KIF2C DNA methylation was reduced in PCa and was inversely linked with KIF2C expression. KIF2C was shown to have a strong relationship with the tumor microenvironment (TME), infiltrating cells, and immune checkpoint genes. Furthermore, high KIF2C expression was significantly resistant to a variety of MAPK signaling pathway-related inhibitors. Our study reveals that KIF2C may be a possible predictive biomarker for assessing prognosis in PCa patients with immune infiltration.
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Affiliation(s)
- Pingxin Zhang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hang Gao
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chunwei Ye
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruping Yan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lu Yu
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chengxing Xia
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Delin Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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40
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Xu H, Jiang C, Chen D, Wu Y, Lu J, Zhong L, Yao F. Analysis of Pan-Cancer Revealed the Immunological and Prognostic Potential of CBX3 in Human Tumors. Front Med (Lausanne) 2022; 9:869994. [PMID: 35573019 PMCID: PMC9096250 DOI: 10.3389/fmed.2022.869994] [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: 02/05/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
Chromobox protein homolog 3 (CBX3) has been recognized as a member of the heterochromatin protein 1 family and participate in transcriptional activation or inhibition, cell differentiation and growth. Despite more and more evidence shows that CBX3 has a critical function in the development of some tumors, no systematic extensive analysis of CBX3 has been reported. Thus, we intended to examine the prognostic significance of CBX3 in 33 tumors and investigate its potential immune function. We employed several bioinformatics methods to explore the potential carcinogenic impact of CBX3 premised on the data sets collected from tumor genome maps, human protein maps, cBioPortal, and genotype tissue expression. The approaches include assessing the link between CBX3 and prognosis of different tumors, immune cell infiltration, micro-satellite instability (MSI), DNA methylation, and tumor mutational burden (TMB). The outcomes illustrated that CBX3 was increasingly expressed in 29 tumors. Moreover, CBX3 exhibited a negative correlation with the prognosis of many tumors. The expression of CBX3 was linked to MSI in 12 tumors and TMB in 16 tumors. In 24 tumors, the expression of CBX3 was linked to DNA methylation. Moreover, the CBX3 expression exhibited a negative relationship with the infiltration level of the majority of immune cells, but showed a positive link to T gamma delta cells, central memory T cells, and T helper cells, especially when invading breast carcinoma, thymic carcinoma, colon carcinoma, cutaneous melanoma, endometrial carcinoma, and lung squamous carcinoma. Our research indicates that CBX3 might be used as a prognostic indicator for different malignant tumors due to its function in tumor genesis as well as tumor immunity.
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Affiliation(s)
- Haitao Xu
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Caihong Jiang
- Department of Pediatric Surgery, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Dangui Chen
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Youzhi Wu
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Jia Lu
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Long Zhong
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Fusheng Yao
- Department of Hematology, Anqing Municipal Hospital, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
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Comprehensive analysis of m 6A regulator-based methylation modification patterns characterized by distinct immune profiles in colon adenocarcinomas. Gene 2022; 821:146250. [PMID: 35151825 DOI: 10.1016/j.gene.2022.146250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/05/2022] [Accepted: 01/21/2022] [Indexed: 01/02/2023]
Abstract
Mounting evidences have indicated that RNA N6-methyladenosine (m6A) modification played important roles in tumor formation and growth. However, it is rarely reported that m6A modifications are involved in the immune regulation and tumor microenvironment (TME) formation. In this study, we aimed to investigate the correlation between m6A modifications and TME regulation of colon adenocarcinoma (COAD) by bioinformatic analysis. NMF algorithm was applied to carry out consensus molecular subtype analysis on 36 selected m6A regulators regarding methylation modification, to identify m6A modification patterns and characteristics of m6A related genes in colon adenocarcinoma (COAD). Further, the relative infiltration levels of different immune cell subsets were quantified by ssGSEA and CIBERSORT algorithms, and a m6Sig scoring scheme was constructed to predict the prognosis and evaluate the response to immunotherapy in the patients with COAD. Among 579 COAD samples, we identified three different m6A modification patterns which were related to different biological pathways and clinical outcomes. Then, a scoring scheme termed "m6Sig score" was developed based on m6A-related characteristic genes, and was utilized to score patients with COAD into groups. We found that COAD patients with lower m6Sig scores exhibited prolonged survival and potentiated immune infiltration, which were associated with higher tumor mutation load, lower PD-L1 expression, and higher mutation rates of SMG (such as TTN and KRAS). Moreover, analysis regarding evaluation of immune response revealed that the patients with lower m6Sig scores had higher Immunophenoscore. Collectively, our study provided in depth insight into the interactions between m6A modification and regulation of TME. In addition, the quantitative evaluation of m6A modification patterns in our results may have implications in further immunotherapy for individual COAD patients.
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Zhao X, Wang J, Wang Y, Zhang M, Zhao W, Zhang H, Zhao L. Interferon‑stimulated gene 15 promotes progression of endometrial carcinoma and weakens antitumor immune response. Oncol Rep 2022; 47:110. [PMID: 35445736 PMCID: PMC9073416 DOI: 10.3892/or.2022.8321] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/14/2021] [Indexed: 11/24/2022] Open
Abstract
Endometrial carcinoma (EC) is one of the most common gynecological cancers with a poor prognosis. Therefore, clarifying the details of the molecular mechanisms is of great importance for EC diagnosis and clinical management. Interferon-stimulated gene 15 (ISG15) plays an important role in the development of various cancers. However, its role in EC remains unclear. High ISG15 expression was observed in EC, which was associated with poor clinical outcomes and pathological stage of patients with EC, thus representing a promising marker for EC progression. Further exploratory analysis revealed that the elevated ISG15 levels in EC were driven by aberrant DNA methylation, independent of copy number variation and specific transcription factor aberrations. Accordingly, knockdown of ISG15 by small interfering RNA attenuated the malignant cellular phenotype of EC cell lines, including proliferation and colony formation in vitro. Finally, investigation of the molecular mechanisms indicated that ISG15 promoted the cell cycle G1/S transition in EC. Furthermore, ISG15 promoted EC progression by activating the MYC proto-oncogene protein signaling pathway. Moreover, ECs with high levels of ISG15 harbored a more vital immune escape ability, evidenced not only by significantly less invasive CD8+ T cells, but also higher expression of T cell inhibitory factors, such as programmed death-ligand 1. These results suggest a tumor-promoting role of ISG15 in EC, which may be a promising marker for diagnosis, prognosis and therapeutic immunity.
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Affiliation(s)
- Xiwa Zhao
- Department of Obstetrics and Gynecology, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Jingjing Wang
- The Research Center, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Yaojie Wang
- The Research Center, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Mengmeng Zhang
- Department of Obstetrics and Gynecology, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Wei Zhao
- Department of Obstetrics and Gynecology, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Hui Zhang
- Department of Obstetrics and Gynecology, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Lianmei Zhao
- The Research Center, The Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
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Hyper-Methylated Hub Genes of T-Cell Receptor Signaling Predict a Poor Clinical Outcome in Lung Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2022:5426887. [PMID: 35432532 PMCID: PMC9007647 DOI: 10.1155/2022/5426887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022]
Abstract
Background Immune checkpoint inhibitors (ICIs) emerge as the first-line treatment of lung adenocarcinoma (LUAD); selection of subpopulations acquiring clinical benefit is required. Associations between epigenetic modulation of tumor microenvironment (TME) and clinical outcome are far from clear. We focused on immune-related genes closely regulated by DNA methylation to identify the potential clinical outcome indicators. Methods We systematically calculated immunophenotype score (IMpS) and classified immunophenotypes based on seven TME features in three independent cohorts. The overlapping of differential expressed genes and methylated probes targeted genes was regarded as genes closely regulated by DNA methylation. Then, probe/gene pairs which highly correlated with each other and IMpS were identified and named as immune-related probe/gene pairs (mIMg). Prognostic mIMg were selected and verified in seven independent validation cohorts. Results Three immune phenotypes were clustered, and similar results were obtained in the three independent training cohorts. C2 displayed as an immunologically hot phenotype, whereas C3 corresponded with immunologically cold phenotype. Average methylation level was decreased from C2 to C3 (C2 > C1 > C3). Similarly, ICIs nonresponders showed global hypo-methylation compared with responders. Genes in mIMg were mainly enriched, especially in T-cell receptor activation, and repressed in noninflamed TME by hyper-methylation. Among mIMg, low expression and hyper-methylation of CD247, LCK, and PSTPIP1 were risk factors of overall survival (OS). ICIs nonresponders were more likely to be hyper-methylated in the three genes. By integrating with the oncogenes status, we demonstrated that EGFR wt and SRGN overexpressed patients were associated with chronic inflammation and immune evasion, showing an immunologically hot phenotype, which might lead to the short OS but derive clinical benefit from ICIs. Conclusions This study identifies hyper-methylation and concurrent repression of CD247, LCK, PSTPIP1 as immune negative indicators and risk factors for prognosis in LUAD. Moreover, EGFR/SRGN axis may participate in immune modification to influence ICIs response and clinical outcome in LUAD.
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A Novel Cognition of Decitabine: Insights into Immunomodulation and Antiviral Effects. Molecules 2022; 27:molecules27061973. [PMID: 35335337 PMCID: PMC8950928 DOI: 10.3390/molecules27061973] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
DNA methylation, as one of the major means of epigenesis change, makes a large difference in the spatial structure of chromatin, transposable element activity and, fundamentally, gene transcription. It has been confirmed that DNA methylation is closely related to innate immune responses. Decitabine, the most efficient available DNA methyltransferase inhibitor, has demonstrated exhilarating immune activation and antiviral effects on multiple viruses, including HIV, HBV, HCV, HPV and EHV1. This review considers the role of decitabine in regulating innate immune responses and antiviral ability. Understanding the complex transcriptional and immune regulation of decitabine could help to identify and validate therapeutic methods to reduce pathogen infection-associated morbidity, especially virus infection-induced morbidity and mortality.
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Pan-Cancer Analysis of Microfibrillar-Associated Protein 2 (MFAP2) Based on Bioinformatics and qPCR Verification. JOURNAL OF ONCOLOGY 2022; 2022:8423173. [PMID: 35211173 PMCID: PMC8863482 DOI: 10.1155/2022/8423173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 11/18/2022]
Abstract
MFAP2 has been reported to play an oncogenic role in several types of human cancers. However, the expression profile of MFAP2 in various cancers and its impact on prognosis and immune infiltration remain unclear. In this study, the mRNA expression and protein expression of MFAP2 in normal tissues, tumor cell lines, and 33 malignant tumor tissues were analyzed comprehensively using Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), and The Cancer Genome Atlas (TCGA), Oncomine and UALCAN databases, and the expression of MFAP2 in different grades and stages of cancers was assessed using Gene Expression Profiling Interactive Analysis 2 (GEPIA2) and Tumor and Immune System Interaction Database (TISIDB). In general, MFAP2 showed distinct expression in most tumor and normal tissues, closely associated with higher tumor grade, higher tumor stage, and poor survival in multiple cancers. A search of the UALCAN database and the cBioPortal database revealed that this difference in mRNA level expression could be partly attributed to abnormal DNA methylation and mutations at the genomic level. In addition, MFAP2 expression was also associated with tumor mutation burden, microsatellite instability, and neoantigens in different cancer types. More importantly, the TIMER and TISIDB databases also showed that MFAP2 levels were significantly correlated with immune infiltration abundance and immune-related gene markers, as well as ESTIMATE scores. By qPCR, MFAP2 expression was validated in four kinds of tumor tissue samples. The present study combined several databases and performed a pan-cancer analysis of the expression profile, methylation, and mutation for MFAP2 and its implications for prognosis and immune infiltration, suggesting that MFAP2 could contribute to malignant properties of many tumors. MFAP2 may be an important biomarker with prognostic value and has the potential to be a target for tumor immunotherapy.
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Du M, Peng Y, Li Y, Sun W, Zhu H, Wu J, Zong D, Wu L, He X. MYC-activated RNA N6-methyladenosine reader IGF2BP3 promotes cell proliferation and metastasis in nasopharyngeal carcinoma. Cell Death Dis 2022; 8:53. [PMID: 35136045 PMCID: PMC8826370 DOI: 10.1038/s41420-022-00844-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/05/2022] [Accepted: 01/21/2022] [Indexed: 12/21/2022]
Abstract
N6-Methyladenosine (m6A) modification is the most abundant RNA modification in eukaryotic cells. IGF2BP3, a well-known m6A reader, is deregulated in many cancers, but its role in nasopharyngeal carcinoma (NPC) remains unclear. In this work, IGF2BP3 was upregulated in NPC tissues and cells. The high level of IGF2BP3 was positively related to late clinical stages, node metastasis, and poor outcomes. Moreover, IGF2BP3 accelerated NPC cell tumor progression and metastasis in vitro and vivo. Upstream mechanism analyses indicated that the high expression of IGF2BP3 in head and neck tumors was mainly due to mRNA level amplification. Luciferase assay and chromatin immunoprecipitation assay (CHIP) depicted that MYC was effectively bound to the promoter of IGF2BP3, thereby improving its transcriptional activity. Results also showed that IGF2BP3 was not only positively correlated with KPNA2 expression but also modulated the expression of KPNA2. m6A RNA immunoprecipitation (MeRIP) and RNA stability experiments verified that silencing IGF2BP3 significantly inhibited the m6A modification level of KPNA2, thereby stabilizing the mRNA stability of KPNA2. Rescue experiments proved that the effect of inhibiting or overexpressing IGF2BP3 on NPC cells was partly reversed by KPNA2. Collectively, MYC-activated IGF2BP3 promoted NPC cell proliferation and metastasis by influencing the stability of m6A-modified KPNA2. Our findings offer new insights that IGF2BP3 may serve as a new molecular marker and potential therapeutic target for NPC treatment.
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Affiliation(s)
- Mingyu Du
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Nanjing, Jiangsu, China
| | - Yi Peng
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Nanjing, Jiangsu, China
| | - Yang Li
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Nanjing, Jiangsu, China
| | - Wenyue Sun
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Nanjing, Jiangsu, China
| | - Huanfeng Zhu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Nanjing, Jiangsu, China
| | - Jing Wu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Nanjing, Jiangsu, China
| | - Dan Zong
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Nanjing, Jiangsu, China
| | - Lirong Wu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Nanjing, Jiangsu, China
| | - Xia He
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, 42 Baiziting Road, Nanjing, Jiangsu, China.
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Zhang H, Kong W, Zhao X, Han C, Liu T, Li J, Song D. N6-Methyladenosine-Related lncRNAs as potential biomarkers for predicting prognoses and immune responses in patients with cervical cancer. BMC Genom Data 2022; 23:8. [PMID: 35042477 PMCID: PMC8767716 DOI: 10.1186/s12863-022-01024-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/11/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Several recent studies have confirmed epigenetic regulation of the immune response. However, the potential role of RNA N6-methyladenosine (m6A) modifications in cervical cancer and tumour microenvironment (TME) cell infiltration remain unclear. RESULTS We evaluated and analysed m6A modification patterns in 307 cervical cancer samples from The Cancer Genome Atlas (TCGA) dataset based on 13 m6A regulators. Pearson correlation analysis was used to identify lncRNAs associated with m6A, followed by univariate Cox regression analysis to screen their prognostic role in cervical cancer patients. We also correlated TME cell infiltration characteristics with modification patterns. We screened six m6A-associated lncRNAs as prognostic lncRNAs and established the prognostic profile of m6A-associated lncRNAs by least absolute shrinkage and choice of operator (LASSO) Cox regression. The corresponding risk scores of the patients were derived based on their prognostic features, and the correlation between this feature model and disease prognosis was analysed. The prognostic model constructed based on the TCGA-CESC (The Cancer Genome Cervical squamous cell carcinoma and endocervical adenocarcinoma) dataset showed strong prognostic power in the stratified analysis and was confirmed as an independent prognostic indicator for predicting the overall survival of patients with CESC. Enrichment analysis showed that biological processes, pathways, and markers associated with malignancy were more common in the high-risk subgroup. Risk scores were strongly correlated with the tumour grade. ECM receptor interactions and pathways in cancer were enriched in Cluster 2, while oxidative phosphorylation and other biological processes were enriched in Cluster 1. The expression of immune checkpoint molecules, including programmed death 1 (PD-1) and programmed death ligand 1 (PD-L1), was significantly increased in the high-risk subgroup, suggesting that this prognostic model could be a predictor of immunotherapy. CONCLUSIONS This study reveals that m6A modifications play an integral role in the diversity and complexity of TME formation. Assessing the m6A modification patterns of individual tumours will help improve our understanding of TME infiltration characteristics and thus guide immunotherapy more effectively. We also developed an independent prognostic model based on m6A-associated lncRNAs as a predictor of overall survival, which can also be used as a predictor of immunotherapy.
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Affiliation(s)
- He Zhang
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100006, China
| | - Weimin Kong
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100006, China.
| | - Xiaoling Zhao
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100006, China
| | - Chao Han
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100006, China
| | - Tingting Liu
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100006, China
| | - Jing Li
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100006, China
| | - Dan Song
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100006, China
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Xu W, Zhu W, Tian X, Liu W, Wu Y, Anwaier A, Su J, Wei S, Qu Y, Zhang H, Ye D. Integrative 5-Methylcytosine Modification Immunologically Reprograms Tumor Microenvironment Characterizations and Phenotypes of Clear Cell Renal Cell Carcinoma. Front Cell Dev Biol 2021; 9:772436. [PMID: 34957104 PMCID: PMC8694268 DOI: 10.3389/fcell.2021.772436] [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: 09/08/2021] [Accepted: 11/01/2021] [Indexed: 01/04/2023] Open
Abstract
The tumor microenvironment (TME) affects the biologic malignancy of clear cell renal cell carcinoma (ccRCC). The influence of the 5-methylcytosine (m5C) epigenetic modification on the TME is unknown. We comprehensively assessed m5C modification patterns of 860 ccRCC samples (training, testing, and real-world validation cohorts) based on 17 m5C regulators and systematically integrated the modification patterns with TME cell-infiltrating characterizations. Our results identified distinct m5C modification clusters with gradual levels of immune cell infiltration. The distinct m5C modification patterns differ in clinicopathological features, genetic heterogeneity, patient prognosis, and treatment responses of ccRCC. An elevated m5C score, characterized by malignant biologic processes of tumor cells and suppression of immunity response, implies an immune-desert TME phenotype and is associated with dismal prognosis of ccRCC. Activation of exhausted T cells and effective immune infiltration were observed in the low m5C score cluster, reflecting a noninflamed and immune-excluded TME phenotype with favorable survival and better responses to immunotherapy. Together, these findings provide insights into the regulation mechanisms of DNA m5C methylation modification patterns on the tumor immune microenvironment. Comprehensive assessment of tumor m5C modification patterns may enhance our understanding of TME cell-infiltrating characterizations and help establish precision immunotherapy strategies for individual ccRCC patients.
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Affiliation(s)
- Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenkai Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wangrui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yuanyuan Wu
- Department of Gastroenterology, Naval Medical Center of PLA, Naval Military Medical University, Shanghai, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shiyin Wei
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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49
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Guo L, Yang H, Zhou C, Shi Y, Huang L, Zhang J. N6-Methyladenosine RNA Modification in the Tumor Immune Microenvironment: Novel Implications for Immunotherapy. Front Immunol 2021; 12:773570. [PMID: 34956201 PMCID: PMC8696183 DOI: 10.3389/fimmu.2021.773570] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/25/2021] [Indexed: 01/24/2023] Open
Abstract
N6-methyladenosine (m6A) methylation is one of the most common modifications of RNA in eukaryotic cells, and is mainly regulated by m6A methyltransferases (writers), m6A demethylases (erasers), and m6A binding proteins (readers). Recently, accumulating evidence has shown that m6A methylation plays crucial roles in the regulation of the tumor immune microenvironment, greatly impacting the initiation, progression, and metastasis processes of various cancers. In this review we first briefly summarizes the m6A-related concepts and detection methods, and then describes in detail the associations of m6A methylation modification with various tumor immune components especially immune cells (e.g., regulatory T cells, dendritic cells, macrophages, and myeloid-derived suppressor cells) in a variety of cancers. We discuss the relationship between m6A methylation and cancer occurrence and development with the involvement of tumor immunity highlighted, suggesting novel markers and potential targets for molecular pathological diagnosis and immunotherapy of various cancers.
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Affiliation(s)
- Liting Guo
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Yang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenfei Zhou
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Shi
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Huang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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50
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Long Q, Huang C, Huang J, Meng Q, Cheng Y, Li Y, He L, Chen M, Zhang C, Wang X, Zhu W, Peng J, Shi D, Zheng F, Dong P, Deng W. Prognostic value of JAK3 promoter methylation and mRNA expression in clear cell renal cell carcinoma. J Adv Res 2021; 40:153-166. [PMID: 36100323 PMCID: PMC9481962 DOI: 10.1016/j.jare.2021.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/13/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Qian Long
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Chunyu Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Jinsheng Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Qi Meng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yanjun Cheng
- Reproductive Center, Shenzhen Maternity & Child Healthcare Hospital, China
| | - Yilin Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Liru He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Miao Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Changlin Zhang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiaonan Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Wancui Zhu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Jin Peng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Dingbo Shi
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Fufu Zheng
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Pei Dong
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China.
| | - Wuguo Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China.
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