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Qu H, Mao M, Wang K, Mu Z, Hu B. Knockdown of ADAM8 inhibits the proliferation, migration, invasion, and tumorigenesis of renal clear cell carcinoma cells to enhance the immunotherapy efficacy. Transl Res 2024; 266:32-48. [PMID: 37992987 DOI: 10.1016/j.trsl.2023.11.003] [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: 08/04/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023]
Abstract
The current study performed bioinformatics and in vitro and in vivo experiments to explore the effects of ADAM8 on the malignant behaviors and immunotherapeutic efficacy of renal clear cell carcinoma (ccRCC) Cells. The modular genes most associated with immune cells were screened. Then, prognostic risk models were constructed by univariate COX analysis, LASSO regression analysis and multivariate COX analysis, and their diagnostic value was determined. The correlation between tumor mutation load (TMB) scores and the prognosis of ccRCC patients was clarified. Finally, six key genes (ABI3, ADAM8, APOL3, MX2, CCDC69, and STAC3) were analyzed for immunotherapy efficacy. Human and mouse ccRCC cell lines and human proximal tubular epithelial cell lines were used for in vitro cell experiments. The effect of ADAM8 overexpression or knockdown on tumor formation and survival in ccRCC cells was examined by constructing subcutaneous transplanted tumor model. Totally, 636 Black module genes were screened as being most associated with immune cell infiltration. Six genes were subsequently confirmed for the construction of prognostic risk models, of which ABI3, APOL3 and CCDC69 were low-risk factors, while ADAM8, MX2 and STAC3 were high-risk factors. The constructed risk model based on the identified six genes could accurately predict the prognosis of ccRCC patients. Besides, TMB was significantly associated with the prognosis of ccRCC patients. Furthermore, ABI3, ADAM8, APOL3, MX2, CCDC69 and STAC3 might play important roles in treatment concerning CTLA4 inhibitors or PD-1 inhibitors or combined inhibitors. Finally, we confirmed that ADAM8 could promote the proliferation, migration and invasion of ccRCC cells through in vitro experiments, and further found that in in vivo experiments, ADAM8 knockdown could inhibit tumor formation in ccRCC cells, improve the therapeutic effect of anti-PD1, and prolong the survival of mice. Our study highlighted the alleviative role of silencing ADAM8 in ccRCC patients.
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Affiliation(s)
- Hongchen Qu
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province 110042, PR China
| | - Minghuan Mao
- Department of Urological Surgery, Fourth affiliated Hospital of China Medical University, Shenyang 110000, PR China
| | - Kai Wang
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province 110042, PR China
| | - Zhongyi Mu
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province 110042, PR China
| | - Bin Hu
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province 110042, PR China.
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Li Y, Yang Y. Label-free quantitative proteomics reveals the mechanisms of Aurora kinase B in renal cell carcinoma. SAGE Open Med 2024; 12:20503121241228474. [PMID: 38516642 PMCID: PMC10956137 DOI: 10.1177/20503121241228474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/05/2024] [Indexed: 03/23/2024] Open
Abstract
Background Renal cell carcinoma is the most common form of kidney cancer which is a global threat to human health, needing to explore effective therapeutic targets and treatment methods. Aurora kinase B acts as an important carcinogenic role in various kinds of tumors, while its mechanism in renal cell carcinoma is indistinct. Herein we explore the underlying mechanism of Aurora kinase B in renal cell carcinoma. Methods and results Label-free quantitative proteomics analysis was employed to analyze the differentially expressed proteins in 786-O cells which were treated with si-Aurora kinase B or si-ctrl. In the current study, 169 differentially expressed proteins were identified. The top 10 upregulated proteins were MX2, IFI44L, ISG20, DDX58, F3, IFI44, ECE1, PRIC285, NIT1, and IFIT2. The top 10 downregulated proteins were FKBP9, FSTL1, DDAH1, TGFB2, HMGN3, COIL, FAM65A, PTPN14, ARFGAP2, and EIF2C2. GO enrichment analysis showed that these differentially expressed proteins participated in biological processes, including defense response to virus, response to virus, and type I interferon signaling pathway. These differentially expressed proteins participated in cellular components, including focal adhesion, cell-substrate adherens junction, cell-substrate junction, and endoplasmic reticulum lumen. These differentially expressed proteins participated in molecule functions, including guanyl nucleotide binding, nucleotidase activity, double-stranded RNA binding, 2'-5'-oligoadenylate synthetase activity, and virus receptor activity. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the significantly changed proteins including OAS3, OAS2, JAK1, TAP1, and RAC1 were involved in Epstein-Barr virus infection. Conclusions Taken together, our results demonstrate the possible mechanisms that Aurora kinase B may participate in renal cell carcinoma. These findings may provide insights into tumorigenesis and a theoretical basis for developing potential therapies of renal cell carcinoma.
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Affiliation(s)
- Yulong Li
- Department of Gastroenterology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Yang Yang
- School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, China
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Chen M, Gao Y, Cao H, Wang Z, Zhang S. Comprehensive analysis reveals dual biological function roles of EpCAM in kidney renal clear cell carcinoma. Heliyon 2024; 10:e23505. [PMID: 38187284 PMCID: PMC10767389 DOI: 10.1016/j.heliyon.2023.e23505] [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: 07/17/2023] [Revised: 10/27/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Background Epithelial cell adhesion molecule (EpCAM), a well-established marker for circulating tumor cells, plays a crucial role in the complex process of cancer metastasis. The primary objective of this investigation is to study EpCAM expression in pan-cancer and elucidate its significance in the context of kidney renal clear cell carcinoma (KIRC). Methods Data obtained from the public database was harnessed for the comprehensive assessment of the EpCAM expression levels and prognostic and clinicopathological correlations in thirty-three types of cancer. EpCAM was validated in our own KIRC sequencing and immunohistochemical cohorts. Subsequently, an in-depth exploration was conducted to scrutinize the interrelationship between EpCAM and various facets, including immune cells, immune checkpoints, and chemotherapy drugs. We employed Cox regression analysis to identify prognostic immunomodulators associated with EpCAM, which were subsequently utilized in the development of a prognostic model. The model was validated in our own clinical cohort and public datasets, and compared with 137 published models. The role of EpCAM in KIRC was explored by biological function experiments in vitro. Results While EpCAM exhibited pronounced overexpression across a wide spectrum of cancer types, a notable reduction was observed in KIRC tissues. As grade increased, EpCAM expression decreased. EpCAM expression decreased in patients without metastasis. EpCAM mRNA and protein levels were used as independent, favorable prognostic factors in patients with KIRC in our own cohort. The expression of EpCAM exhibited strong associations with immune-related pathways, demonstrating an inverse correlation with the majority of immune cell types. Immune checkpoint inhibitors exert better therapeutic effects on patients with low EpCAM expression. In addition, EpCAM can be used as a drug resistance indicator and guide the clinical medication of patients with KIRC. A robust model, which had good predictive accuracy and applicability, showed significant superiority over other models. Importantly, EpCAM played the dual roles of promoting proliferation and resisting metastasis in KIRC. Conclusion In the context of KIRC, EpCAM assumes a surprising dual role, where it not only facilitates cell proliferation but also exerts resistance against the metastatic process. EpCAM serves as a standalone prognostic marker for patients with KIRC, and related models can also effectively predict prognosis. These discoveries offer novel perspectives on the functional significance of EpCAM in the context of KIRC.
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Affiliation(s)
- Mei Chen
- Central Laboratory, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, 570208, China
| | - Yuanhui Gao
- Central Laboratory, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, 570208, China
| | - Hui Cao
- Central Laboratory, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, 570208, China
| | - Zhenting Wang
- Urology, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, 570208, China
| | - Shufang Zhang
- Central Laboratory, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, 570208, China
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Chen X, Zhang T, Ren X, Wei Y, Zhang X, Zang X, Ju X, Qin C, Xu D. CHKB-AS1 enhances proliferation and resistance to NVP-BEZ235 of renal cancer cells via regulating the phosphorylation of MAP4 and PI3K/AKT/mTOR signaling. Eur J Med Res 2023; 28:588. [PMID: 38093375 PMCID: PMC10720114 DOI: 10.1186/s40001-023-01558-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Targeted therapy is pivotal in renal carcinoma treatment, and the dual-inhibitor NVP-BEZ235 has emerged as a promising candidate in preliminary studies. Its effectiveness against renal carcinoma and the mechanisms underlying potential resistance, however, warrant further exploration. This study aims to elucidate these aspects, enhancing our understanding of NVP-BEZ235's future clinical utility. To investigate resistance mechanisms, renal cancer cell lines were exposed to progressively increasing concentrations of NVP-BEZ235, leading to the development of stable resistance. These resistant cells underwent extensive RNA-sequencing analysis. We implemented gene interference techniques using plasmid vectors and lentivirus and conducted regular IC50 assessments. To pinpoint the role of LncRNAs, we utilized FISH and immunofluorescence staining assays, supplemented by RNA pull-down and RIP assays to delineate interactions between LncRNA and its RNA-binding protein (RBP). Further, Western blotting and qRT-PCR were employed to examine alterations in signaling pathways, with an animal model providing additional validation. Our results show a marked increase in the IC50 of NVP-BEZ235 in resistant cell lines compared to their parental counterparts. A significant revelation was the role of LncRNA-CHKB-AS1 in mediating drug resistance. We observed dysregulated expression of CHKB-AS1 in both clinical samples of clear cell renal cell carcinoma (ccRCC) and cell lines. In vivo experiments further substantiated our findings, showing that CHKB-AS1 overexpression significantly enhanced tumor growth and resistance to NVP-BEZ235 in a subcutaneous tumorigenesis model, as evidenced by increased tumor volume and weight, whereas CHKB-AS1 knockdown led to a marked reduction in these parameters. Critically, CHKB-AS1 was identified to interact with MAP4, a key regulator in the phosphorylation of the PI3k/Akt/mTOR pathway. This interaction contributes to a diminished antitumor effect of NVP-BEZ235, highlighting the intricate mechanism through which CHKB-AS1 modulates drug resistance pathways, potentially impacting therapeutic strategies against renal carcinoma.
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Affiliation(s)
- Xinglin Chen
- Urology Centre, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Pudong New District, Shanghai, 201203, China
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No. 300, Guangzhou Street, Nanjing, 210029, Jiangsu Province, China
| | - Tongtong Zhang
- Urology Centre, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Pudong New District, Shanghai, 201203, China
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No. 300, Guangzhou Street, Nanjing, 210029, Jiangsu Province, China
| | - Xiaohan Ren
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No. 300, Guangzhou Street, Nanjing, 210029, Jiangsu Province, China
| | - Yuang Wei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No. 300, Guangzhou Street, Nanjing, 210029, Jiangsu Province, China
| | - Xu Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No. 300, Guangzhou Street, Nanjing, 210029, Jiangsu Province, China
| | - Xinyue Zang
- Urology Centre, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Pudong New District, Shanghai, 201203, China
| | - Xiran Ju
- Urology Centre, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Pudong New District, Shanghai, 201203, China.
| | - Chao Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, No. 300, Guangzhou Street, Nanjing, 210029, Jiangsu Province, China.
| | - Dongliang Xu
- Urology Centre, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, 528 Zhangheng Road, Pudong New District, Shanghai, 201203, China.
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Yao K, Xiaojun Z, Tingxiao Z, Shiyao L, Lichen J, Wei Z, Yanlei L, Jinlong T, Xiaoyan D, Jun Z, Qing B, Jun L. Multidimensional analysis to elucidate the possible mechanism of bone metastasis in breast cancer. BMC Cancer 2023; 23:1213. [PMID: 38066539 PMCID: PMC10704724 DOI: 10.1186/s12885-023-11588-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Breast cancer (BC) patients tend to suffer from distant metastasis, especially bone metastasis. METHODS All the analysis based on open-accessed data was performed in R software, dependent on multiple algorithms and packages. The RNA levels of specific genes were detected using quantitative Real-time PCR as a method of detecting the RNA levels. To assess the ability of BC cells to proliferate, we utilized the CCK8 test, colony formation, and the 5-Ethynyl-20-deoxyuridine assay. BC cells were evaluated for invasion and migration by using Transwell assays and wound healing assays. RESULTS In our study, we identified the molecules involved in BC bone metastasis based on the data from multiple BC cohorts. Then, we comprehensively investigated the effect pattern and underlying biological role of these molecules. We found that in the identified molecules, the EMP1, ACKR3, ITGA10, MMP13, COL11A1, and THY1 were significantly correlated with patient prognosis and mainly expressed in CAFs. Therefore, we explored the CAFs in the BC microenvironment. Results showed that CAFs could activate multiple carcinogenic pathways and most of these pathways play an important role in cancer metastasis. Meanwhile, we noticed the interaction between CAFs and malignant, endothelial, and M2 macrophage cells. Moreover, we found that CAFs could induce the remodeling of the BC microenvironment and promote the malignant behavior of BC cells. Then, we identified MMP13 for further analysis. It was found that MMP13 can enhance the malignant phenotype of BC cells. Meanwhile, biological enrichment and immune infiltration analysis were conducted to present the effect pattern of MMP13 in BC. CONCLUSIONS Our result can improve the understanding of researchers on the underlying mechanisms of BC bone metastasis.
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Affiliation(s)
- Kang Yao
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zhu Xiaojun
- Department of Musculoskeletal Oncology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Collaborative innovation Center for Cancer Medicine, Guangzhou, Guangdong, China
- State Key laboratory of Oncology in South China, Guangzhou, Guangdong, China
| | - Zhao Tingxiao
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Liao Shiyao
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ji Lichen
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zhang Wei
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Li Yanlei
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Tian Jinlong
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ding Xiaoyan
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zhang Jun
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
- Zhejiang Provincial People`s Hospital Bijie Hospital, Bijie, China.
| | - Bi Qing
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
| | - Lv Jun
- Cancer Center, Department of Orthopedics, Affliated People`s Hospital, Zhejiang Provincial People`s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
- Department of Laboratory Medicine, Affliated People`s Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
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Ke ZP, Tao WQ, Zhao G, Cheng K. Role of PPAR-related genes in chronic heart failure: evidence from large populations. BMC Cardiovasc Disord 2023; 23:552. [PMID: 37950149 PMCID: PMC10638691 DOI: 10.1186/s12872-023-03554-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The role of PPAR signaling and its associated genes in the pathogenesis and progression of chronic heart failure (CHF) remains elusive. METHODS We accessed the gene expression profile and relevant baseline information of CHF samples from the Gene Expression Omnibus (GEO) database, specifically from the GSE57338 project. RESULTS From GSE57338 project, we derived the expression value of 126 PPAR-related genes. A protein-protein interaction network was then established to illustrate potential protein interactions. ClueGO analysis results revealed that these genes predominantly participate in functions such as export across plasma membrane, regulation of lipid metabolic process, fatty acid metabolism, circulatory system vascular processes, alcohol metabolism, triglyceride metabolism and regulation of lipid localization and response to nutrient. Using the cytohubba plug-in in Cytoscape, we pinpointed ACADM, PPARG and CPT2 as potential central molecules in HF pathogenesis and progression. Subsequent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis delved into the potential biological role of these three genes in CHF. Immune infiltration analysis suggested that the infiltration level of neutrophils and M2 macrophages might be notably influenced by these genes, thereby playing a role in the CHF mechanism. CONCLUSIONS Our research provides a comprehensive insight into the significance of PPAR associated genes in CHF development. Notably, the genes ACADM, PPARG and CPT2 emerged as potential targets for clinical interventions.
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Affiliation(s)
- Zun-Ping Ke
- Department of Geriatrics, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Wen-Qi Tao
- Department of Cardiology, Jing'an District Centre Hospital of Shanghai, Fudan University, Shanghai, 200040, China
| | - Gang Zhao
- Department of Cardiology, Zhongshan Hospital, Shanghai Institute of Cardiovascular Diseases, Fudan University, Shanghai, China
| | - Kuan Cheng
- Department of Cardiology, Zhongshan Hospital, Shanghai Institute of Cardiovascular Diseases, Fudan University, Shanghai, China.
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Yao Y, Xuan H, Wang J, Gong L, Gao W. Integrative analysis of tertiary lymphoid structures and immune microenvironment in patients with esophageal carcinoma. TUMORI JOURNAL 2023; 109:466-480. [PMID: 37249074 DOI: 10.1177/03008916231176857] [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: 05/31/2023]
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most common upper gastrointestinal malignancies worldwide. Tertiary lymphoid structures (TLS) are tumor-infiltrating immune cells aggregates coupled with stromal cells which are similar to secondary lymphoid organs. The objective of this study is to explore the predictive effects of two common genes associated with TLS models on prognosis and immunotherapy effects in ESCC patients. METHODS Clinical information for ESCC patients in the TCGA(The Cancer Genome Altas) cohort and GSE 53625 were collected. All of the samples were classified as either high score group or low score group based on two TLS signatures, and the association between TLS signatures and survival, clinical indicators, genomic burden, stemness indices analysis, tumor microenvironment and immunotherapy response were performed. Furthermore, the mature TLS was also assessed in ESCC tissue microarray. RESULTS In our study, we quantified the score of TLS_9 and TLS_12, respectively, reflecting the different statuses of TLS (TLS_9 = B and T cells in TLSs; TLS_12 = neogenesis of TLSs). Subsequently, we explored the effect of TLS score on ESCC tumor microenvironment quantified by multiple algorithms. We found that a correlation analysis indicated that TLS_9 and TLS_12 were all positively correlated with CD8+ T cell, NK cells, CD4+ T cells, M1 macrophages and so on. Meanwhile, some cells present a different correlation pattern of TLS_9 and TLS_12, including activated CD4+ memory T cells and Tgd cells. Immune-related analysis revealed that the TLS_12 and TLS_9 scores were all positively correlated with immune dysfunction, yet negatively correlated with immune exclusion. Following this, the biological roles of TLS_9 and TLS_12 scores were investigated. Also, we noticed that the TLS score could significantly affect the CAFs infiltration and be associated with the genomic burden and tumor stemness. In addition, we explored the prognostic value of mature TLS through tissue microarray (TMA). Our result displayed ESCC patients with the presence of mature TLS had a better prognosis than ESCC patients without it. CONCLUSIONS Our study indicated that ESCC patients with the presence of TLS had better outcomes and an inflamed immune microenvironment. In addition, both TLS-9 and TLS-12 gene signatures could be used as potential biomarkers for the immunotherapy of ESCC patients.
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Affiliation(s)
- Yuanshan Yao
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Haojie Xuan
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jing Wang
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Libao Gong
- Department of abdominal oncology, The cancer center of the fifth affiliated hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Wen Gao
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
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Xu C, Xie XL, Kang N, Jiang HQ. Evaluation of ITGB1 expression as a predictor of the therapeutic effects of immune checkpoint inhibitors in gastric cancer. BMC Gastroenterol 2023; 23:298. [PMID: 37667169 PMCID: PMC10478479 DOI: 10.1186/s12876-023-02930-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 08/22/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Gastric cancer (CC) is a disease with high incidence and mortality rate. Immunotherapy is an important method for gastric cancer while lack of effective predictor. Integrins play an important role in the development. We aimed to explore the predictive value of β1 integrin (ITGB1) as a predictor of immunnotherapy in gastric cancer. METHODS Differential expression analysis was conducted using the Gene Expression Profiling Interactive Analysis (GEPIA) 2.0 and GEO databases. GEPIA data were used to evaluate the prognostic value of ITGB1 in gastric cancer (GC). Transcriptomic and clinical data of GC and normal tissues were downloaded from The Cancer Genome Atlas database, and the TIMER database was used to evaluate the association between ITGB1 and immune infiltration. Time-dependent receiver operating characteristic (ROC) curve analysis was used to determine the prognostic value of ITGB1. To verify ITGB1 expression at the protein level, immunohistochemical staining was conducted. In addition, to analyze the correlation of ITGB1 with PD-1 and PD-L1, we examined levels of PD-1 and PD-L1 by IHC and determined the predictive value of ITGB1 for anti-PD-1 therapy in GC by ROC curve analysis. RESULTS Compared with normal tissues, analysis of GEPIA and data at protein levels showed significantly higher expression of ITGB1 in GC. In addition, higher expression of ITGB1 was associated with worse pathological G-staging and tumor T-staging, which suggested that ITGB1 is a risk factor for poor prognosis in GC. The level of ITGB1 expression was positively correlated with CD8 + T cells, neutrophils, macrophages, and dendritic cells. ITGB1 expression was also correlated with PD-L1 expression, and this was further verified at the protein level by immunohistochemical analysis. The area under the ROC curve was 0.808. CONCLUSION ITGB1 may be a promising prognostic biomarker and effective predictor for anti-PD-1 therapy in GC. TRIAL REGISTRATION Retrospectively registered.
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Affiliation(s)
- Chao Xu
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China
- Handan Central Hospital, No.15, Zhonghua Road, Handan, 056001, Hebei Province, China
| | - Xiao-Li Xie
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China
| | - Ning Kang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China
| | - Hui-Qing Jiang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, No. 215, Heping West Road, Shijiazhuang, 050000, Hebei Province, China.
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Chen Y, Wen H, Li Y, Han Y, Tan J, Guo C, Cai C, Liu P, Peng Y, Liu Y, Wang X, Zeng S, Feng Z, Shen H. A multi-omics analysis reveals CLSPN is associated with prognosis, immune microenvironment and drug resistance in cancers. Biol Proced Online 2023; 25:16. [PMID: 37268895 DOI: 10.1186/s12575-023-00201-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/12/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Immunotherapy is effective only in limited patients. It is urgent to discover a novel biomarker to predict immune cells infiltration status and immunotherapy response of different cancers. CLSPN has been reported to play a pivotal role in various biological processes. However, a comprehensive analysis of CLSPN in cancers has not been conducted. METHODS To show the whole picture of CLSPN in cancers, a pan-cancer analysis was conducted in 9125 tumor samples across 33 cancer types by integrating transcriptomic, epigenomic and pharmacogenomics data. Moreover, the role of CLSPN in cancer was validated by CCK-8, EDU, colony formation and flow cytometry in vitro and tumor cell derived xenograft model in vivo. RESULTS CLSPN expression was generally upregulated in most cancer types and was significantly associated with prognosis in different tumor samples. Moreover, elevated CLSPN expression was closely correlated with immune cells infiltration, TMB (tumor mutational burden), MSI (microsatellite instability), MMR (mismatch repair), DNA methylation and stemness score across 33 cancer types. Enrichment analysis of functional genes revealed that CLSPN participated in the regulation of numerous signaling pathways involved in cell cycle and inflammatory response. The expression of CLSPN in LUAD patients were further analyzed at the single-cell level. Knockdown CLSPN significantly inhibited cancer cell proliferation and cell cycle related cyclin-dependent kinase (CDK) family and Cyclin family expression in LUAD (lung adenocarcinoma) both in vitro and in vivo experiments. Finally, we conducted structure-based virtual screening by modelling the structure of CHK1 kinase domain and Claspin phosphopeptide complex. The top five hit compounds were screened and validated by molecular docking and Connectivity Map (CMap) analysis. CONCLUSION Our multi-omics analysis offers a systematic understanding of the roles of CLSPN in pan-cancer and provides a potential target for future cancer treatment.
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Affiliation(s)
- Yihong Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Haicheng Wen
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yin Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ying Han
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jun Tan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Cao Guo
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Changjing Cai
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ping Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yinghui Peng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yihan Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xinwen Wang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ziyang Feng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Li GS, Zhang W, Huang WY, He RQ, Huang ZG, Gan XY, Yang Z, Dang YW, Kong JL, Zhou HF, Chen G. CEP55: an immune-related predictive and prognostic molecular biomarker for multiple cancers. BMC Pulm Med 2023; 23:166. [PMID: 37173675 PMCID: PMC10182662 DOI: 10.1186/s12890-023-02452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Centrosomal protein 55 (CEP55) plays a significant role in specific cancers. However, comprehensive research on CEP55 is lacking in pan-cancer. METHODS In-house and multi-center samples (n = 15,823) were used to analyze CEP55 in 33 cancers. The variance of CEP55 expression levels among tumor and control groups was evaluated by the Wilcoxon rank-sum test and standardized mean difference (SMD). The clinical value of CEP55 in cancers was assessed using receiver operating characteristic (ROC) curves, Cox regression analysis, and Kaplan-Meier curves. The correlations between CEP55 expression and the immune microenvironment were explored using Spearman's correlation coefficient. RESULTS The data of clustered regularly interspaced short palindromic repeats confirmed that CEP55 was essential for the survival of cancer cells in multiple cancer types. Elevated CEP55 mRNA expression was observed in 20 cancers, including glioblastoma multiforme (p < 0.05). CEP55 mRNA expression made it feasible to distinguish 21 cancer types between cancer specimens and their control samples (AUC = 0.97), indicating the potential of CEP55 for predicting cancer status. Overexpression of CEP55 was correlated with the prognosis of cancer individuals for 18 cancer types, exhibiting its prognostic value. CEP55 expression was relevant to tumor mutation burden, microsatellite instability, neoantigen counts, and the immune microenvironment in various cancers (p < 0.05). The expression level and clinical relevance of CEP55 in cancers were verified in lung squamous cell carcinoma using in-house and multi-center samples (SMD = 4.07; AUC > 0.95; p < 0.05). CONCLUSION CEP55 may be an immune-related predictive and prognostic marker for multiple cancers, including lung squamous cell carcinoma.
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Affiliation(s)
- Guo-Sheng Li
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Wei Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Wan-Ying Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Rong-Quan He
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Xiang-Yu Gan
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Zhen Yang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, 530021, Nanning, Guangxi, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Jin-Liang Kong
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, 530021, Nanning, Guangxi, P. R. China
| | - Hua-Fu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China.
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11
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Liu T, Sun L, Li ZZ, Yang K, Chen JM, Han XY, Qi LM, Zhou XG, Wang P. The m6A/m5C/m1A regulator genes signature reveals the prognosis and is related with immune microenvironment for hepatocellular carcinoma. BMC Gastroenterol 2023; 23:147. [PMID: 37170222 PMCID: PMC10173529 DOI: 10.1186/s12876-023-02776-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/20/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND RNA methylation is a crucial in many biological functions, and its aberrant regulation is associated with cancer progression. N6-Methyladenosine (m6A), 5-Methylcytosine (m5C), N1-methyladenosine (m1A) are common modifications of RNA methylation. However, the effect of methylation of m6A/m5C/m1A in hepatocellular carcinoma (HCC) remains unclear. METHOD The transcriptome datasets, clinic information, and mutational data of 48 m6A/m5C/m1A regulator genes were acquired from the TCGA database, and the prognostic hazard model was established by univariate and Least absolute shrinkage and selection operator (Lasso) regression. The multivariate regression was performed to determine whether the risk score was an independent prognostic indicator. Kaplan-Meier survival analysis and ROC curve analysis were used to evaluate the predictive ability of the risk model. Decision curve analysis(DCA)analysis was conducted to estimate the clinical utility of the risk model. We further analyzed the association between risk score and functional enrichment, tumor immune microenvironment, and somatic mutation. RESULT The four-gene (YTHDF1, YBX1, TRMT10C, TRMT61A) risk signature was constructed. The high-risk group had shorter overall survival (OS) than the low-risk group. Univariate and multivariate regression analysis indicated that risk score was an independent prognostic indicator. Risk scores in male group, T3 + T4 group and Stage III + IV group were higher in female group, T1 + T2 group and stage I + II group. The AUC values for 1-, 2-, and 3-year OS in the TCGA dataset were 0.764, 0.693, and 0.689, respectively. DCA analysis showed that the risk score had a higher clinical net benefit in 1- and 2-year OS than other clinical features.The risk score was positively related to some immune cell infiltration and most immune checkpoints. CONCLUSION We developed a novel m6A/m5C/m1A regulator genes' prognostic model, which could be applied as a latent prognostic tool for HCC and might guide the choice of immunotherapies.
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Affiliation(s)
- Ting Liu
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Lei Sun
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Zhi-Zhao Li
- Department of Cardiovascular, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Kun Yang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Jia-Min Chen
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Xiao-Yi Han
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Li-Ming Qi
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Xin-Gang Zhou
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China.
| | - Peng Wang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China.
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12
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Ren L, Yang X, Liu J, Wang W, Liu Z, Lin Q, Huang B, Pan J, Mao X. An innovative model based on N7-methylguanosine-related lncRNAs for forecasting prognosis and tumor immune landscape in bladder cancer. Cancer Cell Int 2023; 23:85. [PMID: 37158958 PMCID: PMC10165842 DOI: 10.1186/s12935-023-02933-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND As a novel type of the prevalent post-transcriptional modifications, N7-methylguanosine (m7G) modification is essential in the tumorigenesis, progression, and invasion of many cancers, including bladder cancer (BCa). However, the integrated roles of m7G-related lncRNAs in BCa remain undiscovered. This study aims to develop a prognostic model based on the m7G-related lncRNAs and explore its predictive value of the prognosis and anti-cancer treatment sensitivity. METHODS We obtained RNA-seq data and corresponding clinicopathological information from the TCGA database and collected m7G-related genes from previous studies and GSEA. Based on LASSO and Cox regression analysis, we developed a m7G prognostic model. The Kaplan-Meier (K-M) survival analysis and ROC curves were performed to evaluate the predictive power of the model. Gene set enrichment analysis (GSEA) was conducted to explore the molecular mechanisms behind apparent discrepancies between the low- and high-risk groups. We also investigated immune cell infiltration, TIDE score, TMB, the sensitivity of common chemotherapy drugs, and the response to immunotherapy between the two risk groups. Finally, we validated the expression levels of these ten m7G-related lncRNAs in BCa cell lines by qRT-PCR. RESULTS We developed a m7G prognostic model (risk score) composed of 10 m7G-related lncRNAs that are significantly associated with the OS of BCa patients. The K-M survival curves revealed that the high-risk group patients had significantly worse OS than those in the low-risk group. The Cox regression analysis confirmed that the risk score was a significant independent prognostic factor for BCa patients. We found that the high-risk group had higher the immune scores and immune cell infiltration. Furthermore, the results of the sensitivity of common anti-BCa drugs showed that the high-risk group was more sensitive to neoadjuvant cisplatin-based chemotherapy and anti-PD1 immunotherapy. Finally, qRT-PCR revealed that AC006058.1, AC073133.2, LINC00677, and LINC01338 were significantly downregulated in BCa cell lines, while the expression levels of AC124312.2 and AL158209.1 were significantly upregulated in BCa cell lines compared with normal cell lines. CONCLUSION The m7G prognostic model can be applied to accurately predict the prognosis and provide robust directions for clinicians to develop better individual-based and precise treatment strategies for BCa patients.
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Affiliation(s)
- Lei Ren
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Xu Yang
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Jinwen Liu
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Weifeng Wang
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Zixiong Liu
- Department of Urology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Qingyuan Lin
- Department of Urology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Bin Huang
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.
| | - Jincheng Pan
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.
| | - Xiaopeng Mao
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.
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13
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Chen S, Zhang S, Chen S, Ma F. The prognostic value and immunological role of CD44 in pan-cancer study. Sci Rep 2023; 13:7011. [PMID: 37117249 PMCID: PMC10147611 DOI: 10.1038/s41598-023-34154-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/25/2023] [Indexed: 04/30/2023] Open
Abstract
To investigate the correlation between cluster of differentiation-44 (CD44) expression and immunotherapy response and identify its possible predictive value in pan-cancer. Datasets of 33 cancer types from The Cancer Genome Atlas (TCGA) database were applied to investigate the relationship of CD44 expression with prognosis, tumor mutational burden (TMB), and microsatellite instability (MSI), and determine its potential prognostic value in pan-cancer. Patients were split into high-risk and low-risk cancer groups based on the survival outcomes of various cancer types. Additionally, the underlying mechanisms of CD44 in the tumor microenvironment (TME) were analyzed using ESTIMATE and CIBERSORT algorithms and Gene Set Enrichment Analysis (GSEA). Subsequently, the biological role of CD44 at single-cell level was investigated using CancerSEA database. Variable expression levels of CD44 between tumor and adjacent normal tissues were identified in pan-cancer datasets, further survival analysis revealed that CD44 expression was associated with multiple clinical annotations and survival indicators. Besides, the expression of CD44 was significantly associated with TMB and MSI in 10 types and 6 types of cancer, respectively, indicating it could be exploited as a potential biomarker predicting immunotherapy outcomes. Meanwhile, CD44 could influence several crucial immune cell-related pathways. and the results revealed by CancerSEA database denoted the correlation of CD44 with malignant phenotype and functional states, further indicating it can serve as a potential therapeutic target in cancer management. Our study demonstrated that CD44 shows great promise as a prognostic biomarker in numerous cancers, which will assist in developing new strategies in cancer management.
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Affiliation(s)
- Shaoyong Chen
- College of Stomatology, Guangxi Medical University, Nanning, Guangxi, China
| | - Siqin Zhang
- College of Stomatology, Guangxi Medical University, Nanning, Guangxi, China
| | - Shaohua Chen
- Guangxi Medical University, Nanning, Guangxi, China.
| | - Fei Ma
- College of Stomatology, Guangxi Medical University, Nanning, Guangxi, China.
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Zeng H, Su K, Chen X, Li X, Wen L, Song Y, Chen L, Li H, Guo L, Han Y. A propensity score matching study on survival benefits of radiotherapy in patients with inoperable hepatocellular carcinoma. Sci Rep 2023; 13:6879. [PMID: 37106014 PMCID: PMC10140032 DOI: 10.1038/s41598-023-34135-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/25/2023] [Indexed: 04/29/2023] Open
Abstract
With the advancements in radiotherapy (RT) in recent years, several studies have shown that RT can significantly prolong the survival of patients with hepatocellular carcinoma (HCC). As a noninvasive treatment option, the application of RT for the treatment of HCC is garnering increasing attention. In this retrospective study, we included data from 13,878 patients with HCC from the Surveillance, Epidemiology, and End Results (SEER) database between 2000 and 2019 and 325 patients with HCC treated in three tertiary hospitals in China between 2015 and 2021. Patient data were divided into RT and non-RT groups based on whether the patients underwent RT. Propensity score matching analysis was performed to minimize the deviation between the RT and non-RT groups, and the Kaplan-Meier method, Cox proportional hazard model, and nomogram were used to assess the efficacy of undergoing RT. The median overall survival (mOS) of the RT group was significantly longer compared with that of the non-RT group for the SEER data (16 months versus 9 months, p < 0.01). Similarly, the survival benefit was more significant in the RT group than in the non-RT group at our hospitals (34.1 months versus 15.4 months, p < 0.01). Furthermore, multivariate Cox analysis revealed that factors, including tumor (T) stage, patient age, tumor grade, serum AFP level, and chemotherapy, also affected patient survival. Moreover, these factors were also used to construct a nomogram. Subgroup analysis of these factors showed that RT was effective in prolonging patient survival in different populations. RT significantly improves the survival time of patients with inoperable HCC, thereby providing a basis for selecting HCC patients who can benefit from RT.
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Affiliation(s)
- Hao Zeng
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, No.25 Taiping Street, Luzhou, Sichuan Province, China
| | - Ke Su
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, No.25 Taiping Street, Luzhou, Sichuan Province, China
| | - Xiaojing Chen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, No.25 Taiping Street, Luzhou, Sichuan Province, China
| | - Xueting Li
- Department of Oncology, 363 Hospital, Chengdu, China
| | - Lianbin Wen
- Department of Geriatric Cardiology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Yanqiong Song
- Department of Radiotherapy, School of Medicine, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, University of Electronic Science and Technology of China, Chengdu, China
| | - Lan Chen
- Department of Oncology and Hematology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Han Li
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, No.25 Taiping Street, Luzhou, Sichuan Province, China
| | - Lu Guo
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yunwei Han
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, No.25 Taiping Street, Luzhou, Sichuan Province, China.
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15
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Tuhongjiang A, Wang F, Zhang C, Pang S, Qu Y, Feng B, Amuti G. Construction of an RNA modification-related gene predictive model associated with prognosis and immunity in gastric cancer. BMC Bioinformatics 2023; 24:147. [PMID: 37061682 PMCID: PMC10105968 DOI: 10.1186/s12859-023-05283-3] [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: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is one of the most common causes of cancer-related fatalities worldwide, and its progression is associated with RNA modifications. Here, using RNA modification-related genes (RNAMRGs), we aimed to construct a prognostic model for patients with GC. METHODS Based on RNAMRGs, RNA modification scores (RNAMSs) were obtained for GC samples from The Cancer Genome Atlas and were divided into high- and low-RNAMS groups. Differential analysis and weighted correlation network analysis were performed for the differential expressed genes (DEGs) to obtain the key genes. Next, univariate Cox regression, least absolute shrinkage and selection operator, and multivariate Cox regression analyses were performed to obtain the model. According to the model risk score, samples were divided into high- and low-risk groups. Enrichment analysis and immunoassays were performed for the DEGs in these groups. Four external datasets from Gene Expression Omnibus data base were used to test the accuracy of the predictive model. RESULTS We identified SELP and CST2 as key DEGs, which were used to generate the predictive model. The high-risk group had a worse prognosis compared to the low-risk group (p < 0.05). Enrichment analysis and immunoassays revealed that 144 DEGs related to immune cell infiltration were associated with the Wnt signaling pathway and included hub genes such as ELN. Overall mutation levels, tumor mutation burden, and microsatellite instability were lower, but tumor immune dysfunction and exclusion scores were greater (p < 0.05) in the high-risk group than in the low-risk group. The validation results showed that the prediction model score can accurately predict the prognosis of GC patients. Finally, a nomogram was constructed using the risk score combined with the clinicopathological characteristics of patients with GC. CONCLUSION This risk score from the prediction model related to the tumor microenvironment and immunotherapy could accurately predict the overall survival of GC patients.
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Affiliation(s)
- Airexiati Tuhongjiang
- Department of Day Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
| | - Feng Wang
- Department of Day Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China.
| | - Chengrong Zhang
- Department of Day Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
| | - Sisi Pang
- Department of Day Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
| | - Yujiang Qu
- Department of Day Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
| | - Bo Feng
- Department of Day Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
| | - Gulimire Amuti
- Department of Day Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, China
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Liu S, Ye Z, Xue VW, Sun Q, Li H, Lu D. KIF2C is a prognostic biomarker associated with immune cell infiltration in breast cancer. BMC Cancer 2023; 23:307. [PMID: 37016301 PMCID: PMC10071625 DOI: 10.1186/s12885-023-10788-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/29/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND The kinesin-13 family member 2C (KIF2C) is a versatile protein participating in many biological processes. KIF2C is frequently up-regulated in multiple types of cancer and is associated with cancer development. However, the role of KIF2C in immune cell infiltration of tumor microenvironment and immunotherapy in breast cancer remains unclear. METHODS The expression of KIF2C was analyzed using Tumor Immune Estimation Resource (TIMER) database and further verified by immunohistochemical staining in human breast cancer tissues. The correlation between KIF2C expression and clinical parameters, the impact of KIF2C on clinical prognosis and independent prognostic factors were analyzed by using TCGA database, the Kaplan-Meier plotter, and Univariate and multivariate Cox analyses, respectively. The nomograms were constructed according to independent prognostic factors and validated with C-index, calibration curves, ROC curves, and decision curve analysis. A gene set enrichment analysis (GSEA) was performed to explore the underlying molecular mechanisms of KIF2C. The degree of immune infiltration was assessed by the Estimation of Stromal and Immune cells in Malignant Tumor tissues using the Expression (ESTIMATE) algorithm and the single sample GSEA (ssGSEA). The Tumor mutational burden and Tumor Immune Dysfunction and Rejection (TIDE) were used to analyze immunotherapeutic efficiency. Finally, the KIF2C-related competing endogenous RNA (ceRNA) network was constructed to predict the putative regulatory mechanisms of KIF2C. RESULTS KIF2C was remarkably up-regulated in 18 different types of cancers, including breast cancer. Kaplan-Meier survival analysis showed that high KIF2C expression was associated with poor overall survival (OS). KIF2C expression was associated with clinical parameters such as age, TMN stage, T status, and molecular subtypes. We identified age, stage, estrogen receptor (ER) and KIF2C expression as OS-related independent prognosis factors for breast cancer. An OS-related nomogram was developed based on these independent prognosis factors and displayed good predicting ability for OS of breast cancer patients. Finally, our results revealed that KIF2C was significantly related to immune cell infiltration, tumor mutational burden, and immunotherapy in patients with breast cancer. CONCLUSION KIF2C was overexpressed in breast cancer and was positively correlated with immune cell infiltration and immunotherapy response. Therefore, KIF2C can serve as a potential biomarker for prognosis and immunotherapy in breast cancer.
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Affiliation(s)
- Shanshan Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology, Carson International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, 518055, China
| | - Ziwei Ye
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology, Carson International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, 518055, China
| | - Vivian Weiwen Xue
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology, Carson International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, 518055, China
| | - Qi Sun
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology, Carson International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, 518055, China
| | - Huan Li
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology, Carson International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, 518055, China
| | - Desheng Lu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology, Carson International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, 518055, China.
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Deng Y, Wang F, Wu X, Du K, Yang Q, Xia T. The m6A-regulation and single cell effect pattern in sunitinib resistance on clear cell renal cell carcinoma: Identification and validation of targets. Front Pharmacol 2023; 14:1131610. [PMID: 37063301 PMCID: PMC10102343 DOI: 10.3389/fphar.2023.1131610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Background: Sunitinib is the main target drug for clear cell renal cell carcinoma. However, the effect of sunitinib is often limited by acquired drug resistance.Methods: The open-accessed data used in this study were obtained from different online public databases, which were analyzed using the R software. The RNA level of specific genes was detected using quantitative Real-Time PCR. Sunitinib-resistant cell lines were constructed based on protocol get from the previous study. Colony formation and Cell Counting Kit-8 assays were applied to detect cell proliferation ability.Results: In this study, through publicly available data and high-quality analysis, we deeply explored the potential biological mechanisms that affect the resistance of sunitinib. Detailed, data from GSE64052, GSE76068 and The Cancer Genome Atlas were extracted. We identified the IFITM1, IL6, MX2, PCOLCE2, RSAD2 and SLC2A3 were associated with sunitinib resistance. Single-cell analysis, prognosis analysis and m6A regulatory network were conducted to investigate their role. Moreover, the MX2 was selected for further analysis, including its biological role and effect on the ccRCC microenvironment. Interestingly, we noticed that MX2 might be an immune-related gene that could affect the response rate of immunotherapy. Then, in vitro experiments validated the overexpression of MX2 in sunitinib-resistance cells. Colony formation assay indicated that the knockdown of MX2 could remarkably inhibit the proliferation ability of 786-O-Res and Caki-1-Res when exposed to sunitinib.Conclusion: In summary, through publicly available data and high-quality analysis, we deeply explored the potential biological mechanisms that affect the resistance of sunitinib. MX2 was selected for further analysis, including its biological role and effect on the ccRCC microenvironment. Finally, in vitro experiments were used to validate its role in ccRCC.
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Affiliation(s)
- Yanxi Deng
- Clinical Laboratory, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Fang Wang
- Clinical Laboratory, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xinhui Wu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Kangming Du
- Department of Cardiothoracic Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qing Yang
- Department of Cardiothoracic Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Qing Yang, ; Ting Xia,
| | - Ting Xia
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Qing Yang, ; Ting Xia,
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Lin X, Deng Y, Ye L, Chen B, Tong J, Shi W, Wang B, Yu B, Tang J. RNA Sequencing Reveals the Differentially Expressed circRNAs between Stable and Unstable Carotid Atherosclerotic Plaques. Genet Res (Camb) 2023; 2023:7006749. [PMID: 37020895 PMCID: PMC10070021 DOI: 10.1155/2023/7006749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Objective. This study aimed to identify circular RNA profiles (circRNAs) via high-throughput RNA sequencing and distinguish the differentially expressed (DE) circRNAs between stable and unstable plaques. Methods. RNA sequencing was performed on unstable and stable carotid plaque samples obtained from patients with carotid artery stenosis. DE circRNAs were screened, and six DE circRNAs were verified using quantitative real-time PCR (qRT-PCR). Functional evaluation of the DE circRNAs was conducted via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Results. We screened 344 DE circRNAs in unstable plaques, consisting of 342 upregulated and 2 downregulated circRNAs. GO analysis showed that the host genes of the upregulated circRNAs were related to ER to Golgi transport vesicle membrane, endocytic vesicle membrane, and Ran GTPase binding. KEGG analysis revealed that the host genes of the upregulated circRNAs were primarily associated with protein processing in endoplasmic reticulum, lysine degradation, homologous recombination, epithelial cell signaling in Helicobacter pylori infection, and yersinia infection. The results of qRT-PCR verified three upregulated DE circRNAs and two downregulated DE circRNAs in unstable plaques. Conclusion. Hsa-circ-0001523, hsa-circ-0008950, hsa-circ-0000571, hsa-circ-0001946, and hsa-circ-0000745 may be involved in regulating the stability of atherosclerotic plaques and serves as a therapeutic target for unstable plaques.
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Zhai X, Chen X, Wan Z, Ge M, Ding Y, Gu J, Hua J, Guo D, Tan M, Xu D. Identification of the novel therapeutic targets and biomarkers associated of prostate cancer with cancer-associated fibroblasts (CAFs). Front Oncol 2023; 13:1136835. [PMID: 36937411 PMCID: PMC10020494 DOI: 10.3389/fonc.2023.1136835] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Globally, prostate cancer remains a leading cause of mortality and morbidity despite advances in treatment. Research on prostate cancer has primarily focused on the malignant epithelium, but the tumor microenvironment has recently been recognized as an important factor in the progression of prostate cancer. Cancer-associated fibroblasts (CAFs) play an important role in prostate cancer progression among multiple cell types in the tumor microenvironment. In order to develop new treatments and identify predictive and prognostic biomarkers for CAFs, further research is needed to understand the mechanism of action of prostate cancer and CAF. In this work, we performed the single-cell RNA sequence analysis to obtain the biomarkers for CAFs, and ten genes were finally regarded as the marker genes for CAFs. Based on the ssGSEA algorithm, the prostate cancer cohort was divided into low- and high-CAFs groups. Further analysis revealed that the CAFs-score is associated with many immune-related cells and immune-related pathways. In addition, between the low- and high-CAFs tissues, a total of 127 hub genes were discovered, which is specific in CAFs. After constructing the prognostic prediction model, SLPI, VSIG2, CENPF, SLC7A1, SMC4, and ITPR2 were finally regarded as the key genes in the prognosis of patients with prostate cancer. Each patient was assigned with the risk score as follows: SLPI* 0.000584811158157081 + VSIG2 * -0.01190627068889 + CENPF * -0.317826812875334 + SLC7A1 * -0.0410213995358753 + SMC4 * 0.202544454923637 + ITPR2 * -0.0824652047622673 + TOP2A * 0.140312081524807 + OR51E2 * -0.00136602095885459. The GSVA revealed the biological features of CAFs, many cancer-related pathways, such as the adipocytokine signaling pathway, ERBB signaling pathway, GnRH signaling pathway, insulin signaling pathway, mTOR signaling pathway and PPAR signaling pathway are closely associated with CAFs. As a result of these observations, similar transcriptomics may be involved in the transition from normal fibroblasts to CAFs in adjacent tissues. As one of the biomarkers for CAFs, CENPF can promote the proliferation ability of prostate cancer cells. The overexpress of CENPF could promote the proliferation ability of prostate cancer cells. In conclusion, we discuss the potential prognostic and therapeutic value of CAF-dependent pathways in prostate cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Mingyue Tan
- Urology Centre, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dongliang Xu
- Urology Centre, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Identification of a Novel Gene Signature Based on Kinesin Family Members to Predict Prognosis in Glioma. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59020414. [PMID: 36837615 PMCID: PMC9959126 DOI: 10.3390/medicina59020414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
Background and Objectives: Extensive research indicates that the kinesin superfamily (KIFs) regulates tumor progression. Nonetheless, the potential prognostic and therapeutic role of KIFs in glioma has been limited. Materials and Methods: Four independent cohorts from The Cancer Genome Atlas (TCGA) database and the Chinese Glioma Genome Atlas (CGGA) database were generated into a large combination cohort for identification of the prognostic signature. Following that, systematic analyses of multi-omics data were performed to determine the differences between the two groups. In addition, IDH1 was selected for the differential expression analysis. Results: The signature consists of five KIFs (KIF4A, KIF26A, KIF1A, KIF13A, and KIF13B) that were successfully identified. Receiver operating characteristic (ROC) curves indicated the signature had a suitable performance in prognosis prediction with the promising predictive area under the ROC curve (AUC) values. We then explored the genomic features differences, including immune features and tumor mutation status between high- and low-risk groups, from which we found that patients in the high-risk group had a higher level of immune checkpoint modules, and IDH1 was identified mutated more frequently in the low-risk group. Results of gene set enrichment analysis (GSEA) analysis showed that the E2F target, mitotic spindle, EMT, G2M checkpoint, and TNFa signaling were significantly activated in high-risk patients, partially explaining the differential prognosis between the two groups. Moreover, we also verified the five signature genes in the Human Protein Atlas (HPA) database. Conclusion: According to this study, we were able to classify glioma patients based on KIFs in a novel way. More importantly, the discovered KIFs-based signature and related characteristics may serve as a candidate for stratification indicators in the future for gliomas.
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Exploration of the Long Noncoding RNAs Involved in the Crosstalk between M2 Macrophages and Tumor Metabolism in Lung Cancer. Genet Res (Camb) 2023; 2023:4512820. [PMID: 36741921 PMCID: PMC9891836 DOI: 10.1155/2023/4512820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/31/2022] [Accepted: 01/07/2023] [Indexed: 01/27/2023] Open
Abstract
Background Complex regulation exists between tumor metabolism and M2 macrophages. Long noncoding RNAs (lncRNAs) are famous for their wide regulatory role. This study aimed to identify the lncRNAs involved in the crosstalk between tumor metabolism and M2 macrophages. Methods The Cancer Genome Atlas was responsible for the public data. R software was responsible for the analysis of public data. Results Based on the input expression profile, we quantified the M2 macrophage infiltration using the CIBERSORT algorithm and found that M2 macrophages were a risk factor for lung cancer. Also, we found that M2 macrophages were correlated with multiple metabolism pathways. Then, 67 lncRNAs involved in both M2 macrophages and related metabolism pathways were identified. A prognosis signature based on AC027288.3, AP001189.3, FAM30A, GAPLINC, LINC00578, and LINC01936 was established, which had good prognosis prediction ability. The clinical parameters and risk score were combined into a nomogram plot for better prediction of the patient's prognosis. A high fit of actual survival and nomogram-predicted survival was found using the calibration plot. Moreover, in low-risk patients, immunotherapy was more effective, while cisplatin and docetaxel were more effective in high-risk patients. Biological enrichment analysis indicated pathways of notch signaling, TGF-β signaling, interferon alpha response, and interferon-gamma response were activated in the high-risk group. Meanwhile, the risk score was associated with tumor metabolism and M2 macrophages. Also, we found that the promoting effect of CAPLINC on M2 macrophage polarization might act through multiple metabolism pathways. Conclusions Our result can provide new insights into the interaction between M2 macrophages and tumor metabolism, as well as the involved lncRNAs, which can provide the direction for future studies.
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Development of a Novel KCNN4-Related ceRNA Network and Prognostic Model for Renal Clear Cell Carcinoma. Anal Cell Pathol 2023. [DOI: 10.1155/2023/2533992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Background. Clear cell renal cell carcinoma (ccRCC) accounts for more than 80% of renal cell carcinomas. Yet, it has not been fully understood about the derivation and progression of the tumor, as well as the long-term benefits from multimodality therapy. Therefore, reliable and applicable molecular markers are urgently needed for the prediction of diagnosis and prognosis of ccRCC patients. Methods. Genetic and clinical information of 533 ccRCC patients from The Cancer Genome Atlas database was collected for comprehensive bioinformatic analyses. UALCAN was used to detect gene expression in paired tumor samples. Two data sets from Gene Expression Omnibus database were analyzed to identify differentially expressed genes (DEGs), and Gene Set Enrichment Analysis was applied for the functional enrichment of DEGs. Tumor Immune Single Cell Hub and Tumor IMmune Estimation Resource databases were separately used for analyses of single-immune cell and immune cell infiltration. Encyclopedia of RNA Interactomes database was explored to predict targeted microRNAs (miRNAs) and corresponding long non-coding RNAs (lncRNAs). Cox regression analysis was performed for the construction of risk signature and prognosis model. Finally, quantitative real-time polymerase chain reaction and western blot were conducted for KCNN4 expression detection in cell lines and clinical samples. Small interfering RNA was employed to knock down KCNN4, and corresponding functional experiments were conducted on ccRCC cells as well. Results. KCNN4 showed elevated expression in tumors and prominent clinical correlation in ccRCC. In total, 41 KCNN4-related genes were enriched, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed they were intimately related to immune-related signaling pathways. Spearman’s analysis revealed the significantly positive correlation of KCNN4 with immune cell infiltration. By integrating hub miRNA-let-7e-5p and four critical lncRNA, a competitive endogenous RNA network-based risk signature was constructed. The prognosis model derived from it showed considerable predictive value for survival of ccRCC patients. Finally, in vitro experiments confirmed the remarkable tumor-promoting role of KCNN4 in ccRCC cells. Conclusion. KCNN4 significantly affected the immune status of tumor microenvironment and immunotherapy elements, through which it promoted tumor progression in ccRCC, and it could be a potential biomarker for prognosis and immunotherapy effects of ccRCC patients.
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Song P, Zhou J, Wu K, Wang W, Gu S. The Underlying Mechanism Involved in Gefitinib Resistance and Corresponding Experiment Validation in Lung Cancer. Mediators Inflamm 2023; 2023:9658912. [PMID: 37205010 PMCID: PMC10188267 DOI: 10.1155/2023/9658912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/19/2023] [Accepted: 04/05/2023] [Indexed: 05/21/2023] Open
Abstract
Background Gefitinib resistance remains a major problem in the treatment of lung cancer. However, the underlying mechanisms involved in gefitinib resistance are largely unclear. Methods Open-accessed data of lung cancer patients were downloaded from The Cancer Genome Atlas Program and Gene Expression Omnibus databases. CCK8, colony formation, and 5-ethynyl-2'-deoxyuridine assays were utilized to evaluate the cell proliferation ability. Transwell and wound-healing assays were utilized to evaluate the cell invasion and migration ability. Quantitative real-time PCR was utilized to detect the RNA level of specific genes. Results Here, we obtained the expression profile data of wild and gefitinib-resistant cells. Combined with the data from the TCGA and GDSC databases, we identified six genes, RNF150, FAT3, ANKRD33, AFF3, CDH2, and BEX1, that were involved in gefitinib resistance in both cell and tissue levels. We found that most of these genes were expressed in the fibroblast of the NSCLC microenvironment. Hence, we also comprehensively investigated the role of fibroblast in the NSCLC microenvironment, including its biological effect and cell interaction. Ultimately, CDH2 was selected for further analysis for its prognosis correlation. In vitro experiments presented the cancer-promoting role of CDH2 in NSCLC. Moreover, cell viability detection showed that the inhibition of CDH2 could significantly decrease the IC50 of gefitinib in NSCLC cells. GSEA showed that CDH2 could significantly affect the pathway activity of PI3K/AKT/mTOR signaling. Conclusions This study is aimed at investigating the underlying mechanism involved in gefitinib resistance to lung cancer. Our research has improved researchers' understanding of gefitinib resistance. Meanwhile, we found that CDH2 could lead to gefitinib resistance through PI3K/AKT/mTOR signaling.
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Affiliation(s)
- Puwei Song
- Department of Thoracic Surgery, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jianghui Zhou
- Department of Thoracic Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Kaiqin Wu
- Department of Thoracic Surgery, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wenli Wang
- Department of Thoracic Surgery, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shaorui Gu
- Department of Thoracic Surgery, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
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Wei S, Chen Z, Ling X, Zhang W, Jiang L. Comprehensive analysis illustrating the role of PANoptosis-related genes in lung cancer based on bioinformatic algorithms and experiments. Front Pharmacol 2023; 14:1115221. [PMID: 36874021 PMCID: PMC9977813 DOI: 10.3389/fphar.2023.1115221] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Background: Recently, PANoptosis has aroused the interest of researchers for its role in cancers. However, the studies that investigated PANoptosis in lung cancer are still few. Methods: The public data were mainly collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus database. R software was utilized for the analysis of public data. Quantitative real-time (qRT) polymerase chain reaction (PCR) was used to measure the RNA level of FADD. The cell proliferation ability was evaluated using the CCK8, colony formation, and 5-ethynyl-2'-deoxyuridine (EdU) assays. Western blot was used to detect the protein level of specific molecules. Flow cytometry analysis and TUNEL staining were used to evaluate cell apoptosis. Results: In our study, we collected the PANoptosis-related genes from previous studies. Through series analysis, we identified the FADD, an adaptor of PANoptosis and apoptosis, for further analysis. Results showed that FADD is one of the prominent risk factors in lung cancer, mainly localized in nucleoplasm and cytosol. We next performed immune infiltration analysis and biological enrichment to illustrate the underlying cause of FADD in lung cancer. Subsequently, we discovered that the patients with a high level of FADD might respond worse to immunotherapy but better to AICAR, bortezomib, docetaxel, and gemcitabine. In vitro experiments indicated that inhibiting FADD could reduce significantly the ability of cancerous lung cells to proliferate. Meanwhile, we found that the knockdown of FADD promotes the apoptosis and pyroptosis. Ultimately, a prognosis signature was identified based on the FADD-regulated genes, which showed satisfactory prediction efficiency on patients with lung cancer. Conclusion: Our result can provide a novel direction for future studies focused on the role of PANoptosis in lung cancer.
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Affiliation(s)
- Shiyou Wei
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhigang Chen
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinyu Ling
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wentian Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lei Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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Leng XF, Wang GF, Yin H, Wei F, Zeng KK, Zhang YQ. Comprehensive Analysis Identifies the PPAR-Targeted Genes Associated with Ovarian Cancer Prognosis and Tumor Microenvironment. PPAR Res 2023; 2023:6637414. [PMID: 37213709 PMCID: PMC10195182 DOI: 10.1155/2023/6637414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/07/2023] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
Background There is a significant role for peroxisome proliferator-activated receptors (PPARs) in the development of cancer. Nevertheless, the role of PPARs-related genes in ovarian cancer (OC) remains unclear. Methods The open-accessed data used for analysis were downloaded from The Cancer Genome Atlas database, which was analyzed using the R software. Results In our study, we comprehensively investigated the PPAR target genes in OC, including their biological role. Meanwhile, a prognosis signature consisting of eight PPAR target genes was established, including apolipoprotein A-V, UDP glucuronosyltransferase 2 family, polypeptide B4, TSC22 domain family, member 1, growth hormone inducible transmembrane protein, renin, dedicator of cytokinesis 4, enoyl CoA hydratase 1, peroxisomal (ECH1), and angiopoietin-like 4, which showed a good prediction efficiency. A nomogram was constructed by combining the clinical feature and risk score. Immune infiltration and biological enrichment analysis were applied to investigate the difference between high- and low-risk patients. Immunotherapy analysis indicated that low-risk patients might respond better to immunotherapy. Drug sensitivity analysis indicated that high-risk patients might respond better to bleomycin, nilotinib, pazopanib, pyrimethamine, and vinorelbine, yet worse to cisplatin and gefitinib. Furthermore, the gene ECH1 was selected for further analysis. Conclusions Our study identified a prognosis signature that could effectively indicates patients survival. Meanwhile, our study can provide the direction for future studies focused on the PPARs in OC.
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Affiliation(s)
- Xiao-Fei Leng
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Gao-Fa Wang
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Hao Yin
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Feng Wei
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Kang-Kang Zeng
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yi-Qun Zhang
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- State Key Laboratory of Ultrasound in Medicine and Engineering, Chongqing Medical University, Chongqing 400016, China
- Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, No. 251, Yaojiayuan Road, Chaoyang District, Beijing, China
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Zeng Z, Yu J, Yang Z, Du K, Chen Y, Zhou L. Investigation of M2 macrophage-related gene affecting patients prognosis and drug sensitivity in non-small cell lung cancer: Evidence from bioinformatic and experiments. Front Oncol 2022; 12:1096449. [PMID: 36591493 PMCID: PMC9797692 DOI: 10.3389/fonc.2022.1096449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Background The progression process of lung cancer can be accelerated by M2 macrophages. However, genes that affect M2 macrophage polarization remain unidentified. Methods The Cancer Genome Atlas, Gene Expression Omnibus, and Arrayexpress databases were used to obtain open-access data. The analysis of public data was mostly performed with R studio. The RNA levels of specific genes were detected using quantitative real-time PCR. The proliferation ability of the cells was assessed by CCK8, colony formation, and EdU assays. Results Based on the multiple datasets, we noticed a poor prognosis in patients with high M2 macrophage infiltration. There were 114 genes differentially expressed between high and low M2 macrophages infiltrated samples, regarded as M2 macrophage-related genes. Subsequently, a prognosis prediction signature consisting of ABHD5, HS3ST2, TM6SF1, CAPZA2, LEPROT, HNMT, and MRO was identified and presented a satisfactory performance. The pathway enrichment results revealed a positive correlation between riskscore and enrichment scores for most immunotherapy-related positive terms. Also, there might be an increase in genomic instability among patients at high risk. Interestingly, low risk patients are most likely to benefit from PD-1 therapy, while high risk patients may benefit from CTLA-4 therapy. Meanwhile, the estimated IC50 of seven drugs differs significantly between two risk groups, including Cisplatin, Docetaxel, Doxorubicin, Gefitinib, Paclitaxel, Sunitinib and Vinorelbine. Moreover, further experiments indicated that HNMT was overexpressed and can enhance the proliferation ability in lung cancer cells. Conclusions In summary, our study identified the molecules significantly affecting M2 macrophage infiltration and identified a prognosis signature that robustly indicated patients prognosis. Moreover, we validated the cancer-promoting effect of HNMT using in vitro experiments.
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Affiliation(s)
- Zhen Zeng
- Department of Emergency, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jiachen Yu
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhuo Yang
- Department of Cardiology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Kangming Du
- Department of Cardiothoracic Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yuewei Chen
- Department of Cardiothoracic Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China,*Correspondence: Yuewei Chen, ; Lei Zhou,
| | - Lei Zhou
- Pain Management, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China,*Correspondence: Yuewei Chen, ; Lei Zhou,
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Wang T, Jian W, Xue W, Meng Y, Xia Z, Li Q, Xu S, Dong Y, Mao A, Zhang C. Integration analysis identifies MYBL1 as a novel immunotherapy biomarker affecting the immune microenvironment in clear cell renal cell carcinoma: Evidence based on machine learning and experiments. Front Immunol 2022; 13:1080403. [PMID: 36591240 PMCID: PMC9794576 DOI: 10.3389/fimmu.2022.1080403] [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: 10/26/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Background Previous studies have identified MYBL1 as a cancer-promoting molecule in numerous types of cancer. Nevertheless, the role of MYBL in renal cancer remains unclear. Methods Genomic and clinical data of clear cell renal cell carcinoma (ccRCC) was get from the Cancer Genome Atlas (TCGA) database. CCK8, colony formation, and 5-ethynyl-2'-deoxyuridine assay were utilized to evaluate the performance of cell proliferation. Cell apoptosis was detected using the flow cytometric analysis. The protein level of MYBL1 in different tissues was evaluated using immunohistochemistry. A machine learning algorithm was utilized to identify the prognosis signature based on MYBL1-derived molecules. Results Here, we comprehensively investigated the role of MYBL1 in ccRCC. Here, we noticed a higher level of MYBL1 in ccRCC patients in both RNA and protein levels. Further analysis showed that MYBL1 was correlated with progressive clinical characteristics and worse prognosis performance. Biological enrichment analysis showed that MYBL1 can activate multiple oncogenic pathways in ccRCC. Moreover, we found that MYBL1 can remodel the immune microenvironment of ccRCC and affect the immunotherapy response. In vitro and in vivo assays indicated that MYBL1 was upregulated in ccRCC cells and can promote cellular malignant behaviors of ccRCC. Ultimately, an machine learning algorithm - LASSO logistics regression was utilized to identify a prognosis signature based on the MYBL1-derived molecules, which showed satisfactory prediction ability on patient prognosis in both training and validation cohorts. Conclusions Our result indicated that MYBL1 is a novel biomarker of ccRCC, which can remodel the tumor microenvironment, affect immunotherapy response and guide precision medicine in ccRCC.
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Affiliation(s)
- Tengda Wang
- Urology Surgery Department, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wengang Jian
- Urology Surgery Department, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei Xue
- Urology Surgery Department, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yuyang Meng
- Urology Surgery Department, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhinan Xia
- Urology Surgery Department, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qinchen Li
- The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Shenhao Xu
- The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Dong
- The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Anli Mao
- The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Cheng Zhang
- Urology Surgery Department, The First Affiliated Hospital of Harbin Medical University, Harbin, China,The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang, China,*Correspondence: Cheng Zhang,
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Integrated Analysis of the Role of Enolase 2 in Clear Cell Renal Cell Carcinoma. DISEASE MARKERS 2022; 2022:6539203. [DOI: 10.1155/2022/6539203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/13/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022]
Abstract
Enolase 2 (ENO2) has increasingly been documented in multiple cancers in recent years. However, the role of ENO2 in clear cell renal carcinoma (ccRCC) has not been fully explored. In the present study, open-access data were downloaded from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and the Human Protein Atlas (HPA) databases. All statistical analyses were performed in R and GraphPad Prism 8 softwares. Results showed that ENO2 was overexpressed in ccRCC tissues and cell lines and correlated with worse clinical features and prognosis. In vitro experiments indicated that the inhibition of ENO2 could hamper the malignant behaviors of ccRCC cells. Gene Set Enrichment Analysis showed that epithelial-mesenchymal transition, KRAS signaling, inflammatory response, angiogenesis, hypoxia, and WNT/β-catenin pathways were upregulated in the ENO2 high-expression group; whereas adipogenesis, DNA repair, and androgen response pathways were downregulated. Immune infiltration analysis indicated that patients with high ENO2 levels might have higher M2 macrophages and lower γβ T cells in the tumor microenvironment, which may account to some extent for the worse prognosis of ENO2. Moreover, it was found that patients with low and high ENO2 expression might be more sensitive to PD-1 therapy and CTLA-4 therapy, respectively. In addition, patients with high ENO2 expression showed lower sensitivity to common chemotherapy drugs for ccRCC, including axitinib, cisplatin, gemcitabine, pazopanib, sunitinib, and temsirolimus. Overall, these results suggest that ENO2 is a potential prognosis biomarker of ccRCC and could affect the malignant biological behavior of cancer cells, highlighting its value as a potential therapeutic target.
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Wang Q, Zhang X, Du K, Wu X, Zhou Y, Chen D, Zeng L. Machine learning identifies characteristics molecules of cancer associated fibroblasts significantly correlated with the prognosis, immunotherapy response and immune microenvironment in lung adenocarcinoma. Front Oncol 2022; 12:1059253. [PMID: 36439484 PMCID: PMC9682016 DOI: 10.3389/fonc.2022.1059253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/24/2022] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a highly lethal disease with a dramatic pro-fibrocytic response. Cancer-associated fibroblasts (CAFs) have been reported to play a key role in lung adenocarcinoma. METHODS Marker genes of CAFs were obtained from the Cell Marker website. Single sample gene set enrichment analysis (ssGSEA) was used for CAFs quantification. R and GraphPad Prism software were utilized for all analysis. Quantitative real-time PCR (qRT-PCR) was utilized to detect the RNA level of specific molecules. RESULTS Based on the ssGSEA algorithm and obtained CAFs markers, the LUAD patients with low- and high-CAFs infiltration were successfully identified, which had different response patterns to immunotherapy. Through the machine learning algorithm - LASSO logistic regression, we identified 44 characteristic molecules of CAFs. Furthermore, a prognosis signature consisting of seven characteristic genes was established, which showed great prognosis prediction ability. Additionally, we found that patients in the low-risk group might have better outcomes when receiving immunotherapy of PD-1, but not CTLA4. Also, the biological enrichment analysis revealed that immune response-related pathways were significantly associated with CAFs infiltration. Meanwhile, we investigated the underlying biological and microenvironment difference in patients with high- and low-risk groups. Finally, we identified that AMPD1 might be a novel target for LUAD immunotherapy. Patients with a high level of AMPD1 were correlated with worse responses to immunotherapy. Moreover, immunohistochemistry showed that the protein level of AMPD1 was higher in lung cancer. Results of qRT-PCR demonstrated that AMPD1 was upregulated in A549 cells compared with BEAS-2B. Meanwhile, we found that the knockdown of AMPD4 can significantly reduce the expression of CTLA4 and PDCD1, but not CD274 and PDCD1LG2. CONCLUSION We comprehensively explored the role of CAFs and its characteristics molecules in LUAD immunotherapy and developed an effective signature to indicate patients prognosis and immunotherapy response. Moreover, AMPD1 was identified as a novel target for lung cancer immunotherapy.
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Affiliation(s)
- Qian Wang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xunlang Zhang
- Department of Geriatric, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Kangming Du
- Department of Vascular Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xinhui Wu
- Department of Geriatric, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yexin Zhou
- Guangxi University of Chinese Medicine, Nanning, China
| | - Diang Chen
- Department of Urology Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Lin Zeng
- Department of Neurosurgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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Xiang Y, Zheng G, Zhong J, Sheng J, Qin H. Advances in Renal Cell Carcinoma Drug Resistance Models. Front Oncol 2022; 12:870396. [PMID: 35619895 PMCID: PMC9128023 DOI: 10.3389/fonc.2022.870396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Renal cell carcinoma (RCC) is the most common form of kidney cancer. Systemic therapy is the preferred method to eliminate residual cancer cells after surgery and prolong the survival of patients with inoperable RCC. A variety of molecular targeted and immunological therapies have been developed to improve the survival rate and prognosis of RCC patients based on their chemotherapy-resistant properties. However, owing to tumor heterogeneity and drug resistance, targeted and immunological therapies lack complete and durable anti-tumor responses; therefore, understanding the mechanisms of systemic therapy resistance and improving clinical curative effects in the treatment of RCC remain challenging. In vitro models with traditional RCC cell lines or primary cell culture, as well as in vivo models with cell or patient-derived xenografts, are used to explore the drug resistance mechanisms of RCC and screen new targeted therapeutic drugs. Here, we review the established methods and applications of in vivo and in vitro RCC drug resistance models, with the aim of improving our understanding of its resistance mechanisms, increasing the efficacy of combination medications, and providing a theoretical foundation for the development and application of new drugs, drug screening, and treatment guidelines for RCC patients.
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Affiliation(s)
- Yien Xiang
- Department of Hepatobiliary and Pancreatic Surgery, Second Hospital of Jilin University, Changchun, China
| | - Ge Zheng
- Department of Hepatobiliary and Pancreatic Surgery, Second Hospital of Jilin University, Changchun, China
| | - Jianfeng Zhong
- Department of Clinical Laboratory, Second Hospital of Jilin University, Changchun, China
| | - Jiyao Sheng
- Department of Hepatobiliary and Pancreatic Surgery, Second Hospital of Jilin University, Changchun, China
| | - Hanjiao Qin
- Department of Radiotherapy, The Second Hospital of Jilin University, Changchun, China
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Du S, Zhong Y, Zheng S, Lyu J. Analysis and Prediction of the Survival Trends of Patients with Clear-Cell Renal Cell Carcinoma: A Model-Based Period Analysis, 2001-2015. Cancer Control 2022; 29:10732748221121226. [PMID: 35981235 PMCID: PMC9393668 DOI: 10.1177/10732748221121226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background Clear-cell renal cell carcinoma (ccRCC) is one of the most common malignant
tumors worldwide whose poor prognosis results in a serious disease burden on
patients. The changing trend of the long-term relative survival rates (RSRs)
of patients with ccRCC was analyzed in this study to evaluate their
treatment results over a 15-year period. Methods This study is a retrospective study, which assessed and predicted the 1-, 3-,
and 5-year survival rates of patients with ccRCC during 2001-2005,
2006-2010, 2011-2015, and 2016-2020 using data extracted from the
Surveillance, Epidemiology, and End Results (SEER) database. Period analysis
was used in this study to analyze the data from the SEER database and to
assess survival differences according to age, sex, race, and socioeconomic
status (SES) during the 15-year study period by comparing Kaplan-Meier
curves. Results During 2001-2015, the 5-year RSR of patients with ccRCC increased from 78.4%
to 83.0%, and the generalized linear model predicted that the 5-year RSR
increased to 85.7% during 2016-2020. The RSR of patients with ccRCC differed
significantly with SES, race, sex, and age. Compared with male patients, the
survival advantage of female patients decreased as their age increased. The
RSR of all patients with ccRCC was also lower in patients with a lower SES
and of black race. Conclusion This study found an improvement in the RSR of patients with ccRCC during
2001-2020. Understanding the change trend of the survival rate of patients
with ccRCC is helpful to improve the design of clinical trials. It also
provides basic data and a scientific basis for evaluating the harm of ccRCC
on the health of affected patients and the effect of cancer prevention, and
developing cancer prevention plans.
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Affiliation(s)
- Sicong Du
- Zhongshan School of Medicine, 74644Sun Yat-sen University, Guangzhou, People's Republic of China.,Department of Clinical Research, 107652The First Affiliated Hospital of Jinan University, Guangzhou, People's Republic of China
| | - Yu Zhong
- School of Public Health, 107652Shaanxi University of Chinese Medicine, Xianyang, People's Republic of China
| | - Shuai Zheng
- School of Public Health, 107652Shaanxi University of Chinese Medicine, Xianyang, People's Republic of China
| | - Jun Lyu
- Department of Clinical Research, 107652The First Affiliated Hospital of Jinan University, Guangzhou, People's Republic of China
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Identification of four hub genes in venous thromboembolism via weighted gene coexpression network analysis. BMC Cardiovasc Disord 2021; 21:577. [PMID: 34861826 PMCID: PMC8642897 DOI: 10.1186/s12872-021-02409-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/26/2021] [Indexed: 11/13/2022] Open
Abstract
Background The pathogenic mechanisms of venous thromboembolism (VT) remain to be defined. This study aimed to identify differentially expressed genes (DEGs) that could serve as potential therapeutic targets for VT. Methods Two human datasets (GSE19151 and GSE48000) were analyzed by the robust rank aggregation method. Gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were conducted for the DEGs. To explore potential correlations between gene sets and clinical features and to identify hub genes, we utilized weighted gene coexpression network analysis (WGCNA) to build gene coexpression networks incorporating the DEGs. Then, the levels of the hub genes were analyzed in the GSE datasets. Based on the expression of the hub genes, the possible pathways were explored by gene set enrichment analysis and gene set variation analysis. Finally, the diagnostic value of the hub genes was assessed by receiver operating characteristic (ROC) analysis in the GEO database. Results In this study, we identified 54 upregulated and 10 downregulated genes that overlapped between normal and VT samples. After performing WGCNA, the magenta module was the module with the strongest negative correlation with the clinical characteristics. From the key module, FECH, GYPA, RPIA and XK were chosen for further validation. We found that these genes were upregulated in VT samples, and high expression levels were related to recurrent VT. Additionally, the four hub genes might be highly correlated with ribosomal and metabolic pathways. The ROC curves suggested a diagnostic value of the four genes for VT. Conclusions These results indicated that FECH, GYPA, RPIA and XK could be used as promising biomarkers for the prognosis and prediction of VT. Supplementary Information The online version contains supplementary material available at 10.1186/s12872-021-02409-4.
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