1
|
Ajadee A, Mahmud S, Hossain MB, Ahmmed R, Ali MA, Reza MS, Sarker SK, Mollah MNH. Screening of differential gene expression patterns through survival analysis for diagnosis, prognosis and therapies of clear cell renal cell carcinoma. PLoS One 2024; 19:e0310843. [PMID: 39348357 PMCID: PMC11441673 DOI: 10.1371/journal.pone.0310843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 09/02/2024] [Indexed: 10/02/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of kidney cancer. Although there is increasing evidence linking ccRCC to genetic alterations, the exact molecular mechanism behind this relationship is not yet completely known to the researchers. Though drug therapies are the best choice after the metastasis, unfortunately, the majority of the patients progressively develop resistance against the therapeutic drugs after receiving it for almost 2 years. In this case, multi-targeted different variants of therapeutic drugs are essential for effective treatment against ccRCC. To understand molecular mechanisms of ccRCC development and progression, and explore multi-targeted different variants of therapeutic drugs, it is essential to identify ccRCC-causing key genes (KGs). In order to obtain ccRCC-causing KGs, at first, we detected 133 common differentially expressed genes (cDEGs) between ccRCC and control samples based on nine (9) microarray gene-expression datasets with NCBI accession IDs GSE16441, GSE53757, GSE66270, GSE66272, GSE16449, GSE76351, GSE66271, GSE71963, and GSE36895. Then, we filtered these cDEGs through survival analysis with the independent TCGA and GTEx database and obtained 54 scDEGs having significant prognostic power. Next, we used protein-protein interaction (PPI) network analysis with the reduced set of 54 scDEGs to identify ccRCC-causing top-ranked eight KGs (PLG, ENO2, ALDOB, UMOD, ALDH6A1, SLC12A3, SLC12A1, SERPINA5). The pan-cancer analysis with KGs based on TCGA database showed the significant association with different subtypes of kidney cancers including ccRCC. The gene regulatory network (GRN) analysis revealed some crucial transcriptional and post-transcriptional regulators of KGs. The scDEGs-set enrichment analysis significantly identified some crucial ccRCC-causing molecular functions, biological processes, cellular components, and pathways that are linked to the KGs. The results of DNA methylation study indicated the hypomethylation and hyper-methylation of KGs, which may lead the development of ccRCC. The immune infiltrating cell types (CD8+ T and CD4+ T cell, B cell, neutrophil, dendritic cell and macrophage) analysis with KGs indicated their significant association in ccRCC, where KGs are positively correlated with CD4+ T cells, but negatively correlated with the majority of other immune cells, which is supported by the literature review also. Then we detected 10 repurposable drug molecules (Irinotecan, Imatinib, Telaglenastat, Olaparib, RG-4733, Sorafenib, Sitravatinib, Cabozantinib, Abemaciclib, and Dovitinib.) by molecular docking with KGs-mediated receptor proteins. Their ADME/T analysis and cross-validation with the independent receptors, also supported their potent against ccRCC. Therefore, these outputs might be useful inputs/resources to the wet-lab researchers and clinicians for considering an effective treatment strategy against ccRCC.
Collapse
Affiliation(s)
- Alvira Ajadee
- Department of Statistics, Bioinformatics Lab (Dry), University of Rajshahi, Rajshahi, Bangladesh
| | - Sabkat Mahmud
- Department of Statistics, Bioinformatics Lab (Dry), University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Bayazid Hossain
- Department of Statistics, Bioinformatics Lab (Dry), University of Rajshahi, Rajshahi, Bangladesh
- Department of Agricultural and Applied Statistics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Reaz Ahmmed
- Department of Statistics, Bioinformatics Lab (Dry), University of Rajshahi, Rajshahi, Bangladesh
- Department of Biochemistry & Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Ahad Ali
- Department of Statistics, Bioinformatics Lab (Dry), University of Rajshahi, Rajshahi, Bangladesh
- Department of Chemistry, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Selim Reza
- Department of Statistics, Bioinformatics Lab (Dry), University of Rajshahi, Rajshahi, Bangladesh
- Center for Biomedical Informatics & Genomics, School of Medicine, Tulane University, New Orleans, LA, United States of America
| | - Saroje Kumar Sarker
- Department of Statistics, Bioinformatics Lab (Dry), University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Nurul Haque Mollah
- Department of Statistics, Bioinformatics Lab (Dry), University of Rajshahi, Rajshahi, Bangladesh
| |
Collapse
|
2
|
Wang K, Ding Y, Liu Y, Ma M, Wang J, Kou Z, Liu S, Jiang B, Hou S. CPA4 as a biomarker promotes the proliferation, migration and metastasis of clear cell renal cell carcinoma cells. J Cell Mol Med 2024; 28:e18165. [PMID: 38494845 PMCID: PMC10945090 DOI: 10.1111/jcmm.18165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/07/2024] [Accepted: 01/24/2024] [Indexed: 03/19/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a commonly occurring and highly aggressive urological malignancy characterized by a significant mortality rate. Current therapeutic options for advanced ccRCC are limited, necessitating the discovery of novel biomarkers and therapeutic targets. Carboxypeptidase A4 (CPA4) is a zinc-containing metallocarboxypeptidase with implications in various cancer types, but its role in ccRCC remains unexplored. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were utilized in order to investigate the differential expression patterns of CPA4. The expression of CPA4 in ccRCC patients was further verified using immunohistochemical (IHC) examination of 24 clinical specimens. A network of protein-protein interactions (PPI) was established, incorporating CPA4 and its genes that were expressed differentially. Functional enrichment analyses were conducted to anticipate the contribution of CPA4 in the development of ccRCC. To validate our earlier study, we conducted real-time PCR and cell functional tests on ccRCC cell lines. Our findings revealed that CPA4 is overexpressed in ccRCC, and the higher the expression of CPA4, the worse the clinical outcomes such as TNM stage, pathological stage, histological grade, etc. Moreover, patients with high CPA4 expression had worse overall survival, disease-specific survival and progress-free interval than patients with low expression. The PPI network analysis highlighted potential interactions contributing to ccRCC progression. Functional enrichment analysis indicated the involvement of CPA4 in the regulation of key pathways associated with ccRCC development. Additionally, immune infiltration analysis suggested a potential link between CPA4 expression and immune response in the tumour microenvironment. Finally, cell functional studies in ccRCC cell lines shed light on the molecular mechanisms underlying the role of CPA4 in promoting ccRCC formation. Overall, our study unveils CPA4 as a promising biomarker with prognostic potential in ccRCC. The identified interactions and pathways provide valuable insights into its implications in ccRCC development and offer a foundation for future research on targeted therapies. Further investigation of CPA4's involvement in immune responses may contribute to the development of immunotherapeutic strategies for ccRCC treatment.
Collapse
Affiliation(s)
- Kongjia Wang
- Department of UrologyQingdao Municipal HospitalQingdao UniversityQingdaoChina
| | - Yixin Ding
- Department of OncologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Yunbo Liu
- Department of UrologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Mingyu Ma
- Department of UrologyQingdao Municipal HospitalQingdao UniversityQingdaoChina
| | - Ji Wang
- Department of UrologyQingdao Municipal HospitalQingdao UniversityQingdaoChina
| | - Zengshun Kou
- Department of UrologyQingdao Municipal HospitalQingdao UniversityQingdaoChina
| | - Shuo Liu
- Department of UrologyQingdao Municipal HospitalQingdao UniversityQingdaoChina
| | - Bo Jiang
- Department of UrologyQingdao Municipal HospitalQingdao UniversityQingdaoChina
| | - Sichuan Hou
- Department of UrologyQingdao Municipal HospitalQingdao UniversityQingdaoChina
| |
Collapse
|
3
|
Zhu YF, Liu ML, Zheng WT, Fu F, Xue ES, Fan XQ, Zhang HP, Lian GT, Ye Q. Predictive Model of CK7 Expression in Patients With Clear Cell Renal Cell Carcinoma by Combined Multimodal Ultrasound Diagnostic Techniques: A Retrospective Study. ULTRASOUND IN MEDICINE & BIOLOGY 2024; 50:520-527. [PMID: 38281886 DOI: 10.1016/j.ultrasmedbio.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/18/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024]
Abstract
OBJECTIVE The aim of the work described here was to develop and validate a predictive model for cytokeratin 7 (CK7) expression in clear cell renal cell carcinoma (ccRCC) patients by combining multimodal ultrasound diagnostic techniques. METHODS This retrospective study enrolled 157 surgically confirmed ccRCC patients. All patients underwent pre-operative multimodal ultrasound diagnostic examinations, including B-mode ultrasound (US), color Doppler flow imaging (CDFI) and contrast-enhanced ultrasound (CEUS). The patients were randomly divided into a training group (103 cases) and a testing group (54 cases). Univariate and multivariate logistic regression analyses were performed in the training group to identify independent indicators associated with CK7 positivity. These indicators were included in the predictive model. Receiver operating characteristic (ROC) curves and calibration curves were used to evaluate the model's discriminative ability and accuracy. Decision curve analysis (DCA) and nomogram visualization were used to assess the clinical utility of the predictive model. RESULTS Univariate logistic regression analysis revealed that US and CDFI observations were not correlated with CK7 expression and could not predict it. Multivariate logistic regression analysis identified age (odds ratio [OR] = 0.953, 95% confidence interval [CI]: 0.909-0.999), wash-in pattern (OR = 0.180, 95% CI: 0.063-0.513) and enhancement homogeneity (OR = 11.610, 95% CI: 1.394-96.675) as independent factors related to CK7 positivity in ccRCC. Incorporating these variables into the predictive model resulted in areas under the receiver operating characteristic curve of 0.812 (95% CI: 0.711-0.913) for the training group and 0.792 (95% CI: 0.667-0.924) for the testing group. The calibration curve and DCA revealed that the model had good accuracy and clinical utility of the model. CONCLUSION The combination of multimodal ultrasound diagnostic techniques in constructing a predictive model for CK7 expression in ccRCC patients has significant predictive value.
Collapse
Affiliation(s)
- Yi-Fan Zhu
- Department of Ultrasound/Fujian Provincial Institute of Ultrasonic Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Mao-Lin Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Wen-Ting Zheng
- Department of Ultrasound/Fujian Provincial Institute of Ultrasonic Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Fen Fu
- Department of Ultrasound/Fujian Provincial Institute of Ultrasonic Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - En-Sheng Xue
- Department of Ultrasound/Fujian Provincial Institute of Ultrasonic Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Xiao-Qing Fan
- Department of Ultrasound/Fujian Provincial Institute of Ultrasonic Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Hui-Ping Zhang
- Department of Ultrasound/Fujian Provincial Institute of Ultrasonic Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Guang-Tian Lian
- Department of Ultrasound/Fujian Provincial Institute of Ultrasonic Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China
| | - Qin Ye
- Department of Ultrasound/Fujian Provincial Institute of Ultrasonic Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian Province, China.
| |
Collapse
|
4
|
Xiang J, Liu W, Liu S, Wang T, Tang H, Yang J. Deciphering the implications of mitophagy-related signatures in clinical outcomes and microenvironment heterogeneity of clear cell renal cell carcinoma. J Cancer Res Clin Oncol 2023; 149:16015-16030. [PMID: 37689589 DOI: 10.1007/s00432-023-05349-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/25/2023] [Indexed: 09/11/2023]
Abstract
BACKGROUND The role of mitophagy in various cancer-associated biological processes is well recognized. Nonetheless, the comprehensive implications of mitophagy in clear cell renal cell carcinoma (ccRCC) necessitate further exploration. METHODS Based on the transcriptomic data encompassing 25 mitophagy-related genes (MRGs), we identified the distinct mitophage patterns in 763 ccRCC samples. Subsequently, a mitophage-related predictive signature with machine learning algorithms was constructed, designated as RiskScore, to quantify the individual mitophagy status in ccRCC patients. Employing multispectral immunofluorescence (mIF) and immunohistochemistry (IHC) staining, we detected the effect of PTEN-induced putative kinase 1 (PINK1) in the prognosis and immune microenvironment of ccRCC. RESULTS Our analysis initially encompassed a comprehensive assessment of the expression profiling, genomic variations, and interactions among the 25 MRGs in ccRCC. Subsequently, the consensus clustering algorithm was applied to stratify ccRCC patients into three clusters with distinct prognostic outcomes, tumor microenvironment (TME) characteristics, and underlying biological pathways. We screened eight pivotal genes (CLIC4, PTPRB, SLC16A12, ENPP5, FLRT3, HRH2, PDK4, and SCD5) to construct a mitophagy-related predictive signature, which showed excellent prognostic value for ccRCC patients. Moreover, patient subgroups divided by the RiskScore showed contrasting expression levels of immune checkpoints (ICPs), abundance of immune cells, and immunotherapy response. Additionally, a nomogram was established with robust predictive power integrating the RiskScore and clinical features. Notably, we observed that PINK1 expression markedly correlated with favorable treatment response and advanced maturation stages of tertiary lymphoid structures, which potentially shed light on enhancing anti-tumor immunity of ccRCC. CONCLUSION Collectively, this study initially developed a signature associated with mitophagy, which demonstrated an excellent ability to predict the clinical prognosis, TME characterization, and responsiveness to targeted therapy and immunotherapy for ccRCC patients. Of particular note is the pivotal role of PINK1 in mediating the treatment response and immune microenvironment for ccRCC patients.
Collapse
Affiliation(s)
- Jianfeng Xiang
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wangrui Liu
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shifan Liu
- Department of Medical Imaging, Medical School of Nantong University, Nantong, China
| | - Tao Wang
- Department of Interventional Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Haidan Tang
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.
| | - Jianfeng Yang
- Department of Surgery, Shangnan Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| |
Collapse
|
5
|
Pu Y, Cai D, Jin L, Xu F, Ye E, Wu L, Mo L, Liu S, Guo Q, Wu G. TREM-1 as a potential prognostic biomarker associated with immune infiltration in clear cell renal cell carcinoma. World J Surg Oncol 2023; 21:156. [PMID: 37217993 DOI: 10.1186/s12957-023-03013-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND The tumor immune microenvironment plays a crucial role in the efficacy of various therapeutics. However, their correlation is not yet completely understood in Clear cell renal cell carcinoma (ccRCC). This study aimed to investigate the potential of TREM-1 as a potential novel biomarker for ccRCC. METHODS We constructed a ccRCC immune prognostic signature. The clinical characteristics, the status of the tumor microenvironment, and immune infiltration were analyzed through the ESTIMATE and CIBERSORT algorithms for the hub gene, while the Gene Set Enrichment Analysis and PPI analysis were performed to predict the function of the hub gene. Immunohistochemical staining was used to detect the expression of TREM-1 in renal clear cell carcinoma tissues. RESULTS The CIBERSORT and ESTIMATE algorithms revealed that TREM-1 was correlated with the infiltration of 12 types of immune cells. Therefore, it was determined that TREM-1 was involved in numerous classical pathways in the immune response via GSEA analysis. In Immunohistochemical staining, we found that the expression of TREM-1 was significantly upregulated with increasing tumor grade in renal clear cell carcinoma, and elevated TREM-1 expression was associated with poor prognosis. CONCLUSIONS The results suggest that TREM-1 may act as an implicit novel prognostic biomarker in ccRCC that could be utilized to facilitate immunotherapeutic strategy.
Collapse
Affiliation(s)
- Yaling Pu
- Taizhou Hospital of Zhejiang Province, Shao Xing University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China
| | - Danyang Cai
- Department of Radiation Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China
| | - Lingling Jin
- Department of Pathology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China
| | - Fenfen Xu
- Department of Pharmacy, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China
| | - Enru Ye
- Department of Pathology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China
| | - Lina Wu
- Department of Pathology, Enze Hospital, Taizhou Enze Medical Center, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China
| | - Licai Mo
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China
| | - Suzhi Liu
- Taizhou Hospital of Zhejiang Province, Shao Xing University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China.
- Department of Neurology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China.
| | - Qunyi Guo
- Department of Hematology and Oncology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China.
| | - Gang Wu
- Department of Pharmacy, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 Ximen Street, TaizhouZhejiang, 317000, Linhai, China.
| |
Collapse
|
6
|
Liu Y, Shi Z, Zheng J, Zheng Z, Sun H, Xuan Z, Bai Y, Fu M, Du Y, Shao C. Establishment and validation of a novel anoikis-related prognostic signature of clear cell renal cell carcinoma. Front Immunol 2023; 14:1171883. [PMID: 37056778 PMCID: PMC10086373 DOI: 10.3389/fimmu.2023.1171883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
BackgroundDespite progression in its treatment, the clinical outcome of patients with clear cell renal cell carcinoma (ccRCC) remains not ideal. Anoikis is a unique form of programmed apoptosis, owing to insufficient cell-matrix interactions. Anoikis plays a crucial role in tumor migration and invasion, and tumor cells could protect themselves through the capacity of anoikis resistance.MethodsAnoikis-related genes (ARGs) were obtained from Genecards and Harmonizome portals. The ARGs related to ccRCC prognosis were identified through univariate Cox regression analysis, then we utilized these ARGs to construct a novel prognostic model for ccRCC patients. Moreover, we explored the expression profile of ARGs in ccRCC using the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database. We also conducted Real-Time Polymerase Chain Reaction (RT-PCR) to probe ARGs expression of the risk score. Finally, we performed correlation analysis between ARGs and tumor immune microenvironment.ResultsWe identified 17 ARGs associated with ccRCC survival, from which 7 genes were chosen to construct a prognostic model. The prognostic model was verified as an independent prognostic indicator. The expression of most ARGs was higher in ccRCC samples. These ARGs were closely correlated with immune cell infiltration and immune checkpoint members, and had independent prognostic value respectively. Functional enrichment analysis demonstrated that these ARGs were significantly associated with multiple types of malignances.ConclusionThe prognostic signature was identified to be highly efficient in predicting ccRCC prognosis, and these ARGs were closely related to tumor microenvironment.
Collapse
Affiliation(s)
- Yankuo Liu
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Zhiyuan Shi
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jianzhong Zheng
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Zeyuan Zheng
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Huimin Sun
- Central Laboratory, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Zuodong Xuan
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yang Bai
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Meiling Fu
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yifan Du
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chen Shao
- Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- *Correspondence: Chen Shao,
| |
Collapse
|
7
|
Yang L, Yu Q, Zhu Y, Ali Mallah M, Wang W, Feng F, Zhang Q. Core genes in lung adenocarcinoma identified by integrated bioinformatic analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2023; 33:243-257. [PMID: 34961365 DOI: 10.1080/09603123.2021.2016660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
This study aims to identify potential core genes of lung adenocarcinoma (LUAD). Three datasets (GSE32863, GSE43458, and GSE116959) were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between LUAD and normal tissues were filtrated by GEO2R tool. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed via Metascape database. The protein-protein interaction (PPI) network was constructed and core genes were identified using STRING and Cytoscape. Core genes expressions and their relevant clinical characteristics were performed via Oncomine and UALCAN databases respectively. The correlation between core genes and immune infiltrates was investigated by TIMER database. Kaplan-Meier plotter was performed for survival analysis. The signal pathway network of core genes was mapped by KEGG Mapper analysis tool. In this study, ten core genes were significantly related to overall survival (OS) of LUAD patients, which can provide clues for prognosis of LUAD.
Collapse
Affiliation(s)
- Liu Yang
- Department of Toxicology, College of Public Health, Zhengzhou University, Zhongyuan District, Zhengzhou, Henan Province, China
| | - Qi Yu
- Department of Toxicology, College of Public Health, Zhengzhou University, Zhongyuan District, Zhengzhou, Henan Province, China
| | - Yonghang Zhu
- Department of Toxicology, College of Public Health, Zhengzhou University, Zhongyuan District, Zhengzhou, Henan Province, China
| | - Manthar Ali Mallah
- Department of Toxicology, College of Public Health, Zhengzhou University, Zhongyuan District, Zhengzhou, Henan Province, China
| | - Wei Wang
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhongyuan District, Zhengzhou, Henan Province, China
| | - Feifei Feng
- Department of Toxicology, College of Public Health, Zhengzhou University, Zhongyuan District, Zhengzhou, Henan Province, China
| | - Qiao Zhang
- Department of Toxicology, College of Public Health, Zhengzhou University, Zhongyuan District, Zhengzhou, Henan Province, China
| |
Collapse
|
8
|
Chen S, Ding H, Wang K, Guo K. Inhibition of Wnt7b reduces the proliferation, invasion, and migration of colorectal cancer cells. Mol Biol Rep 2023; 50:1415-1424. [PMID: 36472725 DOI: 10.1007/s11033-022-08106-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Colorectal cancer is one of the most common gastrointestinal tumors. The role of Wnt7b as a ligand of the Wnt signaling pathway in colorectal cancer remains to be studied. Through bioinformatics online analysis, we found that Wnt7b is abnormally highly expressed in a variety of gastrointestinal tumors. This study mainly explored the effects of Wnt7b regulating the Wnt/β-catenin signaling pathway on the proliferation, migration, and invasion of SW480 cells in colorectal cancer. METHODS AND RESULTS Applying the TCGA data set, Wnt7b was found to be highly expressed in most gastrointestinal tumor samples. Real-time quantitative PCR(q-PCR), Western blotting(WB) results showed that Wnt7b was significantly higher expressed in colorectal cancer cell lines compared with normal intestinal epithelial cells. SW480 cells transfected with the sh-Wnt7b showed successful knockdown of Wnt7b. MTT colorimetry showed the proliferation ability of sh-Wnt7b group decreased significantly compared with the non-transfected group. The results of double staining flow cytometry showed that the sh-Wnt7b group had more apoptosis. Cell scratch test showed that the cell migration rate of sh-wnt7b group considerably reduced. The Transwell invasion experiment demonstrated that the number of cell invasions in the sh-Wnt7b group decreased significantly. After SW480 cells was transfected with sh-Wnt7b, the protein levels of β-catenin, CCND1, and CD44 in this group of cells were detected to be reduced by WB, and the same results were obtained by q-PCR detection of mRNA. CONCLUSION Wnt7b is highly expressed in colorectal cancer cells, which may affect the proliferation, migration, and invasion of colorectal cancer cells by activating the Wnt/β-catenin signaling pathway.
Collapse
Affiliation(s)
- Siyang Chen
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, 430065, Wuhan, China
| | - Hui Ding
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, 430065, Wuhan, China
| | - Kaiyun Wang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, 430065, Wuhan, China
| | - Kaiwen Guo
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, 430065, Wuhan, China.
| |
Collapse
|
9
|
Renal Carcinoma and Angiogenesis: Therapeutic Target and Biomarkers of Response in Current Therapies. Cancers (Basel) 2022; 14:cancers14246167. [PMID: 36551652 PMCID: PMC9776425 DOI: 10.3390/cancers14246167] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Due to the aberrant hypervascularization and the high immune infiltration of renal tumours, current therapeutic regimens of renal cell carcinoma (RCC) target angiogenic or immunosuppressive pathways or both. Tumour angiogenesis plays an essential role in tumour growth and immunosuppression. Indeed, the aberrant vasculature promotes hypoxia and can also exert immunosuppressive functions. In addition, pro-angiogenic factors, including VEGF-A, have an immunosuppressive action on immune cells. Despite the progress of treatments in RCC, there are still non responders or acquired resistance. Currently, no biomarkers are used in clinical practice to guide the choice between the different available treatments. Considering the role of angiogenesis in RCC, angiogenesis-related markers are interesting candidates. They have been studied in the response to antiangiogenic drugs (AA) and show interest in predicting the response. They have been less studied in immunotherapy alone or combined with AA. In this review, we will discuss the role of angiogenesis in tumour growth and immune escape and the place of angiogenesis-targeted biomarkers to predict response to current therapies in RCC.
Collapse
|
10
|
Xia W, Zeng C, Zheng Z, Huang C, Zhou Y, Bai L. Development and Validation of a Novel Mitochondrion and Ferroptosis-Related Long Non-Coding RNA Prognostic Signature in Hepatocellular Carcinoma. Front Cell Dev Biol 2022; 10:844759. [PMID: 36036006 PMCID: PMC9413087 DOI: 10.3389/fcell.2022.844759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/20/2022] [Indexed: 11/22/2022] Open
Abstract
Mitochondrion and ferroptosis are related to tumorigenesis and tumor progression of hepatocellular carcinoma (HCC). Therefore, this study focused on exploring the participation of lncRNAs in mitochondrial dysfunction and ferroptosis using public datasets from The Cancer Genome Atlas (TCGA) database. We identified the mitochondrion- and ferroptosis-related lncRNAs by Pearson's analysis and lasso-Cox regression. Moreover, real-time quantitative reverse transcription PCR (RT-qPCR) was utilized to further confirm the abnormal expression of these lncRNAs. Based on eight lncRNAs, the MF-related lncRNA prognostic signature (LPS) with outstanding stratification ability and prognostic prediction capability was constructed. In addition, functional enrichment analysis and immune cell infiltration analysis were performed to explore the possible functions of lncRNAs and their impact on the tumor microenvironment. The pathways related to G2M checkpoint and MYC were activated, and the infiltration ratio of regulatory T cells and M0 and M2 macrophages was higher in the high-risk group. In conclusion, these lncRNAs may affect mitochondria functions, ferroptosis, and immune cell infiltration in HCC through specific pathways, which may provide valuable insight into the progression and therapies of HCC.
Collapse
Affiliation(s)
- Wuzheng Xia
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital/The First School of Clinical Medicine, Southem Medical University, Guangzhou, China
- Department of Organ Transplant, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cong Zeng
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital/The First School of Clinical Medicine, Southem Medical University, Guangzhou, China
- Department of General Practice, Hospital of South China Normal University, Guangzhou, China
| | - Zehao Zheng
- Department of Organ Transplant, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of General Surger, Shantou University of Medical College, Shantou, China
| | - Chunwang Huang
- Department of Ultrasound, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yu Zhou
- Department of Pancreatic Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Lan Bai
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital/The First School of Clinical Medicine, Southem Medical University, Guangzhou, China
| |
Collapse
|
11
|
Wu Z, Huang T. Bone Marrow Mesenchymal Stem Cell (BMSC)-Derived Exosomal miR-168-5p Inhibits Proliferation and Chemotherapy Resistance in Gastric Cancer by Downregulation of Cyclin D1 and P Glycoprotein. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.2912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
miR-168-5p is indicated as an upstream effector of the tumor suppressor signal pathway in ovarian cancer and bladder cancer, but the role in gastric cancer (GC) remains unknown. This study aims to reveal the expression and significance of miR-168-5p in GC. RT-qPCR analysis was used
to detect the expression of miR-168-5p in GC tissues and plasma, and the relationship of miR-168-5p and CCND1 was evaluated. GC cells were co-cultured with BMSCs or transfected with miR-168-5p mimic. CCK-8 assay and flow cytometry were conducted to assess the effect of miR-168-5p in GC and
the interaction between BMSCs and cancer cell progression. Animal experiment was established to explore the in vivo effect of miR-168-5p. miR-168-5p is poorly expressed in gastric cancer cells and the plasma of patients with gastric cancer. BMSC co-culture is similar to miR-168-5p mimic
induced miR-168-5p expression increase. miR-168-5p overexpression decreased the proliferative, invasive and migratory capacities of GC cells, and promoted apoptosis. Mechanically, miR-168-5p targeted and decreased the expression of CCND1. Additionally, the low miR-168-5p expression in GC was
closely related to poor prognosis and malignant transformation. BMSC exosomes carrying miR-168-5p suppress cell progression in GC when inhibiting the expression of CCND1 and P glycoprotein, which indicates potential diagnostic and prognostic value of miR-168-5p and helps the development of
miR-168-5p-based treatment for drug-resistant GC.
Collapse
Affiliation(s)
- ZhongXin Wu
- Department of General Surgery, Huzhou Central Hospital, Affiliated Cent Hospital HuZhou University, Huzhou City, Zhejiang Province, 313204, China
| | - Tianyi Huang
- Department of Anesthesia and Surgery, Huzhou Central Hospital, Affiliated Cent Hospital HuZhou University, Huzhou City, Zhejiang Province, 313204, China
| |
Collapse
|
12
|
Identification of heterogeneity and prognostic key genes associated with uveal melanoma using single-cell RNA-sequencing technology. Melanoma Res 2022; 32:18-26. [PMID: 34879031 DOI: 10.1097/cmr.0000000000000783] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Uveal melanoma (UM) is the most common intraocular malignancy in adults. The prognosis is poor once metastasis has developed. The treatment of metastatic UM remains challenging nowadays due to lacking a deep understanding of the biological characteristics of this disease. Here, we revealed the cell subpopulations with distinct functional status and the existence of cells with high invasive potential within heterogeneous primary and metastatic UM. The single-cell sequencing data were retrieved from GSE139829 and GSE138433, through which we identified a new cell cluster related to metastatic UM as a unique type of immune cell. The cell-cell communication was conducted by 'Cellchat' to understand the cell crosstalk between these immune cells and their surrounding cells. The crucial signals contributing most to outgoing or incoming signaling of this cell group were identified to reveal the crucial pathway genes. Furthermore, we judged the prognostic value of these candidates on the basis of the data downloaded from The Cancer Genome Atlas. The results demonstrated that the increased IL10, SELPLG, EPHB and ITGB2 signaling pathways could be promising predicting factors for the patient prognosis in UM. Conclusively, we discover the potential key signals of UM for occurrence and metastasis, and also provide a theoretical basis for judging whether there is a high risk of metastasis or recurrence.
Collapse
|
13
|
Guo F, Yan J, Ling G, Chen H, Huang Q, Mu J, Mo L. Screening and Identification of Key Biomarkers in Lower Grade Glioma via Bioinformatical Analysis. Appl Bionics Biomech 2022; 2022:6959237. [PMID: 35035531 PMCID: PMC8759910 DOI: 10.1155/2022/6959237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023] Open
Abstract
Lower-grade glioma (LGG) is a common type of central nervous system tumor. Due to its complicated pathogenesis, the choice and timing of adjuvant therapy after tumor treatment are controversial. This study explored and identified potential therapeutic targets for lower-grade. The bioinformatics method was employed to identify potential biomarkers and LGG molecular mechanisms. Firstly, we selected and downloaded GSE15824, GSE50161, and GSE86574 from the GEO database, which included 40 LGG tissue and 28 normal brain tissue samples. GEO and VENN software identified of 206 codifference expressed genes (DEGs). Secondly, we applied the DAVID online software to investigate the DEG biological function and KEGG pathway enrichment, as well as to build the protein interaction visualization network through Cytoscape and STRING website. Then, the MCODE plug is used in the analysis of 22 core genes. Thirdly, the 22 core genes were analyzed with UNCLA software, of which 18 genes were associated with a worse prognosis. Fourthly, GEPIA was used to analyze the 18 selected genes, and 14 genes were found to be a significantly different expression between LGGs and normal brain tumor samples. Fifthly, hierarchical gene clustering was used to examine the 14 important gene expression differences in different histologies, as well as analysis of the KEGG pathway. Five of these genes were shown to be abundant in the natural killer cell-mediated cytokines (NKCC) and phagosome pathways. The five key genes that may be affected by the immune microenvironment play a crucial role in LGG development.
Collapse
Affiliation(s)
- Fangzhou Guo
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jun Yan
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Guoyuan Ling
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hainan Chen
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qianrong Huang
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Junbo Mu
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ligen Mo
- Department of Neurosurgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China
| |
Collapse
|
14
|
Zhang J, Chen X, Wang J, Zhang P, Han X, Zhang Y, Wang Y, Yang X. Bioinformatics Analysis of Prognostic Value of SPC24 in ccRCC and Pan-Cancer. Int J Gen Med 2022; 15:817-836. [PMID: 35125884 PMCID: PMC8807948 DOI: 10.2147/ijgm.s348859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/31/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Clear cell renal cell carcinoma (ccRCC) is one of the most common diseases in the world, with high morbidity and mortality. Recent studies have revealed the important role of SPC24, a subunit of the Ndc80 complex, in the occurrence and development of carcinoma. However, the latent effect of SPC24 in the progress of ccRCC remains to be further explored. The intent of this research is to investigate whether SPC24 can be used as an index to predict the progression of ccRCC and to explore its relationship with the immune microenvironment and pan-cancer. Materials and Methods Based on data from public databases, we determined the expression level and clinical value of SPC24 in ccRCC and human pan-cancer. RT-qPCR analysis was carried out to detect the expression level of SPC24 in the OSRC/786O (human ccRCC cells) cell lines and HK2 (human normal kidney cells) cell line. The signal transduction pathways activated by different levels of SPC24 expression were explored by Gene Set Enrichment Analysis (GSEA), and the CIBERSORT algorithm was applied to analyze the relationship between infiltrating immune cells and SPC24 expression in ccRCC and pan-cancer tissues. Results SPC24 is overexpressed in ccRCC and several types of tumors, which is associated with poor prognosis. GSEA and CIBERSORT algorithms suggested that the high expression group of SPC24 enriched various pathways including immune-related pathways, and the several infiltrated immunocytes were related to the expression of SPC24. Conclusion Our study revealed that SPC24 is a prognostic factor in ccRCC related to immunomodulation and has generalized value in pan-cancer.
Collapse
Affiliation(s)
- Jipeng Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
| | - Xinlei Chen
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
| | - Jirong Wang
- Department of Urology, The Second Affiliated Hospital of Lanzhou University, Lanzhou, Gansu, People’s Republic of China
| | - Pengfei Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
| | - Xue Han
- Department of Oncology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, People’s Republic of China
| | - Youzhi Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
| | - Yonghua Wang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
- Correspondence: Yonghua Wang; Xiaokun Yang, Department of Urology, The Affiliated Hospital of Qingdao University, No. 16, Jiangsu Road, Shinan District, Qingdao, Shandong, 266071, People’s Republic of China, Email ;
| | - Xiaokun Yang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, People’s Republic of China
| |
Collapse
|
15
|
Xu Y, Kong D, Li Z, Qian L, Li J, Zou C. Screening and identification of key biomarkers of papillary renal cell carcinoma by bioinformatic analysis. PLoS One 2021; 16:e0254868. [PMID: 34358255 PMCID: PMC8345835 DOI: 10.1371/journal.pone.0254868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/05/2021] [Indexed: 12/05/2022] Open
Abstract
Background Papillary renal cell carcinoma (PRCC) is the most common type of renal cell carcinoma after clear cell renal cell carcinoma (ccRCC). Its pathological classification is controversial, and its molecular mechanism is poorly understood. Therefore, the identification of key genes and their biological pathways is of great significance to elucidate the molecular mechanisms of PRCC occurrence and progression. Methods The PRCC-related datasets GSE7023, GSE48352 and GSE15641 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified, and gene ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Cytoscape and STRING were used to construct the protein-protein interaction network (PPI) and perform module analysis to identify hub genes and key pathways. A heatmap of hub genes was constructed using the UCSC cancer genomics browser. Overall survival and recurrence-free survival of patients stratified by the expression levels of hub genes were analysed using Kaplan-Meier Plotter. The online database UALCAN was applied to analyse gene expression based on tissue type, stage, subtype and race. Results A total of 214 DEGs, specifically, 205 downregulated genes and 9 upregulated genes, were identified. The DEGs were mainly enriched in angiogenesis, kidney development, oxidation-reduction process, metabolic pathways, etc. The 17 hub genes identified were mainly enriched in the biological processes of angiogenesis, cell adhesion, platelet degranulation, and leukocyte transendothelial migration. Survival analysis showed that EGF, KDR, CXCL12, REN, PECAM1, CDH5, THY1, WT1, PLAU and DCN might be related to the carcinogenesis, metastasis or recurrence of PRCC. UALCAN analysis showed that low expression of PECAM1 and PLAU in PRCC tissues was related to stage, subtype and race. Conclusions The DEGs and hub genes identified in the present study provide insight into the specific molecular mechanisms of PRCC occurrence and development and may be potential molecular markers and therapeutic targets for the accurate classification and efficient diagnosis and treatment of PRCC.
Collapse
Affiliation(s)
- Yingying Xu
- Department of Nephrology, Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China
| | - Deyang Kong
- Department of Nephrology, Shenzhen Bao’an District Songgang People’s Hospital, Shenzhen, Guangdong, People’s Republic of China
- * E-mail: (CZ); (DK)
| | - Zhongtang Li
- Department of Pediatrics, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, People’s Republic of China
| | - Lingling Qian
- Department of Nephrology, Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China
| | - Junchao Li
- Department of Vasculocardiology Deparment, Taizhou Clinical Medical College of Nanjing Medical University (Taizhou People’s Hospital), Taizhou, Jiangsu, People’s Republic of China
| | - Chunbo Zou
- Department of Nephrology, Taizhou Clinical Medical College of Nanjing Medical University (Taizhou People’s Hospital), Taizhou, Jiangsu, People’s Republic of China
- * E-mail: (CZ); (DK)
| |
Collapse
|
16
|
Cheng X, Wang J, Lu S, Fan W, Wang W. Aurora kinase A (AURKA) promotes the progression and imatinib resistance of advanced gastrointestinal stromal tumors. Cancer Cell Int 2021; 21:407. [PMID: 34332577 PMCID: PMC8325869 DOI: 10.1186/s12935-021-02111-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/24/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Gastrointestinal stromal tumor (GIST) is a common tumor that originates from the alimentary system mesenchyme. Compared to typical gastrointestinal carcinomas, GISTs exhibit unique malignant behaviors. Bioinformatic tools and subsequent experiments were applied to investigate novel targets involved in GIST progression and imatinib resistance. METHODS Differences in gene expression profiles between advanced and nonadvanced GISTs were comprehensively analyzed based on the Gene Expression Omnibus (GEO) dataset GSE136755. A protein-protein interaction (PPI) network was constructed to identify the potential target gene. Gene set enrichment analysis (GSEA) was used to elucidate relevant biological events related to the target gene based on the GSE47911 dataset. Subsequently, immunohistochemistry and Kaplan-Meier analysis were performed to validate the prognostic value of the target gene in GISTs. Overexpression of the target gene was conducted to analyze its function in the proliferation, apoptosis, and imatinib resistance of GIST/T1 cells. RESULTS In the current study, a total of 606 differentially expressed genes (DEGs) were screened based on the GSE136755 dataset, and the upregulated DEGs in advanced GISTs were mainly involved in cell division through functional annotations. The intersecting hub gene, Aurora kinase A (AURKA), was identified by degree and bottleneck algorithms. GSEA revealed that AURKA was involved in cell cycle-related biological processes. Analysis of the Oncomine and GEPIA databases revealed a pattern of elevated AURKA expression in most human malignances. Clinical assays demonstrated that AURKA could be an independent prognostic factor for GISTs. Additionally, overexpression of AURKA was experimentally demonstrated to promote cell proliferation, inhibit cell apoptosis, and enhance imatinib resistance in GIST/T1 cells. CONCLUSIONS These findings indicated that overexpression of AURKA promoted GIST progression and enhanced imatinib resistance, implying that AURKA is a potential therapeutic target for GISTs.
Collapse
Affiliation(s)
- Xiaobin Cheng
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Jinhai Wang
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Sen Lu
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Weina Fan
- Department of Intensive Care Unit, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Weilin Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, #88 Jiefang Road, Hangzhou, Zhejiang, People's Republic of China.
| |
Collapse
|
17
|
Rausch M, Rutz A, Allard PM, Delucinge-Vivier C, Docquier M, Dormond O, Wolfender JL, Nowak-Sliwinska P. Molecular and Functional Analysis of Sunitinib-Resistance Induction in Human Renal Cell Carcinoma Cells. Int J Mol Sci 2021; 22:6467. [PMID: 34208775 PMCID: PMC8235637 DOI: 10.3390/ijms22126467] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/24/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023] Open
Abstract
Resistance in clear cell renal cell carcinoma (ccRCC) against sunitinib is a multifaceted process encompassing numerous molecular aberrations. This induces clinical complications, reducing the treatment success. Understanding these aberrations helps us to select an adapted treatment strategy that surpasses resistance mechanisms, reverting the treatment insensitivity. In this regard, we investigated the dominant mechanisms of resistance to sunitinib and validated an optimized multidrug combination to overcome this resistance. Human ccRCC cells were exposed to single or chronic treatment with sunitinib to obtain three resistant clones. Upon manifestation of sunitinib resistance, morphometric changes in the cells were observed. At the molecular level, the production of cell membrane and extracellular matrix components, chemotaxis, and cell cycle progression were dysregulated. Molecules enforcing the cell cycle progression, i.e., cyclin A, B1, and E, were upregulated. Mass spectrometry analysis revealed the intra- and extracellular presence of N-desethyl sunitinib, the active metabolite. Lysosomal sequestration of sunitinib was confirmed. After treatment with a synergistic optimized drug combination, the cell metabolic activity in Caki-1-sunitinib-resistant cells and 3D heterotypic co-cultures was reduced by >80%, remaining inactive in non-cancerous cells. These results demonstrate geno- and phenotypic changes in response to sunitinib treatment upon resistance induction. Mimicking resistance in the laboratory served as a platform to study drug responses.
Collapse
Affiliation(s)
- Magdalena Rausch
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland; (M.R.); (A.R.); (P.-M.A.); (J.-L.W.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1205 Geneva, Switzerland
| | - Adriano Rutz
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland; (M.R.); (A.R.); (P.-M.A.); (J.-L.W.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland; (M.R.); (A.R.); (P.-M.A.); (J.-L.W.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | | | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, 1206 Geneva, Switzerland; (C.D.-V.); (M.D.)
- Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Olivier Dormond
- Department of Visceral Surgery, Lausanne University Hospital and University of Lausanne, 1015 Lausanne, Switzerland;
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland; (M.R.); (A.R.); (P.-M.A.); (J.-L.W.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Patrycja Nowak-Sliwinska
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland; (M.R.); (A.R.); (P.-M.A.); (J.-L.W.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1205 Geneva, Switzerland
| |
Collapse
|
18
|
Wang L, Lu F, Xu J. Identification of Potential miRNA-mRNA Regulatory Network Contributing to Hypertrophic Cardiomyopathy (HCM). Front Cardiovasc Med 2021; 8:660372. [PMID: 34136543 PMCID: PMC8200816 DOI: 10.3389/fcvm.2021.660372] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/23/2021] [Indexed: 01/14/2023] Open
Abstract
Background: Hypertrophic cardiomyopathy (HCM) is a myocardial disease with unidentified pathogenesis. Increasing evidence indicated the potential role of microRNA (miRNA)-mRNA regulatory network in disease development. This study aimed to explore the miRNA-mRNA axis in HCM. Methods: The miRNA and mRNA expression profiles obtained from the Gene Expression Omnibus (GEO) database were used to identify differentially expressed miRNAs (DEMs) and genes (DEGs) between HCM and normal samples. Target genes of DEMs were determined by miRTarBase. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to identify biological functions of the DEGs and DEMs. miRNA-mRNA regulatory network was constructed to identify the hub genes and miRNAs. Logistic regression model for HCM prediction was established basing on the network. Results: A total of 224 upregulated and 366 downregulated DEGs and 10 upregulated and 14 downregulated DEMs were determined. We identified 384 DEM-targeted genes, and 20 of them were overlapped with the DEGs. The enriched functions include extracellular structure organization, organ growth, and phagosome and melanoma pathways. The four miRNAs and three mRNAs, including hsa-miR-373, hsa-miR-371-3p, hsa-miR-34b, hsa-miR-452, ARHGDIA, SEC61A1, and MYC, were identified through miRNA-mRNA regulatory network to construct the logistic regression model. The area under curve (AUC) values over 0.9 suggested the good performance of the model. Conclusion: The potential miRNA-mRNA regulatory network and established logistic regression model in our study may provide promising diagnostic methods for HCM.
Collapse
Affiliation(s)
- Lin Wang
- Cardiology Department, Tianjin Chest Hospital, Tianjin, China
| | | | | |
Collapse
|
19
|
Identification of hub driving genes and regulators of lung adenocarcinoma based on the gene Co-expression network. Biosci Rep 2021; 40:222428. [PMID: 32196072 PMCID: PMC7108999 DOI: 10.1042/bsr20200295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) remains the leading cause of cancer-related deaths worldwide. Increasing evidence suggests that circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) can regulate target gene expression and participate in tumor genesis and progression. However, hub driving genes and regulators playing a potential role in LUAD progression have not been fully elucidated yet. Based on data from The Cancer Genome Atlas database, 2837 differentially expressed genes, 741 DE-regulators were screened by comparing cancer tissues with paracancerous tissues. Then, 651 hub driving genes were selected by the topological relation of the protein-protein interaction network. Also, the target genes of DE-regulators were identified. Moreover, a key gene set containing 65 genes was obtained from the hub driving genes and target genes intersection. Subsequently, 183 hub regulators were selected based on the analysis of node degree in the ceRNA network. Next, a comprehensive analysis of the subgroups and Wnt, mTOR, and MAPK signaling pathways was conducted to understand enrichment of the subgroups. Survival analysis and a receiver operating characteristic curve analysis were further used to screen for the key genes and regulators. Furthermore, we verified key molecules based on external database, LRRK2, PECAM1, EPAS1, LDB2, and HOXA11-AS showed good results. LRRK2 was further identified as promising biomarker associated with CNV alteration and various immune cells' infiltration levels in LUAD. Overall, the present study provided a novel perspective and insight into hub driving genes and regulators in LUAD, suggesting that the identified signature could serve as an independent prognostic biomarker.
Collapse
|
20
|
Yang L, Cui Y, Sun X, Wang Y. Overexpression of TICRR and PPIF confer poor prognosis in endometrial cancer identified by gene co-expression network analysis. Aging (Albany NY) 2021; 13:4564-4589. [PMID: 33495413 PMCID: PMC7906164 DOI: 10.18632/aging.202417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/03/2020] [Indexed: 12/19/2022]
Abstract
The incidence of endometrial cancer (EC) is intensively increasing. However, due to the complexity and heterogeneity of EC, the molecular targeted therapy is still limited. The reliable and accurate biomarkers for tumor progression are urgently demanded. After normalizing the data from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), we utilized limma and WGCNA packages to identify differentially expressed genes (DEGs). The copy number variations of candidate genes were investigated by cBioPortal. Enrichment pathways analysis was performed by ClueGO and CluePedia. The methylation status was explored by UALCAN. ROC curve and survival analysis were conducted by SPSS and Kaplan–Meier. Infiltration immune cells in microenvironment were analyzed by TISIDB. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were applied to explore potential biological pathways. Immunohistochemistry staining (IHC), cell proliferation, cell apoptosis, colony formation, migration, invasion and scratch-wound assays were performed to investigate the function of key genes in vitro. In this study, four expression profile datasets were integrated to identify candidate genes. Combined with WGCNA analysis, the top ten candidates were screened out, whose abnormal methylation patterns were extremely correlated with their expression level and they were associated with tumor grades and predicted poor survival. GSEA and GSVA demonstrated they were involved in DNA replication and cell cycle transition in EC. Gene silencing of TICRR and PPIF dramatically inhibited cell growth, migration and epithelial-mesenchymal transition (EMT) and enhanced progesterone sensitivity. Additionally, from DrugBank database, cyclosporine may be effective for PPIF targeted therapy. By integrative bioinformatics analysis and in vitro experiments, our study shed novel light on the molecular mechanisms of EC. TICRR and PPIF may promise to be potential therapeutic targets for endometrial cancer.
Collapse
Affiliation(s)
- Linlin Yang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Yunxia Cui
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Xiao Sun
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| | - Yudong Wang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Disease, Shanghai, China
| |
Collapse
|
21
|
Yuan P, Ling L, Gao X, Sun T, Miao J, Yuan X, Liu J, Wang Z, Liu B. Identification of RNA-binding protein SNRPA1 for prognosis in prostate cancer. Aging (Albany NY) 2021; 13:2895-2911. [PMID: 33460399 PMCID: PMC7880319 DOI: 10.18632/aging.202387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023]
Abstract
Prostate cancer is one of the deadliest cancers in men. RNA-binding proteins play a critical role in human cancers; however, whether they have a significant effect on the prognosis of prostate cancer has yet to be elucidated. In the present study, we performed a comprehensive analysis of RNA sequencing and clinical data from the Cancer Genome Atlas dataset and obtained differentially expressed RNA-binding proteins between prostate cancer and benign tissues. We constructed a protein-protein interaction network and Cox regression analyses were conducted to identify prognostic hub RNA-binding proteins. SNRPA1 was associated with the highest risk of poor prognosis and was therefore selected for further analysis. SNRPA1 expression was positively correlated with Gleason score and pathological TNM stage in prostate cancer patients. Furthermore, the expression profile of SNRPA1 was validated using the Oncomine, Human Protein Atlas, and Cancer Cell Line Encyclopedia databases. Meanwhile, the prognostic profile of SNRPA1 was successfully verified in GSE70769. Additionally, the results of molecular experiments revealed the proliferative role of SNRPA1 in prostate cancer cells. In summary, our findings evidenced a relationship between RNA-binding proteins and prostate cancer and indicated the prognostic significance of SNRPA1 in prostate cancer.
Collapse
Affiliation(s)
- Penghui Yuan
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Le Ling
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xintao Gao
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Taotao Sun
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Jianping Miao
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Jihong Liu
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Zhihua Wang
- Department of Urology Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| |
Collapse
|
22
|
Chu G, Jiao W, Yang X, Liang Y, Li Z, Niu H. C3, C3AR1, HLA-DRA, and HLA-E as potential prognostic biomarkers for renal clear cell carcinoma. Transl Androl Urol 2020; 9:2640-2656. [PMID: 33457236 PMCID: PMC7807358 DOI: 10.21037/tau-20-699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Prognostic biomarkers play a vital role in the early detection of the cancer and assessment of prognosis. With advances in technology, a large number of biomarkers of kidney renal clear cell carcinoma (KIRC) have been discovered, but their prognostic value has not been fully investigated, and thus have not been widely used in clinical practice. We aimed to identify the reliable markers associated with the prognosis of KIRC patients. Methods We obtained 72 normal samples and 539 tumor samples from The Cancer Genome Atlas (TCGA), and 23 normal samples and 32 tumor samples from the Gene Expression Omnibus (GEO). Overlapping differentially expressed genes (ODEGs) were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, followed by construction of a protein-protein interaction (PPI) network to screen hub genes. Kaplan-Meier analysis, univariate Cox analysis, multivariate Cox analysis, Wilcoxon signed-rank test, Kruskal-Wallis test, and gene set enrichment analysis (GSEA) were performed to verify the prognostic value and function of the markers we selected. The relationships among gene expression level, tumor immune cell infiltration, and immune-checkpoints were also analyzed. Results A total of 910 genes were screened out, and C3, C3AR1, HLA-DRA, and HLA-E were identified as potential tumor markers. The expression of each gene was closely associated with tumor immune cell infiltration, survival rate, and the patients’ clinical characteristics (P<0.05). C3AR1, HLA-DRA, and HLA-E were also verified as independent prognostic factors of KIRC (P<0.05), and all these potential biomarkers had a close correlation with immune checkpoints. Conclusions C3, C3AR1, HLA-DRA, and HLA-E could be reliable biomarkers of KIRC and may have a significant contribution to make in immunotherapy, thus playing an important role in the improvement of prognosis.
Collapse
Affiliation(s)
- Guangdi Chu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wei Jiao
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xuecheng Yang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ye Liang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhiqiang Li
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Haitao Niu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
23
|
Shi J, Wang K, Xiong Z, Yuan C, Wang C, Cao Q, Yu H, Meng X, Xie K, Cheng Z, Yang H, Chen K, Zhang X. Impact of inflammation and immunotherapy in renal cell carcinoma. Oncol Lett 2020; 20:272. [PMID: 33014151 PMCID: PMC7520756 DOI: 10.3892/ol.2020.12135] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/23/2020] [Indexed: 12/13/2022] Open
Abstract
Substantial research attention has been directed at exploring the mechanisms and treatment of renal cell carcinoma (RCC). Indeed, the association between inflammation and tumor phenotypes has been at the center of cancer research. Concomitant with research on the inflammation response and inflammatory molecules involved in RCC, new breakthroughs have emerged. A large body of knowledge now shows that treatments targeting inflammation and immunity in RCC provide substantial clinical benefits. Adequate analysis and a better understanding of the mechanisms of inflammatory factors in the occurrence and progression of RCC are highly desirable. Currently, numerous RCC treatments targeted at inflammation and immunotherapy are available. The current review describes in detail the link between inflammation and RCC.
Collapse
Affiliation(s)
- Jian Shi
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Keshan Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zhiyong Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Changfei Yuan
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Cheng Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Qi Cao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Huang Yu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiangui Meng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Kairu Xie
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Zhixian Cheng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Hongmei Yang
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Ke Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| |
Collapse
|
24
|
Chen P, Zhang Z, Chen X. Overexpression of PKMYT1 Facilitates Tumor Development and Is Correlated with Poor Prognosis in Clear Cell Renal Cell Carcinoma. Med Sci Monit 2020; 26:e926755. [PMID: 33024069 PMCID: PMC7549326 DOI: 10.12659/msm.926755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Protein kinase membrane-associated tyrosine/threonine (PKMYT1) has been found in many tumors, but its association with clear cell renal cell carcinoma (ccRCC) remains unclear. MATERIAL AND METHODS PKMYT1 expression in ccRCC was examined in the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Tumor Immune Estimation Resource databases. The correlation between PKMYT1 expression and clinicopathological parameters was explored via the chi-square test. Receiver operating characteristic curves were used to estimate the diagnostic performance of PKMYT1. Kaplan-Meier curves, a Cox model, nomogram, time-dependent receiver operating characteristic curves, and decision curve analysis (DCA) were used to evaluate the prognostic value and clinical utility of PKMYT1. Genes coexpressed with PKMYT1 in ccRCC were identified based on TCGA, the gene expression profiling interactive, and cBioPortal. Gene Set Enrichment Analysis revealed biological pathways associated with PKMYT1 in ccRCC. RESULTS Weighted gene coexpression network analysis identified PKMYT1 as one of the genes most significantly correlated with progression of histological grade. PKMYT1 was significantly upregulated in ccRCC compared with normal tissue (P<0.001), with a trend toward differentiating between individuals with ccRCC and those who were healthy (area under the curve=0.942). High PKMYT1 expression was correlated with unsatisfactory survival (hazard ratio=1.67, P=0.001), indicating that it is a risk factor for ccRCC. A nomogram incorporating PKMYT1 level was created and showed a clinical net benefit. PKMYT1 was strongly positively correlated with the anti-silencing function of 1B histone chaperone (ASF1B) gene in ccRCC. CONCLUSIONS PKMYT1 is upregulated in ccRCC and its presence indicates poor prognosis, making it a potential therapeutic target for ccRCC.
Collapse
Affiliation(s)
- Peng Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China (mainland)
| | - Ziying Zhang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China (mainland).,Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China (mainland)
| | - Xiang Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China (mainland)
| |
Collapse
|
25
|
Ma CG, Xu WH, Xu Y, Wang J, Liu WR, Cao DL, Wang HK, Shi GH, Zhu YP, Qu YY, Zhang HL, Ye DW. Identification and validation of novel metastasis-related signatures of clear cell renal cell carcinoma using gene expression databases. Am J Transl Res 2020; 12:4108-4126. [PMID: 32913492 PMCID: PMC7476160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Patients with clear cell renal cell carcinoma (ccRCC) typically face aggressive disease progression when metastasis occurs. Here, we screened and identified differentially expressed genes in three microarray datasets from the Gene Expression Omnibus database. We identified 112 differentially expressed genes with functional enrichment as candidate prognostic biomarkers. Lasso Cox regression suggested 10 significant oncogenic hub genes involved in earlier recurrence and poor prognosis of ccRCC. Receiver operating characteristic curves validated the specificity and sensitivity of the Cox regression penalty used to predict prognosis. The area under the curve indexes of the integrated genes scores were 0.758 and 0.772 for overall and disease-free survival, respectively. The prognostic values of ADAMTS9, C1S, DPYSL3, H2AFX, MINA, PLOD2, RUNX1, SLC19A1, TPX2, and TRIB3 were validated through an analysis of 10 hub genes in 380 patients with ccRCC from a real-world cohort. The expression levels of were of high prognostic value for predicting metastatic potential. These findings will likely significantly contribute to our understanding of the underlying mechanisms of ccRCC, which will enhance efforts to optimize therapy.
Collapse
Affiliation(s)
- Chun-Guang Ma
- Department of Urology, Fudan University Shanghai Cancer CenterShanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, P. R. China
| | - Wen-Hao Xu
- Department of Urology, Fudan University Shanghai Cancer CenterShanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, P. R. China
| | - Yue Xu
- Department of Ophthalmology, The First Affiliated Hospital of Soochow UniversitySuzhou 215000, P. R. China
| | - Jun Wang
- Department of Urology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineGuangzhou 510060, Guangdong, P. R. China
| | - Wang-Rui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical College for NationalitiesGuangxi, P. R. China
| | - Da-Long Cao
- Department of Urology, Fudan University Shanghai Cancer CenterShanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, P. R. China
| | - Hong-Kai Wang
- Department of Urology, Fudan University Shanghai Cancer CenterShanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, P. R. China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer CenterShanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, P. R. China
| | - Yi-Ping Zhu
- Department of Urology, Fudan University Shanghai Cancer CenterShanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, P. R. China
| | - Yuan-Yuan Qu
- Department of Urology, Fudan University Shanghai Cancer CenterShanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, P. R. China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer CenterShanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, P. R. China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer CenterShanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan UniversityShanghai 200032, P. R. China
| |
Collapse
|
26
|
Zhai W, Lu H, Dong S, Fang J, Yu Z. Identification of potential key genes and key pathways related to clear cell renal cell carcinoma through bioinformatics analysis. Acta Biochim Biophys Sin (Shanghai) 2020; 52:853-863. [PMID: 32556097 DOI: 10.1093/abbs/gmaa068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 10/17/2019] [Accepted: 12/26/2019] [Indexed: 12/16/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common malignancy of the genitourinary system and is associated with high mortality rates. However, the molecular mechanism of ccRCC pathogenesis is still unclear, which translates to few effective diagnostic and prognostic biomarkers. In this study, we conducted a bioinformatics analysis on three Gene Expression Omnibus datasets and identified 437 differentially expressed genes (DEGs) related to ccRCC development and prognosis, of which 311 and 126 genes are respectively down-regulated and up-regulated. The protein-protein interaction network of these DEGs consists of 395 nodes and 1872 interactions and 2 prominent modules. The Staphylococcus aureus infection and complement and coagulation cascades are significantly enriched in module 1 and are likely involved in ccRCC progression. Forty-two hub genes were screened, of which von Willebrand factor, TIMP metallopeptidase inhibitor 1, plasminogen, formimidoyltransferase cyclodeaminase, solute carrier family 34 member 1, hydroxyacid oxidase 2, alanine-glyoxylate aminotransferase 2, phosphoenolpyruvate carboxykinase 1, and 3-hydroxy-3-methylglutaryl-CoA synthase 2 are possibly related to the prognosis of ccRCC. The differential expression of all nine genes was confirmed by quantitative real-time polymerase chain reaction analysis of the ccRCC and normal renal tissues. These key genes are potential biomarkers for the diagnosis and prognosis of ccRCC and warrant further investigation.
Collapse
Affiliation(s)
- Wenxin Zhai
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Haijiao Lu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200000, China
| | - Shenghua Dong
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Jing Fang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Zhuang Yu
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| |
Collapse
|