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Wolszczak-Biedrzycka B, Dorf J, Matowicka-Karna J, Wojewódzka-Żeleźniakowicz M, Żukowski P, Zalewska A, Maciejczyk M. Significance of nitrosative stress and glycoxidation products in the diagnosis of COVID-19. Sci Rep 2024; 14:9198. [PMID: 38649417 PMCID: PMC11035544 DOI: 10.1038/s41598-024-59876-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024] Open
Abstract
Nitrosative stress promotes protein glycoxidation, and both processes can occur during an infection with the SARS-CoV-2 virus. Therefore, the aim of this study was to assess selected nitrosative stress parameters and protein glycoxidation products in COVID-19 patients and convalescents relative to healthy subjects, including in reference to the severity of COVID-19 symptoms. The diagnostic utility of nitrosative stress and protein glycoxidation biomarkers was also evaluated in COVID-19 patients. The study involved 218 patients with COVID-19, 69 convalescents, and 48 healthy subjects. Nitrosative stress parameters (NO, S-nitrosothiols, nitrotyrosine) and protein glycoxidation products (tryptophan, kynurenine, N-formylkynurenine, dityrosine, AGEs) were measured in the blood plasma or serum with the use of colorimetric/fluorometric methods. The levels of NO (p = 0.0480), S-nitrosothiols (p = 0.0004), nitrotyrosine (p = 0.0175), kynurenine (p < 0.0001), N-formylkynurenine (p < 0.0001), dityrosine (p < 0.0001), and AGEs (p < 0.0001) were significantly higher, whereas tryptophan fluorescence was significantly (p < 0.0001) lower in COVID-19 patients than in the control group. Significant differences in the analyzed parameters were observed in different stages of COVID-19. In turn, the concentrations of kynurenine (p < 0.0001), N-formylkynurenine (p < 0.0001), dityrosine (p < 0.0001), and AGEs (p < 0.0001) were significantly higher, whereas tryptophan levels were significantly (p < 0.0001) lower in convalescents than in healthy controls. The ROC analysis revealed that protein glycoxidation products can be useful for diagnosing infections with the SARS-CoV-2 virus because they differentiate COVID-19 patients (KN: sensitivity-91.20%, specificity-92.00%; NFK: sensitivity-92.37%, specificity-92.00%; AGEs: sensitivity-99,02%, specificity-100%) and convalescents (KN: sensitivity-82.22%, specificity-84.00%; NFK: sensitivity-82,86%, specificity-86,00%; DT: sensitivity-100%, specificity-100%; AGE: sensitivity-100%, specificity-100%) from healthy subjects with high sensitivity and specificity. Nitrosative stress and protein glycoxidation are intensified both during and after an infection with the SARS-CoV-2 virus. The levels of redox biomarkers fluctuate in different stages of the disease. Circulating biomarkers of nitrosative stress/protein glycoxidation have potential diagnostic utility in both COVID-19 patients and convalescents.
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Affiliation(s)
- Blanka Wolszczak-Biedrzycka
- Department of Psychology and Sociology of Health and Public Health, University of Warmia and Mazury in Olsztyn, 10-900, Olsztyn, Poland.
| | - Justyna Dorf
- Department of Clinical Laboratory Diagnostics, Medical University of Bialystok, 15-089, Białystok, Poland
| | - Joanna Matowicka-Karna
- Department of Clinical Laboratory Diagnostics, Medical University of Bialystok, 15-089, Białystok, Poland
| | | | - Piotr Żukowski
- Department of Restorative Dentistry, Croydon University Hospital, 530 London Road, Croydon, Surrey, CR7 7YE, UK
| | - Anna Zalewska
- Independent Laboratory of Experimental Dentistry, Medical University of Bialystok, 15-089, Białystok, Poland
| | - Mateusz Maciejczyk
- Department of Hygiene, Epidemiology and Ergonomics, Medical University of Bialystok, 15-089, Białystok, Poland
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Li Z, Chen Y, Zhang B, Xie L, Shi B. Global trends and hotspots in Cyclin-dependent Kinase Subunit 2 research from 1999 to 2022: A bibliometric and visualized analysis. Medicine (Baltimore) 2023; 102:e36319. [PMID: 38050288 PMCID: PMC10695487 DOI: 10.1097/md.0000000000036319] [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: 05/15/2023] [Accepted: 09/18/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Cyclin-dependent Kinase Subunit 2 is a protein closely related to the regulation of the cell cycle. In recent years, there has been an increasing number of research articles on this topic. However, there is a lack of comprehensive synthesis and evaluation in the field of CKS2 research. This study aims to summarize and visualize the literature distribution, research hotspots, and development trends of CKS2 based on bibliometric methods. METHODS Publications from 1999 to 2022 were extracted from the Web of Science. Citespace was used to analyze the relevant information of each article. RESULTS A total of 138 publications focused on CKS2 showed a positive growth trend from 1999 to 2022 and were published by 27 countries. The most prolific countries are China and the USA. The most prolific institution is Scripps Research Institute. The most prolific author is Steven I. Reed from Scripps Research Institute. The most cited article is published by Todd R Golub. The most cited author is Hanna-Stina Martinsson-Ahlzen. The journal with the most published articles is International Journal of Oncology. The high frequency keywords suggest that expression and function of CKS2 in cancer are dominated topics. The clusters and burst words suggest that expression and function of CKS2 still active in the future. CONCLUSION SUBSECTIONS The results of this bibliometric analysis provide information on the state and trends in CKS2 from 1999 to 2022. It is helpful for scholars to pinpoint hot issues and discover new areas of study.
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Affiliation(s)
- Ziteng Li
- School of Acupuncture-Tuina, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuanzhen Chen
- Neck-Shoulder and Lumbocrural Pain Hospital of Shandong First Medical University, Jinan, China
| | - Bo Zhang
- Neck-Shoulder and Lumbocrural Pain Hospital of Shandong First Medical University, Jinan, China
| | - Liangyu Xie
- Neck-Shoulder and Lumbocrural Pain Hospital of Shandong First Medical University, Jinan, China
| | - Bin Shi
- Neck-Shoulder and Lumbocrural Pain Hospital of Shandong First Medical University, Jinan, China
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3
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Chen Q, Fu Y, Liu X, Wang P, Dai S, Zhu F, Liu T, Xu W, Wu J. Aberrant expression of CKS2 induced by ELK1 contributes to malignant progression of pancreatic cancer. Mol Carcinog 2023; 62:1947-1959. [PMID: 37642304 DOI: 10.1002/mc.23627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/20/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Cyclin-dependent kinase subunit 2 (CKS2) has been reported to promote various malignancies. This study investigated the functional role of CKS2 in pancreatic cancer (PC). An analysis of abnormally expressed genes and their prognostic value for PC was performed by using the Gene Expression Profiling Interactive Analysis (GEPIA) database and performing immunohistochemical staining on 64 samples of tumor tissue. CCK-8 assays, EdU staining, colony formation assays, flow cytometry, and a xenograft tumor model were used to analyze the biological function of CKS2 in PC. Our results revealed that CKS2 was expressed at significantly higher levels in PC tissues than in adjacent normal tissues, and a high level of CKS2 expression was associated with a poor prognosis for patients with PC. Moreover, functional assays revealed that CKS2 knockdown suppressed cell proliferation, induced cell cycle S phase, G2/M phase arrest, and apoptosis in vitro, and also reduced tumor growth in vivo. In addition, CKS2 knockdown increased the levels of Bax, caspase-3, P53, P21, and GADD45α expression, but decreased Bcl-2, Cyclin B1, CDK1, Cyclin A, and Cdc25C expression. CKS2 overexpression produced the opposite effects of CKS2 knockdown. Furthermore, we found that ELK1 protein regulated transcription of the CKS2 gene. In conclusion, our findings suggest that CKS2 expression is regulated by ELK1, which could possibly serve as prognostic indicator and therapeutic target for PC.
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Affiliation(s)
- Qiuyang Chen
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
- Department of Hepatopancreatobiliary Surgery, The Affiliated Jiangyin Hospital of Southeast University Medical College, Wuxi, China
| | - Yue Fu
- Department of Gastrointestinal Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Xinchun Liu
- Department of Gastrointestinal and Anal Surgery, The Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peng Wang
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Shangnan Dai
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Feng Zhu
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Tongtai Liu
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Wenbin Xu
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Junli Wu
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
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Rakic A, Anicic R, Rakic M, Nejkovic L. Integrated Bioinformatics Investigation of Novel Biomarkers of Uterine Leiomyosarcoma Diagnosis and Outcome. J Pers Med 2023; 13:985. [PMID: 37373974 DOI: 10.3390/jpm13060985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Uterine leiomyosarcomas (uLMS) have a poor prognosis and a high percentage of recurrent disease. Bioinformatics has become an integral element in rare cancer studies by overcoming the inability to collect a large enough study population. This study aimed to investigate and highlight crucial genes, pathways, miRNAs, and transcriptional factors (TF) on uLMS samples from five Gene Expression Omnibus datasets and The Cancer Genome Atlas Sarcoma study. Forty-one common differentially expressed genes (DEGs) were enriched and annotated by the DAVID software. With protein-protein interaction (PPI) network analysis, we selected ten hub genes that were validated with the TNMplotter web tool. We used the USCS Xena browser for survival analysis. We also predicted TF-gene and miRNA-gene regulatory networks along with potential drug molecules. TYMS and TK1 correlated with overall survival in uLMS patients. Finally, our results propose further validation of hub genes (TYMS and TK1), miR-26b-5p, and Sp1 as biomarkers of pathogenesis, prognosis, and differentiation of uLMS. Regarding the aggressive behavior and poor prognosis of uLMS, with the lack of standard therapeutic regimens, in our opinion, the results of our study provide enough evidence for further investigation of the molecular basis of uLMS occurrence and its implication in the diagnosis and therapy of this rare gynecological malignancy.
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Affiliation(s)
- Aleksandar Rakic
- The Obstetrics and Gynecology Clinic Narodni Front, 11000 Belgrade, Serbia
| | - Radomir Anicic
- The Obstetrics and Gynecology Clinic Narodni Front, 11000 Belgrade, Serbia
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Marija Rakic
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia
| | - Lazar Nejkovic
- The Obstetrics and Gynecology Clinic Narodni Front, 11000 Belgrade, Serbia
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
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Cyclin-Dependent Kinase Subunit 2 (CKS2) as a Prognostic Marker for Stages I-III Invasive Non-Mucinous Lung Adenocarcinoma and Its Role in Affecting Drug Sensitivity. Cells 2022; 11:cells11162611. [PMID: 36010686 PMCID: PMC9406629 DOI: 10.3390/cells11162611] [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: 07/18/2022] [Revised: 08/11/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
With the aim of improving the prognosis of patients with lung adenocarcinoma (LUAD), we identified the biomarker related to the sensitivity of patients to chemotherapy drugs and explored the potential mechanisms. As a cell cycle-related protein, CKS2 has an essential role to play in tumor progression and prognosis. CKS2 expression was measured using TCGA RNA-sequencing data and immunohistochemistry. The sensitivity data of tumor cells to chemotherapeutic drugs for lung cancer was acquired from the Cancer Therapeutics Response Portal (CTRP) database. A range of bioinformatics methods was used to explore the mechanisms of CKS2 upregulation. The biological functions of CKS2 were predicted using GO and KEGG enrichment analysis, as well as GSEA. CKS2 expression was up-regulated in stages I-III invasive non-mucinous lung adenocarcinoma and varied significantly between various histological subtypes. High CKS2 expression worsened the prognosis of patients. The CKS2 expression level was linked to the sensitivity of LUAD cells to carboplatin and paclitaxel. CKS2 upregulation was associated with the immune microenvironment, mRNA methylation, and competing endogenous RNAs (ceRNAs). CKS2 can serve as a diagnostic and prognostic biomarker for stages I-III invasive non-mucinous lung adenocarcinoma and modulate the effect of paclitaxel and carboplatin by regulating microtubule binding and influencing carboplatin binding to DNA.
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Tian L, Liao Y. Identification of G6PC as a potential prognostic biomarker in hepatocellular carcinoma based on bioinformatics analysis. Medicine (Baltimore) 2022; 101:e29548. [PMID: 35984176 PMCID: PMC9388022 DOI: 10.1097/md.0000000000029548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has high mortality and incidence rates around the world with limited therapeutic options. There is an urgent need for identification of novel therapeutic targets and biomarkers for early diagnosis and predicting patient survival with HCC. Several studies (GSE102083, GSE29722, GSE101685, and GSE112790) from the GEO database in HCC were screened and analyzed by GEO2R, gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were conducted with the Database for Annotation, Visualization and Integrated Discovery. The protein-protein interaction network was plotted and the module analysis was performed using Search Tool for the Retrieval of Inter-acting Genes/Proteins database and Cytoscape. The expression and survival of key genes were identified using UALCAN, Kaplan-Meier Plotter and ONCOMINE online databases, and the immune infiltration level of key genes was analyzed via the Tumor Immune Estimation Resource (TIMER) database. Through database analysis, eight key genes were finally screened out, and the expressions of cyclin-dependent kinase regulatory subunit 2 and glucose-6-phosphatase catalytic (G6PC), which were closely related to the survival of HCC patients, was detected by using UALCAN. Further analysis on the differential expression of G6PC in multiple cancerous tumors and normal tissues revealed low expression in many solid tumors by Oncomine and TIMER. In addition, Kaplan-Meier plotter and UALCAN database analysis to access diseases prognosis suggested that low expression of G6PC was significantly associated with poor overall survival in HCC patients. Finally, TIMER database analysis showed a significant negative correlation between G6PC and infiltration levels of six kinds of immune cells. The somatic copy number alterations of G6PC were associated with B cells, CD8+ T cells, CD4+ T cells, macrophages, dentritic cells and neutrophils. These bioinformatic data identified G6PC as a potential key gene in the diagnosis and prognosis of HCC.
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Affiliation(s)
- Li Tian
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China
- Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China
- Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yong Liao
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China
- Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China
- Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Yong Liao, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China. Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China. Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China (e-mail: )
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7
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Comprehensive Expression Profiling and Molecular Basis of CDC28 Protein Kinase Regulatory Subunit 2 in Cervical Cancer. Int J Genomics 2022; 2022:6084549. [PMID: 35935749 PMCID: PMC9352497 DOI: 10.1155/2022/6084549] [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: 03/05/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
More and more evidence suggests the oncogenic function of overexpressed CDC28 protein kinase regulatory subunit 2 (CKS2) in various human cancers. However, CKS2 has rarely been studied in cervical cancer. Herein, taking advantage of massive genetics data from multicenter RNA-seq and microarrays, we were the first group to perform tissue microarrays for CKS2 in cervical cancer. We were also the first to evaluate the clinical significance of CKS2 with large samples (980 cervical cancer cases and 422 noncancer cases). We further excavated the mechanism of the tumor-promoting activities of CKS2 in cervical cancer through analysis of genetic mutation profiles, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) significant enrichment of genes coexpressed with CKS2. According to the results, expression data from multilevels unanimously supported the overexpression of CKS2 in cervical cancer. Patients with cervical cancer in stage II from inhouse microarrays had significantly higher expression of CKS2, and CKS2 overexpression had an adverse impact on the disease-free survival status of cervical cancer patients in GSE44001. Both mutation types of mRNA high and mRNA low appeared in cervical cancer cases from the TCGA Firehose project. Gene coexpressed with CKS2 participated in pathways including the cell cycle, estrogen signaling pathway, and DNA replication. In summary, upregulated CKS2 is closely associated with the malignant clinical development of cervical cancer and might serve as a valuable therapeutic target in cervical cancer.
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Chen L, Hu K, Liu Y, Liu L, Tang J, Qin X. Knockdown of replication protein A 3 induces protective autophagy and enhances cisplatin sensitivity in lung adenocarcinoma by inhibiting AKT/mTOR signaling via binding to cyclin-dependent kinases regulatory subunit 2. Drug Dev Res 2022; 83:1589-1599. [PMID: 35903032 DOI: 10.1002/ddr.21978] [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: 12/09/2021] [Revised: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 11/08/2022]
Abstract
Replication protein A 3 (RPA3) is a significant component of replication protein A and has been documented to function as an oncogene in several types of cancers. However, the role and underlying mechanism of RPA3 in lung adenocarcinoma (LUAD) remains unknown. In this study, messenger expression of RPA3 and survival probability in LUAD were predicted by the UALCAN database. The combination of RPA3 with cyclin-dependent kinases regulatory subunit 2 (CKS2) were characterized by the humanbase and STRING databases and verified by co-immunoprecipitation. Cell viability was assessed by Cell Counting Kit-8 assay and colony formation assay. Flow cytometric analysis and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay were used to determine cell cycle and cell apoptosis, respectively. The expressions of protein kinase B/mammalian target of rapamycin (AKT/mTOR) pathway and autophagy-related proteins were examined by western blot assay. Significantly, we revealed that RPA3 expression was upregulated in LUAD and is associated with poor prognosis in LUAD patients. RPA3 and CKS2 expression was highly expressed in LUAD cell lines and the interaction between RPA3 and CKS2 was confirmed. RPA3 silencing inhibited A549 cell viability, blocked cell cycle and promoted cell apoptosis, as well as induction of autophagy and inhibition of AKT/mTOR signaling. CKS2 overexpression reversed the effects of RPA3 silencing on A549 cells. In addition, RPA3 knockdown enhanced cisplatin sensitivity of A549 cells through blocking the AKT/mTOR signaling. These results suggested that RPA3 might control LUAD cell autophagy and enhance cisplatin sensitivity by regulation of AKT/mTOR signaling via targeting CKS2.
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Affiliation(s)
- Lijun Chen
- Department of Gerneral Theory of Surgery, Medical College, Hunan University of Medicine, Huaihua, Hunan, China
| | - Ke Hu
- Department of Gerneral Theory of Surgery, Medical College, Hunan University of Medicine, Huaihua, Hunan, China
| | - Yu Liu
- Department of Gerneral Theory of Surgery, Medical College, Hunan University of Medicine, Huaihua, Hunan, China
| | - Lingli Liu
- Department of Gerneral Theory of Surgery, Medical College, Hunan University of Medicine, Huaihua, Hunan, China
| | - Juanjuan Tang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaobing Qin
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
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Gao L, Chen G, Liang ZQ, Li JD, Li DM, Tang YL, Tang D, Huang ZG, Chen JH, Luo JY, Zeng JH, Dang YW, Feng ZB. Expression Profile and Molecular Basis of Cyclin-Dependent Kinases Regulatory Subunit 2 in Endometrial Carcinoma Detected by Diversified Methods. Pathol Oncol Res 2022; 28:1610307. [PMID: 35693634 PMCID: PMC9184457 DOI: 10.3389/pore.2022.1610307] [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: 01/07/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022]
Abstract
Purpose: Our purpose was to systematically appraise the clinicopathological significance and explore the molecular bases of CKS2 in endometrial carcinoma. Patients and Methods: We measured the clinicopathological significance of CKS2 using diverse methods of public RNA-seq, microarrays, and in-house tissue microarrays to investigate the molecular basis of CKS2 in endometrial carcinoma through upstream transcriptional analysis, immune infiltration correlation analysis, and co-expression analysis. Results: Both the analysis for public RNA-seq plus the microarray data and in-house tissue microarray confirmed the significant overexpression of CKS2 in a total of 1,021 endometrial carcinoma samples compared with 279 non-cancer endometrium samples (SMD = 2.10, 95% CI = 0.72-3.48). The upregulated CKS2 was significantly related to the lymph node metastasis and advanced clinical grade of endometrial carcinoma patients (p < 0.001). Mutation types such as amplification and mRNA occurred with high frequency in the CKS2 gene in endometrial carcinoma patients. A series of miRNAs and transcription factors, such as hsa-miR-26a, hsa-miR-130a, hsa-miR-30, E2F4, MAX, and GABPA, were predicted to regulate the transcription and expression of CKS2. Significant links were found between CKS2 expression and the infiltration level of B cells, CD4+ T cells, and neutrophils in endometrial carcinoma. CKS2-coexpressed genes were actively involved in pathways such as the mitotic cell cycle process, PID aurora B pathway, and prolactin signaling pathway. Conclusion: The overexpressed CKS2 showed positive correlations with the clinical progression of endometrial carcinoma and was associated with various cancer-related biological processes and pathways, showing potential as a promising clinical biomarker for endometrial carcinoma.
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Affiliation(s)
- Li Gao
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zi-Qian Liang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jian-Di Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Dong-Ming Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yu-Lu Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Deng Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jun-Hong Chen
- Department of Pathology, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Jia-Yuan Luo
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiang-Hui Zeng
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People's Hospital, Nanning, China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhen-Bo Feng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Qu G, Wang D, Xu W, Guo W. Comprehensive Analysis of the Correlation Between Pyroptosis-Related LncRNAs and Tumor Microenvironment, Prognosis, and Immune Infiltration in Hepatocellular Carcinoma. Front Genet 2022; 13:867627. [PMID: 35559014 PMCID: PMC9087742 DOI: 10.3389/fgene.2022.867627] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/25/2022] [Indexed: 01/04/2023] Open
Abstract
Background: Accumulating evidence shows that pyroptosis plays a crucial role in hepatocellular carcinoma (HCC). However, the relationship between pyroptosis-related long non-coding RNAs (lncRNAs) and HCC tumor characteristics remains enigmatic. We aimed to explore the predictive effect of pyroptosis-related lncRNAs (PRLs) in the prognosis of HCC. Methods: We comprehensively analyzed the role of the PRLs in the tumor microenvironment and HCC prognosis by integrating genomic data from patients of HCC. Consensus clustering analysis of PRLs was applied to identify HCC subtypes. A prognostic model was then established with a training cohort from The Cancer Genome Atlas (TCGA) using univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Further, we evaluated the accuracy of this predictive model using a validation set. We predicted IC50s of commonly used chemotherapeutic and targeted drugs through the R package pRRophetic. Results: Based on pyroptosis-related lncRNAs, a prognostic risk signature composed of seven PRLs (MKLN1AS, AL031985.3, SNHG4, GHRLOS, AC005479.2, AC099850.4, and AC026412.3) was established. For long-term prognosis of HCC patients, our model shows excellent accuracy to forecast overall survival of HCC individuals both in training set and testing set. We found a significant correlation between clinical features and the risk score. Patients in the high-risk group had tumor characteristics associated with progression such as aggressive pathological grade and stage. Besides that, gene set enrichment analysis (GSEA) showed that cell cycle and focal adhesion were significantly enriched in the high-risk group. Conclusion: The association of the risk model constituted by these seven pyroptosis-related lncRNAs with clinical prognosis, tumor microenvironment, chemotherapy and small molecule drugs was evaluated. Our study provides strong evidence for individualized prediction of prognosis, shedding light on immunotherapy in HCC patients.
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Affiliation(s)
- Guangzhen Qu
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Dong Wang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Weiyu Xu
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Wei Guo
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing, China
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Wang Z, Zhang M, Wu Y, Yu Y, Zheng Q, Li J. CKS2 Overexpression Correlates with Prognosis and Immune Cell Infiltration in Lung Adenocarcinoma: A Comprehensive Study based on Bioinformatics and Experiments. J Cancer 2021; 12:6964-6978. [PMID: 34729099 PMCID: PMC8558665 DOI: 10.7150/jca.63625] [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: 06/07/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
Objective: Cyclin-dependent kinase regulatory subunit 2 (CKS2) plays a vital role in regulation of the cell cycle and cancer progression. However, the role of CKS2 in lung adenocarcinoma (LUAD) remains unkonwn. Here, we examined the prognostic value and biological functions of CKS2 in LUAD by using omics data of 1,235 LUAD samples from TCGA, GEO, and our own cohort as well as data of in vitro experiments. Methods: Kaplan-Meier was conducted to evaluate the prognostic value of CKS2 expression. The association between CKS2 expression level and tumor immune infiltration was explored using the single-sample Gene Set Enrichment Analysis (ssGSEA) and TIMER database. Functional enrichment analyses were performed to annotate the biological functions of CKS2 in LUAD. Furthermore, a series of in vitro experiments and immunohistochemistry were performed for validation. Results: CKS2 overexpression was correlated with the advanced stage, TP53 status, PD-L1 expression, and DNA hypomethylation. Moreover, patients with LUAD and high CKS2 expression exhibited poor overall survival. Functional enrichment analysis indicated that CKS2 was involved in cell division, cell cycle, DNA replication. Experiments in vitro indicated that CKS2 knockdown decreased the invasion and proliferation of LUAD cells and facilitated their apoptosis. ssGSEA and TIMER analysis revealed a negative correlation between CKS2 expression and the immune cell infiltration. Conclusions: In summary, High CKS2 expression was associated with poor prognosis and low levels of infiltrating immune cells in LUAD as well as with malignant phenotypes. Therefore, CKS2 may be a promising prognostic biomarker and therapeutic target in LUAD.
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Affiliation(s)
- Zhiping Wang
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Mengyan Zhang
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Yahua Wu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Yilin Yu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Qunhao Zheng
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Jiancheng Li
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
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Hu M, Li Z, Qiu J, Zhang R, Feng J, Hu G, Ren J. CKS2 (CDC28 protein kinase regulatory subunit 2) is a prognostic biomarker in lower grade glioma: a study based on bioinformatic analysis and immunohistochemistry. Bioengineered 2021; 12:5996-6009. [PMID: 34494924 PMCID: PMC8806895 DOI: 10.1080/21655979.2021.1972197] [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] [Indexed: 12/19/2022] Open
Abstract
Gliomas account for the highest cases of primary brain malignancies. Whereas previous studies have demonstrated the roles of CDC28 Protein Kinase Regulatory Subunit 2 (CKS2) in various cancer types, its functions in lower grade gliomas (LGGs) remain elusive. This study aimed to profile the expression and functions of CKS2 in LGG. Multiple online databases such as The Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), Gene Expression Profiling Interactive Analysis 2nd edition (GEPIA2), Tumor Immune Estimation Resource 2nd edition (TIMER2.0) as well as Gene Expression Omnibus (GEO) were used in this study. Immunohistochemistry (IHC) was performed to evaluate CKS2 protein expression. Our data demonstrated upregulation of CKS2 in LGG tissues at both mRNA and protein level, especially in grade III gliomas. Similarly, there was increased expression of CKS2 in isocitrate dehydrogenase 1 (IDH1) wildtype gliomas. In addition, increased DNA copy number and DNA hypomethylation might be associated with the upregulation of the CKS2 in LGG. Using the Kaplan–Meier survival analysis and the Cox regression analysis, CKS2 was shown to be independently associated with poor prognosis of LGG patients. Receiver operating characteristic (ROC) analysis revealed that CKS2 could effectively predict the 1-, 3- and 5-year survival rates of LGG patients. Enrichment analyses revealed that CKS2 was mainly involved in the regulation of the cell cycle in LGG. Taken together, our study demonstrated that CKS2 might be a candidate prognostic biomarker for LGG and could predict the survival rates of LGG patients. Abbreviations: LGG: lower grade glioma; CKS2: CDC28 protein kinase regulatory subunit 2; TCGA: The Cancer Genome Atlas; CGGA: the Chinese Glioma Genome Atlas; GEO: Gene Expression Omnibus; GEPIA: Gene Expression Profiling Interactive Analysis; TIMER: Tumor Immune Estimation Resource; IHC: immunohistochemistry; qRT-PCR: quantitative real-time polymerase chain reaction; PBS: phosphate buffered saline; DAB: diaminobenzidine tetrachloride; OS: overall survival; CAN: copy number alteration; IDH: Isocitrate dehydrogenase; GSEA: Gene Set Enrichment Analysis; DEG: differentially expressed gene; KEGG: Kyoto encyclopedia of genes and genomes; GO: Gene ontology; BP: biological process; CC: cellular component; MF: molecular function; NES: normalized enrichment score; NOM: nominal; FDR: false discovery rate
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Affiliation(s)
- Menglong Hu
- Department of Pathology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zongkuo Li
- Department of Pathology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jinhuan Qiu
- Department of Pathology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ruizhen Zhang
- Department of Pathology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Junkai Feng
- Department of Pathology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Guiming Hu
- Department of Pathology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jingli Ren
- Department of Pathology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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13
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Liu G, Singha M, Pu L, Neupane P, Feinstein J, Wu HC, Ramanujam J, Brylinski M. GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. J Cheminform 2021; 13:58. [PMID: 34380569 PMCID: PMC8356453 DOI: 10.1186/s13321-021-00540-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/31/2021] [Indexed: 12/22/2022] Open
Abstract
Traditional techniques to identify macromolecular targets for drugs utilize solely the information on a query drug and a putative target. Nonetheless, the mechanisms of action of many drugs depend not only on their binding affinity toward a single protein, but also on the signal transduction through cascades of molecular interactions leading to certain phenotypes. Although using protein-protein interaction networks and drug-perturbed gene expression profiles can facilitate system-level investigations of drug-target interactions, utilizing such large and heterogeneous data poses notable challenges. To improve the state-of-the-art in drug target identification, we developed GraphDTI, a robust machine learning framework integrating the molecular-level information on drugs, proteins, and binding sites with the system-level information on gene expression and protein-protein interactions. In order to properly evaluate the performance of GraphDTI, we compiled a high-quality benchmarking dataset and devised a new cluster-based cross-validation protocol. Encouragingly, GraphDTI not only yields an AUC of 0.996 against the validation dataset, but it also generalizes well to unseen data with an AUC of 0.939, significantly outperforming other predictors. Finally, selected examples of identified drugtarget interactions are validated against the biomedical literature. Numerous applications of GraphDTI include the investigation of drug polypharmacological effects, side effects through offtarget binding, and repositioning opportunities.
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Affiliation(s)
- Guannan Liu
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Manali Singha
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Limeng Pu
- Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Prasanga Neupane
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Joseph Feinstein
- Department of Computer Science, Brown University, Providence, RI, 02902, USA
| | - Hsiao-Chun Wu
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - J Ramanujam
- Division of Electrical and Computer Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA.,Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA. .,Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Kim HJ, Kim J. OTUD6A Is an Aurora Kinase A-Specific Deubiquitinase. Int J Mol Sci 2021; 22:ijms22041936. [PMID: 33669244 PMCID: PMC7919836 DOI: 10.3390/ijms22041936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/25/2022] Open
Abstract
Aurora kinases are serine/threonine kinases required for cell proliferation and are overexpressed in many human cancers. Targeting Aurora kinases has been a therapeutic strategy in cancer treatment. Here, we attempted to identify a deubiquitinase (DUB) that regulates Aurora kinase A (Aurora-A) protein stability and/or kinase activity as a potential cancer therapeutic target. Through pull-down assays with the human DUB library, we identified OTUD6A as an Aurora-A-specific DUB. OTUD6A interacts with Aurora-A through OTU and kinase domains, respectively, and deubiquitinates Aurora-A. Notably, OTUD6A promotes the protein half-life of Aurora-A and activates Aurora-A by increasing phosphorylation at threonine 288 of Aurora-A. From qPCR screening, we identified and validated that the cancer gene CKS2 encoding Cyclin-dependent kinases regulatory subunit 2 is the most upregulated cell cycle regulator when OTUD6A is overexpressed. The results suggest that OTUD6A may serve as a therapeutic target in human cancers.
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