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Li C, Peng S, Tang C. Retracted article: MicroRNA-4521 targets hepatoma up-regulated protein (HURP) to inhibit the malignant progression of breast cancer. Bioengineered 2024; 15:1996016. [PMID: 34699315 PMCID: PMC10826620 DOI: 10.1080/21655979.2021.1996016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 10/20/2022] Open
Abstract
Changwen Li, Sen Pengb, and Chuangang Tanga. MicroRNA-4521 targets hepatoma up-regulated protein (HURP) to inhibit the malignant progression of breast cancer. Bioengineered. 2021 Oct. doi: 10.1080/21655979.2021.1996016.Since publication, significant concerns have been raised about the compliance with ethical policies for human research and the integrity of the data reported in the article.When approached for an explanation, the authors provided some original data but were not able to provide all the necessary supporting information. As verifying the validity of published work is core to the scholarly record's integrity, we are retracting the article. All authors listed in this publication have been informed.We have been informed in our decision-making by our editorial policies and the COPE guidelines.The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as 'Retracted.'
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Affiliation(s)
- Changwen Li
- Department of Breast Surgery, Xuzhou Central Hospital, Xuzhou, Jiangsu Province, China
| | - Sen Peng
- Department of Pathology, Xuzhou Central Hospital, Xuzhou, Jiangsu Province, China
| | - Chuangang Tang
- Department of Breast Surgery, Xuzhou Central Hospital, Xuzhou, Jiangsu Province, China
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Li J, Liu Q, Zhang T, Du Q. Bioinformatics Analysis Reveals CDK1 and DLGAP5 as Key Modulators of Tumor Immune Cell Infiltration in Hepatocellular Carcinoma. Cancer Manag Res 2024; 16:1597-1608. [PMID: 39559249 PMCID: PMC11572444 DOI: 10.2147/cmar.s478426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 11/01/2024] [Indexed: 11/20/2024] Open
Abstract
Introduction Hepatocellular carcinoma (HCC), a prevalent and aggressive form of cancer, poses significant challenges due to its limited therapeutic options. This study aims to leverage multi-omics data from liver cancer to identify potential therapeutic targets for HCC. Methods We employed an integrative approach by analyzing various omics datasets related to liver cancer. Through comprehensive data mining and analysis, we identified key genes that are significantly associated with HCC. To gain insights into their biological roles and underlying mechanisms, we constructed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway networks. Specifically, we focused on genes that exhibited high expression levels in HCC and were correlated with poor patient prognosis. Among these, CDK1 and DLGAP5 emerged as promising candidates and were further investigated for their potential involvement in tumor immune cell infiltration and HCC progression. Results Our analysis revealed that CDK1 and DLGAP5 are highly expressed in HCC tissues compared to normal liver tissues, and their elevated expression is associated with unfavorable clinical outcomes. Furthermore, through GO and KEGG pathway analyses, we found that these genes are implicated in critical biological processes and signaling pathways relevant to HCC pathogenesis. Notably, CDK1 and DLGAP5 were shown to be associated with tumor immune cell infiltration, suggesting their potential role in modulating the tumor microenvironment and promoting HCC progression. Discussion These findings provide valuable insights into the development of novel therapeutic approaches for HCC.
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Affiliation(s)
- Jiajing Li
- The Diagnostics Laboratory, Affiliated Hospital to Zunyi Medical University, Zunyi, Guizhou, 563000, People’s Republic of China
| | - Qi Liu
- Affiliated Hospital to Zunyi Medical University, Zunyi, Guizhou, 563000, People’s Republic of China
| | - Ting Zhang
- Affiliated Hospital to Zunyi Medical University, Zunyi, Guizhou, 563000, People’s Republic of China
| | - Qian Du
- Department of Endoscopy and Digestive System, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, 550002, People’s Republic of China
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Yan F, Yuan WQ, Wu SM, Yang YH, Cui DJ. Novel mechanisms of intestinal flora regulation in high-altitude hypoxia. Heliyon 2024; 10:e38220. [PMID: 39498080 PMCID: PMC11534185 DOI: 10.1016/j.heliyon.2024.e38220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 11/07/2024] Open
Abstract
Background This study investigates the molecular mechanisms behind firmicutes-mediated macrophage (Mψ) polarization and glycolytic metabolic reprogramming through HIF-1α in response to intrinsic mucosal barrier injury induced by high-altitude hypoxia. Methods Establishing a hypoxia mouse model of high altitude, we utilized single-cell transcriptome sequencing to identify key cell types involved in regulating intestinal mucosal barrier damage caused by high-altitude hypoxia. Through proteomic analysis of colonic tissue Mψ and metabolomic analysis of Mψ metabolites, we determined crucial proteins and metabolic pathways influencing intestinal mucosal barrier damage induced by high-altitude hypoxia. Mechanistic validation was conducted using RAW264.7 Mψ in vitro by assessing cell viability with CCK-8 assay following treatment with different metabolites. The hypoxia mouse model was further validated in vivo by transplanting gut microbiota of Firmicutes. Histological examinations through H&E staining assessed colonic cell morphology and structure, while the FITC-dextran assay evaluated intestinal tissue permeability. Hypoxia probe signal intensity in mouse colonic tissue was assessed via metronidazole staining. Various experimental techniques, including flow cytometry, immunofluorescence, ELISA, Western blot, and RT-qPCR, were employed to study the impact of HIF-1α/glycolysis pathway and different gut microbiota metabolites on Mψ polarization. Results Bioinformatics analysis revealed that single-cell transcriptomics identified Mψ as a key cell type, with their polarization pattern playing a crucial role in the intestinal mucosal barrier damage induced by high-altitude hypoxia. Proteomics combined with metabolomics analysis indicated that HIF-1α and the glycolytic pathway are pivotal proteins and signaling pathways in the intestinal mucosal barrier damage caused by high-altitude hypoxia. In vitro cell experiments demonstrated that activation of the glycolytic pathway by HIF-1α led to a significant upregulation of mRNA levels of IL-1β, IL-6, and TNFα while downregulating mRNA levels of IL-10 and TGFβ, thereby promoting M1 Mψ activation and inhibiting M2 Mψ polarization. Further mechanistic validation experiments revealed that the metabolite butyric acid from Firmicutes bacteria significantly downregulated the protein expression of HIF-1α, GCK, PFK, PKM, and LDH, thus inhibiting the HIF-1α/glycolytic pathway that suppresses M1 Mψ and activates M2 Mψ, consequently alleviating the hypoxic symptoms in RAW264.7 cells. Subsequent animal experiments confirmed that Firmicutes bacteria inhibited the HIF-1α/glycolytic pathway to modulate Mψ polarization, thereby mitigating intestinal mucosal barrier damage in high-altitude hypoxic mice. Conclusion The study reveals that firmicutes, through the inhibition of the HIF-1α/glycolysis pathway, mitigate Mψ polarization, thereby alleviating intrinsic mucosal barrier injury in high-altitude hypoxia.
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Affiliation(s)
- Fang Yan
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, No.83, East Zhongshan Road, Guiyang, Guizhou, China
- Medical College of Guizhou University, Guiyang, Guizhou, China
| | - Wen-qiang Yuan
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, No.83, East Zhongshan Road, Guiyang, Guizhou, China
- Medical College of Guizhou University, Guiyang, Guizhou, China
| | - Shi-min Wu
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, No.83, East Zhongshan Road, Guiyang, Guizhou, China
- Zunyi Medical University, Zunyi, 563006, China
| | - Yun-han Yang
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, No.83, East Zhongshan Road, Guiyang, Guizhou, China
- Medical College of Guizhou University, Guiyang, Guizhou, China
| | - De-jun Cui
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, No.83, East Zhongshan Road, Guiyang, Guizhou, China
- Medical College of Guizhou University, Guiyang, Guizhou, China
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Balasundaram A, Mitra TS, Tayubi IA, Zayed H, Doss GPC. Deciphering the miRNA-mRNA Interaction Landscape between Breast Cancer and Triple-Negative Breast Cancer: An Integrated Bioinformatics Approach. ACS OMEGA 2024; 9:24379-24395. [PMID: 38882157 PMCID: PMC11170726 DOI: 10.1021/acsomega.4c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/13/2024] [Accepted: 04/19/2024] [Indexed: 06/18/2024]
Abstract
Breast cancer (BC) is globally recognized as the second most prevalent form of cancer. It predominantly affects women and can be categorized into distinct types based on the overexpression of specific cancer receptors.The key receptors implicated in this context are the human epidermal growth factor receptor-2 (HER2), estrogen receptor (ER), and progesterone receptor (PR), alongside a particularly intricate subclass known as triple-negative breast cancer (TNBC). This subclassification is critical for the stratification of breast cancer and informs therapeutic decision-making processes. Due to a lack of therapeutic targets, such as growth factor receptors, TNBC is the most aggressive type. Hence, identifying targetable regulators such as miRNAs could pave the way for potential therapeutic interventions. To identify common differentially expressed mRNAs (DE-mRNAs) in BC, including TNBC, we leveraged two data sets from the GEO collection and The Cancer Genome Atlas (TCGA). Significant DE-mRNAs were identified through PPI, MCODE, CytoNCA, and CytoHubba analyses. Following this, miRNAs were predicted using mirDIP. We utilized GSE42568, GSE185645, and TCGA and identified 159 common DE-mRNAs. Using Cytoscape plug-ins, we identified the 10 most significant DE-mRNAs in BC. Using mirDIP, target miRNAs for 10 DE-mRNAs were identified. We conducted an advanced analysis on the TNBC GEO data set (GSE45498) to corroborate the significance of shared DE-mRNAs and DE-miRNAs in TNBC. We identified four downregulated DE-miRNAs, including hsa-miR-802, hsa-miR-1258, hsa-miR-548a-3p, and hsa-miR-2053, significantly associated with TNBC. Our study revealed significant miRNA-mRNA interactions, specifically hsa-miR-802/MELK, hsa-miR-1258/NCAPG, miR-548a-3p/CCNA2, and hsa-miR-2053/NUSAP1, in both BC and TNBC. The observed downregulation of hsa-miR-548a-3p is associated with diminished survival rates in BC patients, emphasizing their potential utility as prognostic indicators. Furthermore, the differential expression of mRNAs, including CCNB2, UBE2C, MELK, and KIF2C, correlates with reduced survival outcomes, signifying their critical role as potential targets for therapeutic intervention in both BC and TNBC. These findings highlight specific regulatory mechanisms that are potentially crucial for understanding and treating these cancer types.
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Affiliation(s)
- Ambritha Balasundaram
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Tanisha Saurav Mitra
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Iftikhar Aslam Tayubi
- Department of Computer Science, Faculty of Computing and Information Technology, Rabigh (FCITR), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha 2713, Qatar
| | - George Priya C Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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Li Y, Yang S, Qi L, Li Y, Wang X. Identification of a Group of Therapeutic Targets and Prognostic Biomarker for Triple Negative Breast Cancer. Adv Ther 2024; 41:1621-1636. [PMID: 38421558 DOI: 10.1007/s12325-024-02806-z] [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: 11/10/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
INTRODUCTION Triple-negative breast cancer (TNBC) is a highly heterogeneous disease. Mining differentially expressed genes of TNBC is helpful to explore new therapeutic targets. This study aimed to investigate diagnostic biomarker genes in TNBC compared to normal tissue. Additionally, we explored the functions and prognostic value of these key genes as well as potential targeted drugs that could affect these genes. METHODS Differential gene expression analysis was conducted using the R software with data from the Gene Expression Omnibus (GEO) database. Then, the identified differentially expressed genes (DEGs) were used to construct a protein-protein interaction (PPI) network using the Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape software. The mRNA expression levels of key genes were analyzed using the UALCAN database with data from The Cancer Genome Atlas (TCGA). Enrichment and survival analyses were performed using R software. In addition, potential compounds showing sensitivity to key genes were identified by gene set cancer analysis (GSCA). RESULTS Compared with normal tissues, a total of 203 DEGs were upregulated in TNBC. These DEGs participated in various biological processes including nuclear division, microtubule binding, cell cycle, and the p53 signaling pathway. Through the PPI network analysis, ten key genes were identified, among which four genes showed significant correlation with poor progression-free interval (PFI) in patients with TNBC. Moreover, the four survival-related genes were found to act as sensitive therapeutic targets. CONCLUSION The identified four key genes were considered new biomarkers for diagnosis and prognosis and also potential therapeutic targets for TNBC.
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Affiliation(s)
- Yan Li
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China
| | - Shengjie Yang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China
| | - Lu Qi
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China
| | - Yinjuan Li
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China
| | - Xinghe Wang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, No. 10 Tieyi Road, Haidian District, Beijing, 100038, China.
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Forooghi Pordanjani T, Dabirmanesh B, Choopanian P, Mirzaie M, Mohebbi S, Khajeh K. Extracting Potential New Targets for Treatment of Adenoid Cystic Carcinoma using Bioinformatic Methods. IRANIAN BIOMEDICAL JOURNAL 2023; 27:294-306. [PMID: 37873683 PMCID: PMC10707816 DOI: 10.61186/ibj.27.5.294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/25/2023] [Indexed: 12/17/2023]
Abstract
Background Adenoid cystic carcinoma is a slow-growing malignancy that most often occurs in the salivary glands. Currently, no FDA-approved therapeutic target or diagnostic biomarker has been identified for this cancer. The aim of this study was to find new therapeutic and diagnostic targets using bioinformatics methods. Methods We extracted the gene expression information from two GEO datasets (including GSE59701 and GSE88804). Different expression genes between adenoid cystic carcinoma (ACC) and normal samples were extracted using R software. The biochemical pathways involved in ACC were obtained by using the Enrichr database. PPI network was drawn by STRING, and important genes were extracted by Cytoscape. Real-time PCR and immunohistochemistry were used for biomarker verification. Results After analyzing the PPI network, 20 hub genes were introduced to have potential as diagnostic and therapeutic targets. Among these genes, PLCG1 was presented as new biomarker in ACC. Furthermore, by studying the function of the hub genes in the enriched biochemical pathways, we found that insulin-like growth factor type 1 receptor and PPARG pathways most likely play a critical role in tumorigenesis and drug resistance in ACC and have a high potential for selection as therapeutic targets in future studies. Conclusion In this study, we achieved the recognition of the pathways involving in ACC pathogenesis and also found potential targets for treatment and diagnosis of ACC. Further experimental studies are required to confirm the results of this study.
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Affiliation(s)
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Peyman Choopanian
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saleh Mohebbi
- ENT and Head & Neck Research Center, the Five Senses Health Institute, Rasoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
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High Expression of DLGAP5 Indicates Poor Prognosis and Immunotherapy in Lung Adenocarcinoma and Promotes Proliferation through Regulation of the Cell Cycle. DISEASE MARKERS 2023; 2023:9292536. [PMID: 36712920 PMCID: PMC9879687 DOI: 10.1155/2023/9292536] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 01/21/2023]
Abstract
Background Lung adenocarcinoma (LUAD) is one of the most common types of cancer in the respiratory system, with a high mortality and recurrence rate. The role of disc large-associated protein 5 (DLGAP5) in LUAD progression and tumor microenvironment (TME) remains unclear. This study is aimed at revealing the functional role of DLGAP5 in LUAD based on bioinformatics analysis and experimental validation. Methods Differential expression analysis, protein-protein interaction (PPI) network, and Cox regression analysis were applied to screen potential prognostic biomarkers. The mRNA and protein levels of DLGAP5 were analyzed using The Cancer Genome Atlas (TCGA) and the Human Protein Atlas (HPA) databases. The CCK-8 and colony formation assays were performed to assess the effect of DLGAP5 on cell proliferation. RNA sequencing (RNA-seq) and enrichment analyses were utilized to explore the biological functions of DLGAP5. Furthermore, flow cytometry was used to explore the role of DLGAP5 on the cell cycle. The ssGSEA algorithm in the R package "GSVA" was applied to quantify immune infiltrating cells, and the tumor immune dysfunction and exclusion (TIDE) algorithm was used to predict the efficacy of immunotherapy. Moreover, analyses using the cBioPortal and MethSurv databases were performed to evaluate the mutation and methylation of DLGAP5, respectively. Finally, the prognostic value of DLGAP5 was estimated using the TCGA and the Gene Expression Omnibus (GEO) databases. The nomogram model was constructed using the TCGA-LUAD cohort and evaluated by adopting calibration curves, time-dependent receiver operating characteristic (ROC) curves, and decision curve analysis (DCA). Results DLGAP5 mRNA and protein abundance were significantly elevated in LUAD, and knockdown of DLGAP5 remarkably suppressed lung cancer cell proliferation through induction of cell cycle G1 arrest. In addition, DLGAP5 expression was positively correlated with Th2 cells and negatively correlated with B cells, T follicular helper cells, and mast cells. LUAD patients with high DLGAP5 expression may be resistant to immunotherapy. Hypermethylation levels of the cg23678254 site of DLGAP5 or its enhanced expression were unfavorable for the survival of LUAD patients. Meanwhile, DLGAP5 expression was associated with TNM stages, tumor status, and therapy outcome. Notably, the prognostic model constructed based on DLGAP5 expression exhibited great predictive capability, which was promising for clinical applications. Conclusion DLGAP5 promotes lung cancer cell proliferation through regulation of the cell cycle and is associated with multiple immune infiltrating cells. Furthermore, DLGAP5 predicts poor prognosis and response to immunotherapy in lung adenocarcinoma.
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Yan C, Niu Y, Wang X. Blood transcriptome analysis revealed the crosstalk between COVID-19 and HIV. Front Immunol 2022; 13:1008653. [PMID: 36389792 PMCID: PMC9650272 DOI: 10.3389/fimmu.2022.1008653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/29/2022] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND The severe coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has resulted in the most devastating pandemic in modern history. Human immunodeficiency virus (HIV) destroys immune system cells and weakens the body's ability to resist daily infections and diseases. Furthermore, HIV-infected individuals had double COVID-19 mortality risk and experienced worse COVID-related outcomes. However, the existing research still lacks the understanding of the molecular mechanism underlying crosstalk between COVID-19 and HIV. The aim of our work was to illustrate blood transcriptome crosstalk between COVID-19 and HIV and to provide potential drugs that might be useful for the treatment of HIV-infected COVID-19 patients. METHODS COVID-19 datasets (GSE171110 and GSE152418) were downloaded from Gene Expression Omnibus (GEO) database, including 54 whole-blood samples and 33 peripheral blood mononuclear cells samples, respectively. HIV dataset (GSE37250) was also obtained from GEO database, containing 537 whole-blood samples. Next, the "Deseq2" package was used to identify differentially expressed genes (DEGs) between COVID-19 datasets (GSE171110 and GSE152418) and the "limma" package was utilized to identify DEGs between HIV dataset (GSE37250). By intersecting these two DEG sets, we generated common DEGs for further analysis, containing Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) functional enrichment analysis, protein-protein interaction (PPI) analysis, transcription factor (TF) candidate identification, microRNAs (miRNAs) candidate identification and drug candidate identification. RESULTS In this study, a total of 3213 DEGs were identified from the merged COVID-19 dataset (GSE171110 and GSE152418), and 1718 DEGs were obtained from GSE37250 dataset. Then, we identified 394 common DEGs from the intersection of the DEGs in COVID-19 and HIV datasets. GO and KEGG enrichment analysis indicated that common DEGs were mainly gathered in chromosome-related and cell cycle-related signal pathways. Top ten hub genes (CCNA2, CCNB1, CDC20, TOP2A, AURKB, PLK1, BUB1B, KIF11, DLGAP5, RRM2) were ranked according to their scores, which were screened out using degree algorithm on the basis of common DEGs. Moreover, top ten drug candidates (LUCANTHONE, Dasatinib, etoposide, Enterolactone, troglitazone, testosterone, estradiol, calcitriol, resveratrol, tetradioxin) ranked by their P values were screened out, which maybe be beneficial for the treatment of HIV-infected COVID-19 patients. CONCLUSION In this study, we provide potential molecular targets, signaling pathways, small molecular compounds, and promising biomarkers that contribute to worse COVID-19 prognosis in patients with HIV, which might contribute to precise diagnosis and treatment for HIV-infected COVID-19 patients.
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Affiliation(s)
- Cheng Yan
- *Correspondence: Cheng Yan, ; Xuannian Wang,
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ASPM, CDC20, DLGAP5, BUB1B, CDCA8, and NCAPG May Serve as Diagnostic and Prognostic Biomarkers in Endometrial Carcinoma. Genet Res (Camb) 2022; 2022:3217248. [PMID: 36186000 PMCID: PMC9509287 DOI: 10.1155/2022/3217248] [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: 05/03/2022] [Revised: 07/09/2022] [Accepted: 07/27/2022] [Indexed: 12/04/2022] Open
Abstract
Uterine Corpus Endometrial Carcinoma (UCEC), the most common gynecologic malignancy in developed countries, remains to be a major public health problem. Further studies are surely needed to elucidate the tumorigenesis of UCEC. Herein, intersecting 203 differentially expressed genes (DEGs) were identified with the GSE17025, GSE63678, and The Cancer Genome Atlas-UCEC datasets. The Gene Ontology/Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and protein-protein interaction (PPI) network were performed on those 203 DEGs. Intriguingly, 6 of the top 10 nodes in the PPI network were related to unfavorable prognosis, that is, ASPM, CDC20, DLGAP5, BUB1B, CDCA8, and NCAPG. The mRNA and protein expression levels of the 6 hub genes were elevated in UCEC tissues compared to normal tissues. Higher expression of the 6 hub genes was associated with poor prognostic clinicopathological characteristics. The receiver operating characteristic curve suggested the significant diagnostic ability of the 6 hub genes for UCEC. Then, underlying pathogeneses of UCEC including promoter methylation level, TP53 mutation status, genomic genetic variation, and immune cells infiltration were analyzed. The mRNA expression level of the 6 hub genes was also higher in cervical squamous cell carcinoma and endocervical adenocarcinoma, uterine carcinosarcoma, and ovarian serous cystadenocarcinoma tissues than in corresponding normal tissues. In conclusion, ASPM, CDC20, DLGAP5, BUB1B, CDCA8, and NCAPG may be considered diagnostic and prognostic biomarkers in UCEC.
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Rao X, Cao H, Yu Q, Ou X, Deng R, Huang J. NEAT1/MALAT1/XIST/PKD--Hsa-Mir-101-3p--DLGAP5 Axis as a Novel Diagnostic and Prognostic Biomarker Associated With Immune Cell Infiltration in Bladder Cancer. Front Genet 2022; 13:892535. [PMID: 35873473 PMCID: PMC9305813 DOI: 10.3389/fgene.2022.892535] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/16/2022] [Indexed: 12/24/2022] Open
Abstract
Background: The clinical value of the biomarkers of bladder cancer (BC) is limited due to their low sensitivity or specificity. As a biomarker, DLG associated protein 5 (DLGAP5) is a potential cell cycle regulator in cancer cell carcinogenesis. However, its functional part in BC remains unclear. Therefore, this study aims to identify DLGAP5 expression in BC and its potential diagnostic and prognostic values. Eventually, it predicts the possible RNA regulatory pathways of BC.Methods: Data on DLGAP5 expression levels in BC and normal bladder tissues were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. The receiver operating characteristic (ROC), Kaplan–Meier survival curves, and the univariate and multivariate Cox regression analysis determined the diagnostic and prognostic values of DLGAP5 in BC patients. Finally, the StarBase predicted the target RNAs and constructed networks using Cytoscape.Results: DLGAP5 expression was significantly upregulated in BC tissue, verified by the TCGA (p < 0.001), GSE3167, GSE7476, and GSE65635 datasets (p < 0.01). BC patients with increased DLGAP5 had poor overall survival (OS) (p = 0.01), disease specific survival (DSS) (p = 0.006) and progress free interval (DFI) (p = 0.007). The area under the ROC curve (AUC) was 0.913. The multivariate Cox analysis identified that lymphovascular invasion (p = 0.007) and DLGAP5 (p = 0.002) were independent prognostic factors.Conclusion: Increased DLGAP5 expression was closely associated with a poor prognosis in BC patients. In this case, DLGAP5 might be a diagnostic and prognostic biomarker for BC. DLGAP5 expression might be regulated by NEAT1/MALAT1/XIST/PKD--Hsa-mir-101-3p pathways.
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Affiliation(s)
- Xiaosheng Rao
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haiyan Cao
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Qingfeng Yu
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiuyu Ou
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ruiqi Deng
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jinkun Huang
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Jinkun Huang,
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Li Z, Ma Z, Xue H, Shen R, Qin K, Zhang Y, Zheng X, Zhang G. Chromatin Separation Regulators Predict the Prognosis and Immune Microenvironment Estimation in Lung Adenocarcinoma. Front Genet 2022; 13:917150. [PMID: 35873497 PMCID: PMC9305311 DOI: 10.3389/fgene.2022.917150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Abnormal chromosome segregation is identified to be a common hallmark of cancer. However, the specific predictive value of it in lung adenocarcinoma (LUAD) is unclear. Method: The RNA sequencing and the clinical data of LUAD were acquired from The Cancer Genome Atlas (TACG) database, and the prognosis-related genes were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were carried out for functional enrichment analysis of the prognosis genes. The independent prognosis signature was determined to construct the nomogram Cox model. Unsupervised clustering analysis was performed to identify the distinguishing clusters in LUAD-samples based on the expression of chromosome segregation regulators (CSRs). The differentially expressed genes (DEGs) and the enriched biological processes and pathways between different clusters were identified. The immune environment estimation, including immune cell infiltration, HLA family genes, immune checkpoint genes, and tumor immune dysfunction and exclusion (TIDE), was assessed between the clusters. The potential small-molecular chemotherapeutics for the individual treatments were predicted via the connectivity map (CMap) database. Results: A total of 2,416 genes were determined as the prognosis-related genes in LUAD. Chromosome segregation is found to be the main bioprocess enriched by the prognostic genes. A total of 48 CSRs were found to be differentially expressed in LUAD samples and were correlated with the poor outcome in LUAD. Nine CSRs were identified as the independent prognostic signatures to construct the nomogram Cox model. The LUAD-samples were divided into two distinct clusters according to the expression of the 48 CSRs. Cell cycle and chromosome segregation regulated genes were enriched in cluster 1, while metabolism regulated genes were enriched in cluster 2. Patients in cluster 2 had a higher score of immune, stroma, and HLA family components, while those in cluster 1 had higher scores of TIDES and immune checkpoint genes. According to the hub genes highly expressed in cluster 1, 74 small-molecular chemotherapeutics were predicted to be effective for the patients at high risk. Conclusion: Our results indicate that the CSRs were correlated with the poor prognosis and the possible immunotherapy resistance in LUAD.
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Affiliation(s)
- Zhaoshui Li
- Qingdao Medical College, Qingdao University, Qingdao, China
- Cardiothoracic Surgery Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Zaiqi Ma
- Cardiothoracic Surgery Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Hong Xue
- Heart Center Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Ruxin Shen
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Kun Qin
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Yu Zhang
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xin Zheng
- Cancer Center Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
- *Correspondence: Xin Zheng, ; Guodong Zhang,
| | - Guodong Zhang
- Thoracic Surgery Department, Shandong Cancer Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Xin Zheng, ; Guodong Zhang,
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Zeng X, Shi G, He Q, Zhu P. Screening and predicted value of potential biomarkers for breast cancer using bioinformatics analysis. Sci Rep 2021; 11:20799. [PMID: 34675265 PMCID: PMC8531389 DOI: 10.1038/s41598-021-00268-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/08/2021] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is the most common cancer and the leading cause of cancer-related deaths in women. Increasing molecular targets have been discovered for breast cancer prognosis and therapy. However, there is still an urgent need to identify new biomarkers. Therefore, we evaluated biomarkers that may aid the diagnosis and treatment of breast cancer. We searched three mRNA microarray datasets (GSE134359, GSE31448 and GSE42568) and identified differentially expressed genes (DEGs) by comparing tumor and non-tumor tissues using GEO2R. Functional and pathway enrichment analyses of the DEGs were performed using the DAVID database. The protein-protein interaction (PPI) network was plotted with STRING and visualized using Cytoscape. Module analysis of the PPI network was done using MCODE. The associations between the identified genes and overall survival (OS) were analyzed using an online Kaplan-Meier tool. The redundancy analysis was conducted by DepMap. Finally, we verified the screened HUB gene at the protein level. A total of 268 DEGs were identified, which were mostly enriched in cell division, cell proliferation, and signal transduction. The PPI network comprised 236 nodes and 2132 edges. Two significant modules were identified in the PPI network. Elevated expression of the genes Discs large-associated protein 5 (DLGAP5), aurora kinase A (AURKA), ubiquitin-conjugating enzyme E2 C (UBE2C), ribonucleotide reductase regulatory subunit M2(RRM2), kinesin family member 23(KIF23), kinesin family member 11(KIF11), non-structural maintenance of chromosome condensin 1 complex subunit G (NCAPG), ZW10 interactor (ZWINT), and denticleless E3 ubiquitin protein ligase homolog(DTL) are associated with poor OS of breast cancer patients. The enriched functions and pathways included cell cycle, oocyte meiosis and the p53 signaling pathway. The DEGs in breast cancer have the potential to become useful targets for the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Xiaoyu Zeng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Gaoli Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qiankun He
- School of Life Sciences, Zhengzhou University, Zhengzhou, China.
| | - Pingping Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China.
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Li W, Hu X, Li Y, Song K. Cytotoxicity and growth-inhibiting activity of Astragalus polysaccharides against breast cancer via the regulation of EGFR and ANXA1. J Nat Med 2021; 75:854-870. [PMID: 34043154 DOI: 10.1007/s11418-021-01525-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/03/2021] [Indexed: 12/17/2022]
Abstract
Astragalus polysaccharide (APS) has been frequently used as an adjuvant agent responsible for its immunoregulatory activity to enhance efficacy and reduce toxicity of chemotherapy used in the management of breast cancer. However, the other synergism mechanism of APS remains unclear. This study was performed to evaluate the potential targets and possible mechanism behind APS in vivo direct anti-tumor activity on breast cancer. Multiple biological detections were conducted to investigate the protein and mRNA expression levels of key targets. In total, 116 down-regulated and 73 up-regulated differential expressed genes (DEGs) were examined from 7 gene expression datasets. Top ten hub genes were obtained in four typical protein-protein interaction (PPI) network of DEGs involved in each specific biological process (BP, cell cycle, cell proliferation, cell apoptosis and death) that was related to inhibitory activity of APS in vitro against breast cancer cell lines. Four common DEGs (EGFR, ANXA1, KIF14 and IGF1) were further identified in the above four BP-PPI networks, among which EGFR and ANXA1 were the hub genes that were potentially linked to the progression of breast cancer. The results of biological detections indicated that the expression of EGFR in breast cancer cells was down-regulated, while the expression of ANXA1 was markedly increased in response to APS. In conclusion, the present study may provide potential molecular therapeutic targets and a new insight into the mechanism of APS against breast cancer.
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Affiliation(s)
- Wenfang Li
- School of Life Science and Technology, Weifang Medical University, Weifang, 261053, China
| | - Xueyan Hu
- State Key Laboratory of Fine Chemicals, Dalian R&D Center for Stem Cell and Tissue Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Yanjie Li
- School of Pharmacy, Weifang Medical University, Weifang, 261053, China
| | - Kedong Song
- State Key Laboratory of Fine Chemicals, Dalian R&D Center for Stem Cell and Tissue Engineering, Dalian University of Technology, Dalian, 116024, China.
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