Syndecan Family Gene and Protein Expression and Their Prognostic Values for Prostate Cancer.
Ontology highlight
ABSTRACT:
SUBMITTER: Santos NJ
PROVIDER: S-EPMC8395474 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The replication protein A (RPA)1-4 family are single-stranded DNA-binding proteins that are essential components of DNA replication, repair and recombination, and cell cycle regulation. The present study aimed to evaluate the prognostic value of the RPA family members in patients with gastric cancer (GC), using datasets retrieved from the Oncomine public database. Datasets were retrieved for the purpose of comparing the RPA expression levels between GC and normal tissues. Additionally, Kaplan-Meier analysis was used to compare the overall survival (OS) times of GC patients that expressed different levels of RPA proteins. RPA1, 2, and 3 expression levels were all significantly upregulated in gastric intestinal-type, diffuse gastric, and gastric mixed adenocarcinomas, compared with those in normal mucosal tissues. Moreover, high mRNA expression levels of RPA3 and 4 predicted poorer OS times in all GCs, as well as patients with human epidermal growth factor receptor 2-negative and -positive GC. The high-risk group, separated by RPA signature, showed a poorer outcome than the low-risk group. RPA3 was the most strongly correlated with CD4+ T-cell levels. In conclusion, RPAs are novel prognostic indicators in GC, and can also predict the features of immunological diseases. Future experimental investigation into the roles of RPAs concerning the pathogenesis and development of GC may provide a novel biomarker or therapeutic target, improving the prognosis of patients with GC.
| S-EPMC7038973 | biostudies-literature
Project description:The homeobox A cluster (HOXA) gene family, comprising 11 members, is involved in a wide spectrum of biological functions in human cancers. However, there is little research on the expression profile and prognostic values of HOXA genes in laryngeal squamous cell cancer (LSCC). Based on updated public resources and integrative bioinformatics analysis, we assessed the expression profile and prognostic values of the HOXA family members. Expression and methylation data on HOXA family members were obtained from The Cancer Genome Atlas (TCGA). The prognostic values of HOXA members and clinical features were identified. A gene set enrichment analysis (GSEA) was conducted to explore the mechanism underlying the involvement of HOXA members in LSCC. The associations between tumor immune infiltrating cells (TIICs) and the HOXA family members were evaluated using the Tumor Immune Estimation Resource (TIMER) database. HOXA2 and HOXA4 were downregulated and HOXA7 and HOXA9-13 were upregulated in LSCC. Upregulation of HOXA10, HOXA11, and HOXA13, along with two clinical characteristics (M stage and gender), were associated with a poor LSCC prognosis based on the results of univariate and multivariate Cox proportional hazards regression analyses. Although there were no significant correlations between TIICs and HOXA members, the GSEA results indicated that HOXA members participate in multiple biological processes underlying tumorigenesis. This study comprehensively analyzed the HOXA members, providing insights for further investigation of the HOXA family members as potential targets in LSCC.
| S-EPMC7136465 | biostudies-literature
Project description:Background: Gastric cancer (GC) remains the fifth most commonly diagnosed malignancy worldwide, with a poor prognosis. The lysyl oxidase (LOX) family, a type of secreted copper-dependent amine oxidases, is comprised of LOX and four LOX-like (LOXL) 1-4 isoforms and has been reported to be dysregulated in a number of different type cancers. However, the diverse expression patterns and prognostic values of LOX family in GC have yet to be systematically analyzed. Methods: ONCOMINE, GEPIA, UALCAN, Kaplan-Meier Plotter, LOGpc, cBioPortal, GeneMANIA and Metascape databases were utilized in this study to analyze the expression, prognostic values, mutations and functional networks of LOX family in GC. Results: The mRNA expression levels of LOX, LOXL1 and LOXL2 were significantly higher in GC, the expression level of LOXL3 was contrary in different databases, while the expression level of LOXL4 made no difference; the expression levels of LOX, LOXL1 and LOXL3 were higher in stages 2-4 than that of normal tissues and stage 1, while the mRNA level of LOXL2 in stage 1-4 was higher than normal tissues; patients with high expression of LOX and LOXL 2-4 had poor OS; the genes correlated with LOX and LOXL2 were enriched in extracellular matrix organization, vasculature development and skeletal system development. Conclusion: Our results indicated that the LOX family, especially LOX and LOXL2, might play an important role in GC oncogenesis, and they may become biomarkers for predicting tumor prognosis and potential targets for tumor therapy.
| S-EPMC8812723 | biostudies-literature
Project description:Accumulated studies have provided controversial evidences of expression patterns and prognostic value of the GATA family in human ovarian cancer. In the present study, we accessed the distinct expression and prognostic roles of 7 individual members of GATA family in ovarian cancer (OC) patients through Oncomine analysis, CCLE analysis, Human Protein Atlas (HPA), Kaplan-Meier plotter (KM plotter) database, cBioPortal and Metascape. Our results indicated that GATA1, GATA3, GATA4 and TRPS1 mRNA and protein expression was significantly higher in OC than normal samples. High expression of GATA1, GATA2, and GATA4 were significantly correlated with better overall survival (OS), while increased GATA3 and GATA6 expression were associated with worse prognosis in OC patients. GATA1, GATA2, GATA3 and GATA6 were closely related to the different pathological histology, pathological grade, clinical stage and TP53 mutation status of OC. The genetic variation and interaction of the GATA family may be closely related to the pathogenesis and prognosis of OC, and the regulatory network composed of GATA family genes and their neighboring genes are mainly involved in Notch signaling pathway, Th1 and Th2 cell differentiation and Hippo signaling pathway. Transcriptional GATA1/2/3/4/6 could be prognostic markers and potential therapeutic target for OC patients.
| S-EPMC9052646 | biostudies-literature
Project description:The "A Disintegrin and Metalloproteinase with Thrombospondin Motif" (ADAMTS) family of genes is involved in the occurrence and development of different cancers. However, the prognostic value of these genes in gastric cancer (GC) has not been revealed. The present study was thus conducted to determine the prognostic value for the ADAMTS family of genes in GC. First, we evaluated the mRNA expression levels of the ADAMTS family in GC patients using a GEPIA dataset. Thereafter, we determined the prognostic value of these genes by analyzing their mRNA level using the Kaplan-Meier Plotter database. The mRNA expression level of ADAMTS12 was randomly validated by qRT-PCR and meta-analysis while its coexpression genes were derived using Coexpedia. Finally, we performed Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses using the OmicShare Tools. Compared to normal tissues, expression of ADAMTS2 and 12 was significantly higher while that of ADAMTS1, 13, and 15 was significantly lower in GC tissues. According to the RNA-seq and gene chip data, the ADAMTS family (6, 7, 12, 15, and 18) of genes was closely related to the prognosis of GC, and their high expression levels were associated with poor prognosis and survival time. In addition, ADAMTS12 was highly expressed in 20 pairs of GC tissues based on RT-PCR (P=0.016) and meta-analysis (SMD: 0.73, 95% CI: 0.32-1.14, P < 0.001). GO and KEGG pathway analyses indicated that the ADAMTS12 coexpressed genes were enriched in the pathways of extracellular matrix organization, extracellular matrix structural constituent, extracellular matrix, and protein digestion and absorption. Herein, we discovered the prognostic values and biological roles of the ADAMTS genes in GC.
| S-EPMC7455834 | biostudies-literature
Project description:BackgroundHead and neck squamous cell carcinoma (HNSC) ranks as the sixth most common malignancy. The identification of highly specific and sensitive prognostic markers and potential drug targets can contribute to enhanced patient prognosis and individualized treatments. Heat shock proteins (HSPs) act as molecular chaperones and play a crucial role in maintaining cell homeostasis. Recently, research has indicated that HSPs also act as "evil chaperones" in cancer development.MethodsIn this study, we assessed the expression of HSPs in HNSC patients using the ONCOMINE, GEPIA, and UALCAN databases. Mutations of HSP genes were also analysed using the cBioPortal database. Additionally, the expression levels of HSPs were verified using the Human Protein Altas (THPA) database.ResultsWe found that the expression levels of HSPH1, HSPD1, SERPINH1, HSPA4, and HSP90AA1 were significantly higher in tissues from HNSC patients compared with normal tissues. Moreover, HSPH1, HSPD1, SERPINH1, HSPA4 and HSP90AA1 expressions were linked to disease progression. Survival analysis with the GEPIA and OncoLnc databases indicated that upregulation of HSPH1, HSPD1, SERPINH1, HSPA4 and HSP90AA1 was related to poor overall survival (OS).ConclusionThis study suggests that the HSPH1, HSPD1, SERPINH1, HSPA4 and HSP90AA1 genes are potential clinical targets and prognostic biomarkers for patients with HNSC.
| S-EPMC7278206 | biostudies-literature
Project description:Non-small cell lung cancer (NSCLC) is a highly malignant type of cancer with a poor 5-year survival rate. The development of prognostic biomarkers and novel drug targets are required in order to improve the survival for NSCLC patients. Signal transducer and activator of transcription (STAT) proteins are cytoplasmic transcription factors known to play key roles in many cellular biological processes. However, the roles of STAT family members in the development and progression of NSCLC have not yet been apparently determined. Our study investigated the roles of STATs in the prognosis of NSCLC using cBioPortal, Human Protein Atlas, ONCOMINE, and Kaplan-Meier Plotter databases. High mutation rate of STATs existed in both lung adenocarcinoma (ADE) patients and squamous cell carcinoma (SCC) patients. High mRNA expression of STAT2 was significantly associated with shorter overall survival (OS) in NSCLC patients, while increased STAT5 and STAT6 were associated with better OS in NSCLC patients. We further found that increased mRNA expressions of STAT2 and STAT3 predicted unfavorable overall survival (OS) while high mRNA expression of STAT5B and STAT6 related to favorable OS for lung ADE patients. However, no significant correlation was identified for lung SCC patients. In stratified survival analysis, high expression of STAT2 predicted poor prognosis in stage II NSLCC patients, surgical margins negative patients and female patients. Taken together, our results illustrated that STAT5B and STAT6 could be effective prognostic biomarkers for survivals of NSCLC patients. And STAT2 might be a promising therapeutic target for the treatment of NSCLC as well as ADE.
| S-EPMC6731411 | biostudies-literature
Project description:Background A disintegrin-like and metalloproteinase domain with thrombospondin type 1 motifs (ADAMTS)-like proteins, including ADAMTSL1-6 and papilin, which are part of the mammalian ADAMTS superfamily, appear to be relevant to extracellular matrix function and the regulation of ADAMTS protease activity. Their roles in tumor initiation and progression and regulating the tumor microenvironment (TME) are now recognized. Methods In the present study, a comprehensive investigation of the pan-cancer effects of ADAMTSLs and their associations with patient survival, drug responses, and the TME was performed by integrating The Cancer Genome Atlas (TCGA) data and annotated data resources. Results The expression of ADAMTSL family members was found to be dysregulated in many cancer types. More importantly, their expression was frequently associated with patients’ overall survival (OS), drug responses, and the TME. ADAMTSL1, ADAMTSL4, and ADAMTSL5 were primarily associated with aggressive phenotypes, while PAPLN was more frequently associated with a favorable prognosis. In a non-small cell lung cancer (NSCLC) cohort, Thrombospondin Type 1 Domain Containing 4 (THSD4) (ADAMTSL6) and Papilin (PAPLN) were associated with immune checkpoint inhibitor (ICI) sensitivity in samples from the Gene Expression Omnibus repository (GSE135222). Twenty and 30 proteins related to THSD4 and PAPLN, respectively, were identified through a proteomic analysis of 18 Chinese lung adenocarcinoma patients. Conclusions Our findings extend understandings of the role of the ADAMTSL family in cancers and are a valuable resource on their clinical utility. This article provides insight into the clinical importance of next-generation sequencing technology to identify novel biomarkers for prognosis and investigate therapeutic strategy for clinical benefit.
| S-EPMC8576672 | biostudies-literature
Project description:OBJECTIVE:Exhibiting high consistence in sequence and structure, S100 family members are interchangeable in function and they show a wide spectrum of biological processes, including proliferation, apoptosis, migration, inflammation and differentiation and the like. While the prognostic value of each individual S100 in ovarian cancer is still elusive. In current study, we investigated the prognostic value of S100 family members in the ovarian cancer. METHODS:We used the Kaplan Meier plotter (KM plotter) database, in which updated gene expression data and survival information are from 1657 ovarian cancer patients, to assess the relevance of individual S100 family mRNA expression to overall survival in various ovarian cancer subtypes and different clinicopathological features. RESULTS:It was found that high expression of S100A2 (HR?=?1.18, 95%CI: 1.04-1.34, P?=?0.012), S100A7A (HR?=?1.3, 95%CI: 1.04-1.63, P?=?0.02),S100A10 (HR?=?1.2, 95%CI: 1.05-1.38, P?=?0.0087),and S100A16 (HR?=?1.23, 95%CI: 1-1.51, P?=?0.052) were significantly correlated with worse OS in all ovarian cancer patients, while the expression of S100A1 (HR?=?0.87, 95%CI: 0.77-0.99, P?=?0.039), S100A3 (HR?=?0.83, 95%CI: 0.71-0.96, P?=?0.0011), S100A5 (HR?=?0.84, 95%CI: 0.73-0.97, P?=?0.017), S100A6 (HR?=?0.84, 95%CI: 0.72-0.98, P?=?0.024), S100A13 (HR?=?0.85, 95%CI:0.75-0.97, P?=?0.014) and S100G (HR?=?0.86, 95%CI: 0.74-0.99, P?=?0.041) were associated with better prognosis. Furthermore, we assessed the prognostic value of S100 expression in different subtypes and the clinicopathological features, including pathological grades, clinical stages and TP53 mutation status, of ovarian cancer patients. CONCLUSION:Comprehensive understanding of the S100 family members may have guiding significance for the diagnosis and outcome of ovarian cancer patients.
| S-EPMC6296138 | biostudies-literature
Project description:Chromobox (CBX) family proteins are canonical components in polycomb repressive complexes 1 (PRC1), with epigenetic regulatory function and transcriptionally repressing target genes via chromatin modification. A plethora of studies have highlighted the function specifications among CBX family members in various cancer, including lung cancer, colon cancer and breast cancer. Nevertheless, the functions and prognostic roles of distinct CBX family members in breast cancer (BC) remain elusive. In this study, we reported the prognostic values of CBX family members in patients with BC through analysis of a series of databases, including CCLE, ONCOMINE, Xena Public Data Hubs, and Kaplan-Meier plotter. It was found that the mRNA expression of CBX family members were noticeably higher in BC than normal counterparts. CBX2 was highly expressed in Basal-like and HER-2 subtypes, while CBX4 and CBX7 expressions were enriched in Luminal A and Luminal B subtypes of BC. Survival analysis revealed that CBX1, CBX2 and CBX3 mRNA high expression was correlated to worsen relapse-free survival (RFS) for all BC patients, while CBX4, CBX5, CBX6 and CBX7 high expression was correlated to better RFS in this setting. Noteworthily, CBX1 and CBX2 were associated with chemoresistance whereas CBX7 was associated with tamoxifen sensitivity, as well as chemosensitivity in breast tumors. Therefore, we propose that CBX1, CBX2 and CBX7 are potential targets for BC treatment. The results might be beneficial for better understanding the complexity and heterogeneity in the molecular underpinning of BC, and to develop tools to more accurately predict the prognosis of patients with BC.
| S-EPMC5696189 | biostudies-literature