scholarly journals Pan-cancer analysis identifies FAM49B as an immune-related prognostic maker for hepatocellular carcinoma

2022 ◽  
Vol 13 (1) ◽  
pp. 278-289
Author(s):  
Feng Xu ◽  
Jionghuang Chen ◽  
Dihua Huang
Keyword(s):  
Hepatocellular Carcinoma ◽  
Pan Cancer ◽  
Prognostic Maker

scholarly journals DUXAP8 a Pan-Cancer Prognostic Marker Involved in the Molecular Regulatory Mechanism in Hepatocellular Carcinoma: A Comprehensive Study Based on Data Mining, Bioinformatics, and in vitro Validation

2019 ◽  
Vol Volume 12 ◽  
pp. 11637-11650 ◽  
Author(s):  
Chaosen Yue ◽  
Chaojie Liang ◽  
Pengyang Li ◽  
Lijun Yan ◽  
Dongxin Zhang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Data Mining ◽  
Prognostic Marker ◽  
Regulatory Mechanism ◽  
Pan Cancer ◽  
Comprehensive Study

scholarly journals Cyclin-Dependent Kinase and Antioxidant Gene Expression in Cancers with Poor Therapeutic Response

2020 ◽  
Vol 13 (2) ◽  
pp. 26
Author(s):  
George S. Scaria ◽  
Betsy T. Kren ◽  
Mark A. Klein
Keyword(s):  
Hepatocellular Carcinoma ◽  
Pancreatic Cancer ◽  
Antioxidant Defense ◽  
Treatment Strategies ◽  
The Cancer Genome Atlas ◽  
Cyclin Dependent Kinase ◽  
Critical Pathways ◽  
Cancer Genome Atlas ◽  
Antioxidant Gene Expression ◽  
Pan Cancer

Pancreatic cancer, hepatocellular carcinoma (HCC), and mesothelioma are treatment-refractory cancers, and patients afflicted with these cancers generally have a very poor prognosis. The genomics of these tumors were analyzed as part of The Cancer Genome Atlas (TCGA) project. However, these analyses are an overview and may miss pathway interactions that could be exploited for therapeutic targeting. In this study, the TCGA Pan-Cancer datasets were queried via cBioPortal for correlations among mRNA expression of key genes in the cell cycle and mitochondrial (mt) antioxidant defense pathways. Here we describe these correlations. The results support further evaluation to develop combination treatment strategies that target these two critical pathways in pancreatic cancer, hepatocellular carcinoma, and mesothelioma.

scholarly journals Pan-cancer analysis of the oncogenic role of discs large homolog associated protein 5 (DLGAP5) in human tumors

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Neng Tang ◽  
Xiaolin Dou ◽  
Xing You ◽  
Qiman Shi ◽  
Mujing Ke ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Carcinoma ◽  
Cell Lines ◽  
Cellular Proliferation ◽  
Germ Cell Tumors ◽  
Enrichment Analysis ◽  
Human Tumors ◽  
Testicular Germ Cell ◽  
Pan Cancer

Abstract Background In recent years, there have been many studies on the relationship between DLGAP5 and different types of cancers, yet there is no pan-cancer analysis of DLGAP5. Therefore, this study aims to analyze the roles of DLGAP5 in human tumors. Methods Firstly, we evaluated the expression level of DLGAP5 in 33 types of tumors throughout the datasets of TCGA (Cancer Genome Atlas) and GEO (Gene Expression Synthesis). Secondly, we used the GEPIA2 and Kaplan-Meier plotter to conduct Survival prognosis analysis. Additionally, cBioPortal web was utilized to analyze the genetic alteration of DLGAP5, after which we selected hepatocellular carcinoma (HCC) cell lines to define the function of DLGAP5. Last but not least, we performed immune infiltration analysis and DLGAP5-related gene enrichment analysis. Results DLGAP5 is highly expressed in most type of cancers, and there is a significant correlation between the expression of DLGAP5 and the prognosis of cancer patients. We have observed that DLGAP5 promotes the proliferation and invasion of hepatocellular carcinoma (HCC) cell lines. We also found that DLGAP5 expression was related with the CD8+ T-cell infiltration status in kidney renal clear cell carcinoma, uveal melanoma, and thymoma, and cancer-associated fibroblast infiltration was observed in breast invasive carcinoma, kidney renal papillary cell carcinoma and testicular germ cell tumors. In addition, enrichment analysis revealed that cell cycle- and oocyte meiosis-associated functions were involved in the functional mechanism of DLGAP5. Conclusions Taken together, our unpresented pan-cancer analysis of DLGAP5 provides a relatively integrative understanding of the oncogenic role of DLGAP5 in various tumors. DLGAP5 may prompt HCC cellular proliferation, invasion and metastasis. All of these provides solid basement and will promote more advanced understanding the role of DLGAP5 in tumorigenesis and development from the perspective of clinical tumor samples and cells.

scholarly journals 1304Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the EPIC study

2021 ◽  
Vol 50 (Supplement_1) ◽  
Author(s):  
Marie Breeur ◽  
Pietro Ferrari ◽  
Julie Schmidt ◽  
Ruth Travis ◽  
Tim Key ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cancer Risk ◽  
Statistical Power ◽  
Conditional Logistic Regression ◽  
Total Sample ◽  
Case Control ◽  
Cancer Site ◽  
Case Control Studies ◽  
Cancer Types ◽  
Pan Cancer

Abstract Background Metabolomics studies in cancer epidemiology have mostly focused on single metabolite-cancer site associations. Pan-cancer analyses may have larger statistical power when identifying metabolites showing consistent associations across cancer sites, while allowing the identification of site-specific associations. Methods Data from seven cancer-specific case-control studies nested within the European Prospective Investigation into Cancer and Nutrition Cohort (EPIC) were pooled, resulting in a total sample of 7,957 case-control pairs from eight cancer types (breast, colorectal, endometrial, gallbladder, kidney, localized prostate and advanced prostate cancer, and hepatocellular carcinoma). A total of 117 pre-diagnostic blood metabolites were measured. After clustering the most highly correlated ones together, we studied the association between 50 features (metabolites or clusters of metabolites) and cancer risk in multivariate penalized conditional logistic regression models controlled for body mass index using the data shared lasso. Results We identified: (i) 8 features with consistent associations across cancer sites: e.g., glutamine and C4-acylcarnitine, one cluster of lysophosphatidylcholines and one of phosphatidylcholines were inversely associated with cancer, while C10-acylcarnitine, valine and proline showed positive associations; (ii) 11 features with heterogeneous associations across cancer sites: e.g., arginine was positively associated with colorectal cancer only, while one cluster of sphingomyelins was associated inversely with hepatocellular carcinoma and positively with endometrial cancer. Conclusions Our pan-cancer analysis notably identified metabolites showing consistent associations with cancer risk across different cancer-types. Key messages Our results could lead to the identification of common pathways shared across different cancer types.

scholarly journals Diagnostic significance and carcinogenic mechanism of pan-cancer gene POU5F1 in liver hepatocellular carcinoma

2020 ◽  
Author(s):  
Dingdong He ◽  
Xiaokang Zhang ◽  
Jiancheng Tu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Meta Analysis ◽  
Diagnostic Value ◽  
Gene Set Enrichment Analysis ◽  
Clinicopathological Parameters ◽  
Cancer Gene ◽  
Hub Genes ◽  
Liver Hepatocellular Carcinoma ◽  
The Impact ◽  
Pan Cancer

Abstract Background The prognostic and clinicopathological significance of POU Class 5 Homeobox 1 (POU5F1) among various cancers is disputable heretofore. The diagnostic value and function mechanism of POU5F1 in liver hepatocellular carcinoma (LIHC) have not been studied thoroughly. Methods An integrative strategy of meta-analysis, bioinformatics and wet-lab approach was used to explore the diagnostic and prognostic significance of POU5F1 in various types of tumors, especially in LIHC. Meta-analysis was utilized to investigate the impact of POU5F1 on prognosis and clinicopathological parameters in various cancers. The expression level and diagnostic value of POU5F1 were assessed by qPCR in plasma collected from LIHC patients and controls. The correlation between POU5F1 and tumor infiltrating immune cells (TIICs) in LIHC was evaluated by CIBERSORT. Gene set enrichment analysis (GSEA) was performed based on TCGA. Hub genes and related pathways were identified on the basis of co-expression genes of POU5F1. Results Elevated POU5F1 was associated with poor OS, DFS, RFS and DSS in various cancers. POU5F1 was confirmed as an independent risk factor for LIHC and correlated with tumor occurrence, stage and invasion depth. The combination of POU5F1 and AFP in plasma was with high diagnostic validity (AUC = 0.902, P < 0.001). Specifically, the level of POU5F1 was correlated with infiltrating levels of B cells, T cells, dendritic cells and monocytes in LIHC. GSEA indicated POU5F1 participated in multiple cancer related pathways and cell proliferation pathways. Moreover, CBX3, CCHCR1 and NFYC were filtered as the central hub genes of POU5F1. Conclusions Our study identified POU5F1 as a pan-cancer gene could not only be a prognostic and diagnostic biomarker in various cancers, especially in LIHC, but functionally carcinogenic in LIHC.

Hepatocellular carcinoma with ARID1A mutation is associated with higher TMB and poor survival.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e16667-e16667 ◽  
Author(s):  
Yaorong Peng ◽  
Bowen Gao ◽  
Zhenyu Zhou ◽  
Tingting Chen ◽  
Wenzhuan Xie ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cancer Patients ◽  
Gene Mutation ◽  
Sequencing Data ◽  
Coding Region ◽  
Poor Prognostic Factor ◽  
Synonymous Mutations ◽  
Significant Difference ◽  
Chinese Cohort ◽  
Pan Cancer

e16667 Background: Hepatocellular carcinoma (HCC) is a heterogeneous disease that lacks molecular predictors of response to available treatments. AT-rich interactive domain 1A (ARID1A), a SWI/SNF chromatin remodeling gene, is commonly mutated in human cancers and hypothesized to be a tumor suppressor gene. In recent years, immune checkpoint blockade immunotherapies (ICIs) are promising therapies for multiple cancers including HCC, and tumor mutation burden (TMB) was an important biomarker to predict the efficacy of ICIs. Besides, previous research reported that ARID1A deficiency was associated with mismatch repair (MMR) in cancer, and may cooperated with ICIs. Methods: Whole exome sequencing data of 10336 pan-cancer patients including 353 HCC patients was obtained from the Cancer Genome Altas (TCGA). Next generation sequencing (NGS) data of 15849 pan-cancer patients including 1926 HCC patients from Chinese clinical dataset were analyzed to explore the correlation between ARID1A gene mutation and TMB. TMB was defined as total number of somatic non-synonymous mutations in coding region. Prognostic data of 136 HCC patients were obtained from the MSK-IMPACT Clinical Sequencing Cohort (MSKCC). Results: In total, 8.62% (891/10336) of pan-cancer patients in TCGA harboring ARID1A mutation and 8.47% (3188/37628) in Chinese cohort, while mutant percentage of HCC was 9.35% (33/353) in TCGA, 9.03% (174/1926) in Chinese cohort, the alternation frequency of ARID1A in two cohorts was no significant difference (P = 0.3334). The medium TMB level of ARID1A mutant group was higher than wild-type group with significant difference both in Chinese pan-cancer and HCC (medium TMB level, P < 0.0001). Results of 18 kinds of ARID1A mutated tumors patients in TCGA cohort indicated that ARID1A mutation was an independent risk factor in liver cancer affecting overall survival (OS, HR 2.43, 95% IC 1.07-5.54, P = 0.0286). Besides, Kaplan-Meier analysis was performed on HCC patients in MSKCC cohort, ARID1A statue resulted in significantly shorter OS (median, 12.2 vs 21.43 months; HR 2.5; P = 0.0092). Conclusions: The results indicated that ARID1A gene mutation was a poor prognostic factor in hepatocellular carcinoma, and these mutational states were associated with higher TMB level, which might be a potential positive biomarker of immunotherapy.

scholarly journals Diagnostic significance and carcinogenic mechanism of pan‐cancer gene POU5F1 in liver hepatocellular carcinoma

2020 ◽  
Vol 9 (23) ◽  
pp. 8782-8800
Author(s):  
Dingdong He ◽  
Xiaokang Zhang ◽  
Jiancheng Tu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cancer Gene ◽  
Diagnostic Significance ◽  
Liver Hepatocellular Carcinoma ◽  
Pan Cancer

scholarly journals Comprehensive Pan-Cancer Genomic Analysis Reveals PHF19 as a Carcinogenic Indicator Related to Immune Infiltration and Prognosis of Hepatocellular Carcinoma

2022 ◽  
Vol 12 ◽  
Author(s):  
Zheng-yi Zhu ◽  
Ning Tang ◽  
Ming-fu Wang ◽  
Jing-chao Zhou ◽  
Jing-lin Wang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Tumor Microenvironment ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Interaction Network ◽  
Suppressor Cells ◽  
Cell Receptor ◽  
Phd Finger ◽  
Immune Infiltration ◽  
Pan Cancer

BackgroundAs a crucial constituent part of Polycomb repressive complex 2, PHD finger protein 19 (PHF19) plays a pivotal role in epigenetic regulation, and acts as a critical regulator of multiple pathophysiological processes. However, the exact roles of PHF19 in cancers remain enigmatic. The present research was primarily designed to provide the prognostic landscape visualizations of PHF19 in cancers, and study the correlations between PHF19 expression and immune infiltration characteristics in tumor microenvironment.MethodsRaw data in regard to PHF19 expression were extracted from TCGA and GEO data portals. We examined the expression patterns, prognostic values, mutation landscapes, and protein-protein interaction network of PHF19 in pan-cancer utilizing multiple databases, and investigated the relationship of PHF19 expression with immune infiltrates across TCGA-sequenced cancers. The R language was used to conduct KEGG and GO enrichment analyses. Besides, we built a risk-score model of hepatocellular carcinoma (HCC) and validated its prognostic classification efficiency.ResultsOn balance, PHF19 expression was significantly higher in cancers in comparison with that in noncancerous samples. Increased expression of PHF19 was detrimental to the clinical prognoses of cancer patients, especially HCC. There were significant correlations between PHF19 expression and TMB or MSI in several cancers. High PHF19 levels were critically associated with the infiltration of myeloid-derived suppressor cells (MDSCs) and Th2 subsets of CD4+ T cells in most cancers. Enrichment analyses revealed that PHF19 participated in regulating carcinogenic processes including cell cycle and DNA replication, and was correlated with the progression of HCC. Intriguingly, GSEA suggested that PHF19 was correlated with the cellular components including immunoglobulin complex and T cell receptor complex in HCC. Based on PHF19-associated functional gene sets, an eleven-gene prognostic signature was constructed to predict HCC prognosis. Finally, we validated pan-cancer PHF19 expression, and its impacts on immune infiltrates in HCC.ConclusionThe epigenetic related regulator PHF19 participates in the carcinogenic progression of multiple cancers, and may contribute to the immune infiltration in tumor microenvironment. Our study suggests that PHF19 can serve as a carcinogenic indicator related to prognosis in pan-cancer, especially HCC, and shed new light on therapeutics of cancers for clinicians.

scholarly journals Pan-cancer analysis identifies ITIH1 as a novel prognostic indicator for hepatocellular carcinoma

Aging ◽  
2021 ◽  
Author(s):  
Qing-hua Chang ◽  
Ting Mao ◽  
Yan Tao ◽  
Tao Dong ◽  
Xuan-xuan Tang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Prognostic Indicator ◽  
Pan Cancer
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