Genetic variants in the exon region of versican predict survival of patients with resected early-stage hepatitis B virus-associated hepatocellular carcinoma

Prognostic value of genotyping in hepatocellular carcinoma: A systematic review

Primary liver cancer is the sixth most commonly diagnosed cancer and the third leading cause of cancer death. Advances in sequencing technology are opening genomics to widespread application for diagnosis and research. The poor prognosis of advanced HCC warrants a personalized approach. The objective was to assess the value of genotyping for risk stratification and prognostication of HCC. We performed a systematic review of manuscripts published on MEDLINE from 1 January 2009 to 1 January 2022, addressing the value of genotyping for HCC risk stratification and prognostication. Publication information for each has been collected using a standardized data extraction form. Twenty-five articles were analysed. This study showed that various genomics approaches (i.e., NGS, SNP, CASP or polymorphisms in circadian genes' association) provided predictive and prognostic information, such as disease control rate, median progression-free survival, and shorter median overall survival. Genotyping, which advances in understanding the molecular origin, could be a solution to predict prognosis or treatment response in patients with HCC.

Joint effect of THBS2 and VCAN accelerating the poor prognosis of gastric cancer

OBJECTIVE

Gastric cancer is the most common malignant tumor of the digestive system. The progression from gastritis to gastric cancer may be related to genetic factors, but the specific molecular mechanism remains unclear. Therefore, an in-depth study of the molecular mechanism of gastritis and gastric cancer is significant.

METHODS

We downloaded two gene profiles, GSE2669 and GSE116312, from the Gene Expression Omnibus (GEO) database. This study aims to apply bioinformatics technology to mine differentially expressed genes (DEGs), DEGs annotation, protein-protein interaction (PPI) network creation, and hub gene identification and expression between gastric cancer patients and gastritis patients. Overall survival analysis of hub genes, analysis by comparative toxicogenomics database for hub genes in gastric cancer, THBS2 and VCAN protein expression by immunohistochemistry for gastric cancer and gastritis as well as design of the biological process (BP) neural network was implemented.

RESULTS

The MSLN, SPP1, THBS2, SPARC, FN1, IGFBP7, VCAN were up-regulated in gastric carcinoma samples, while FGA was down-regulated. The protein expression of THBS2 and VCAN in gastric cancer was significantly higher than that in gastritis. VCAN protein expression was positively associated with tumor invasion (P = 0.011) and HER2 overexpression (P = 0.031). Strong correlation among THBS2, VCAN, and gastric cancer based on the BP neural network.

CONCLUSION

THBS2 and VCAN may be potential targets for improving gastric cancer patients' diagnosis and clinical efficacy.

Angiogenesis-Related Gene Expression Signatures Predicting Prognosis in Gastric Cancer Patients

Simple Summary

To elucidate the role of angiogenesis as a prognostic signature in gastric cancer, we analyzed the expression level of 36 angiogenesis-related genes (ARGs) from Stomach Adenocarcinoma (STAD) from The Cancer Genome Atlas (TCGA). Consensus clustering analysis showed two major angiogenesis-related types: one related to more aggressive clinicopathological characteristics and worse survival, and the other related to lower tumor, lymph node, metastasis (TNM) stage and better outcomes. Our analysis of TCGA with a least absolute shrinkage and selection operator (LASSO) regression model identified 10 genes associated with overall survival in gastric cancer patients. With this gene signature, we computed angiogenesis-related gene signature risk scores for individual cancer patients that predicted overall and disease-free survival, which were further validated in the independent dataset Asian Cancer Research Group (ACRG). Moreover, an overall survival (OS)-related nomogram was established and had better performance in prognosis prediction than TNM stage. Our analysis provides a comprehensive map of ARGs that can be serve as useful biomarkers for gastric cancer.

Abstract

Increasing evidence indicates that angiogenesis is crucial in the development and progression of gastric cancer (GC). This study aimed to develop a prognostic relevant angiogenesis-related gene (ARG) signature and a nomogram. The expression profile of the 36 ARGs and clinical information of 372 GC patients were extracted from The Cancer Genome Atlas (TCGA). Consensus clustering was applied to divide patients into clusters 1 and 2. Least absolute shrinkage and selection operator (LASSO) Cox regression analyses were used to identify the survival related ARGs and establish prognostic gene signatures, respectively. The Asian Cancer Research Group (ACRG) (n = 300) was used for external validation. Risk score of ARG signatures was calculated, and a prognostic nomogram was developed. Gene set enrichment analysis of the ARG model risk score was performed. Cluster 2 patients had more advanced clinical stage and shorter survival rates. ARG signatures carried prognostic relevance in both cohorts. Moreover, ARG-risk score was proved as an independent prognostic factor. The predictive value of the nomogram incorporating the risk score and clinicopathological features was superior to tumor, lymph node, metastasis (TNM) staging. The high-risk score group was associated with several cancer and metastasis-related pathways. The present study suggests that ARG-based nomogram could serve as effective prognostic biomarkers and allow a more precise risk stratification.

Development of cancer prognostic signature based on pan-cancer proteomics

Utilizing genomic data to predict cancer prognosis was insufficient. Proteomics can improve our understanding of the etiology and progression of cancer and improve the assessment of cancer prognosis. And the Clinical Proteomic Tumor Analysis Consortium (CPTAC) has generated extensive proteomics data of the vast majority of tumors. Based on CPTAC, we can perform a proteomic pan-carcinoma analysis. We collected the proteomics data and clinical features of cancer patients from CPTAC. Then, we screened 69 differentially expressed proteins (DEPs) with R software in five cancers: hepatocellular carcinoma (HCC), children’s brain tumor tissue consortium (CBTTC), clear cell renal cell carcinoma (CCRC), lung adenocarcinoma (LUAD) and uterine corpus endometrial carcinoma (UCEC). GO and KEGG analysis were performed to clarify the function of these proteins. We also identified their interactions. The DEPs-based prognostic model for predicting over survival was identified by least absolute shrinkage and selection operator (LASSO)-Cox regression model in training cohort. Then, we used the time-dependent receiver operating characteristics analysis to evaluate the ability of the prognostic model to predict overall survival and validated it in validation cohort. The results showed that the DEPs-based prognostic model could accurately and effectively predict the survival rate of most cancers.

VUp-Regulation of VCAN Promotes the Proliferation, Invasion and Migration and Serves as a Biomarker in Gastric Cancer

Background

Versican (VCAN), a significant protein of extracellular matrix (ECM), is capable of accumulating in tumor stroma and critically impacts malignant transforming process and tumor progressing process. Promoted VCAN expression was identified in numerous malignant tumors and showed relationships to cancer relapse and ineffective breast, prostate, and many other cancer types of patients. Nevertheless, the molecular capability and prognosis importance exhibited by VCAN are infrequently presented in gastric cancer (GC).

Methods

According to 5 GC tissues and corresponding general tissues, mRNA expression profiles were taken here. VCAN expression in tissues was confirmed by quantitative reverse transcription polymerase reaction (qRT-PCR). The effect generated by VCAN expression on cell proliferating, invading and migrating processes was assessed in vitro with knockdown and overexpression strategies. Moreover, the relationships between immune response and VCAN expression in GC were assessed with the use of the software online.

Results

There are 181 genes up-regulated and 530 genes down-regulated in GC. According to pathway study, the mentioned differently expressed mRNAs showed correlations with a number of vital physiological processes, cellular components, molecular functions and critical cancer signal pathways. VCAN was reported to be noticeably promoted in GC tissues and related to individual cancer age, race, and stages. VCAN was up-regulated in 16 GC tissues compared to adjacent non-tumorous tissue specimens via qRT-PCR. GC patients exhibiting higher VCAN expression had less post-progression survival (PPS), first progression (FP) and overall survival (OS). Experimental processes in vitro revealed VCAN knockdown hindered, proliferated, invaded, and migrated levels of GC cells, whereas overexpression of VCAN played the opposite effect. Immune factors may interact with VCAN mRNA in GC, and VCAN was found noticeably linked with regulatory T cells (Tregs).

Conclusion

According to the mentioned results, VCAN critically impacts GC progression. Accordingly, VCAN is likely to be a potentially feasible prognosis marking element and a prominent cancer drug for GC patients.

Comprehensive review of Hepatitis B Virus-associated hepatocellular carcinoma research through text mining and big data analytics

PubMed was text mined to glean insights into the role of Hepatitis B virus (HBV) in hepatocellular carcinoma (HCC) from the massive number of publications (9249) available to date. Reports from ∼70 countries identified >1300 human genes associated with either the Core, Surface or X gene in HBV-associated HCC. One hundred and forty-three of these host genes, which can potentially yield 1180 biomolecular interactions, each were reported in at least three different publications to be associated with the same HBV. These 143 genes function in 137 pathways, involved mainly in the cell cycle, apoptosis, inflammation and signalling. Fourteen of these molecules, primarily transcriptional regulators or kinases, play roles in several pathways pertinent to the hallmarks of cancers. 'Chronic' was the most frequent word used across the 9249 abstracts. A key event in chronic HBV infection is the integration of HBV into the host genome. The advent of cost-effective, next-generation sequencing technology facilitated the employment of big-data analytics comprehensively to characterize HBV-host integration within HCC patients. A total of 5331 integration events were reported across seven publications, with most of these integrations observed between the Core/X gene and the introns of genes. Nearly one-quarter of the intergenic integrations are within repeats, especially long interspersed nuclear elements (LINE) repeats. Integrations within 13 genes were each reported by at least three different studies. The human gene with the most HBV integrations observed is the TERT gene where a total of 224 integrations, primarily at its promoter and within the tumour tissue, were reported by six of seven publications. This unique review, which employs state-of-the-art text-mining and data-analytics tools, represents the most complete, systematic and comprehensive review of nearly all the publications associated with HBV-associated HCC research. It provides important resources to either focus future research or develop therapeutic strategies to target key molecules reported to play important roles in key pathways of HCC, through the systematic analyses of the commonly reported molecules associated with the various HBV genes in HCC, including information about the interactions amongst these commonly reported molecules, the pathways in which they reside as well as detailed information regarding the viral and host genes associated with HBV integration in HCC patients. Hence this review, which highlights pathways and key human genes associated with HBV in HCC, may facilitate the deeper elucidation of the role of HBV in hepato-carcinogenesis, potentially leading to timely intervention against this deadly disease.