Transcriptome profiling of cancer tissues in Chinese patients with gastric cancer by high-throughput sequencing

Ontologies and Knowledge Graphs in Oncology Research

The complexity of cancer research stems from leaning on several biomedical disciplines for relevant sources of data, many of which are complex in their own right. A holistic view of cancer—which is critical for precision medicine approaches—hinges on integrating a variety of heterogeneous data sources under a cohesive knowledge model, a role which biomedical ontologies can fill. This study reviews the application of ontologies and knowledge graphs in cancer research. In total, our review encompasses 141 published works, which we categorized under 14 hierarchical categories according to their usage of ontologies and knowledge graphs. We also review the most commonly used ontologies and newly developed ones. Our review highlights the growing traction of ontologies in biomedical research in general, and cancer research in particular. Ontologies enable data accessibility, interoperability and integration, support data analysis, facilitate data interpretation and data mining, and more recently, with the emergence of the knowledge graph paradigm, support the application of Artificial Intelligence methods to unlock new knowledge from a holistic view of the available large volumes of heterogeneous data.

Comprehensive analysis of prognostic genes in gastric cancer

Background: Gastric cancer is associated with high mortality, and effective methods for predicting prognosis are lacking. We aimed to identify potential prognostic markers associated with the development of gastric cancer through bioinformatic analyses.

Methods: Gastric cancer-associated gene expression profiles were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The key genes involved in the development of gastric cancer were obtained by differential expression analysis, coexpression analysis, and short time-series expression miner (STEM) analysis. The potential prognostic value of differentially expressed genes was further evaluated using a Cox regression model and risk scores. Hierarchical clustering was applied to validate the impact of key genes on the overall survival of gastric cancer patients.

Results: A total of 1381 genes were consistently dysregulated in the development of gastric cancer. Among them, 186 genes affected the overall survival of gastric cancer patients. The following genes had areas under the receiver operating characteristic curve greater than 0.9 in both datasets and were therefore considered key genes: ADAM12, CEP55, LRFN4, INHBA, ADH1B, DPT, FAM107A, and LOC100506388. LRFN4, DPT, and LOC100506388 were identified as potential prognostic genes for gastric cancer through a nomogram. Overexpression of LRFN4 and LOC100506388 was associated with a higher risk of gastric cancer. Finally, we found that tumors were infiltrated with high levels of Th2 cells and mast cells, and the infiltration levels were associated with overall survival in gastric cancer patients.

Conclusions: We found that key dysregulated genes may have a prognostic value for the development of gastric cancer.

CHPF promotes gastric cancer tumorigenesis through the activation of E2F1

Chondroitin polymerizing factor (CHPF) is an important glycosyltransferase involved in the biosynthesis of chondroitin sulfate. However, the relationship between CHPF and gastric cancer has not been fully investigated. CHPF expression in gastric cancer tissues was detected by immunohistochemistry and correlated with gastric cancer patient prognosis. Cultured gastric cancer cells and human gastric epithelial cell line GES1 were used to investigate the effects of shCHPF and shE2F1 on the development and progression of gastric cancer by MTT, western blotting, flow cytometry analysis of cell apoptosis, colony formation, transwell and gastric cancer xenograft mouse models, in vitro and in vivo. In gastric cancer tissues, CHPF was found to be significantly upregulated, and its expression correlated with tumor infiltration and advanced tumor stage and shorter patient survival in gastric cancer. CHPF may promote gastric cancer development by regulating cell proliferation, colony formation, cell apoptosis and cell migration, while knockdown induced the opposite effects. Moreover, the results from in vivo experiments demonstrated that tumor growth was suppressed by CHPF knockdown. Additionally, E2F1 was identified as a potential downstream target of CHPF in the regulation of gastric cancer, and its knockdown decreased the CHPF-induced promotion of gastric cancer. Mechanistic study revealed that CHPF may regulate E2F1 through affecting UBE2T-mediated E2F1 ubiquitination. This study showed, for the first time, that CHPF is a potential prognostic indicator and tumor promoter in gastric cancer whose function is likely carried out through the regulation of E2F1.

RNA Sequencing for Gene Expression Profiles in Peripheral Blood Mononuclear Cells with Ankylosing Spondylitis RNA

Several previous studies have attempted to investigate the regulatory mechanisms underlying gene expression in ankylosing spondylitis (AS). However, the specific molecular pathways underlying this condition remain unclear. Previous research used next-generation RNA sequencing to identify a series of differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMCs) when compared between patients with AS and healthy controls, thus implying that these DEGs may be related to AS. Furthermore, by screening these DEGS, it may be possible to facilitate clinical diagnosis and optimize treatment strategies. In order to test this hypothesis, we recruited 15 patients with AS and 15 healthy controls. We randomly selected five subjects from each group of patients for RNA sequencing analysis. Sequence reads were generated by an Illumina HiSeq2500 platform and mapped on to the human reference genome using HISAT2. We successfully identified 973 significant DEGs (p < 0.05) in PBMCs. When compared with controls, 644 of these genes were upregulated (with a fold change (FC) > 2) in AS patients and 329 were downregulated (FC < 0.5). Our analysis identified numerous genes related to immune response. Gene Ontology (GO) analysis indicated that these DEGs were significantly related to the positive regulation of epidermal growth factor-activated receptor activity, the positive regulation of the ERBB (erb-b2 receptor tyrosine kinase) signaling pathway, the differentiation of trophoblast giant cells, oxygen transport, immune-related pathways, and inflammation-related pathways. The DEGs were also closely related to the TNF and NF-κB signaling pathways. Six DEGs were verified by quantitative real-time polymerase chain reaction (qRT-PCR). Receiver operating characteristic (ROC) curve analysis indicated that IL6 may represent a useful biomarker for diagnosing AS. The development of new biomarkers may help us to elucidate the specific mechanisms involved in the development and progression of AS.

Radiotherapy benefited the survival of patients with intestinal-type gastric adenocarcinoma: a SEER population-based study

BACKGROUND

Currently, the role of adjuvant radiotherapy (RT) in the treatment of patients with intestinal-type gastric adenocarcinoma (IGA) has not been well established. This study aimed to elucidate the survival impact of RT on such patients.

METHODS

The Surveillance, Epidemiology, and End Results (SEER) database was utilized to select eligible patients. The recruited patients were dichotomized into those not received RT versus those received RT. The 1:1 propensity score matching (PSM) analysis was conducted to balance the confounding factors between the two comparison groups. The categorical variables were assessed by Chi-square test. Cancer-specific survival (CSS) and overall survival (OS) of the patients were compared by Kaplan-Meier (KM) methods. Cox proportional hazard models were used to identify prognostic factors associated with CSS.

RESULTS

A total of 3572 eligible patients were enrolled for our analysis, of which, 2896(81.1%) patients did not receive RT and 676(18.9%) patients received RT. Before PSM, except race and tumor size, significant differences in patients' baseline characteristics were observed in no RT versus RT group. The KM plots before PSM indicated that RT exerted significant survival benefits for the recruited patients (p < 0.001). After PSM, most confounders were well balanced between the two comparison groups. The KM plots showed significantly superior CSS and OS in the RT group (p < 0.05). Grade IV, stage II-IV, and N3 were identified as independent risk factors, while LN examined > 15 and RT were independent protective factors for favorable prognosis. Subgroup survival analysis revealed that RT brought a significant CSS advantage for the stage IV patients.

CONCLUSION

Based on PSM analysis of the cohort from SEER database, RT showed significant survival benefits for patients with IGA. Our study supports adjuvant RT for this specific cohort.

Genome-wide transcriptome profiling of ex-vivo precision-cut slices from human pancreatic ductal adenocarcinoma

Ex-vivo tumor tissue culture systems are used as models to test specific anti-cancer drugs. Their main advantage is that they are closely comparable with the in vivo tumor in their host organism. We previously reported that precision-cut organotypic tissue slices of pancreatic ductal adenocarcinoma (PDAC) can be successfully cultured ex-vivo for at least 4 days. In order to study how culturing might affect transcription patterns, we now performed genome-wide transcriptome profiling of both baseline (0 h) and explanted tumors at daily intervals (24, 48 and 72 h) after start of culturing. The total-RNA from five samples of surgically resected human PDAC tumors at baseline and at different time points in culture was sequenced. Differential gene expression analysis of the whole transcriptome, testing 58,713 genes and over 206,000 transcripts, found that only a small number of genes showed significant changes in expression between baseline and cultured samples. The cultured tumor slices showed upregulation of a median of 12, 10 and 15 genes and downregulation of a median of 15, 12 and 25 genes at 24, 48 and 72 h in culture, respectively. One sample had morphologically increasing loss of tissue viability (range 0-18%). The vascular endothelial growth factor A (VEGFA) was significantly upregulated during the entire culture period in this case. Pathway over-representation analysis suggested that VEGFA together with the PTGS2 gene were upregulated at the same time as HIF-1-triggered cell apoptosis via NF-ĸB and the AP-1 activating factor was induced. Indeed, increased areas of apoptotic lesions were visible in this sample after 24 hours of culture. In conclusion, genome-wide transcriptome analysis supports that ex-vivo cultured tissue slices of PDAC may be a representative model of the original tumor. Transcriptome analysis was found to be a valuable complement to morphology for evaluation of ex-vivo cultures of PDAC.