Bioinformatic analysis of potential hub genes in gastric adenocarcinoma

High Expression of THY1 in Intestinal Gastric Cancer as a Key Factor in Tumor Biology: A Poor Prognosis-Independent Marker Related to the Epithelial-Mesenchymal Transition Profile

Gastric cancer (GC) is an important cancer-related death worldwide. Among its histological subtypes, intestinal gastric cancer (IGC) is the most common. A previous work showed that increased expression of the THY1 gene was associated with poor overall survival in IGC. Furthermore, it was shown that IGC tumor cells with high expression of THY1 have a greater capacity for tumorigenesis and metastasis in vitro. This study aimed to identify molecular differences between IGC with high and low expression of THY1. Using a feature selection method, a group of 35 genes were found to be the most informative gene set for THY1high IGC tumors. Through a classification model, these genes differentiate THY1high from THY1low tumors with 100% of accuracy both in the test subset and the independent test set. Additionally, this group of 35 genes correctly clustered 100% of the samples. An extensive validation of this potential molecular signature in multiple cohorts successfully segregated between THY1high and THY1low IGC tumors (>95%), proving to be independent of the gene expression quantification methodology. These genes are involved in central processes to tumor biology, such as the epithelial-mesenchymal transition (EMT) and remodeling of the tumor tissue composition. Moreover, patients with THY1high IGC demonstrated poor survival and a more advanced clinicopathological staging. Our findings revealed a molecular signature for IGC with high THY1 expression. This signature showed EMT and remodeling of the tumor tissue composition potentially related to the biology of IGC. Altogether, our results indicate that THY1high IGC tumors are a particular subset of tumors with a specific molecular and prognosis profile.

Emergency exploratory laparotomy and radical gastrectomy in patients with gastric cancer combined with acute upper gastrointestinal bleeding

BACKGROUND

Gastric cancer (GC) is a prevalent malignant tumor worldwide and ranks as the fourth leading cause of cancer-related mortality. Upper gastrointestinal bleeding (UGIB) is a frequent complication of GC. Radical gastrectomy and palliative therapy are widely used surgical procedures in the clinical management of GC. This study intends to probe the clinical efficacy and safety of radical gastrectomy and palliative therapy on the basis of exploratory laparotomy in patients with GC combined with UGIB, hoping to provide valuable information to aid patients in selecting the appropriate surgical intervention.

AIM

To investigate the clinical efficacy and safety of exploratory laparotomy + radical gastrectomy and palliative therapy in patients with GC and UGIB combined.

METHODS

A total of 89 GC patients admitted to the First Affiliated Hospital of the University of South China between July 2018 and July 2020 were selected as participants for this study. The 89 patients were divided into two groups: radical resection group (n = 46) treated with exploratory laparotomy + radical gastrectomy and Palliative group (n = 43) treated with palliative therapy. The study compared several variables between the two groups, including surgical duration, intraoperative blood transfusion volume, postoperative anal exhaust time, off-bed activity time, length of hospitalization, and incidence of complications such as duodenal stump rupture, anastomotic obstruction, and postoperative incision. Additionally, postoperative immune function indicators (including CD3+, CD4+, CD8+, CD4+/CD8+, and CD3+/HLADR+), immunoglobulin (IgG and IgM), tumor markers (CEA, CA199, and CA125), and inflammatory factors (IL-6, IL-17, and TNF-α) were assessed. The surgical efficacy and postoperative quality of life recovery were also evaluated. The patients were monitored for survival and tumor recurrence at 6 mo, 1 year, and 2 years post-surgery.

RESULTS

The results indicated that the duration of operation time and postoperative hospitalization did not differ between the two surgical procedures. However, patients in the radical resection group exhibited shorter intraoperative blood loss, anus exhaust time, off-bed activity time, and inpatient activity time than those in the Palliative group. Although there was no substantial difference in the occurrence of postoperative complications, such as duodenal stump rupture and anastomotic obstruction, between the radical resection group and Palliative group (P > 0.05), the radical resection group exhibited higher postoperative immune function indicators (including CD3+, CD4+, CD8+, etc.) and immunoglobulin levels (IgG, IgM) than the Palliative group, while tumor markers and inflammatory factors levels were lower than those in the radical resection group. Additionally, surgical efficacy, postoperative quality of life, and postoperative survival rates were higher in patients who underwent radical gastrectomy than in those who underwent palliative therapy. Moreover, the probability of postoperative tumor recurrence was lower in the radical gastrectomy group compared to the palliative therapy group, and these differences were all statistically significant (P < 0.05).

CONCLUSION

Compared to palliative therapy, exploratory laparotomy + radical gastrectomy can improve immune function, reduce the levels of tumor markers and inflammatory factors, improve surgical efficacy, promote postoperative quality of life recovery, enhance survival rates, and attenuate the probability of tumor recurrence.

GHRL as a prognostic biomarker correlated with immune infiltrates and progression of precancerous lesions in gastric cancer

Objective

Ghrelin is a protein that regulate appetite and energy balance in the human body, which is encoded by the ghrelin prepropeptide gene (GHRL). GHRL is linked with carcinogenesis and immune regulation. However, the correlation of GHRL to prognosis and tumor-infiltrating lymphocytes in gastric cancer (GC) remains unclear.

Methods

In this study, we assessed the transcriptional expression, prognosis, and different clinicopathological features about GHRL and the correlation between GHRL and tumor infiltration immune cells in GC patients based on the data published in the following databases: TIMER, GEPIA, GEO, STRING, UALCAN, TISIDB, and Kaplan-Meier Plotter. Furthermore, R software analysis for GC Correa' cascade was also provided. Finally, GHRL expression in GC tissues was assayed using quantitative real-time polymerase chain reaction and immunohistochemistry.

Results

We found that GHRL expression in GC samples was lower than in normal samples and verified by quantitative PCR (qPCR) and immunohistochemistry. However, sample type, cancer stage, and worse survival were correlated to high GHRL expression. We also found that the expression of GHRL in dysplasia was significantly lower than that in CNAG and in GC. High GHRL expression was connected with immunomodulators, chemokines, and infiltrating levels of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells in GC.

Conclusions

GHRL is a prognostic biomarker for GC patients, and it is correlated with progression of precancerous lesions in GC. It might lead to poor prognosis by regulating tumor immune microenvironment. Studies are important to explore therapeutic targeting GHRL in the future.

Highly perturbed genes and hub genes associated with type 2 diabetes in different tissues of adult humans: a bioinformatics analytic workflow

Type 2 diabetes (T2D) has a complex etiology which is not yet fully elucidated. The identification of gene perturbations and hub genes of T2D may deepen our understanding of its genetic basis. We aimed to identify highly perturbed genes and hub genes associated with T2D via an extensive bioinformatics analytic workflow consisting of five steps: systematic review of Gene Expression Omnibus and associated literature; identification and classification of differentially expressed genes (DEGs); identification of highly perturbed genes via meta-analysis; identification of hub genes via network analysis; and downstream analysis of highly perturbed genes and hub genes. Three meta-analytic strategies, random effects model, vote-counting approach, and p value combining approach, were applied. Hub genes were defined as those nodes having above-average betweenness, closeness, and degree in the network. Downstream analyses included gene ontologies, Kyoto Encyclopedia of Genes and Genomes pathways, metabolomics, COVID-19-related gene sets, and Genotype-Tissue Expression profiles. Analysis of 27 eligible microarrays identified 6284 DEGs (4592 downregulated and 1692 upregulated) in four tissue types. Tissue-specific gene expression was significantly greater than tissue non-specific (shared) gene expression. Analyses revealed 79 highly perturbed genes and 28 hub genes. Downstream analyses identified enrichments of shared genes with certain other diabetes phenotypes; insulin synthesis and action-related pathways and metabolomics; mechanistic associations with apoptosis and immunity-related pathways; COVID-19-related gene sets; and cell types demonstrating over- and under-expression of marker genes of T2D. Our approach provided valuable insights on T2D pathogenesis and pathophysiological manifestations. Broader utility of this pipeline beyond T2D is envisaged.

Collagen Family and Other Matrix Remodeling Proteins Identified by Bioinformatics Analysis as Hub Genes Involved in Gastric Cancer Progression and Prognosis

Gastric cancer has remained in the top five cancers for over ten years, both in terms of incidence and mortality due to the shortage of biomarkers for disease follow-up and effective therapies. Aiming to fill this gap, we performed a bioinformatics assessment on our data and two additional GEO microarray profiles, followed by a deep analysis of the 40 differentially expressed genes identified. PPI network analysis and MCODE plug-in pointed out nine upregulated hub genes coding for proteins from the collagen family (COL12A1, COL5A2, and COL10A1) or involved in the assembly (BGN) or degradation of collagens (CTHRC1), and also associated with cell adhesion (THBS2 and SPP1) and extracellular matrix degradation (FAP, SULF1). Those genes were highly upregulated at the mRNA and protein level, the increase being correlated with pathological T stages. The high expression of BGN (p = 8 × 10⁻¹²), THBS2 (p = 1.2 × 10⁻⁶), CTHRC1 (p = 1.1 × 10⁻⁴), SULF1 (p = 3.8 × 10⁻⁴), COL5A1 (p = 1.3 × 10⁻⁴), COL10A1 (p = 5.7 × 10⁻⁴), COL12A1 (p = 2 × 10⁻³) correlated with poor overall survival and an immune infiltrate based especially on immunosuppressive M2 macrophages (p-value range 4.82 × 10⁻⁷–1.63 × 10⁻¹³). Our results emphasize that these genes could be candidate biomarkers for GC progression and prognosis and new therapeutic targets.