The prognostic value of ADRA1 subfamily genes in gastric carcinoma

Tracing the pathways and mechanisms involved in the anti-breast cancer activity of glycyrrhizin using bioinformatics tools and computational methods

A complete investigation to understand the pathways that could be affected by glycyrrhizin (licorice), as anti-breast cancer (BC) agent, has not been performed to date. This study aims to investigate the pathways involved in the anti-cancer activity of glycyrrhizin against BC. For this purpose, the target genes of glycyrrhizin were obtained from the ChEMBL database. The BC-associated genes for three types of BC (breast carcinoma, malignant neoplasm of breast, and triple-negative breast neoplasms) were retrieved from DisGeNET. The target genes of glycyrrhizin and the BC-associated genes were compared, and the genes with disease specificity index (DSI) > 0.6 were selected for further evaluation using in silico methods. The protein-protein interaction (PPI) network was constructed, and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed. The potential complexes were further evaluated using molecular dynamics (MD) simulation. The results revealed that among 80 common genes, ten genes had DSI greater than 0.6, which included POLK, TACR2, MC3R, TBXAS1, HH1R, SLCO4A1, NPY2R, ADRA2C, ADRA1A, and SLCO2B1. The binding affinity of glycyrrhizin to the cognate proteins and binding characteristics were assessed using molecular docking and binding free energy calculations (MM/GBSA). POLK, TBXAS1, and ADRA1A showed the highest binding affinity with -8.9, -9.3, and -9.6 kcal/mol, respectively. The final targets had an association with BC at several stages of tumor growth. By affecting these targets, glycyrrhizin could influence and control BC efficiently. MD simulation suggested the pathways triggered by the complex glycyrrhizin-ADRA1A were more likely to happen.Communicated by Ramaswamy H. Sarma.

Identification and Validation of Immune Cells and Hub Genes in Gastric Cancer Microenvironment

Gastric cancer (GC) is the most common malignant tumor in the digestive system, traditional radiotherapy and chemotherapy are not effective for some patients. The research progress of immunotherapy seems to provide a new way for treatment. However, it is still urgent to predict immunotherapy biomarkers and determine novel therapeutic targets. In this study, the gene expression profiles and clinical data of 407 stomach adenocarcinoma (STAD) patients were downloaded from The Cancer Genome Atlas (TCGA) portal, and the abundance ratio of immune cells in each sample was obtained via the “Cell Type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT)” algorithm. Five immune cells were obtained as a result of abundance comparison, and 295 immune-related genes were obtained through differential gene analysis. Enrichment, protein interaction, and module analysis were performed on these genes. We identified five immune cells associated with infiltration and 20 hub genes, of which five genes were correlated with overall survival. Finally, we used Real-time PCR (RT-PCR) to detect the expression differences of the five hub genes in 18 pairs of GC and adjacent tissues. This research not only provides cellular and gene targets for immunotherapy of GC but also provides new ideas for researchers to explore immunotherapy for various tumors.

Identifying Novel Psoriatic Disease Drug Targets Using a Genetics-Based Priority Index Pipeline

BACKGROUND

Despite numerous genome-wide association studies conducted in psoriasis and psoriatic arthritis, only a small fraction of the identified genes has been therapeutically targeted.

OBJECTIVE

We sought to identify and analyze potential therapeutic targets for psoriasis and psoriatic arthritis (PsA) using the priority index (Pi), a genetics-dependent drug target prioritization approach.

METHODS

Significant genetic variants from GWAS for psoriasis, PsA, and combined psoriatic disease were annotated and run through the Pi pipeline. Potential drug targets were identified based on genomic predictors, annotation predictors, pathway enrichment, and pathway crosstalk.

RESULTS

Several gene targets were identified for psoriasis and PsA that demonstrated biological associations to their respective diseases. Some are currently being explored as potential therapeutic targets (i.e. ICAM1, NF-kB, REV3L, ADRA1B for psoriasis; CCL11 for PsA); others have not yet been investigated (i.e. LNPEP, LCE3 for psoriasis; UBLCP1 for PsA). Additionally, many nodal points of potential intervention were identified as promising therapeutic targets. Of these, some are currently being studied such as TYK2 for psoriasis, and others have yet to be explored (i.e. PPP2CA, YAP1, PI3K, AKT, FOXO1, RELA, CSF2, IFNGR1, IFNGR2 for psoriasis; GNAQ, PLCB1, GNAI2 for PsA).

CONCLUSION

Through Pi, we identified data-driven candidate therapeutic gene targets and pathways for psoriasis and PsA. Given the sparse PsA specific genetic studies and PsA specific drug targets, this analysis could prove to be particularly valuable in the pipeline for novel psoriatic therapies.

Comparative Study of Organoids from Patient-Derived Normal and Tumor Colon and Rectal Tissue

Colon and rectal tumors, often referred to as colorectal cancer, show different gene expression patterns in studies that analyze whole tissue biopsies containing a mix of tumor and non-tumor cells. To better characterize colon and rectal tumors, we investigated the gene expression profile of organoids generated from endoscopic biopsies of rectal tumors and adjacent normal colon and rectum mucosa from therapy-naive rectal cancer patients. We also studied the effect of vitamin D on these organoid types. Gene profiling was performed by RNA-sequencing. Organoids from a normal colon and rectum had a shared gene expression profile that profoundly differed from that of rectal tumor organoids. We identified a group of genes of the biosynthetic machinery as rectal tumor organoid-specific, including those encoding the RNA polymerase II subunits POLR2H and POLR2J. The active vitamin D metabolite 1α,25-dihydroxyvitamin D3/calcitriol upregulated stemness-related genes (LGR5, LRIG1, SMOC2, and MSI1) in normal rectum organoids, while it downregulated differentiation marker genes (TFF2 and MUC2). Normal colon and rectum organoids share similar gene expression patterns and respond similarly to calcitriol. Rectal tumor organoids display distinct and heterogeneous gene expression profiles, with differences with respect to those of colon tumor organoids, and respond differently to calcitriol than normal rectum organoids.

Glutathione Peroxidase 8 as a Prognostic Biomarker of Gastric Cancer: An Analysis of The Cancer Genome Atlas (TCGA) Data

Background

Glutathione peroxidase 8 (GPX8) has previously been shown to play a role in Keshan disease. In the present study, we explored the prognostic relevance of GPX8 expression in patients with gastric cancer (GC) based upon The Cancer Genome Atlas (TCGA) data.

Material/Methods

We assessed the relationship between the expression of GPX8 and clinicopathological findings in GC patients via logistic regression analyses, Kruskal-Wallis tests, and Wilcoxon signed-rank tests. We further assessed the prognostic relevance of specific variables using Kaplan-Meier and Cox regression analyses. We lastly conducted gene set enrichment analyses (GSEA).

Results

We detected a significant association between elevated GPX8 levels and more advanced GC tumor stage (OR=5.92 for I vs. IV), as well as more advanced T (OR=22.91 for T1 vs. T4) and N classification (OR=1.82 for N0 vs. N3). We found worse prognosis in patients expressing high levels of GPX8 relative to those with lower expression of this gene (P=0.021). In a univariate analysis, we found high GPX8 expression was strongly correlated with worse OS (hazard ratio [HR]: 1.05; 95% confidence interval [CI]: 1.01–1.08; P=0.018), and multivariate analysis confirmed that GPX8 expression independently predicts GC patient OS (HR: 1.04; CI: 1.00–1.08, P=0.041). GSEA revealed that elevated GPX8 expression was associated with enrichment of pathways consistent with MAPK signaling, JAK/STAT signaling, TGF-β signaling, melanoma, and basal cell carcinoma.

Conclusions

The expression of GPX8 may have prognostic relevance, being positively associated with worse OS in GC patients.