An integrated mRNA–microRNA regulatory network identified INHBA and has-miR-135a-5p as predictors of gastric cancer recurrence

Sample management: a primary critical starting point for successful omics studies

Biological samples collected from cohort studies are widely utilized in molecular genetic studies and are typically stored long term for future applications, such as omics analyses. The extent of sample availability is determined by proper sample handling, and it is of primary importance for successful omics studies. However, questions on whether samples in long-term storage are properly available for omics experiments has been raised, because the quality and availability of such samples remain unknown until their actual utilization. In that perspective, several guidelines for proper sample management have been suggested. In addition, several researchers assessed how improper management damages sample using mock sample and suggested a set of requirements for sample handling. In this review, we present several considerations for sample handling eligible for omics studies. Focusing on birth cohorts, we describe the types of samples collected from which omics data were generated. This review ultimately aims to provide proper guidelines for sample handling for successful human omics studies.

Entrectinib Induces Apoptosis and Inhibits the Epithelial-Mesenchymal Transition in Gastric Cancer with NTRK Overexpression

Tropomyosin receptor kinase (TRK) and receptor tyrosine kinase (RTK class VII) expression are important in many human diseases, especially cancers, including colorectal, lung, and gastric cancer. Using RNA sequencing analysis, we evaluated the mRNA expression and mutation profiles of gastric cancer patients with neurotropic tropomyosin receptor kinase (NTRK) 1-3 overexpression (defined as a ≥2.0-fold change). Furthermore, we screened eight TRK inhibitors in NCI-N87, SNU16, MKN28, MKN7, and AGS cells. Among these inhibitors, entrectinib showed the highest inhibitory activity; therefore, this drug was selected for analysis of its therapeutic mechanisms in gastric cancer. Entrectinib treatment induced apoptosis in NTRK1-3-expressing and VEGFR2-expressing NCI-N87 and AGS cells, but it had no effect on NTRK1-3-, VEGFR2-, TGFBR1-, and CD274-expressing MKN7 cells. SNU16 and MKN28 cells with low NTRK1-3 expression were not affected by entrectinib. Therefore, a mechanistic study was conducted in NCI-N87 (high expression of NTRK1-3 but mutation of NTRK3), AGS (high expression of NTRK1-3) and MKN28 (low expression of NTRK1-3) gastric cancer cell lines. Entrectinib treatment significantly reduced expression levels of phosphorylated NFκB, AKT, ERK, and β-catenin in NCI-N87 and AGS cells, whereas it upregulated the expression levels of ECAD in NCI-N87 cells. Together, these results suggest that entrectinib has anti-cancer activity not only in GC cells overexpressing pan NTRK but also in VEGFR2 GC cells via the inhibition of the pan NTRK and VEGFR signaling pathways.