Objective Non-small-cell lung cancer (NSCLC) accounts for >85% of lung cancers, and its incidence is increasing. We explored expression differences between NSCLC and normal cells and predicted potential target sites for detection and diagnosis of NSCLC. Methods Three microarray datasets from the Gene Expression Omnibus database were analyzed using GEO2R. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were conducted. Then, the String database, Cytoscape, and MCODE plug-in were used to construct a protein–protein interaction (PPI) network and screen hub genes. Overall and disease-free survival of hub genes were analyzed using Kaplan-Meier curves, and the relationship between expression patterns of target genes and tumor grades were analyzed and validated. Gene set enrichment analysis and receiver operating characteristic curves were used to verify enrichment pathways and diagnostic performance of hub genes. Results In total, 293 differentially expressed genes were identified and mainly enriched in cell cycle, ECM–receptor interaction, and malaria. In the PPI network, 36 hub genes were identified, of which 6 were found to play significant roles in carcinogenesis of NSCLC: CDC20, ECT2, KIF20A, MKI67, TPX2, and TYMS. Conclusion The identified target genes can be used as biomarkers for the detection and diagnosis of NSCLC.
DNA methylation alteration is frequently observed in exogenous gene silencing and may play important roles in the genetic stability of traits. Cashmere is derived from the secondary hair follicles (SHFs) of cashmere goats, which are morphogenetically distinct from primary hair follicles (PHFs). Here, in light of having initially produced 15 Tβ4 overexpression (Tβ4-OE) cashmere goats which had more SHFs than the wild type (WT) goats, and produced more cashmere, we produced Tβ4-OE offsprings both via somatic cell nuclear transfer (SCNT) and via natural mating (NM). However, the desired trait exhibited lower fixation in the line-bred offspring compared to the SCNT offspring. Integrative analysis of methylation and transcriptional profiles showed that this might be due to the influence of methylation on the expression of differentially expressed genes (DEGs) between generations, which was mutually consistent with the results of the functional and pathway enrichment analysis of differentially methylated regions (DMRs) and DEGs. Overall, our study systematically describes the DNA methylation characteristics between generations of cashmere goats and provides a basis for improving genetic stability.
Increasing cashmere yield is one of the important goals of cashmere goat breeding. To achieve this goal, we screened the key genes that can improve cashmere performance. In this study, we used the RNA raw datasets of the skin and dermal papilla cells of secondary hair follicle (SHF-DPCs) samples of hair follicle (HF) anagen and telogen of Albas cashmere goats and identified a set of significant differentially expressed genes (DEGs). To explore potential associations between gene sets and SHF growth features and to identify candidate genes, we detected functional enrichment and constructed protein-protein interaction (PPI) networks. Through comprehensive analysis, we selected Thymosin β4 (Tβ4), Rho GTPase activating protein 6 (ARHGAP6), ADAM metallopeptidase with thrombospondin type 1 motif 15, (ADAMTS15), Chordin (CHRD), and SPARC (Osteonectin), cwcv and kazal-like domains proteoglycan 1 (SPOCK1) as candidate genes. Gene set enrichment analysis (GSEA) for these genes revealed Tβ4 and ARHGAP6 have a close association with the growth and development of SHF-DPCs. However, the expression of Tβ4 in the anagen was higher than that in the telogen, so we finally chose Tβ4 as the ultimate research object. Overexpressing Tβ4 promoted and silencing Tβ4 inhibited the proliferation of SHF-DPCs. These findings suggest that Tβ4 can promote the growth and development of SHF-DPCs and indicate that this molecule may be a valuable target for increasing cashmere production.
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