Identification of key protein-coding genes and lncRNAs in spontaneous neutrophil apoptosis

Abstract

Polymorphonuclear leukocytes (PMNs) are the most abundant cells of the innate immune system in humans, and spontaneous PMN apoptosis plays crucial roles in maintaining neutrophil homeostasis and resolving inflammation. However, the detailed mechanisms of spontaneous PMN apoptosis remain to be elucidated. By analysis of the public microarray dataset GSE37416, we identified a total of 3050 mRNAs and 220 long non-coding RNAs (lncRNAs) specifically expressed during PMN apoptosis in a time-dependent manner. By short time-series expression miner (STEM) analysis, Gene Ontology analysis, and lncRNA-mRNA co-expression network analyses, we identified some key molecules specifically related to PMN apoptosis. STEM analysis identified 12 gene profiles with statistically significance, including 2 associated with apoptosis. Protein-protein interaction (PPI) network analysis of the genes from 2 profiles and lncRNA-mRNA co-expression network analysis identified a 12-gene hub (including NFκB1 and BIRC3) associated with apoptosis, as well as 2 highly correlated lncRNAs (THAP9-AS1, and AL021707.6). We experimentally examined the expression profiles of two mRNA (NFκB1 and BIRC3) and two lncRNAs (THAP9-AS1 andAL021707.6) by quantitative real-time polymerase chain reaction to confirm their time-dependent expressions. These data altogether demonstrated that these genes are involved in the regulation of spontaneous neutrophil apoptosis and the corresponding gene products could also serve as potential key regulatory molecules for PMN apoptosis and/or therapeutic targets for over-reactive inflammatory response caused by the abnormality in PMN apoptosis.

Development of a Machine Learning-Based Autophagy-Related lncRNA Signature to Improve Prognosis Prediction in Osteosarcoma Patients

“…They regulate gene expression at the transcriptional and post-transcriptional levels and play a protumorigenic or tumor suppressor role in various human cancers, including breast, gastric, colorectal, and liver cancers (Choi et al, 2019;Feng et al, 2019;Ni et al, 2019;Song et al, 2019). Increasing evidence shows that the role of lncRNAs in cancer pathogenesis is partly mediated by the regulation of various autophagy-related proteins, in addition to proteins involved in cell proliferation, apoptosis, and metastasis (Chi et al, 2019;Jiang N. et al, 2019;Zheng et al, 2019). For instance, the lncRNA XIST inhibits autophagy in osteosarcoma cells by acting as a sponge for miR-375-3p, thereby regulating the AKT/mTOR signaling pathway (Sun et al, 2019).…”

The Crosstalk Between Long Non-Coding RNAs and Various Types of Death in Cancer Cells

“…A large numbers of regulatory genes are involved in the mechanisms by which animals adjust mitosis, discover cell abnormalities, and initiate programmed cell death. 23 Mitosis is stimulated by some of these regulatory genes, while other regulatory genes inhibit mitosis or cause programmed cell death. For cancer and other diseases characterized by the regulation of abnormal cell death, studying the mechanisms of different types of cell death is important.…”

The role of long noncoding RNA THAP9‐AS1 in the osteogenic differentiation of dental pulp stem cells via the miR‐652‐3p/VEGFA axis

“…Trihydroxyacetophenone domain containing 9 antisense RNA 1 (THAP9‐AS1) has been reported to function as an oncogene by promoting cell growth in pancreatic ductal adenocarcinoma [14]. THAP9‐AS1 is involved in the apoptosis of spontaneous neutrophil [15]. In addition, THAP9‐AS1 has been reported to upregulate yes‐associated protein (YAP) expression, [14] and YAP induces osteo/odontogenesis and mineralization in human DPSCs [16].…”