RNA-seq of NPL knock-down in THP1 cells

The NPL encodes an enzyme that regulates cellular concentrations of sialic acid (N-acetyl-neuraminic acid) by mediating the reversible conversion of sialic acid into N-acetylmannosamine and pyruvate. As functions of NPL gene in obesity and gluco-metabolic phenotypes is not studied, we knocked down NPL in THP1 cells to understand its roles in modulating the human monocyte-macrophage expression network. Transduction of THP1 cells by NPL-specific lentiviral shRNA stably knocked down its expression at baseline monocytes and in the PMA-induced macrophage state. Global transcriptomic analysis by RNA-seq validated the downregulation of NPL, and comparison of NPL knockdown cells with control-shRNA treated cells further identified 1,183 differentially expressed genes (DEGs). Genes downregulated by the NPL knockdown were significantly enriched for cytokine production, while upregulated genes were enriched for extracellular structure organization. We further compared the effect of macrophage conditioned media (MCM) derived from NPL-shRNA and control-shRNA-expressing THP1 macrophages on SGBS adipocytes. Compared to unconditioned media, MCM derived from either of the THP1 cells differentially regulated key genes involved in adipocyte function and IR. The expression of ADIPOQ, peroxisome proliferator activated receptor gamma (PPARG), and glucose transporter-4 (SLC2A4/GLUT4) was downregulated, while expression of LEP was upregulated in SGBS cells treated with MCM starting from day 4 of the in vitro differentiation. However, PPARG was less repressed and LEP was less activated when SGBS adipocytes were treated on day 4 differentiation with MCM from NPL-shRNA-THP1 cells, suggesting knockdown of NPL partially ameliorated macrophage-induced inflammation of adipocytes. Overall design: RNA-seq was performed in the NPL-shRNA and control-shRNA expressing THP1 cells at 48hr PMA treated condition