RNA-seq of Mouse Liver after low-dose LPS injection

C-type lectin receptors (CLRs) are a family of pattern recognition receptors that sense diverse microbial and damage-associated molecular patterns. Many CLRs, like Mincle and Dectin-3, are upregulated by TLR4 signaling. In Alcohol-associated Hepatitis (AH), where alcohol consumption leads to leakage of bacterial LPS, TLR4 upregulates CLR expression and increases the diversity of what the immune system can detect, which we call secondary immune surveillance. Previously, we found human monocytes upregulate CLRs in response to LPS/TLR4 signaling with much higher expression in AH. In this study, we broaden our understanding of secondary immune surveillance. We find that CLRs are upregulated by many kinds of TLR signaling. We used Mincle-KO mice to dissect how loss of one CLR impacts tissue inflammation. Mincle-KO mice were protected from liver inflammation caused by LPS, but experienced worse adipose tissue inflammation, suggesting a shift in the site of injury.We then performed bulk RNA-seq of livers from these mice including WT, Mincle-Het, and Mincle-KO. Mice were given low-dose (0.7g/kg) LPS or saline by intraperitoneal injection for 24 hours. Then animals were sacrificed, and livers perfused and removed for RNA isolation. RNA was isolated using the Zymo Direct-zol kit, and libraries were made using the Takara SMART-Seq Total RNA High Input (RiboGone Mammalian) kit. Libraries were pooled and sequenced with an Illumina NovaSeq to generate more than 2 billion paired-end reads of 100 bp with a median of 18 million reads per sample.