Quantitative digital pathology reveals association of cell-specific transcription with NAFLD disease activity.

Background & Aims: The I148M variant (rs738409) in patatin-like phospholipase domain-containing protein 3 (PNPLA3) is by far the most important genetic determinant of non-alcoholic fatty liver disease (NAFLD). However, in the context of NAFLD, the transcriptional regulation of in human liver cells is not known. In this study, we aimed to define the relationship between transcription and disease characteristics of human NAFLD.

Methods: The abundance of and collagen 1α () transcripts was quantified at single-cell resolution using RNAscope® in 87 patients with NAFLD. We examined the association of and transcript levels with NAFLD disease severity, defined by histology.

Results: While the majority of transcripts were found in hepatocytes, approximately 7% of -positive cells co-express , representing activated myofibroblasts. There is no association between the rs738409 genotype and the level of transcript. The overall transcript abundance is lower in zone 1 hepatocytes, patients with higher body mass index, and those with advanced liver fibrosis. The negative association between the transcript levels and liver fibrosis is largely driven by -positive cells. A significant proportion of mRNA is seen in the nucleus. The cytoplasmic-to-nuclear mRNA ratio is inversely associated with NAFLD disease activity.

Conclusions: transcript abundance and nuclear-to-cytoplasmic translocation are negatively associated with hepatic steatosis and NAFLD disease activity, while its abundance in activated myofibroblasts is inversely associated with the stage of liver fibrosis.

Lay Summary: A genetic variant in patatin-like phospholipase domain-containing protein 3 (or ) is the most important genetic determinant of non-alcoholic fatty liver disease (NAFLD). However, it is not known how transcriptional regulation of the gene contributes to the disease characteristics of human NAFLD. Herein, we show that the mRNA levels of , particularly in the cytoplasm, are negatively associated with the severity of NAFLD in humans.