The transcription factor ZNF469 regulates collagen production in liver fibrosis [LX2_CUTRUN_ZNF]

Non-alcoholic fatty liver disease (NAFLD)—characterized by excess accumulation of fat in the liver—now affects one third of the world's population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis. Overall design: Human immortalized stellate cel lline (LX2) were grown in standard conditions. Cells were transfected with a piggybac transposon vector expressing full length human ZNF469 gene or human ZNF469 with deleted zinc finger (dZF). 3 days after transfection, stable lines were selected with puromycin at 1 microgram/mL. After selection, cells were treated with doxycycline (1 microgram/mL) to induce expression of ZNF469 or dz-ZNF469 for 24 hours. Samples were then processed for CUT&RUN.