Transcriptome profiling reveals HNF4A as the gatekeeper of the hepatic acute-phase response

Abstract

Liver-specific genes regulating homeostatic functions are markedly repressed following an inflammatory stimulus. Conversely, transcriptional resources are reallocated to boost acute-phase genes, driving the systemic immune reaction termed the acute phase response (APR). While the liver-enriched transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) directs expression of more than 50% of hepatic genes, its role in the APR is poorly investigated.

To analyze inflammatory gene profile in hepatocytes, we adopted an in vitro APR model of LPS-treated differentiated HepaRG (dHepaRG) cells. RNA sequencing and transcription factor enrichment of the downregulated gene set directed our research focus to HNF4A. The APR resulted in a rapid repression of HNF4A RNA and protein levels. Consequently, reduced binding of HNF4A to regulatory regions of acute-phase genes serum amyloid A (SAA) and haptoglobin (HP) was followed by a chromatin-opening and derepression of these genes. Vice versa, HNF4A overexpression potently inhibited activation of acute-phase genes by maintaining a repressive chromatin state. This result was reproducible in a liver organoid model, where HNF4A overexpression protected from severe loss of liver function while limiting the APR.

We demonstrate that a rapid repression of HNF4A levels and activity is required to enable a transcriptomic switch during the hepatic acute-phase response. HNF4A overexpression impaired acute-phase gene expression while preserving liver functionality, offering potential for the treatment of liver dysfunction during systemic inflammation or sepsis.