Abstract
Hepatocyte nuclear factor 1A (HNF1A) is the master regulator of liver homeostasis and organogenesis and regulates many aspects of hepatocyte functions. It acts as a tumor suppressor in the liver, evidenced by the increased proliferation in HNF1A knockout (KO) hepatocytes. Hence, we postulated that any loss-of-function variation in the gene structure or composition (mutation) could trigger dysfunction, including disrupted transcriptional networks in liver cells. From the International Cancer Genome Consortium (ICGC) database of cancer genomes, we identified several HNF1A mutations located in the functional Pit-Oct-Unc (POU) domain. In our biochemical analysis, we found that the HNF1A POU-domain mutations Y122C, R229Q and V259F suppressed HNF4A promoter activity and disrupted the binding of HNF1A to its target HNF4A promoter without any effect on the nuclear localization. Our results suggest that the decreased transcriptional activity of HNF1A mutants is due to impaired DNA binding. Through structural simulation analysis, we found that a V259F mutation was likely to affect DNA interaction by inducing large conformational changes in the N-terminal region of HNF1A. The results suggest that POU-domain mutations of HNF1A downregulate HNF4A gene expression. Therefore, to mimic the HNF1A mutation phenotype in transcription networks, we performed siRNA-mediated knockdown (KD) of HNF4A. Through RNA-Seq data analysis for the HNF4A KD, we found 748 differentially expressed genes (DEGs), of which 311 genes were downregulated (e.g., HNF1A, ApoB and SOAT2) and 437 genes were upregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping revealed that the DEGs were involved in several signaling pathways (e.g., lipid and cholesterol metabolic pathways). Protein–protein network analysis suggested that the downregulated genes were related to lipid and cholesterol metabolism pathways, which are implicated in hepatocellular carcinoma (HCC) development. Our study demonstrates that mutations of HNF1A in the POU domain result in the downregulation of HNF1A target genes, including HNF4A, and this may trigger HCC development through the disruption of HNF4A–HNF1A transcriptional networks.
Highlights
Liver cancer is a major contributor to the cancer burden and one of the leading causes of cancer-dependent deaths worldwide [1,2]
The mutant amino acid residues are strictly conserved among various species (Figure 1B); the asterisks in red specify the locations of the POU domain mutations (Y122C, R229Q and V259F)
hepatocyte nuclear factor 1A (HNF1A) mutations were identified in diabetes, and their functional effect was validated [31,50,51]; only very few studies have suggested that HNF1A mutations identified in hepatocellular carcinoma (HCC) are associated with the development and progression of HCC [32]
Summary
Liver cancer is a major contributor to the cancer burden and one of the leading causes of cancer-dependent deaths worldwide [1,2]. The common risk factors for liver cancer development include alcohol consumption, hepatitis B and C virus infection, and metabolic diseases [3,4]. Next-generation sequencing (NGS) analysis data for liver cancer patients in which the most significantly mutated genes were TP53, CTNNB1, and TERT have been reported [7]. Besides these major driver gene mutations, other driver and tumor suppressor genes with well-established roles in liver function have been found. The overexpression of HNF1A suppressed the proliferation of HCC and induced the expression of liver-specific genes in HCC cells, which caused cell cycle arrest [14]. While the role of HNF1A in different cancers has recently been examined [15,16,17], only a few studies have demonstrated a critical link between HNF1A mutations and the development of liver cancer
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