Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis

Abstract

Hepatocellular carcinoma (HCC) has a high mortality rate and early detection of HCC is crucial for the application of effective treatment strategies. HCC is typically caused by either viral hepatitis infection or by fatty liver disease. To diagnose and treat HCC it is necessary to elucidate the underlying molecular mechanisms. As a major cause for development of HCC is fatty liver disease, we here investigated anomalies in regulation of lipid metabolism in the liver. We applied a tailored network-based approach to identify signaling hubs associated with regulation of this part of metabolism. Using transcriptomics data of HCC patients, we identified significant dysregulated expressions of lipid-regulated genes, across many different lipid metabolic pathways. Our findings, however, show that viral hepatitis causes HCC by a distinct mechanism, less likely involving lipid anomalies. Based on our analysis we suggest signaling hub genes governing overall catabolic or anabolic pathways, as novel drug targets for treatment of HCC that involves lipid anomalies.

Figure 1.

Signaling hubs of liver lipid metabolism. (A) Hub genes of signaling between lipid sensors (PPAR-α, β/δ and γ) and lipid enzymes were identified from an integrated signaling network. Hepatic lipid enzymes were chosen from a curated genome-scale metabolic model for liver cells, iHepatocyte2322 and classified into 37 lipid metabolic pathways. For every lipid pathway, we identified top-100 signaling hub genes separately. (B) Hub genes overlapping across lipid pathways were shown in a heatmap. Each row indicates hub genes involved in a certain lipid pathway (if involved, they were colored as black). Most of the largely overlapping genes, referred to as global hubs, were genes supporting nuclear receptor, including PPAR, signaling, such as RXRs, HDACs and nuclear receptor (NR) co-activators/-repressors. Known lipid regulators, SREBPs, LXRα and HNF-4α were less overlapping and therefore referred to as local hubs. Also, based on the HPO database, we examined whether hub genes (C) or sensors/enzymes (D) are associated with a lipid anomaly phenotype and both hub genes and sensors/enzymes were significantly overlapped with known lipid anomaly genes in the database. Next, we examined if (E) identified hub genes of liver lipid metabolism were specifically overlapping with gens associated with liver tissue phenotype. Likewise, we identified signaling hubs of lipid metabolism in other tissues, such as (F) bone marrow and (G) kidney and compared them with genes associated with their tissue phenotypes. Interestingly, those signaling hubs were significantly overlapping with their tissue phenotypic genes. Abbreviations: FA, fatty acid; FFA, free fatty acid; UFA, unsaturated fatty acid; PUFA, poly-unsaturated fatty acid.

Figure 2.

Dysregulated expressions of signaling hubs and enzymes across lipid pathways, in patients with HCC. For each lipid pathway, we examined differential expressions of enzymes (top) and signaling hubs (bottom), between tumor samples and matched control samples. Lipid pathways were classified into four major categories: catabolism, anabolism, pooling and transport. Many enzymes in catabolic and transport pathways were dysregulated at the gene expression level. On the other hand, many hub genes in anabolic and pooling pathways were dysregulated at the gene expression level. Abbreviations: same as Figure 1.

Figure 3.

Distinct expressions of signaling hubs and enzymes revealed in HCC patients with viral hepatitis. In two patient groups of HCC, (A and B) a patient group with viral hepatitis B and C and (C and D) a patient group without viral hepatitis, we separately examined differential expressions of signaling hubs and enzymes. Interestingly, in patients with viral hepatitis, (A) most pathways’ enzymes and (B) signaling hubs were less dysregulated. Of note, fatty acid biosynthesis pathways (a red bracket), called de novo lipogenesis pathways, did not reach the statistical significance of P-value = 0.05, suggesting that viral hepatitis leads to HCC, irrespective of lipid anomalies. Abbreviations: same as Figure 1.

Figure 4.

In-group specificity of signaling hubs. In order to distinguish catabolism- and anabolism-specific hub genes, we measured the in-group specificity of hub genes in catabolic or anabolic pathways. Notably, hubs shown only in anabolic pathways (blue) tend to be located in top-left region (high anabolic specificity and low catabolic specificity). On the other hand, hubs shown only in catabolic pathways (red) tend to be in bottom-right region. We also found significant differences of catabolic and anabolic specificity between two hub groups (red and blue) by t-tests (P-values, 3.74 × 10⁻¹¹ and 3.72 × 10⁻¹⁰, respectively). Based on in-group specificities, we identified catabolic or anabolic signaling hubs.