Liver cancer cell lines distinctly mimic the metabolic gene expression pattern of the corresponding human tumours

Zeribe C Nwosu,Matthias P Ebert,Barbara Sitek,Steven Dooley,Christoph Meyer,Dominik A Megger,Stefan Wölfl,Jonathan Sleeman,Ute Hofmann,Melanie Rothley,Nadia Battello,Weronika Piorońska

doi:10.1186/s13046-018-0872-6

Abstract

BackgroundAlthough metabolism is profoundly altered in human liver cancer, the extent to which experimental models, e.g. cell lines, mimic those alterations is unresolved. Here, we aimed to determine the resemblance of hepatocellular carcinoma (HCC) cell lines to human liver tumours, specifically in the expression of deregulated metabolic targets in clinical tissue samples.MethodsWe compared the overall gene expression profile of poorly-differentiated (HLE, HLF, SNU-449) to well-differentiated (HUH7, HEPG2, HEP3B) HCC cell lines in three publicly available microarray datasets. Three thousand and eighty-five differentially expressed genes in ≥2 datasets (P < 0.05) were used for pathway enrichment and gene ontology (GO) analyses. Further, we compared the topmost gene expression, pathways, and GO from poorly differentiated cell lines to the pattern from four human HCC datasets (623 tumour tissues). In well- versus poorly differentiated cell lines, and in representative models HLE and HUH7 cells, we specifically assessed the expression pattern of 634 consistently deregulated metabolic genes in human HCC. These data were complemented by quantitative PCR, proteomics, metabolomics and assessment of response to thirteen metabolism-targeting compounds in HLE versus HUH7 cells.ResultsWe found that poorly-differentiated HCC cells display upregulated MAPK/RAS/NFkB signaling, focal adhesion, and downregulated complement/coagulation cascade, PPAR-signaling, among pathway alterations seen in clinical tumour datasets. In HLE cells, 148 downregulated metabolic genes in liver tumours also showed low gene/protein expression – notably in fatty acid β-oxidation (e.g. ACAA1/2, ACADSB, HADH), urea cycle (e.g. CPS1, ARG1, ASL), molecule transport (e.g. SLC2A2, SLC7A1, SLC25A15/20), and amino acid metabolism (e.g. PHGDH, PSAT1, GOT1, GLUD1). In contrast, HUH7 cells showed a higher expression of 98 metabolic targets upregulated in tumours (e.g. HK2, PKM, PSPH, GLUL, ASNS, and fatty acid synthesis enzymes ACLY, FASN). Metabolomics revealed that the genomic portrait of HLE cells co-exist with profound reliance on glutamine to fuel tricarboxylic acid cycle, whereas HUH7 cells use both glucose and glutamine. Targeting glutamine pathway selectively suppressed the proliferation of HLE cells.ConclusionsWe report a yet unappreciated distinct expression pattern of clinically-relevant metabolic genes in HCC cell lines, which could enable the identification and therapeutic targeting of metabolic vulnerabilities at various liver cancer stages.

Highlights

Metabolism is profoundly altered in human liver cancer, the extent to which experimental models, e.g. cell lines, mimic those alterations is unresolved
Differentiated hepatocellular carcinoma (HCC) cell lines are phenotypically more ‘cancer-like’ and possess tumour molecular portraits To identify human HCC metabolic gene patterns distinctly mimicked in vitro – the correlated proteomic and metabolite-level alterations, as well as cell-specific response to targeting metabolism – we started with comparing the genomic profile of six frequently used human HCC cell lines (Fig. 1a)
In light of the growing relevance of genomics in refining clinical HCC subclasses and therapeutic prospects [1, 2, 41], we identify for the first time, a set of human HCC-derived metabolic genes concordantly or discordantly expressed in vitro

Summary

Introduction

Metabolism is profoundly altered in human liver cancer, the extent to which experimental models, e.g. cell lines, mimic those alterations is unresolved. Similar to human HCC, the corresponding cell lines used for in vitro studies are heterogeneous in their molecular and phenotypic portraits. HCC cell lines show dissimilar expression levels of many known cancer-associated proteins such as caveolin-1 (CAV1), alpha fetoprotein (AFP), and WNT signaling molecules [7,8,9]. Such distinct molecular and phenotypic background, which is seen in cell lines of other cancer types, often raise the question of the extent to which cell lines mimic (or “recapitulate”) original human tumour profile. A thorough characterization of the shared molecular signatures between HCC cell lines and the counterpart primary tumours is highly needed for defining core and novel alterations that can be investigated in vitro with the highest prospect of clinical translation

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