Dynamic modelling of an ACADS genotype in fatty acid oxidation - Application of cellular models for the analysis of common genetic variants

PLoS One. 2019 May 23;14(5):e0216110. doi: 10.1371/journal.pone.0216110. eCollection 2019.

Abstract

Background: Genome-wide association studies of common diseases or metabolite quantitative traits often identify common variants of small effect size, which may contribute to phenotypes by modulation of gene expression. Thus, there is growing demand for cellular models enabling to assess the impact of gene regulatory variants with moderate effects on gene expression. Mitochondrial fatty acid oxidation is an important energy metabolism pathway. Common noncoding acyl-CoA dehydrogenase short chain (ACADS) gene variants are associated with plasma C4-acylcarnitine levels and allele-specific modulation of ACADS expression may contribute to the observed phenotype.

Methods and findings: We assessed ACADS expression and intracellular acylcarnitine levels in human lymphoblastoid cell lines (LCL) genotyped for a common ACADS variant associated with plasma C4-acylcarnitine and found a significant genotype-dependent decrease of ACADS mRNA and protein. Next, we modelled gradual decrease of ACADS expression using a tetracycline-regulated shRNA-knockdown of ACADS in Huh7 hepatocytes, a cell line with high fatty acid oxidation-(FAO)-capacity. Assessing acylcarnitine flux in both models, we found increased C4-acylcarnitine levels with decreased ACADS expression levels. Moreover, assessing time-dependent changes of acylcarnitine levels in shRNA-hepatocytes with altered ACADS expression levels revealed an unexpected effect on long- and medium-chain fatty acid intermediates.

Conclusions: Both, genotyped LCL and regulated shRNA-knockdown are valuable tools to model moderate, gradual gene-regulatory effects of common variants on cellular phenotypes. Decreasing ACADS expression levels modulate short and surprisingly also long/medium chain acylcarnitines, and may contribute to increased plasma acylcarnitine levels.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acyl-CoA Dehydrogenase / genetics*
  • Acyl-CoA Dehydrogenase / metabolism
  • Carnitine / analogs & derivatives
  • Carnitine / genetics
  • Carnitine / metabolism
  • Cell Line, Tumor
  • Fatty Acids / genetics*
  • Fatty Acids / metabolism*
  • Female
  • Genetic Variation / genetics*
  • Genome-Wide Association Study / methods
  • Genotype
  • Hepatocytes / metabolism
  • Humans
  • Male
  • Middle Aged
  • Mitochondria / genetics
  • Mitochondria / metabolism
  • Oxidation-Reduction
  • Phenotype

Substances

  • Fatty Acids
  • acylcarnitine
  • Acyl-CoA Dehydrogenase
  • Carnitine

Grant support

The study was supported by the Else Kröner-Fresenius Foundation, Bad Homburg v. d. H., Germany; by a grant from the German Federal Ministry of Education and Research (BMBF) Grant no. 0315494A (project SysMBo); and by the grant Clinical Cooperation Group ‘Nutrigenomics and type 2 diabetes’ received from the Helmholtz Zentrum München, München-Neuherberg, Germany, and the Technische Universität München, Freising-Weihenstephan, Germany. RE was supported by the German Federal Ministry of Education and Research (BMBF) Grant 01EA1307; FS by the European Union's Seventh Framework Program (FP7-Health-F5-2012) under grant agreement n°305280 (MIMOmics) and by a PhD student fellowships from the “Studienstiftung des Deutschen Volkes"; JK by a grant from the German Helmholtz Association, “Initiative and Networking Fund”; FJT by the European Research Council (starting grant “LatentCauses”); LH by the grant LA2595/3-1 from the German Research Foundation (DFG). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich (TUM) in the framework of the Open Access Publishing Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The author Dr. Michael Salomon (MS) declares commercial affiliation / employment with the commercial company SIRION Biotech GmbH (Martinsried, Germany). The funder provided support in the form of salaries for author MS, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of the author was related to Investigation, Methodology, and Writing - review & editing, as articulated in the ' author contributions section'.