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

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

Matejka K1,2,3,4,5, Stückler F6, Salomon M7, Ensenauer R8,9,10, Reischl E11,12, Hoerburger L13, Grallert H3,4,5,11,12, Kastenmüller G14, Peters A3,12,15, Daniel H2,16, Krumsiek J6,17, Theis FJ6,18, Hauner H1,2,3,4,5,19, Laumen H1,2,3,4,5,13,20,21.

Author information

1
Chair of Nutritional Medicine, Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany.
2
ZIEL-Research Center for Nutrition and Food Sciences, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany.
3
German Center for Diabetes Research (DZD), Neuherberg, Germany.
4
Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, Neuherberg, Germany.
5
Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Technische Universität München, Freising-Weihenstephan, Germany.
6
Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
7
SIRION Biotech GmbH, Martinsried, Germany.
8
Research Center, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, München, Germany.
9
Experimental Pediatrics and Metabolism, Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
10
Institute of Child Nutrition, Max Rubner-Institut, Karlsruhe, Germany.
11
Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.
12
Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany.
13
Paediatric Nutritional Medicine, Else Kröner-Fresenius-Centre for Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany.
14
Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
15
German Research Center for Cardiovascular Disease (DZHK-Munich partner site), Neuherberg, Germany.
16
Chair of Physiology of Human Nutrition, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany.
17
Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States of America.
18
Department of Mathematical Science, Technische Universität München, Garching, Germany.
19
Else Kröner-Fresenius-Center for Nutritional Medicine, Klinikum rechts der Isar, Technische Universität München, München, Germany.
20
Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany.
21
Research Unit Protein Science, Helmholtz Zentrum München, Neuherberg, Germany.

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.

Conflict of interest statement

The author Dr. Michael Salomon (MS) declares commercial affiliation / employment with the commercial company SlRJON Biotech GmbH (Martinsried, Germany). This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.

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