Genetic, metabolic, and molecular insights into the diverse outcomes of diet-induced obesity in mouse

Alexis Maximilien Bachmann
EPFL, 2021
EPFL thesis

Abstract

Overweight and obesity are increasingly common public health issues worldwide, leading to a wide range of diseases from metabolic syndrome to steatohepatitis and cardiovascular diseases. While the increase in the prevalence of obesity is partly attributable to changes in lifestyle (i.e. increased sedentarity and changes in eating behaviour), the metabolic and clinical impacts of these obesogenic conditions varies between sexes and genetic backgrounds. The conception of personalised treatments of obesity and its complications require a thorough understanding of the diversity of responses to environmental stimuli such as high-fat diet intake. In this thesis, by analysing nine genetically diverse mouse strains, we show that much like humans, mice respond to high-fat diet in a genetic- and sex-dependent manner. Physiological and molecular responses to high-fat diet are associated with the expression of genes involved in immunity and mitochondrial function. Finally, we find that mitochondrial function and mitochondrial supercomplex assembly may explain part of the diversity of physiological responses. By exploring the complex interactions between genetics and metabolic phenotypes via gene expression and molecular traits, we shed light on the importance of genetic background and sex in determining metabolic outcomes. In addition to providing the community with an extensive resource for optimizing future experiments, this work serves as an exemplary design for more generalizable translational studies.

Official source

https://infoscience.epfl.ch/record/289802?ln=en

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Alexis Maximilien Bachmann
EPFL, 2021
EPFL thesis

Abstract

Official source

https://infoscience.epfl.ch/record/289802?ln=en

About this result

Related concepts (23)

Related concepts

Related publications (130)

Related publications

Genome-wide association (GWA) studies aim to dissect the relationship between genotype and phenotype. So far, the focus has been on nuclear genetic determinants as variation in the mitochondrial genome is often low in the study cohorts. Despite this observation, mitochondrial genomic variants are increasingly linked to metabolic and neurological disorders. Thus, there is much to gain from studying how mitochondrial variation interacts with nuclear variation and/or environment, and how this subsequently affects phenotypes. In my thesis I address these topics using Drosophila melanogaster as a model system, and specifically the Drosophila Genetic Reference Panel (DGRP). The DGRP consists of 200 sequenced and genetically diverse Drosophila populations and has been extensively used to study a wide-range of quantitative traits. However, in all of these studies, researchers have focussed on the influence of nuclear genetic variants in the absence of a high-resolution map of mitochondrial variants. To address this problem, we have developed a high-throughput method to specifically sequence mitochondrial DNA that enabled us to characterize mitochondrial genomic variation to an unprecedented depth. On average, each DGRP line had 25 mitochondrial variants (1 in 600 bp) and that most of the variants detected were unique for each line. However, we also found that some variants are more prevalent and show they can be used to construct mitochondrial haplotypes. We then used these haplotypes to test whether mitochondrial variation affected previously published phenotypes. We detected significant associations with 12 out of 259 publicly accessible phenotypes and found that these were mostly related to metabolism and responses to environmental cues. We selected one of the significant phenotypes, food intake in males, to verify our findings. We demonstrated the effect of mitochondrial haplotypes on the phenotype by swapping mitochondria from ¿high food intake¿ lines with mitochondria from ¿low food intake¿ lines and vice versa. We observed that, largely independent of the nuclear background, DGRP lines with a ¿high food intake mitochondria¿ consumed more food and concomitantly, DGRP lines with the ¿low food intake mitochondria¿ consumed less food. Furthermore, we investigated the influence of natural genetic variation was on the response to a high-fat diet. We designed a control and a high-fat diet and fed this to >100 DGRP lines and measured the lifespan on each diet. On average, lifespan was decreased by 48% on a high-fat diet, however this ranged from an increase of 2% to a decrease of 60% accentuating the complexity of the underlying genetic architecture. Our dataset was relatively small and limited our genome-wide and mitochondrial haplotype association analyses. Nonetheless, our GWA analysis detected variants related to genes involved in lipid metabolism and mitochondria but we did not detect significant associations with mitochondrial haplotypes. This suggests that while mitochondrial function may be important for the response to a high-fat diet, it is not dependent on the mitochondrial haplotype. Taken together, the work described in my thesis demonstrates the significance of accounting for mitochondrial haplotypes in phenotype association analyses. By doing so, it can open up new insights into genotype-to-phenotype relationships and gene regulation.

EPFL2018

Development and application of experimental tools to elucidate the gene regulatory network underlying adipogenesis

Carine Delattre-Gubelmann

Excess fat mass in obese individuals, which is characterized by an increase of white adipocyte cell size and number, significantly raises the risk of developing metabolic syndrome symptoms as well as cancer. A detailed understanding of the transcriptional mechanisms mediating white adipocyte differentiation (i.e., adipogenesis) is required to counteract the growing obesity epidemics. In this thesis, we have implemented two combinatory approaches to detect new protein-DNA interactions in the mouse, one of which targets the adipogenic gene regulatory network (GRN) that underlies the white adipocyte differentiation process. As a first approach to shed light on GRNs, we have developed and validated a powerful approach that combines a high-throughput yeast one-hybrid-based (Y1H) system to detect transcription factors (TFs)-DNA element interactions, together with a novel microfluidics-based technique, enabling the identification and characterization of individual binding sites for detected TFs within the respective regulatory sequences at unprecedented throughput and resolution. Using well-described regulatory elements as well as an uncharacterized enhancer which can play also a role in adipogenesis, we show that our approach in a first phase uncovers many known as well as novel TF-DNA interactions, of which a large proportion were independently validated. In addition, we further demonstrate how our approach can be used in a second phase to characterize detected interactions by enabling the generation of a relative DNA occupancy landscape over the length of the respective DNA element. Furthermore, we provide evidence that this system enables the detection of novel interactions that may have in vivo relevance. Given the strict requirements for direct and well-characterized protein-DNA interaction data to generate and model gene regulatory networks, the presented two-tiered approach should be of great value to enhance our understanding of the regulatory principles underlying mouse gene expression. To identify transcription factors involved in white adipocyte differentiation, we overexpressed TFs in preadipocytes and quantified their effect on differentiation. To this end, we have created a mouse open-reading frame resource consisting of more than 750 fully sequence-verified TF clones. We transferred these TF clones to a Tet-On lentiviral vector and used them to infect white preadipocytes. Based on microscopy-assisted quantification of lipids after induction of differentiation, we identified putatively novel TF candidates that strongly enhanced differentiation based on the increased lipid accumulation, indicating a potential role in adipogenesis. Gene expression and ChIP-seq experiments have been performed for the three top candidates (ZEB1, ZFP30 and ZFP277) to further study their function within the adipogenic regulatory network. To assess whether the effect of these TFs on adipogenesis could be reproduced in vivo, murine adipose stromal-vascular fraction containing adipocyte precursor cells were implanted into mice fed a high-fat diet, after each of the three TF candidates were knockdown or overexpressed in these cells. This experiment and the RNA-seq analyses are currently being processed while this thesis is being written. Furthermore, due to the absence of quantitative real-time PCR (qPCR) primer designing tools that would allow for gene-specific expression profiling in a high-throughput fashion, we design a user-friendly platform: GETPrime. This platform uniquely combines and automates several features critical to optimal qPCR primer design for all annotated Homo sapiens, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster and Danio rerio genes in the Ensembl database. GETPrime primers have been extensively validated experimentally, demonstrating their high quality as well as high transcript specificity in complex samples.

EPFL2013

Pharmacological Inhibition of Poly(ADP-Ribose) Polymerases Improves Fitness and Mitochondrial Function in Skeletal Muscle

Johan Auwerx, Carlos Canto Alvarez, Wei Li, Keir Joe Menzies, Laia Morato Fornaguera, Laurent Mouchiroud, Norman Lionel Moullan, Eija Riitta Pirinen, Kristina Schoonjans, Evan Graehl Williams, Hongbo Zhang

We previously demonstrated that the deletion of the poly(ADP-ribose) polymerase (Parp)-1 gene in mice enhances oxidative metabolism, thereby protecting against diet-induced obesity. However, the therapeutic use of PARP inhibitors to enhance mitochondrial function remains to be explored. Here, we show tight negative correlation between Parp-1 expression and energy expenditure in heterogeneous mouse populations, indicating that variations in PARP-1 activity have an impact on metabolic homeostasis. Notably, these genetic correlations can be translated into pharmacological applications. Long-term treatment with PARP inhibitors enhances fitness in mice by increasing the abundance of mitochondrial respiratory complexes and boosting mitochondrial respiratory capacity. Furthermore, PARP inhibitors reverse mitochondrial defects in primary myotubes of obese humans and attenuate genetic defects of mitochondrial metabolism in human fibroblasts and C. elegans. Overall, our work validates in worm, mouse, and human models that PARP inhibition may be used to treat both genetic and acquired muscle dysfunction linked to defective mitochondrial function.

Elsevier2014

Development and application of experimental tools to elucidate the gene regulatory network underlying adipogenesis

Carine Delattre-Gubelmann

EPFL2013

EPFL2018