Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population

The manner by which genotype and environment affect complex phenotypes is one of the fundamental questions in biology. In this study, we quantified the transcriptome--a subset of the metabolome--and, using targeted proteomics, quantified a subset of the liver proteome from 40 strains of the BXD mouse genetic reference population on two diverse diets. We discovered dozens of transcript, protein, and metabolite QTLs, several of which linked to metabolic phenotypes. Most prominently, Dhtkd1 was identified as a primary regulator of 2-aminoadipate, explaining variance in fasted glucose and diabetes status in both mice and humans. These integrated molecular profiles also allowed further characterization of complex pathways, particularly the mitochondrial unfolded protein response (UPR(mt)). UPR(mt) shows strikingly variant responses at the transcript and protein level that are remarkably conserved among C. elegans, mice, and humans. Overall, these examples demonstrate the value of an integrated multilayered omics approach to characterize complex metabolic phenotypes.

Mitochondrial unfolded protein response, its molecular mechanism and physiological impact

Virginija Jovaisaite

Mitochondria are the main producers of ATP, the energy currency of the cell, and they perform a wide array of other fundamental functions. These organelles are essential not only for cellular metabolism, but also for organismal physiology and lifespan. A recently discovered mitochondrial unfolded protein response (UPRmt) maintains the mitochondrial proteostasis by managing protein quality control (PQC) network during proteotoxic stress. Recent findings show that activation of this repair pathway improves mitochondrial function and is associated with increased longevity. My thesis aims to expand the knowledge about the UPRmt by exploring its molecular mechanism and impact on mitochondrial stress induced longevity. We performed three studies: Identification of two epigenetic UPRmt regulators (chapter 2). In collaboration with Prof. Dillinâs laboratory (UCB, USA), we identified the conserved histone demethylases jmjd-1.2/PHF8 and jmjd-3.1/JMJD3 as positive regulators of UPRmt and longevity in response to mitochondrial electron transport chain (ETC) dysfunction across species. A systems genetics analysis of data from the BXD mouse genetic reference population (GRP) further indicates conserved roles of the mammalian orthologs of these demethylases in longevity and UPRmt signaling. These findings illustrate an evolutionary conserved epigenetic mechanism that determines the rate of aging, downstream of mitochondrial perturbations. Relation between UPRmt and TCA cycle (chapter 3). We investigated the effects of genetic perturbations of the TCA cycle on the UPRmt and lifespan. We found that downregulation of several TCA cycle enzymes induces UPRmt, but they have divergent effects on lifespan. Restricting the knockdown of these genes to early larval development stages had positive effects on longevity, which was dependent on UPRmt. We analysed the transcriptomes of C. elegans with knockdown of these TCA cycle genes and compared them with those obtained after the knockdown of other mitochondrial genes, which are known to induce the UPRmt. We identified a core set of transcripts, which change in common and which likely represent a signature of mitochondrial dysfunction associated with UPRmt induction. Bioinformatic analysis of UPRmt (chapter 4). In two collaborative studies, we investigated the UPRmt using newly collected data from the BXD mouse GRP. In the first study, we quantified the transcriptome and proteome from 40 strains of the BXD mouse GRP on two different diets. Integrated molecular profiles were used to characterize the UPRmt, which shows strikingly variant responses at the transcript and protein level that are conserved between C.elegans, mice and humans. In the second study, whole genomes of BXD GRP strains were sequenced to detect sequence variants, which were then used to find novel associations within a high coverage phenome of various traits. One of the novel associations included a missense mutation in fumarate hydratase that controls variation in the UPRmt in both mouse and C. elegans. In summary, our work characterized novel epigenetic regulators of UPRmt and associated mitochondrial stress induced longevity, described the connection between the UPRmt and the TCA cycle, and illustrated the conservation of UPRmt in a mouse GRP. These results expand the knowledge about the UPRmt and promote further investigation of its role in longevity and mitochondrial diseases.

EPFL2016

Identification of genetic determinants and pharmacological modulators of mitochondrial function

Pénélope Andreux

Increased life expectancy goes hand in hand with a higher incidence of age-related diseases that affect the nervous and metabolic systems, such as type 2 diabetes, cancer, Parkinson’s and Alzheimer’s disease. These complex diseases are a product of the combined actions of large networks of genes, and environmental factors, such as diet, exercise, drug use, and levels of acute and chronic stress. One of the main challenges in biomedical research is determining how these factors interact to influence human healthspan, in order to develop effective strategies for the diagnosis, prevention, and treatment of these chronic multifactorial diseases. A strategy that has emerged in the last decade is the modulation of mitochondrial function. Accumulating evidence support the involvement of mitochondrial dysfunction in the pathogenesis of type 2 diabetes, Parkinson’s disease, cancer, and to a lesser extent, Alzheimer’s disease. Mitochondrial processes are regulated by a highly dynamic and complex network of enzymes and transcription factors. One of the best characterized branches of this network is the AMPK/SIRT1 pathway and its downstream effectors. Recently, additional pathways important for the regulation of mitochondrial function have been described such as mitochondrial fusion and fission, specific autophagy of mitochondria, termed mitophagy, and mitochondrial unfolded protein response (UPRmt). These recent discoveries have extended the scope of potential therapeutic targets. This thesis describes the development of two complementary approaches to identify novel genetic and pharmacological determinants of mitochondrial function. 1. The first approach aims to identify novel genetic determinants of the regulatory networks that control metabolism in general, and mitochondrial function in particular, by using the mouse BXD genetic reference population (GRP). Chapter II summarizes the analysis of 140 metabolic traits in 42 BXD strains, and demonstrates the suitability and usefulness of the BXD GRP for the identification of genetic regulators of metabolism. 2. The second approach is focused on the development of pharmacological tests for the identification and characterization of novel drugs that modulate mitochondrial phenotypes. Chapter III presents the establishment and validation of a platform of mitochondrial assays in two species, i.e. mammalian cells and the worm C.elegans. A successful example of its use is shown in chapter IV, where the role of copper in tumorigenesis is elucidated by applying these mitochondrial assays Altogether, these two synergistic approaches pave the way that will lead to the identification of novel key factors and treatments for mitochondrial diseases and pathologies associated with mitochondrial dysfunction.

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.