A method to identify and validate mitochondrial modulators using mammalian cells and the worm C-elegans

Mitochondria are semi-autonomous organelles regulated by a complex network of proteins that are vital for many cellular functions. Because mitochondrial modulators can impact many aspects of cellular homeostasis, their identification and validation has proven challenging. It requires the measurement of multiple parameters in parallel to understand the exact nature of the changes induced by such compounds. We developed a platform of assays scoring for mitochondrial function in two complementary models systems, mammalian cells and C. elegans. We first optimized cell culture conditions and established the mitochondrial signature of 1,200 FDA-approved drugs in liver cells. Using cell-based and C. elegans assays, we further defined the metabolic effects of two pharmacological classes that emerged from our hit list, i.e. imidazoles and statins. We found that these two drug classes affect respiration through different and cholesterol-independent mechanisms in both models. Our screening strategy enabled us to unequivocally identify compounds that have toxic or beneficial effects on mitochondrial activity. Furthermore, the cross-species approach provided novel mechanistic insight and allowed early validation of hits that act on mitochondrial function.

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

Metabolic and microenvironmental strategies to accelerate hematopoietic recovery post-aplasia

Vasco Ledebur de Antas de Campos

The procedure-associated mortality rate of bone marrow transplantations (BMT) remains close to 25%. The BMT is therefore only indicated for life-threatening diseases, with no replacement of this technology to be expected in the foreseeable future. Modest improvements such as the use of G-CSF to accelerate hematopoietic recovery significantly reduce mortality. Hematopoietic stem cells (HSC) reside in the bone marrow (BM) and are mainly quiescent, dividing only to self-renew. Via extracellular signals and interactions with other cells of the BM (microenvironment), a stable HSC pool is maintained, while hematopoietic progenitor cells (HPC) proliferate and differentiate to mature blood cell types. Marrow adipocytes (BMA) have recently been recognized as a hematopoietic regulatory entity, although the mechanisms by which it interacts with HSCs and HPCs (HSPC) in vivo, remain unknown. During the hematopoietic recovery period post-BMT, HSPCs increase their metabolism as a response to hematopoietic stress, partly modulated by the microenvironment. In this work we identified novel pharmacological approaches to accelerate hematopoietic recovery in the post-BMT period, addressed via two strategies: (i) by directly modulating HSC metabolism, and (ii) by regulating the differentiation of BMA. Increasing oxidative phosphorylation, combined with an impaired mitochondrial stress response, can severely compromise the regenerative capacity of HSCs. Here we demonstrate that the NAD+-boosting agent Nicotinamide Riboside (NR) reduces mitochondrial activity within HSCs through increased mitophagy, the recycling mechanism of damaged mitochondria. We observed in vitro NR treatment of HSCs to lead to increased asymmetric HSC divisions, which resulted in a significantly enlarged pool of progenitor cells, without HSC exhaustion. Dietary supplementation of NR to mice undergoing BMT accelerated blood recovery and improved survival. We therefore established a novel link between HSC mitochondrial stress, mitophagy and stem cell fate decision. Recent studies have suggested BMA maintain HSCs quiescent, which, may be detrimental to the increased expansion of HPCs in the recovery phase post-BMT. BM stromal cells (BMSC) are the cellular precursors of both adipocytes and osteoblasts, and they have been strongly implicated in supporting hematopoiesis by secreting cytokines such as SCF and Cxcl12. We observed that adipocytes quickly accumulate the marrow space of mice undergoing BMT, followed by an expansion hematopoiesis-supportive multipotent Sca1+/CD24+ stromal cells, coinciding with hematopoietic recovery. We developed a novel screening platform using Digital Holographic Microscopy (DHM), quantifying in vitro adipocytic differentiation non-invasively, allowing for follow-up co-cultures with HSPCs. Using the OP9 BMSC-line, we modulated adipocyte differentiation prior to co-culture using a pharmacological approach and observed that high adipocytic content was associated to a decrease in HPC expansion. We perfomed a screening of over 4000 FDA-approved drugs and natural compounds and identified one to efficiently prevent adipocytic differentiation and maintain the hematopoietic supportive capacity of OP9 stroma. Altogether, this work opens the door to alternative strategies accelerating hematopoietic reconstitution and unveils the potential to improve recovery of patients undergoing BMT.

EPFL2019

Enhancing mitochondrial quality control to fight neuromuscular degeneration in aging and disease

Mario Romani

Loss of mitochondrial function and proteostasis typify aging and age-associated degenerative disorders such as Alzheimer's disease and muscle aging. To date, no cure or preventive measure is available to manage these conditions. Alterations of cellular proteostasis, such as accumulation of misfolded or aggregated proteins, can directly affect mitochondrial homeostasis leading to activation of specific mitochondrial stress pathways capable of maintaining mitochondrial function. However, the contribution of these pathways in age-associated diseases characterized by proteotoxic aggregates is largely unknown. My thesis aims to understand the connection between cellular and mitochondrial proteostasis with a particular focus on mitochondrial stress pathways involved in the response to proteotoxic stress. To this end, I performed 2 studies: Reduction of Amyloid-beta proteotoxicity through activation of mitochondrial quality control: Accumulation of Amyloid-beta (Aß) peptidic aggregates, generated by the miscleavage of amyloid precursor protein (APP), is often associated with mitochondrial dysfunction. However, it is largely unknown how mitochondria react to these proteotoxic insults. We identified a cross-species conserved mitochondrial stress response, from nematodes to humans, activated during Aß proteotoxic stress. This response entails key mitochondrial quality control pathways such as the mitochondrial unfolded protein response (UPRmt) and mitophagy. Importantly, activation of these pathways through administration of mitochondrial regulators Doxycycline and the NAD+ booster nicotinamide riboside (NR), was sufficient to reduce Aß accumulation and proteotoxicity in nematodes and human cell lines. Moreover, boosting mitochondrial quality control in vivo in a mouse model of Alzheimer's disease with the compound NR led to a reduction of brain Aß plaques and preservation of cognitive function. Skeletal muscle aging is characterized by amyloid-like protein aggregates: Skeletal muscle aging is characterized by accumulation of dysfunctional mitochondria and misfolded proteins. However, the connection between these two hallmarks of muscle aging remains elusive. We found that aged skeletal muscles present a similar perturbation of mitochondrial and APP processing pathways when compared to muscles from inclusion body myositis patients (IBM), a disease characterized by intracellular protein deposits containing also Aß aggregates. In line with this, we identified amyloid-like aggregates in aged muscle closely resembling the ones observed during IBM with concomitant mitochondrial dysfunction. Strategies aiming at restoring mitochondrial homeostasis led to activation of the mitochondrial quality control accompanied by a reduction of amyloid-like aggregates in vitro and in vivo in mammalian and nematode systems. In summary, our work demonstrated that amyloidosis characterizes muscle, and possibly brain, aging in a similar fashion to what is observed in muscle and brain tissues from IBM and Alzheimer's patients, respectively. Importantly, restoring mitochondrial homeostasis through activation of mitochondrial quality control is sufficient to alleviate protein aggregation and improve tissue function in aging, IBM and Alzheimer's disease models.

EPFL2021