Prof. Dr. Aleksandra Trifunovic

Research Area: Mitochondrial Stress Responses in Disease and Ageing

Branches: GeneticsImmunologyStem Cell Biology

Website: Trifunovic Lab

Prof. Dr. Aleksandra Trifunovic, Ageing Grad School Cologne

1. Research background:

Mitochondria are essential organelles found in every eukaryotic cell, required to convert food into usable energy. The mitochondrial oxidative phosphorylation (OXPHOS), which produces the majority of cellular energy in the form of ATP, is controlled by two distinct genomes: the nuclear and the mitochondrial genome (mtDNA). Mutations in mitochondrial genes encoded by either genome could cause mitochondrial disorders, and have emerged as a key factor in a myriad of “common” diseases, including Parkinson’s and Alzheimer’s Disease, Type 2 Diabetes, and are strongly linked to the aging process. Despite all this, it is surprising that our understanding of the mechanisms governing the mitochondrial gene expression, its reliance on the complex nature of dual genome control and associated pathologies remains superficial, with therapeutic interventions largely unexplored. Remarkably, mitochondria are now also viewed as main regulators of signal transduction. Within a last few year, multiple mitochondria-centric signaling mechanisms have been proposed, including release of multiple metabolites, and the scaffolding of signaling complexes on the outer mitochondrial membrane. It has also been shown that mitochondrial dysfunction causes induction of stress responses, bolstering the idea that mitochondria communicate their fitness to the rest of the cell. Studies in this area are not only of basic scientific interest, but may also provide new avenues towards treatment of mitochondrial dysfunction in a variety of human diseases and ageing.

2. Research questions addressed by the group:

When mitochondria experience stress or when dysfunction occurs, the organelle sends signals to the cell nucleus, which launches different types of adaptive cell responses. Transcription factors are activated and stimulate the expression of specific sets of genes, whose products enable the cell to adapt to the changes. Most recent scientific advances reveal that mitochondria also play a central role in proinflammatory signalling, on one side as a signalling platform, but also as an active producer of potent damage-associated molecular patterns (DAMPs) that control activation of innate immunity and the inflammatory response. We aim to further understand these largely unknown mechanisms that play a central role in determining the extent of tissue specific defect arising from the respiratory deficiency and systemic metabolic and inflammatory changes. The primary focus of our research is in deciphering the precise signaling cascade of the pathogenic mechanisms leading to mitochondrial diseases and ageing, with the ultimate goal of identifying new therapeutic targets and strategies.

Our group has successfully advanced research approaches that focus on the communication between mitochondria and other parts of the cell. We have shown that mitochondrial dysfunction is sensed independently of the respiratory chain deficiency, questioning current view on molecular mechanisms contributing to the development of mitochondrial diseases (1, 2). We reported that the pathway for induction of mtUPR differs between C. elegans and mice (3-5). We also look for novel pathways involved in the adaptation of cells and organisms to mitochondrial dysfunction that could lead to prolongation of lifespan (6), or discovery of novel homeostatic pathways (7, 8). Recently, we reported that mitochondrial stress response is regulated by an intricate interplay between three transcription factors: CHOP, C/EBPβ, and ATF4 and tissues specific cytokines  (9, 10).

3. Possible project(s):

1. Quality control of respiratory chain

Mitochondria are highly dynamic and stress-responsive organelles that are renewed, maintained and removed by a number of different mechanisms. Recent findings bring more evidence for the focused, defined, and regulatory function of the intramitochondrial proteases extending far beyond the traditional concepts of damage control and stress responses. Until recently, the macrodegradation processes, such as mitophagy, were promoted as the major regulator of OXPHOS remodeling and turnover. However, the spatiotemporal dynamics of the OXPHOS system can be greatly modulated by the intrinsic mitochondrial mechanisms acting apart from changes in the global mitochondrial dynamics. This, in turn, may substantially contribute to the shaping of the metabolic status of the cell.

We have recently described the salvage pathway as the mechanism that safeguard against the accumulation of dysfunctional CI arising from the inactivation of the N-module subunits due to attrition caused by its constant activity under physiological conditions (7, 8). Now, we would like to further explore proteolytic control of OXPHOS function by mitochondrial matrix proteases CLPP and LONP1 under physiological and pathophysiological conditions. 

2. Dissecting the regulation and consequences of acute to chronic mitoISR switch

Cells developed various ways of dealing with disturbances in mitochondrial respiratory chain biogenesis or function. Over the last few years it became clear that one specific pathway has been activated in response to perturbation in OXPHOS activity, preceding other adaptive changes in mitochondrial biogenesis or antioxidant defence, namely the mitochondrial integrated stress response (mitoISR). Acute to chronic switch in mitoISR is characterized by reactivation of suppressed cap-dependent translation in the constant presence of an insult (mitochondrial dysfunction) Our recently published data show that this might be one of the most deleterious events in vivo.

Now, we will primarily use differentiated C2C12 cells initially treated with OXPHOS assembly inhibitor actinonin. This will allow us to follow dose-dependent activation of stress responses, possible cycling in the stress responses and understanding the crosstalk between metabolic remodeling and translational suppression In parallel, using CRISPR/Cas9 technology, we will create several mitochondrial mutant lines of the same parental C2C12 cell line. Ultimately, we would like to test some of the findings in vivo in mice models already present in the lab.

4. Applied Methods and model organisms:

The group mainly uses in vivo transgenic mouse models to tackle specific questions of mitochondrial pathophysiology. Many of the transgenic mice models are developed within the group. The group relies mainly on various molecular biology techniques to understand the complex signaling pathways, many of which are specifically developed to understand the mitochondrial physiology. To tackle complex molecular mechanisms of specific processes in details, we often turn to mammalian cell-based models and different biochemical approaches. As one of the main aims is to understand the consequences of energy depletion in cells and the organism as a whole, the lab has established many different bioenergetic approaches in vitroand in vivo, and this expertise are provided to the Cologne research community.

5. Desirable skills and qualifications:

Applicants should have a strong theoretical and practical background in molecular biology, cell biology, genetics and/or biochemistry. A genuine enthusiasm for scientific research is expected. A high ability for problem solving through analytical thinking is beneficial.

6. References and key publications:

  1. S. A. Dogan et al., Tissue-specific loss of DARS2 activates stress responses independently of respiratory chain deficiency in the heart. Cell Metab  19, 458-469 (2014).
  2. M. Aradjanski et al., DARS2 protects against neuroinflammation and apoptotic neuronal loss, but is dispensable for myelin producing cells. Hum Mol Genet  26, 4181-4189 (2017).
  3. C. Becker et al., CLPP deficiency protects against metabolic syndrome but hinders adaptive thermogenesis. EMBO Rep  19, e45126 (2018).
  4. K. Szczepanowska et al., CLPP coordinates mitoribosomal assembly through the regulation of ERAL1 levels. EMBO J  35, 2566-2583 (2016).
  5. D. Seiferling et al., Loss of CLPP alleviates mitochondrial cardiomyopathy without affecting the mammalian UPRmt. EMBO Rep  17, 953-964 (2016).
  6. M. Herholz et al., KLF-1 orchestrates a xenobiotic detoxification program essential for longevity of mitochondrial mutants. Nat Commun  10, 3323 (2019).
  7. K. Szczepanowska et al., A salvage pathway maintains highly functional respiratory complex I. Nat Commun  11, 1643 (2020).
  8. A. Rumyantseva, M. Popovic, A. Trifunovic, CLPP deficiency ameliorates neurodegeneration caused by impaired mitochondrial protein synthesis. Brain  145, 92-104 (2022).
  9. S. Kaspar et al., Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR. Sci Adv 7,  (2021).
  10. M. Croon et al., FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction. Sci Adv  8, eabn7105 (2022).