PhD Positions:

Project proposals for Call No. 26/01

Clara Correia-Melo
Dissecting host-microbiome metabolism in aging
Dissecting host-microbiome metabolism in aging Cellular senescence is marked by irreversible cell cycle arrest and the secretion of pro-inflammatory and oxidative factors that impair tissue function. In the gut, senescent intestinal fibroblasts disrupt intestinal stem cell differentiation, contributing to functional decline. Emerging evidence further implicates senescence in driving microbial dysbiosis with age. Our previous work in eukaryotic microbial systems has shown that metabolic interactions between cells and their surrounding environment critically influence cellular aging, viability, and drug response. Despite extensive focus on protein-mediated signaling in senescence, the metabolic dimension of this intercellular communication has been largely overlooked-often due to the use of metabolite-rich culture media that obscure physiologically relevant metabolic interactions. To address this, we have developed a high-throughput platform to analyze human cells cultured in Human Plasma-Like Medium (HPLM), which better mimics in vivo conditions. Using this platform, we will profile the intracellular metabolome and senescence-associated extracellular metabolic environment of human colonic cells, and assess their impact on a panel of ~80 representative gut bacterial strains. This study will identify metabolic conditions that modulate dysbiosis, potentially informing the development of metabolism-targeted therapies for aging and age-related diseases. By integrating bacterial proteomics, metabolomics, and metabolic modeling, we will uncover the molecular mechanisms through which senescence-derived exometabolomes alter microbial fitness, shedding light on the metabolic drivers of dysbiosis in aging.

Dennis de Bakker
Characterization and mitigation of blood–brain barrier dysfunction in short-lived turquoise killifish
The blood–brain barrier (BBB) protects the brain from peripheral threats such as pathogens and immune cells. Age-related breakdown of the BBB is associated with a decline in brain function and neurodegenerative diseases, yet the underlying mechanisms and functional consequences remain poorly understood. This lack of knowledge hampers the development of therapeutic strategies aimed at maintaining BBB function throughout life.
In the proposed LGSA project, cutting-edge technologies will be employed to characterize and mitigate age-related BBB breakdown using a 4-step plan. The rapidly aging turquoise killifish model will be used, as it spontaneously develops age-related brain degeneration and cognitive decline.
I. The candidate will begin by performing whole-brain clearing and light-sheet microscopy to map the vascular system of young and old killifish brains.
II. To identify the dynamics and sites of BBB breakdown, the candidate will inject a fluorescent dye intraperitoneally that enters the brain only when the BBB is compromised. Dye accumulation in post-mortem brains of young and old fish will be compared, and possibilities to live record dye entry in vivo will be explored.
III. To characterize the cell types and molecular pathways involved in BBB breakdown, the candidate will employ single-cell RNA sequencing of GFP-positive vascular cells from young and old killifish brains using available transgenic lines.
IV. Based on the generated insights, the candidate will develop a pharmacological approach to mitigate BBB breakdown in aging killifish.
Taken together, the candidate will contribute to a deeper understanding of BBB breakdown using state-of-the-art methodologies within a well-funded, supportive research environment. The findings generated here will help to establish a framework for BBB-targeted therapies within the context of aging and neurodegenerative diseases.

Melike Dönertas
Comparative Systems Biology of Aging
Comparative Systems Biology of Aging The biology of aging involves complex interactions among gene regulation, microbiome dynamics, and evolutionary processes. This project invites an excellent doctoral candidate to investigate aging mechanisms through a systems biology approach, with the flexibility to pursue one or more of the following directions: (1) comparative analysis of age-related changes in gene expression and microbiome composition across short- and long-lived species or populations; (2) integrative analysis of multi-omic datasets to identify pharmacological or lifestyle interventions that mitigate aging phenotypes; and/or (3) analysis of tissue- and cell-type-specific identity shifts during aging, including their molecular drivers and functional consequences. Depending on the candidate’s background and interests, the project can involve experimental data generation (e.g., metagenomics, RNA-seq, scRNA-seq, proteomics) or be conducted entirely computationally. The overarching goal is to uncover conserved and targetable features of aging, offering both a mechanistic understanding and translational potential. Relevant References: Izgi, H., Han, D., Isildak, U., Huang, S., Kocabiyik, E., Khaitovich, P., Somel, M., & Dönertaş, H. M. (2022). Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity. eLife, 11, e68048. https://doi.org/10.7554/eLife.68048 Dönertaş, H. M., Fabian, D. K., Fuentealba, M., Partridge, L., & Thornton, J. M. (2021). Common genetic associations between age-related diseases. Nature Aging, 1(4), 400–412. https://doi.org/10.1038/s43587-021-00051-5 Dönertaş, H. M., Fuentealba, M., Partridge, L., & Thornton, J. M. (2019). Identifying Potential Ageing-Modulating Drugs In Silico. Trends in Endocrinology and Metabolism: TEM, 30(2), 118–131. https://doi.org/10.1016/j.tem.2018.11.005 Turan, Z. G., Parvizi, P., Dönertaş, H. M., Tung, J., Khaitovich, P., & Somel, M. (2019). Molecular footprint of Medawar’s mutation accumulation process in mammalian aging. Aging Cell, 348, e12965. https://doi.org/10.1111/acel.12965 Dönertaş, H. M., Fuentealba Valenzuela, M., Partridge, L., & Thornton, J. M. (2018). Gene expression-based drug repurposing to target aging. Aging Cell, 17(5), e12819. https://doi.org/10.1111/acel.12965

Christoph Englert
The role of cellular senescence in lifespan determination and regeneration in the short-lived killifish Nothobranchius furzeri
Keywords: senescence: reporter line, nitroreductase/metronidazole, cell ablation, regeneration
Abstract: To study the molecular and cellular underpinnings of aging and regeneration we are using the African turquoise killifish Nothobranchius furzeri. Despite its very short lifespan of 6 – 12 months, this species shares many features with mammalian aging including telomere shortening, accumulation of senescent cells (SCs), cognitive decline and loss of regenerative capacity, just to name a few. The unique combination of rapid aging and high regenerative capacity makes N. furzeri an ideal organism for investigating both the detrimental effects of SC accumulation during aging and their beneficial roles in processes such as tissue regeneration. To study the impact of SCs we will generate a model in which we can ablate SCs in an inducible and organ-specific manner. This model will build on the transparent killifish line "klara" that we have generated earlier. This line carries a cdkn1a-eGFP-NTR reporter, which allows the visualization of cdkn1a-expressing cells in living animals as well as in whole organ explants and tissue sections. Quantification of these cdkn1a-expressing (potentially senescent) cells revealed an age-dependent increase in these cells across different tissues. In initial experiments the nitroreductase (NTR) allele was not sufficient to completely ablate SCs in vivo. In a future project we will integrate an improved and more efficient NTR allele (NTR 2.0) into the reporter line. This will allow the targeted ablation of SCs via the ntr/metronidazole system. Initial tests confirmed efficient metronidazole-induced cell death in primary fibroblasts from our reporter. We are currently characterizing SCs in different organs of killifish by a comprehensive approach employing RNA-Seq, single cell RNA-sequencing and proteomics. To this end we have established a DNA-damaging agent-induced senescence model in primary killifish fibroblasts. In addition, we are characterizing SCs in living animals and ex vivo. Through these approaches we aim to identify a transcriptomic and proteomic signature of SCs in N. furzeri. In addition, we also want to address a potential heterogeneity of SCs depending on the tissue, cell type, stimulus or temporal stage of the SCs. In the future we want to combine SC characterization with their selective removal to gain insights into the role of SCs in health span, life span, and regeneration. Possibly we will also generate additional in vivo senescent reports, depending on the results of the senescence marker analysis. The latter shall be used to guide the development of anti-aging interventions.

Maria Ermolaeva
Extreme weight-loss trajectories: implications for aging and healthspan
In recent years, societal pressure to maintain a slim body shape, combined with the increasing availability of effective weight-loss medications such as GLP-1 receptor agonists (Ozempic and others), has led to a rise in rapid and excessive weight loss. In some cases, individuals lose weight faster or to a greater extent than is biologically optimal, maintain very low body weight for extended periods, or experience rapid weight regain after discontinuing drug intake. This often results in repeated cycles of weight loss and regain, commonly referred to as “yo-yo” weight patterns. These extreme weight-loss trajectories are largely new at the population level and were rare in the past. For this reason, their long-term effects on health are still poorly understood. In particular, it is unclear how rapid, excessive, or cyclical weight loss influences aging processes, stress resilience, and overall health during later life. In this project, established dietary restriction and refeeding paradigms will be applied in a short-lived model organism C. elegans to systematically examine how extreme dieting patterns affect aging and healthspan. The work will focus on lifespan, stress responses, and age-related functional decline, providing insight into the long-term biological consequences of extreme weight-loss trajectories. The project builds on preliminary data demonstrating negative effects of rapid weight loss on cognitive and learning abilities of young animals. It will employ a combination of whole-animal functional assays, omics-based approaches for mechanistic analysis, and genetic validation experiments in animals of different ages.

Christoph Kaether
Novel Mechanisms of Microcephaly Driven by Early Secretory Pathway Proteins
Mutations in YIPF5 and IER3IP1, membrane proteins that cycle between the endoplasmic reticulum (ER) and the Golgi apparatus, lead to a severe neurodevelopmental disorder known as MEDS (Microcephaly, Epilepsy, and Diabetes Syndrome). Our previous research demonstrated that YIPF5 and IER3IP1 are critical regulators of protein export from ER exit sites (ERES), specifically affecting the trafficking of a subset of secreted and membrane-bound proteins. This project aims to elucidate the molecular mechanisms by which YIPF5 and IER3IP1 control cargo export from ERES and to investigate how these processes impact neuronal development and contribute to the pathogenesis of microcephaly. To this end, we employ a multidisciplinary approach combining live-cell imaging in cultured primary neurons and human iPSC-derived neurons, proteomic and biochemical analyses of protein-protein interactions, and in vivo studies using mouse models. More information can be found in Anitei et al. DOI 0.1007/s00018-024-05386-x

Janine Kirstein
Analysis of neuronal susceptibility towards proteotoxic stress with aging
Our lab uses the nematode C. elegans to study the vulnerability and resilience of neurons to proteotoxic stress with the progression of aging. We identified neurons that are vulnerable towards the aggregation and toxicity of amyloid proteins such as Abeta and showed an early onset of Abeta aggregation and functional deterioration. Your project would start with this observation to identify factors that render a neuron susceptible or resistant towards proteotoxic damage with aging. You will use recently established tools in our lab such as neuronal FACS as well as proximity labelling that allow you to isolate individual neurons to study their transcriptome and proteome across aging. The data will reveal which factors are depleted or enriched and thus lead to a comprehensive understanding which molecular pathways regulate the resilience of neurons and will also reveal specific factors such as components of the proteostasis network. These pathways and factors will then be studied in neurodegenerative disease models such as Alzheimer’s disease and Huntington’s disease that are established in our lab by advanced imaging techniques such as fluorescence lifetime imaging. Neuronal function will be assessed using GCaMP analyses and neuron-specific functional assays such as learning, memory retention and chemotaxis. You will have the chance to work with an extensive network of cooperation partners of our lab located in Germany and abroad as we are part of several national and international consortia to advance your PhD training.

K.Lenhard Rudolph
Developmental influences on epigenetic changes that shape the pace of aging
Growth signaling, cell proliferation, and metabolic state are fundamental features of development that are tightly coupled to organismal aging. In C. elegans, mutations in the daf-2 gene that attenuate insulin/IGF signaling result in a profound extension of lifespan (Kenyon et al., 1993). Notably, this longevity phenotype depends on the temporal availability of the stress response factor HSF-1 during development (Volovik et al., 2012), suggesting that early-life stress response pathways may establish a durable epigenetic state required for delayed aging in long-lived daf-2 mutants. Consistent with this concept, reduced growth hormone signaling during development in mice is associated with increased lifespan (Bartke et al., 2016), and diminished growth and metabolic signaling in early life delays hematopoietic stem cell aging (Suo et al.; Rudolph, 2022). Despite these observations, the mechanisms by which developmental growth and metabolic cues are integrated into long-lasting epigenomic states that influence aging remain poorly defined. In the present work, we used inducible mouse models to transiently suppress the DNA methylation regulators Dnmt3a or Tet2 during defined embryonic or postnatal windows, thereby perturbing DNA methylation dynamics during development. These interventions resulted in altered body weight trajectories and an acceleration of hematopoietic stem cell aging in early adulthood. Based on our preliminary results, we propose that Tet and Dnmt enzymes act as key molecular sensors or effectors that translate developmental growth and metabolic signals into stable epigenomic configurations, which in turn influence the tempo of organismal aging. We will test this hypothesis by determining how developmental modulation of growth and metabolism affects the rate of epigenomic aging and lifespan, and by assessing whether transient suppression of Dnmt or Tet genes during specific developmental phases is sufficient to disrupt these long-term aging trajectories.

Dario Riccardo Valenzano
Evolutionary Origins, Diversification, and Activity of Transposable Elements During Aging
We are offering a PhD position to investigate the role of transposable elements (TEs) in genome evolution and aging. This project with focus on the natural short-lived in African killifishes, an emerging model organism in aging research. Killifish genomes are rich in repetitive elements, with TEs accounting for a significant proportion of their genomic content. These elements show remarkable sequence diversity and expression patterns across species, suggesting that TE diversification may be a major driver of evolutionary separation within this group. However, the evolutionary origins of many TEs, including endogenous retroviruses (ERVs), and their functional consequences on genome dynamics remain poorly understood. It is still unclear how specific TE families originated, whether they have been horizontally transferred, and to what extent they remain active, particularly in the context of aging and cell-type specific genome instability. To address these questions, the candidate will combine comparative genomics, long-read sequencing, and transcriptomic profiling across multiple killifish species. The candidate will use phylogenetic methods to trace TE origins, and integrate single-cell and bulk transcriptomics to assess TE expression and potential mobilization in different tissues and age groups. Experimental work may include TE expression validation and the development of functional assays to explore TE-driven genome instability during aging. We expect to identify lineage-specific TEs, reconstruct their evolutionary history, and detect active or reactivated elements in aging tissues. These findings will provide conceptual insights into how genome structure and instability evolve and generate technological advances in TE detection and annotation in non-model systems.

Claudia Waskow
Mechanisms of T cell immune aging in mice - histone modification as driver of aging?
Genome integrity is fundamental to organismal longevity and physiological function. We have previously demonstrated that the histone methyltransferase (HMT) SETD1A is essential for maintaining genomic stability in murine hematopoietic stem and progenitor cells (HSPCs). While SETD1A is critical for in vivo T cell differentiation or maintenance, its role in safeguarding the T cell genome remains unexplored. Our current research aims to elucidate how SETD1A deficiency drives T cell imbalance and to define the cooperative mechanism by which SETD1A and TRP53 prevent genomic instability and subsequent acceleration of immune aging.

Katarzyna Winek
Exploring the role of the microbiota–brain–body axis in ischemic stroke
The gut microbiota – a commensal community accompanying the host lifelong - plays a significant role in host physiology and may influence disease development. In this project, the PhD candidate will investigate the complex interplay between the brain, body and bacterial gut microbiota in the context of ischemic stroke, a major acute central nervous system disorder. Our goal is to unravel mechanisms underlying microbiota-brain communication after stroke, with a focus on neural signaling pathways, microbial metabolites and signaling molecules, and host immune responses. Employing both in vitro and in vivo models, we will integrate advanced methodologies including single-cell and single-nucleus sequencing, flow cytometry and FACS, microscopic imaging, metagenomics, proteomics, and computational analyses. Ultimately, we aim to provide mechanistic insights into the microbiota-brain-body signaling and identify druggable targets, paving the way for novel therapeutic strategies.

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