Cell division mechanisms are highly conserved, yet mechanistic requirements vary between species and cell types. For example, while epithelial cells round up for mitosis, hematopoietic cells grow in suspension, maintaining their round shape throughout the cell cycle. Division of cells with distinct morphologies likely requires specialized machineries, yet cell type-specific mitotic mechanisms remain largely unexplored. Understanding specialized cell division machineries might profoundly improve anti-cancer therapies. Many chemotherapeutic drugs target universal cell division pathways, resulting in toxicity due to mitotic perturbation of hematopoiesis, yet the majority of cancers are of epithelial origin. Thus, exploiting cell type-specific vulnerabilities has the potential to increase the specificity of chemotherapy. The aim of this work is to explore how mitotic mechanisms adapt to diverse challenges in different human cell types and growth geometries. I plan to uncover cell type-specific mitotic pathways by genome-wide CRISPR/Cas9 screening, complemented with a candidate-based approach. First, I will use two screening approaches to compare cellular machineries required for chromosome segregation and cytokinesis. Second, I will explore how epithelial and hematopoietic cells accommodate different demands for shape changes during division by investigating cell type-specific regulation of cortex contractility during mitotic entry and cytokinesis. Overall, this project will shed light on how cell division mechanisms accommodate specialized requirements in multicellular organisms, with the tremendous potential to uncover tissue-specific targets for cancer therapy.

The aim of this proposal is to gain insight into the mechanisms of chromatin reprogramming to totipotency in mammals. Totipotency is the potential of a cell to generate all cell types of an organism including extraembryonic tissues. Whilst induced reprogramming to pluripotency by the Yamanaka factors is relatively inefficient and takes days to weeks, natural reprogramming to totipotency occurs within hours in the one-cell embryo or zygote. How zygotic reprogramming is achieved is poorly understood. We will approach this fundamental question by studying the chromatin state of totipotent cells and their precursors. We will determine how higher-order chromatin organization changes during epigenetic reprogramming in zygotes and primordial germ cells, using both mouse embryos and human/mouse primordial germ cell-like cells. We will use our understanding of the zygotic chromatin state to identify candidate pioneer factors and to test their role in promoting totipotency and genome activation. The results of the project will provide insights into how reprogramming alters genome organization and promotes establishment of a totipotent chromatin “ground state”. This project is led by a strong multi-disciplinary team bringing together expertise in polymer physics (Mirny), ovary organoids (Saitou), biochemistry and single-molecule imaging (Peters) and zygote biology (Tachibana-Konwalski).

Skin is a remarkable tissue requiring dynamic and robust behaviors. It acts as a tight bi-directional barrier while being constantly exposed to mechanical stress. The epithelial layer of the skin, the epidermis, acts as load-bearing layer. The presence of tension in the epidermis is critical for its function, however it also constantly threatens the integrity of this tissue which quickly degenerates in the presence of impaired mechanical reinforcement of cell adhesions or the cytoskeleton. Thus it is critical to uncover the poorly understood mechanisms of mechanical stress protection and mechanoadaptation in the epidermis specifically. It is becoming evident that the rheological changes in the nucleus, nuclear envelope, and modifications in chromatin architecture are critical for cellular adaptation and recovery from external mechanical cues, but the mechanisms and precise functional implications of this regulation are unclear. This project aims to investigate the mechanisms and functional consequences of dynamic remodeling of perinuclear actin and heterochromatin in regulating nuclear rheology and thereby the mechanical stress response of epidermal stem cells. Second, based on the preliminary data from the host laboratory, I will test whether strain-induced poly-ADP ribosylation is a mechanopreotective mechanism which, by placing the DNA damage repair machinery in close proximity to the sites of DNA damage enhances the efficiency of repair upon mechanical stress. These studies will unravel molecular mechanisms that allow cells to adapt to mechanical stress through dynamic regulation of nuclear rheology.

RNA modifications have been proposed to affect various aspects of RNA biology, including translation and RNA stability. However, how these effects are mediated is not fully understood. Drosophila melanogaster embryonic development is an excellent model to study the effects of RNA modifications, as RNAs with critical roles during development are highly post transcriptionally regulated. I propose to develop and apply a new method to detect the RNA modification 5-methylcytosine (5mC) transcriptome wide at single nucleotide resolution in the Drosophila embryo. This strategy relies on reverse transcription of RNA and subsequent digestion of the RNA-DNA hybrid with a modification dependent restriction enzyme. The digestion sites are ligated to an adapter containing a T7 promoter, facilitating amplification of the RNA-5mC containing regions. Next, RNA library preparation and Illumina sequencing will reveal the site of modification at the start of the sequence read. The application of this technology will identify the modified RNA species together with the exact location of the modification in Drosophila embryos. In combination with spatial transcriptomics and RNA localization data, in a second step I will elucidate the role of RNA modification status on RNA localization and translation. To reveal the functional consequences of RNA-5mC, I will use affinity purification in combination with mass spectrometry to identify RNA-5mC reader proteins. The abundant genetic tools available in Drosophila will allow me to assess the functional consequences of the removal of each of the reader proteins on the modified transcripts and on a whole organism phenotypical level.

Tumor-infiltrating T cells (TILs) are critical participants in controlling tumor growth, metastatic potential, and ultimate lethality of many cancers. These immune cells act contextually within the tumor microenvironment to either promote tumor clearance or facilitate tumor growth. This is exemplified in the recent successes of the immune checkpoint inhibitors, anti-CTLA-4 and anti-PD-1. In these treatments, subsets of patients experience remarkable tumor regression mediated by rescue of ‘partially exhausted’ CD8+ T cells (peTILs) and negation of the immunosuppressive functions of regulatory T cells (Tregs). However, the dominant molecular pathways preventing TIL-mediated tumor rejection remain obscure. Identification and detailed investigation of these pathways is of fundamental importance in order to understand immune responses to aberrant tissue growth. Recently, the gene LAYN has been identified as highly expressed in the tumor microenvironment and associated with the suppressive signature of Tregs, as well as the exhausted state of CD8+ T cells. Strikingly, high LAYN expression on Tregs correlated with poor clinical outcomes in multiple cancers. Our laboratory has independently observed high LAYN expression on TILs in melanoma patients. As there is a lack of knowledge regarding layilin biology (only 17 publications to date) we propose to comprehensively dissect the functional role of layilin on tumor-infiltrating T cells. We hypothesize that layilin signaling acts to augment Treg suppressive capacity while attenuating CD8+ TIL cytotoxic activity. To address this hypothesis we have generated novel tools to delete or over express layilin in both human and mouse TILs.

Consciousness is probably the biological construct we are most intimately familiar with, yet our understanding of its possible functions remains quite poor. Various – sometimes contradicting – accounts range from denying it from having any functional role to considering it a prerequisite for all high-level functioning. Here, I propose a new experimental approach which will hopefully enable us to make the much-needed leap towards a genuine theory of consciousness. I argue that most current methodologies have drifted away from the studied phenomenon: conscious vs. unconscious processing of information. While the latter is held to occur regularly in everyday lives, it takes on a very different form in the lab, when probed using psychophysical techniques which commonly rely on artificial operationalizations having little resemblance to real-life processes. And the stimuli are typically highly degraded, arguably evoking weak signals (and, in turn, non-robust findings). Instead, I suggest two novel ways to get closer to real-life unconscious processing of stimuli with which subjects can interact: the first – a unique method we developed to suppress, for the first time, real-life, actual 3D objects. The second – a virtual reality protocol which mimics unconscious processing of stimuli in real-life environments (e.g., driving or walking). These two experimental paths enable us to examine the processing of strong, non-degraded, real-life/real-life-like stimuli. I propose 7 experiments that – if successful – promise to fundamentally change the way consciousness and its functions are studied and open a new branch of study, with far-reaching theoretical and practical implications.

Some epigenetic marks are heritable in plants, such as cytosine DNA methylation in the CG dinucleotide context. Because epigenetic marks evolve at rates that are much faster than DNA, they are a potential agent for rapid adaptation to a changing environment, provided they impact fitness. Recent advances in sequencing technology have generated valuable resources, including genomes and more recently methylomes. These data have furthered our understanding about the repressive role of DNA methylation on transposable elements. Surprisingly, however, the role of gene body methylation (gbM) remains enigmatic. gbM is characterized by DNA methylation in the CG context within the body of genes – i.e., between the transcription start site and the transcription termination site – and it is associated with constitutive genes that have moderate to high expression levels. There are two explanations for this phenomenon. One is that gbM is a neutral consequence of transcription without any functional significance. Alternatively, gbM may be functional, in which case it will be subjected to natural selection. This project will search for footprints of selection acting on gbM levels, utilizing ~1000 methylomes available for Arabidopsis thaliana. I will adapt classical population genetic approaches, such as the McDonald-Kreitman test and analyses of the site frequency spectrum, to the study of gbM. By doing so, I will determine whether gbM is under selection in plants and also extend analytical approaches to population methylomic data. If selection on gbM level is detected, the study of the affected genes and their expression patterns may offer clues about gbM function.

The human microbiota produces a wide range of diffusible and cell-associated molecules, many of which are crucial for immune and metabolic homeostasis. The human immune system contains dendritic cells (DC), which sense bacteria-derived molecules through innate immune receptors and initiate an immune reaction that can be immunogenic or tolerogenic in tone. Previous studies have examined the effect of just a single or a few bacterial molecule(s) on the immune system. However, it is not yet understood how the immune system integrates a complex combination of numerous and diverse microbiota-derived molecules and 'decides' what kind of an immune response to mount. In this research, I will systematically elucidate the combinatorial effects of multiple microbiota-derived factors on DCs and identify genes in DCs underlying the integration of multiple signals. In Aim1, a large library of molecules from the microbiota and microenvironment will be generated. The library includes novel unpublished microbiota-derived molecules, in addition to commercially available microbial molecules and microenvironmental factors (i.e., tissue-specific cytokines). In Aim2, DCs will be cultured with combinatorial sets of molecules, and their transcriptional profiles and cytokine expression will be determined by multiplexed RNA-seq analysis. In Aim3, sets of genes required for DC responses will be identified by genome-wide CRISPRi/a screening and comprehensively analyzed using computational techniques. In Aim4, the results of the in vitro analysis will be tested in vivo using mouse experiments in which germ-free mice are colonized by genetically modified bacteria expressing multiple molecules.

The goal of my proposal is to harness protein homeostasis (proteostasis) to restore adult neural stem cell (NSC) function. Ageing is associated with a striking decrease in adult stem cell function in all tissues. In the nervous system, the number of NSCs and their ability to exit quiescence and to produce new neurones decline dramatically during ageing, which may underlie age-dependent decline in cognitive function. Similarly, disruptions in the proteostasis machinery are associated with accelerated ageing and neurodegenerative diseases. Thus, understanding the molecular mechanisms NSCs use to maintain proteostasis, and how they change with age, may help uncover ways to preserve their regenerative potential during ageing. Recent evidence in the Brunet laboratory has revealed that quiescent NSCs (qNSC) accumulate more aggregates than their activated counterparts, with even higher aggregation seen in old qNSCs. In the proposed project, I will carry out a genome-wide genetic screen to identify proteins involved in the formation of aggregates in qNSCs during ageing and will perform cutting-edge mass spectrometry to identify the proteins present in these aggregates. I will then use this knowledge to determine the function of the aggregates in NSCs, with the goal of restoring old NSC function. Completion of these studies will provide unique mechanistic insights into the regulation of protein aggregation during ageing in regenerative cells and their differentiated progeny. This work will pave the way for building new methods for the ‘rejuvenation’ of old cells and the restoration of proteome solubility, crucial steps in countering age-related decline and pathologies.

This project takes a novel approach to study how host organisms combat against pathogens. In general, hosts use resistance to attack and eliminate pathogens, but an alternative method is to employ tolerance, which protects tissues from damage without affecting pathogen burden. The molecular mechanisms of resistance are well established, but the regulation of tolerance is poorly known. Mammals activate tolerance mechanisms when they confront energy-constraining periods, such as infection or starvation. They temporarily abandon the maintenance of body temperature and engage in torpor, which protects organs from tissue damage. Since torpor enables organs to sustain stress without tissue damage, understanding the protective mechanisms might lead to discovery of novel treatment strategies against infections, which might be applicable to other human conditions as well. In the proposed work, I aim to study 1) how animals enter torpor, 2) what are the metabolic signatures of torpid animals and 3) how torpor affects organismal fitness during infections. To accomplish these goals, I will use lipopolysaccharide (LPS) to induce torpor in mice. First, I aim to identify which tissue senses LPS to induce torpor using tissue-specific knock-out mice for TLR4, which is the receptor for LPS. Next, I will perform untargeted metabolomics and transcriptomics to identify metabolic regulators of torpor. Finally, I will ask if torpor affects tissue damage during E. coli infection by assessing immunopathology of the infected animals. The proposed work will expand our understanding of tolerance mechanisms and will, possibly, provide novel strategies to treat infections.

G-protein coupled receptors (GPCRs) regulate virtually all physiological processes and represent the most common drug target. Apart from the classical signaling, involving the activation of heterotrimeric G-protein, GPCRs also initiate parallel signaling events by interacting with ß-arrestins. ß-arrestins serve as key junctions that receive input from receptors and route the signal to various effectors within the cell. The discovery of signal transduction through ß-arrestins underscores the multifaceted functionality of GPCRs and opens new horizons for future studies. Mapping the extensive GPCR-ß-arrestin-mediated signaling networks offers a possibility to design drugs with greater specificity of action and fewer side effects. However, a detailed structural understanding of interactions between GPCRs and ß-arrestins is still lacking. In this project, I will elucidate the molecular mechanisms of ß-arrestin-1 recruitment by the clinically important ß2-adrenergic receptor (ß2AR). To achieve this goal, I will employ a combination of structural and biophysical methods, such as X-ray crystallography, cryo-electron microscopy and double electron-electron resonance. The project will be performed in the laboratory of Professor Lefkowitz (Duke University, Durham, North Carolina, USA), a leading expert in GPCR biology. I aim to obtain the conformational snapshots of ß2AR-ß-arrestin complex at high resolution, identify the binding interface of the receptor and ß-arrestin and elucidate the dynamics of the complex upon ligand binding. These results will provide a holistic understanding of ß-arrestin recruitment by ß2AR and facilitate the development of novel pathway-specific drugs.

Phenotypic plasticity describes how a single genotype can generate a range of alternative phenotypes. The concept is exemplified by complex trait divergence between monozygotic co-twin pairs. Recently the Pospisilik lab identified a genetic circuit that regulates phenotypic plasticity by buffering against the emergence of alternate epigenetic states. The original Trim28(+/D9) line used for that work represents the first in vivo model for exploring the impact of mammalian polyphenism on complex trait biology and disease. Intriguingly, both gain- and loss- of function mutations in Trim28 have previously been associated with cancer. Here, I propose focusing on Trim28(+/D9) haploinsufficiency to assess for the first time the impact of bi-stable, epigenetically determined phenotypic variation on cancer. I will monitor tumour latency, progression and spectrum using in vivo imaging and assess tumour heterogeneity down to the single-cell level. In order to gain mechanistic insight, I will use unbiased in vivo shRNA-mediated oncosuppressor screening followed by molecular dissection using human and mouse organotypic cultures in vitro. My overarching scientific goal is to understand the non-genetic roots of cancer. The unique tools, knowledge and environment of the Pospisilik lab are ideal for assessing how non-genetic variation regulates cancer susceptibility, triggering and progression. If successful, these data will not only drive me much closer to these goals, they will reveal a first gene-gene-environment framework for understanding cancerogenesis in the context of phenotypic variation and epigenetic bi-stability.

In recent years there is a growing realization that many species are at risk of extinction due to habitat loss, while the spread of invasive species increases. These changes could influence the stability and function of ecosystems. Our ability to predict how perturbations, such as species extinctions and invasions, affect stability would help protect biodiversity, for example by restoring "keystone species" to sustain ecosystem structure and stability. The aim of the proposed project is to quantify and predict the impact of removal and addition of species on communities. Using a well-defined set of microbial species, we will construct synthetic communities composed of subsets of this set. We will study the effect of removal/addition of species from/to each subset on the species’ abundances. Specifically, the extinction of species as a result of the removal of other species would be of great interest since it will allow the identification of keystone species. These measurements would form a large dataset of experimentally validated co-occurrence networks, and would enable us to identify properties that make communities more vulnerable to the addition or removal of particular species. Next, we will test whether species’ pairwise interactions can be used to predict the community structure. For this aim, we will develop an experimental framework to map the pairwise interactions between all species, their directions and strengths. Finally, we will develop a mathematical model to predict extinction and invasion effects on a given ecosystem.

Non-coding segments - introns are removed from precursor messenger RNAs (pre-mRNAs) through a process known as pre-mRNA splicing, which is catalyzed by two large ribonucleoprotein (RNP) complexes, the ‘major’ and the ‘minor’ spliceosome. While recent structural studies of the major spliceosome have tremendously advanced our understanding of the basic splicing mechanism, the structure and mechanism of the minor spliceosome remains largely elusive. The minor spliceosome differs in its composition and specificity and no comparable structural insights are available. Therefore I propose to use cryo-electron microscopy (cryo-EM) to study the assembly of the minor spliceosome on its specific pre-mRNA substrates. To achieve this, I will extract endogenous complexes directly from human cells. Affinity tags that I will introduce into the genome by CRISPR/Cas9 gene editing techniques will enable me to purify this large RNP machine from nuclear extracts. I will reconstitute the minor spliceosome on substrate RNAs and analyze them for their composition and homogeneity by mass spectrometry and negative stain EM. Ultimately, I want to obtain atomic models of those complexes by cryo-electron microscopy. My studies will close the gap in knowledge between both spliceosomes in terms of structural insights and thus i) reveal new aspects about the evolution of the splicing mechanism, since the minor spliceosome might constitute a more simple system that is closer related to lower eukaryotes, and ii) provide a molecular understanding on diseases related to malfunctions of the minor spliceosome as well as opportunities for site-specific targeting of the major spliceosome in cancer.

Embryonic development and organ morphogenesis entail both the correct differentiation of cells into given lineages and their proper positioning along the body axes. During gastrulation in the zebrafish embryo, specification of the germ layers is concurrent to internalization movements, which reposition the future mesendoderm precursors underneath the prospective ectoderm. Nodal/TGF-ß signalling is important for both processes, raising the possibility that cell differentiation and tissue shaping may be coupled. Yet the existence, nature and spatiotemporal scale of the mutual feedback between these processes is still poorly understood. To address this fundamental question, I will follow three lines of research: (1) characterize with high spatiotemporal resolution the dynamics of Nodal-mediated mesendoderm fate acquisition and internalization along the dorsal-ventral margin of the germ ring; (2) dissect the molecular mechanism by which Nodal-mediated cell fate specification is linked to mesendoderm internalization; and, finally, (3) explore whether cell internalization feeds back onto mesendoderm fate specification, via mechanotransduction pathways. This exploratory research project will provide a map of cell specification with unprecedented cellular and tissue resolution and establish a framework to understand how gastrulation movements are coordinated with ongoing fate acquisition and embryonic axes establishment. Since there are striking similarities between the molecular mechanisms underlying tumour growth and metastasis and those governing gastrulation, this work is likely to provide key insights to the understanding of both embryonic development and cancer progression.

It has become increasingly evident that the transcriptional activity of a gene is intrinsically linked to its positioning within the nucleus. A distinctive subnuclear structure is the nucleolus, which is mainly formed upon transcription of ribosomal RNA (rRNA) genes. Hundreds to thousands of rRNA genes are tandemly arrayed in megabase-size rDNA clusters. The model plant Arabidopsis thaliana carries two unlinked rDNA clusters, with natural variation in rDNA cluster-activity, meaning that some strains express only one or the other cluster, and some both. Because large genomic regions adjacent to the actively transcribed rDNA cluster(s) –thus associated with the nucleolus– are expressed at lower levels than the genome average, I expect large-scale variation in gene activity. My goal is to investigate how variation in rDNA cluster-usage and its consequent reshaping of 3D genome architecture impact not only the expression of adjacent protein-coding genes, but also how genome-wide gene regulatory networks (GRNs) can adapt to such large-scale differences in gene expression. I propose to take full advantage of the diversity of genetic resources available in A. thaliana, including experimental populations, a large catalog of genomes and transcriptomes, as well as its accessibility for genetic engineering to pursue the following aims: (1) investigate the impact of rDNA-cluster usage on GRNs in natural strains, (2) swap rDNA expression patterns using crosses, and assess effects on GRNs, and (3) induce targeted inversions and translocations using CRISPR-Cas9 technology to directly test the functional consequences of gene-positioning with respect to active rDNA clusters.

A primary feature of highly-social animals, like humans, is the tendency to help one another. These behaviors, where one animal helps another without immediate benefit to itself, are known as prosocial behaviors. While there has been considerable research into how the brain controls social behaviors driven by fear or aggression, there has been almost no investigation of brain mechanisms of prosocial behaviors– when one animal aids another. We will conduct the first mechanistic investigation of the microcircuits underlying prosocial behaviors. To this end, we will utilize the natural food-sharing behaviors of Egyptian fruit bats; where provider-bats feed scrounger-bats; and will conduct wireless single-unit electrophysiological recordings from multiple freely-behaving bats living and interacting together in a colony. We will investigate two brain areas: (i) Medial prefrontal cortex, specifically infralimbic cortex– a brain area linked in humans to prosocial behaviors– where we will investigate neural correlates of prosocial feeding events. (ii) Hippocampus– an area involved in social memory and strongly connected with the prefrontal cortex– where we will investigate how other animals are recognized, a key component of prosocial behaviors. We will further introduce ethological manipulations to the freely-behaving colony to determine how natural variations, such as changes in competition or resource-availability, impacts prosocial behaviors and their neural representations. Finally we will switch a provider bat to a scrounger, by adding weight to create temporary ‘handicap’– and investigate the changes in the underlying neural representations of both oneself and others.

Skeletal muscle has the capacity to regenerate after injury. This process involves an orchestra of cells and factors that sequentially intervene to repair muscle fibers. Muscle regeneration is particularly vital for muscle disorders and aged muscle in which myofibers are constantly degrading. In contrast to the classical approach in studying muscle regeneration, this project focuses on exploring the intrinsic capacity of damaged myofiber to self-repair. We observed that after local injury, nearby nuclei migrate to the damaged site where they become internalized, re-organize chromatin and begin rotating. This cell response coincides with repair of the injury and has never been previously described. Interestingly this process is impaired in aged myofibers that are incapable of repair post injury. We therefore propose to study the intrinsic capacity of myofibers to repair. We will first explore the underlying mechanisms driving nuclear migrations to the damaged site after local injury. We will then establish how chromatin is re-organized for myofiber self-repair. Finally, we will investigate the failing mechanisms in aged myofibers. The difference between intrinsic myofiber repair and regeneration most likely stems from the severity of the injury, with minor damage triggering the intrinsic repair program. The capacity of myofibers to self-repair may be the first line of defense to muscle injury. Exploring the mechanisms of this newly observed process could reveal novel therapeutic strategies to maintain myofiber integrity. This could delay the involvement of the multi-cellular regenerative process, usually overwhelmed or diminished in muscle disorders and old age.

What makes us human? Understanding the evolutionary emergence of human traits is important both for fundamental knowledge and our capacity to treat diverse diseases. In this project I aim to understand molecular mechanisms governing human speech development. FoxP2 is a highly conserved transcription factor, dubbed the ‘speech gene’ because families with mutations in this protein have speech deficits. Two amino acids variants in FoxP2 have been subject to strong selection in our lineage. Introducing them into mice increases vocalization. Yet these mutations do not localize to FoxP2’s DNA-binding domain. Rather, they bracket a long prion-like domain near its N-terminus. Preliminary results show that these variants enhance FoxP2’s capacity to form ‘infectious’ prion-like aggregates. Remarkably, FoxP2 aggregates arise naturally, and in a developmentally regulated manner in the neural crest. I aim to characterize the physiological function of FoxP2 prion-like aggregation during neural crest differentiation, identify the developmental consequences of the evolutionarily selected mutations in this protein, and ultimately identify molecular mechanism(s) by which FoxP2 regulates cellular differentiation. I will test the importance of FoxP2’s prion domain using a series of powerful genetic and cell biological approaches. Subsequently, I will investigate the regulation of prion formation during development. Finally, as a long-term goal I will test if aggregation alone, or templated propagation of the prion per se, is required for normal differentiation. If fulfilled, the aims of this proposal thus have the potential to transform our understanding of human development and evolution.

Dendritic cells, a type of white blood cell, are the sentinels of the immune system. Upon infection with a pathogenic microbe, such as a bacteria or fungus, dendritic cells can ingest the microbe by a process call phagocytosis. Dendritic cells then kill the ingested microbe by huge amounts of hydrogen peroxide, a disinfectant, and subsequently degrade the microbe by enzymes. This releases protein fragments from the microbes which can be presented to T cells, another type of white blood cell. T cells thereby learn to recognize the microbe and can mount a pathogen-specific immune response.
Dendritic cells need to be able to ingest many different types of microbes with a large variation in motilities, sizes and shapes, ranging from very small viruses to fungal hyphens. Although it is well-known that many types of pathogens use their shape and motility to try to avert immune responses, the underlying cell biological mechanisms are still largely unknown. The goal of this project is to address how microbe shape and motility affect their processing by dendritic cells for T cell activation.
We plan to chemically engineer bacteria-sized artificial particles with well-defined but highly irregular shapes, such as star-shaped particles. These particles will be equipped with chemical engines that are fuelled by hydrogen peroxide (produced by the dendritic cells) to generate motion. We expect that the shape and forces exerted by these particles will affect their transport and processing within the crowded environment of dendritic cells. The behaviour of these particles will be studied in well-defined dense suspensions that mimic the complex environment within dendritic cells. These biophysical experiments will be combined with experiments with dendritic cells isolated from the blood of healthy volunteers. This will allow a full quantitative understanding of how pathogen shape and motility affect their fate in dendritic cells.
This study will lead to a better understanding of how pathogens use their shape and motilities to avoid clearance by the immune system. Moreover, understanding how microbe shape and motilities affect immune responses will allow us to generate particles that elicit very fast and strong immune responses or, conversely, no (or very slow) immune responses, which will aid in the design of improved vaccines and carriers for drug delivery.