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Funding
Funding
HFSP supports novel, innovative and interdisciplinary basic research focused on the complex mechanisms of living organisms. A clear emphasis is placed on novel collaborations that bring biologists together to focus on problems at the frontier of the life sciences.
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Awardees
Awardees
In this section you find information about the awardees in the HFSP scientific programs. This includes a searchable database of HFSP awardees, information on the HFSP Nakasone Award and other achievements by HFSP awardees.
- News & Impact
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Events
Events
HFSP promotes and participates in several events every year. We are committed to bringing together the scientific community and forging new opportunities to network and have scientific discussions that help to create bridges and partnerships for the future of frontier science.
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About
About
The Human Frontier Science Program is a program of funding for frontier research in the life sciences. It is implemented by the International Human Frontier Science Program Organization (HFSPO) with its office in Strasbourg. Here you can find all you need to know about the HFSPO.
Awardees
2023
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Grant Awardees - Early Career
Experimentally evolving budding yeast cell size to test scaling laws in cell biology
FUMASONI Marco (ITALY)
- Fundação GIMM - Gulbenkian Institute for Molecular Medicine - Lisbon - PORTUGAL
GIOMETTO Andrea (ITALY)
- Cornell University - Ithaca - United States
Genome and organelle sizes vary with cell volume following scaling laws that are thought to reflect physical and molecular constraints on life. Despite cell size spans over several orders of magnitude across the tree of life, individual species are able to maintain a characteristic, narrow range of volumes, following a handful of homeostatic principles. To cover a large range of sizes, scaling patterns were derived by comparing distantly related species, highlighting their conservation but limiting causal inference. On the other hand, much of the work on the mechanisms that maintain size homeostasis was done in single species, which typically cover cell size ranges that are too narrow to investigate scaling patterns. The molecular and physical links that govern size scaling patterns and homeostasis principles, and how they evolve to produce the variability we observe in nature have remained elusive. To overcome previous limitations, we will evolve and engineer a panel of much larger/smaller Saccharomyces cerevisiae cells, aiming at finding the physical or evolutionary limits for this species. We will track genomic and cellular changes associated with the altered size, identify causative mutations, and dissect the mechanisms they act on. Single cell measurements in a genetically amenable species over an unprecedented range of sizes will allow us to test the robustness of homeostasis principles and scaling laws in cell biology, and observe how evolution can alter physical constraints on cell, genome and organelle size.
2023
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Grant Awardees - Early Career
Unraveling the multi-layer relationship between archaeal symbionts and their viruses
QUAX Tessa (NETHERLANDS)
- University of Groningen (Rijksuniversiteit Groningen (RUG)) - Groningen - NETHERLANDS
GHOSAL Debnath (INDIA)
- University of Melbourne (Melbourne University) - Melbourne - AUSTRALIA
GOOD Benjamin (United States)
- The Board of Trustees of the Leland Stanford Junior University - Stanford - United States
SAKAI Hiroyuki (JAPAN)
- Soka University - Tokyo - JAPAN
Associations between organisms and viruses are complex and encompass everything from beneficial to parasitic relationships. Here we will map the molecular mechanisms that underlie the interactions between crenarchaea, their DPANN archaeal symbionts and their viruses. Archaea are ubiquitous microorganisms in the environment, but the number of isolated species is modest and their cell biology remains underexplored. They are regarded direct ancestors of eukaryotes and important for understanding the origin and evolution of life. Current knowledge of microorganism–virus interactions relies primarily on laboratory studies of one virus and one cell. Yet, based on culture independent approaches, the fraction of microbial species that is involved in a symbiotic relationship is estimated to be considerable, although most are unculturable. Symbiotic microorganisms sustain relationships with another organism (called the host) over a considerable fraction of the life of the host. In addition, this relationship is beneficial for at least one of the organisms. Since symbionts often lack anti-viral defence systems, it has been hypothesized that symbionts can protect their host-cells from viral infection, by serving as decoy. However, empirical relevance of this hypothesis has not yet been tested.
Recently multiple fast-growing symbiotic archaea belonging to the phylum DPANN were isolated by HS, which now offers the exciting possibility to unravel molecular mechanisms underlying viral infection in a symbiotic system. The aerobic fast-growth allows us to apply to this system recently developed imaging techniques. We will combine virology, microbiology, microscopy and structural biology with mathematical modelling to connect the microscopic properties of the individual cells with the emergent behavior at the population level. This will allow us to assess if symbiotic DPANN serve as viral decoys.
Viruses of DPANN archaea are not studied, even though these archaea are widespread. With this project, we will generate unprecedented detail of their infection cycles, structure and the biology of their DPANN hosts, which will lay foundations for a novel field of research.
This project will be one of the first to study viral infection in a symbiotic system, and thus provide essential insights into the impact of viruses on symbiotic organisms, which are so widespread in nature.
2023
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Long-Term Fellowships - LTF
Unraveling limb size determinants using mouse-jerboa chimera
GOEL Isha (INDIA)
ARMI - Monash University - Clayton - AUSTRALIA
ROSELLO DIEZ Alberto (Host supervisor)
Background: From a tiny insect to a giant blue whale the diversity in the animal kingdom is truly remarkable. An understanding of this poorly explored variation in size of organisms can provide a more elaborate map of evolution and will be useful in commercial applications such as increasing meat production from specific body parts. Given the complexity of the animal body, it is more practical to start with one organ that can offer a high range of diversity among different species such as the limb. The differences in size and proportions demonstrating their adaptations during evolution open a door to the factors controlling organ size. Two main steps can be distinguished during limb growth: the patterning phase, in which the different limb segments are specified, and the post-patterning phase, where most of the elongation and differentiation take place.
Aim: We aim to generate jerboa iPSCs for the first time to study how they form limbs in host mouse embryos. We plan to compare the development of chimeric jerboa-mouse limbs with that of normal mouse limbs so that their intrinsic differences can be found.
Central hypothesis: Based on classic and recent studies, we hypothesize that final limb size is controlled by the signal balance during the patterning phase, whereas internal limb proportions are tuned by intrinsic differences in the tempo of the post patterning phase. This predicts that if early limb bud cells are placed within the signal environment of a different species, the limb bud cells will adapt the duration of their patterning phase, leading to a change in the limb size, while the internal proportions will be preserved. This decoupling between intrinsic and extrinsic processes will allow us to identify the key genes and networks involved in the control of limb size.
Experiments: The experiments will take place in three stages: 1) Preparation of jerboa iPSCs under the expert supervision of Dr. Rio Tsutsumi, Kyoto University. The jiPSCs will be chemically transformed in four stages and then characterized by RNA-seq and teratome assays for pluripotency. They will be modified for GFP expression 2) Preparation of hindlimb-less mouse model (Hoxb6-Cre; Ctnnb1(flox/flox)) and complementation of its blastocyst with jiPSCs. Litters will be collected to characterize the expression of segment markers Meis1/2, Hoxa11, Hoxa13 by in situ hybridisation, characterize bone length by micro-CT. Morphological and size analysis will be done according to protocols from the Cooper Lab 3) Relative RNA-seq and ATAC-seq analysis of transcriptome and accessible chromatin of limbs.
Conclusion: These experiments are designed to generate the first iPSC line from jerboa providing new resources for research. jiPSCs are expected to form most of the hindlimb in chimeric animals. The size and genetic analysis of the developed hindlimb will provide an insight into what aspects of limb growth are controlled by intrinsic mechanisms, and which aspects by extrinsic ones.
2023
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Grant Awardees - Program Grants
Cellular and molecular basis of bilaterian symmetry
PAVLOPOULOS Anastasios (GREECE)
- FORTH Institute of Molecular Biology and Biotechnology (IMBB-FORTH) - Heraklion - GREECE
GUIGNARD Léo (FRANCE)
- Universite D'aix Marseille - Marseille - FRANCE
XIE Liangqi (frank) (CHINA)
- Cleveland Clinic Foundation - Cleveland - United States
One of the most pervasive, yet poorly understood, hallmarks of most metazoans is bilateral symmetry. The external left and right sides of bilaterians develop separately but somehow manage to produce symmetric matching halves, presumably via deterministic developmental programs, homeostatic buffering mechanisms or combinations thereof. We will probe these mechanisms in a crustacean embryonic epithelial monolayer that acquires a stereotypic, geometrically ordered and bilaterally symmetric tissue architecture composed of less than a thousand cells, while maintaining the capacity to restore left/right symmetry after unilateral cell ablations. Through live imaging with multi-view light-sheet fluorescence microscopy and image analysis of intact and ablated embryos, we will first decompose the shaping of each side into the individual cell contributions to quantify their levels of stereotypy and variability across sides, embryos and conditions during the normal emergence of bilateral symmetry and during its restoration after cell ablation. Guided by these cellular maps, we will then screen for spatially and temporally structured gene networks operating at the beginning, middle and end of the restoration process, using a genome-wide time-course profiling of gene expression and chromatin accessibility with established spatially resolved methods. To probe the regulatory rules of symmetry, we will also develop a new method for dual spatial transcriptomics and epigenomics by converting and amplifying the open chromatin DNA regions into polyadenylated RNA molecules that will be assayed together with cellular mRNA on existing platforms for spatial transcriptomics. We will devise novel computational frameworks to register the cellular atlases from the microscopy datasets with the molecular atlases from the multi-omics datasets in time and space, and to generate average, statistical representations from multiple input embryos. Data integration will enable us to measure at cellular resolution the intraindividual and interindividual variability between sides and across embryos, respectively, and to probe the qualitative and quantitative differences in the corrective molecular and cellular mechanisms that bilaterians have evolved to promote symmetry by buffering the effects of inherent developmental noise (developmental stability) and the effects of perturbation (canalization).
2023
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Long-Term Fellowships - LTF
Utilizing spatial transcriptomics for uncovering the hypoxic transcriptional landscape of tumors
GUSTAFSSON Johan (SWEDEN)
Cancer program - Broad Institute (Eli and Edythe L. Broad Institute of MIT and Harvard ) - Cambridge - United States
GETZ Gad (Host supervisor)
The tumor microenvironment is characterized by a dense extracellular matrix in combination with leaky and irregular vasculature, creating acidic hypoxic tumor regions with small influx of oxygen and nutrients. Most therapies, such as radiation therapy, immune therapies, and chemotherapy are ineffective in these regions due to lack of oxygen, limited drug influx, immune exclusion, and low proliferation rate. Effective ways to target the cancer cells in hypoxic regions are lacking and means to address this problem could potentially improve the clinical outcome for many groups of patients.
An important step towards finding effective treatments targeting hypoxic regions is to understand their biology. The arrival of spatial transcriptomics has made possible high-resolution studies of the transcriptional landscape in tumors. In spatial transcriptomics, spots containing 1-10 cells are sequenced and associated with a physical coordinate from a thin tissue section, forming a spatial network of gene expression. Hypoxic regions can be identified using immunofluorescence staining for hypoxic markers, enabling identification of biological traits per level of hypoxia. In this project, we will collaborate with the Human Tumor Atlas Network (HTAN) to obtain spatial transcriptomics data overlayed with hypoxia staining from lung and breast cancer patient samples.
The first aim is to establish a method to determine the level of hypoxia per spot based on staining for hypoxic markers, but also from the transcriptomic profiles for use with datasets without staining information.
The second aim is to identify regions within the hypoxia range with similar cellular behavior.
The third aim is to explore and understand the biology and identify potential drug targets in each hypoxic region. To this end, I intend to use methods such as differential expression analysis, gene set enrichment analysis, genome-scale metabolic modeling, and utilize gene essentiality information from the DepMap database.
The fourth aim is to collaborate with the PRISM lab at the Broad Institute, which performs high-throughput screening for drug targets in hundreds of cell lines. To validate our biological theories and provide potential drug targets for hypoxic regions, we will develop a hypoxic setup to test previously identified drug targets as well as perform screening of existing drug libraries for the hypoxic regions previously identified.
In this project, I will bring my metabolic systems biology knowledge into the Getz lab and learn about spatial transcriptomics and cancer biology. The results are envisioned to be an atlas over the transcriptional landscape in tumors defined per region of hypoxia and a list of potential drug targets for these regions. These could serve to find a complementary treatment to existing therapies, specifically targeting the hypoxic regions, which could lead to combination treatments with an increased survival chance for cancer patients.
2023
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Long-Term Fellowships - LTF
Investigating the mechanistic role of the gut microbiome in modulating depressive behavior in mice
GUZZETTA Katherine (USA)
D-BSSE - Eidgenoessische Technische Hochschule Zuerich (ETH Zürich) - Zurich - SWITZERLAND
PLATT Randall (Host supervisor)
Background: Depression is the leading cause of disability worldwide, creating immense psychological and economic burdens for individuals, families and society. Despite depression’s pervasiveness, the pathology and mechanism of action for treatments remain elusive, and roughly half of patients do not improve with antidepressant use. The high global prevalence, poor treatment efficacy and lack of mechanistic understanding has created a large knowledge gap that needs to be addressed to better understand the disease and help patients.
The gut microbiota is an emerging contributor to depression onset and recovery, and can regulate brain function, behavior, and mood of its host by altering the metabolome and immune system. Intriguingly, gut microbial composition is altered in depressed individuals, post-antidepressant treatment and by stress. However, the exact pathways by which these microbes act on the brain, including in depression, remain elusive largely due to an inability to mechanistically interrogate microbe-host interactions.
Overall aim: Uncover how the gut microbiota contributes to the development and recovery from stress-induced depressive behavior (initially in mice).
Hypothesis: The gut microbiota contributes to stress-induced depressive behavior and amelioration through microbe-host signaling (including modulating host serotonin levels and aryl hydrocarbon receptor immune signaling through microbial tryptophan metabolism), and manipulating these pathways is sufficient to augment depressive-like phenotypes in mice.
Experimental Approach: To reveal how stress and antidepressants impact the gut microbiome and physiology of mice, I will analyze behavior and physiology (gene expression, corticosterone/neurotransmitter levels, etc) and use contemporary multi-omics methods (metagenomics/transcriptomics) combined with the novel Record-seq technology recently created by the host laboratory (Schmidt, Nature, 2018; Schmidt, Science, 2022). My bioinformatics analysis will focus on understanding microbe-host pathways altered by stress and alleviated by antidepressant (fluoxetine or probiotic) consumption. I will then functionally validate key findings using CRISPR-based manipulation of top identified pathways in the gut microbiome (with host institutional knowledge) and microbiota transplantation to reveal novel mechanisms by which the gut microbiota contributes to anti-depressive or depressive-like behavior.
Conclusions: This research has the potential to shift paradigms for depression research by incorporating novel microbiome-based techniques and centering the gut microbiota in the pathophysiology of depression. This project will expand on my background of the microbiota-gut-brain axis and allow me to pursue new scientific disciplines and techniques, including CRISPR, microbial engineering, bioinformatics, and Record-seq. The use of cutting-edge non-invasive methods (Record-seq) also provides an entry point for follow-up clinical studies.
2023
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Long-Term Fellowships - LTF
Investigating the cross talk between glioma cells and oligodendrocytes in brain tumors
HAN Jichang (CHINA, PEOPLE'S REPUBLIC OF)
SCCC - Miller School of Medicine of the University of Miami - Coral Gables - United States
IAVARONE Antonio (Host supervisor)
Glioblastoma multiforme (GBM) is the most common high-grade glioma in adults and has an exceptionally dismal prognosis. Neuronal activity has recently emerged as a critical regulator of GBM progression by regulating membrane depolarization of glioma cells via neuron-glioma synapses or secreting neurotrophic factors from neurons. Oligodendrocytes can wrap around axonal segments, enabling fast saltatory conduction of action potentials and supporting axons' energy metabolism. Whether a functional interaction between oligodendrocytes and cancer cells drives GBM remains unknown. To better understand the interactions between tumor and non-tumor cells, the host lab analyzed larger scRNAseq dataset of GBM to uncover the ligand-receptor interactions from the tumor microenvironment (TME) using a recently developed single-cell tumor-host interaction (scTHI) tool and identified that the oligodendrocytes express high levels of NLGN1 that interacts with NRXN3 expressed by neuronal tumor cells.
We propose a model wherein oligodendrocytes directly interact with the tumor cells through ligand-receptor interactions and generate oligodendrocyte-glioma myelin sheaths to promote cancer development. This proposal will uncover the functional downstream consequences of the newly identified ligand-receptor interactions and how they drive glioma progression. A key innovative component of our proposal will be to interrogate the ability of glioma cells to form functional myelin sheaths with oligodendrocytes thus hijacking the normal activities of oligodendrocytes.
A diverse range of cutting-edge techniques will be used to address these goals. To distinguish and verify the interactions between tumor and non-tumor cell types in GBM, I will deploy spatial transcriptomic technology and multiplexed error-robust fluorescence in situ hybridization (MERFISH). For these analyses, a panel of genes will be designed based on the host lab scRNA-seq data and cell-type/state annotations, to decipher spatial and functional organization. I will also investigate the ultrastructure of oligodendrocyte-glioma myelin sheaths in mouse models and patient tumors by enhanced focused ion beam scanning electron microscopy (FIB-SEM) technology enabling high-throughput, large volume, and high-resolution 3D imaging. Finally, to elucidate the molecular mechanisms of ligand-receptor interactions governing tumor growth or oligodendrocyte recruitment in glioma, I propose to examine the gene expression profiling and gene set enrichment analysis of ligand-null (CRISPR-KO) versus parental ligand-wild-type in cell lines or genetically engineered mouse models of gliomas.
The outcome of this work will unravel the regulation and functional impact of the crosstalk between glioma cells and oligodendrocytes in GBM and provide the key knowledge for the design of innovative therapies. It will also provide the paradigm-shift discovery and functional characterization of myelination as driver of GBM progression.
2023
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Grant Awardees - Early Career
Dark oxygen production: Assessing an overlooked microbial process in Earth's hidden ecosystems
RUFF S. emil (GERMANY)
- Marine Biological Laboratory - Woods Hole - United States
HEMINGWAY Jordon (United States)
- Swiss Federal Institue of Technology - Zurich - SWITZERLAND
KRAFT Beate (GERMANY)
- University of Southern Denmark (Syddansk Universitet, SDU) - Odense - DENMARK
Most gaseous oxygen (O2) on Earth is produced via oxygenic photosynthesis. However, new evidence indicates that O2 is also produced in permanently dark ecosystems. This so-called “dark oxygen production” (DOP) can proceed via abiotic chemical reactions or via microbial dismutation of chlorite and nitric oxide—metabolisms fundamentally different from photosynthesis. Recent work suggests that microbial DOP is widespread in groundwater ecosystems, yet definitive evidence is lacking to date. Our team has the abilities, instruments, and expertise to provide such evidence and elucidate the origins, processes, and production rates of groundwater O2. We hypothesize that microbial DOP is a globally relevant process in groundwater ecosystems today, and that groundwater aquifers represent model systems to study O2 production and consumption in the deep geologic past, as well as in subsurface ecosystems of other celestial bodies.
We propose an international, multi-disciplinary project to provide comprehensive insights into the geochemistry, microbiology, and ecology of DOP. Our combined expertise leverages three key technological advances: (1) triple- and clumped-oxygen isotope analyses, which can unambiguously link O2 to biological DOP origins (led by PI Hemingway), (2) determination of DOP rates and fluxes at unprecedented resolution using nanomolar O2 concentration measurements (led by PI Kraft), and (3) high-throughput analyses of O2-producing enzymes and pathways present in complex communities using genome sequencing and protein mass spectrometry (led by PI Ruff). We will apply these techniques to a sample set from diverse aquifers spanning a broad range of ecosystems in Canada, Finland, Germany, Switzerland, and the USA. We expect several key outcomes. First, we will determine the first ever triple- and clumped-oxygen isotope signatures of DOP by different biotic and abiotic sources, values that are needed to decipher natural signals. Second, we will use stable isotope-labelling to determine rates of microbial DOP in groundwaters, critical measurements that are lacking to date. Finally, we will conduct the first global survey of key microbial lineages and genes to understand the diversity, abundance, and activity of microbes involved in DOP. These insights are crucial to understand groundwater aquifers, which represent Earth’s largest source of drinking water.
2023
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Long-Term Fellowships - LTF
Disentangling microbiome effects on plant adaptation
HERNANDEZ-TERAN Alejandra (MEXICO)
EEB - The Regents of the University of California (Irvine) - Irvine - United States
REBOLLEDA-GOMEZ Maria (Host supervisor)
It is increasingly clear that microbes can influence host health and fitness. In particular, microbes affect important developmental transitions like metamorphosis in mosquitoes and flowering time. The timing of these transitions is central for organisms responses in changing environments. However, we do not know which microbes alter such traits and how they do it, or whether it is adaptive for the microbes or a consequence of their metabolism.
Through integration of life-history models, microbial physiology, community selection, and plant evolutionary ecology, my goal is to understand microbial effects on plant developmental timing. The ultimate goal is to generate predictive models of when are microbes more likely to impact plant development, which microbial functions are involved, and how are these interactions going to change with an increasingly variable environment. One intriguing hypothesis is that since microbes are indicators of environmental and ecological conditions, they can provide accurate information about optimal phenology to the plant hosts while integrating to noisy variation. I will use flowering time in Arabidopsis thaliana as a experimental system to determine how microbial community function might change with changes in temperature.
Recently, Dr. Rebolleda-Gomez developed a predictive model microbial community change across temperatures in simple carbon sources. In collaboration with members of the lab, I will extend these models to more complex communities. Using this data I will be able to analyse the information and reliability of changes in microbial functions over time (compared to the temperature series alone) to evaluate the quality of microbes as cues. These mathematical approaches are new to me, but as part of my postdoctoral formation at UCI I will benefit from the expertise in microbial ecology of Dr. Rebolleda-Gomez and time series analyses of Dr. Symons (a close collaborator). Using recently developed theory on community level selection, I will select from different substrates, microbes that significantly affect flowering time and inoculate A. thaliana lines with different flowering plasticity. I will test the effect of such communities in different thermal conditions to determine when and why plants respond to microbes. Using omics approaches, I will characterize from the selected microbial communities the metabolic functions that are associated with either late or early flowering time. Finally, I will incorporate our insights into predictive life-history models to evaluate possible effects of microbes on plant adaptation to climate change. Altogether, this project will allow me to gain insights into the mechanisms by which microbial communities affect plant phenology, and to hypothesize about the evolutionary implications. This fellowship will allow me to learn the mathematical and experimental tools necessary to generate predictive models of microbiome effects on plant development.
2023
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Long-Term Fellowships - LTF
Growth and folding of a wing origami
HIROKAWA Soichi (USA)
Faculté des Sciences - Developmental Biology Institute of Marseille (Institut de Biologie du Développement Marseille, IBDM) - Marseilles - FRANCE
LECUIT Thomas (Host supervisor)
Tissue folding is widespread in morphogenesis. It often arises due to geometric frustration associated with growth mismatch. One of the big questions is how organisms take advantage of the local mechanics, differential growth, and physical and geometric boundary conditions of tissues to drive this folding. One such example may be found in the final stages of Drosophila wing development. During metamorphosis, the wing elongates along the body of the fly as a planar sheet before anchoring to the hard cuticle layer encasing it. From 30 hours into metamorphosis up to 96 hours when metamorphosis ends, the wing has grown by more than an order of magnitude in surface area. The wing manages to continue to grow in the confined space over these 66 hours by folding. During this period, as the wing continues to grow, it also becomes thinner and develops more folds. However, the driving mechanism for this folding phenomenon and the level of variability in the shape change across individual wings are not known. We propose to study how the physical and geometric constraints on the wing and the differential growth of the cellular layer and its attached extracellular matrix (ECM) allows the wing to fold. This project will be an incorporation of live imaging in 3D through the highly robust Gal4-UAS system to identify geometric changes to the wing as it develops folds and will require an analysis of 3D-reconstructed images to identify the patterns of shapes that emerge and the recurrence or variability of these patterns across wings of different individuals. A key piece to better understanding the role of this differential growth between the cells and the ECM as well as the constraints on the folding process will involve genetic and physical perturbation of the wings to further study how making alterations to the development of the wing changes its folding pattern. These include using recently developed optogenetic systems to spatially control changes to local cellular growth rates and the use of genetic mutants to examine how the changing the expression level of genes and the distribution of their resultant proteins affect the boundary or growth conditions on the wing and thus affect the folding pattern. We will also examine how the wings unfold at various time points during development by removing the boundary that encases them and watch how they unravel. We expect these experiments and the concurrent analyses will allow us to understand how boundary conditions that confine the wing and the differential growth and material properties between cell and ECM combine to allow the fly to continue to develop its wings under spatial confinement.
2023
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Long-Term Fellowships - LTF
Rock-paper-scissors dynamics between mobile genetic elements
HUISMAN Jana Sanne (NETHERLANDS)
Physics - Massachusetts Institute of Technology - MIT - Cambridge - United States
GORE Jeff (Host supervisor)
The ecology of bacteria is directly tied to the ecology of the mobile genetic elements (MGEs) that infect them. These elements act as parasites or symbionts, spreading horizontally between bacteria and shaping the genetic repertoire of their hosts. MGEs can be beneficial when carrying traits like metabolic pathways, virulence genes, or antibiotic resistance, which allow their host bacteria to thrive in new environments. Yet, they are also costly due to the expression of the encoded genes. Additionally, evidence is emerging of extensive interaction and competition between MGEs. Many MGEs co-circulate in natural bacterial populations and co-carriage within the same bacterial host is common. However, little is known about “coexistence conditions” for MGEs: how can diverse MGEs be maintained in the same population? And how does this affect the bacterial community in which they circulate?
We aim to address these questions for plasmids, a type of MGE frequently implicated in the spread of antibiotic resistance. Plasmids commonly code for genes that prevent further infection by similar plasmids (“superinfection”). We hypothesize this naturally leads to non-transitive interactions between plasmids that compete for the same bacterial hosts, and that this can maintain a diversity of plasmids even in the absence of selection for plasmid-borne traits. Non-transitive interactions work like the game “rock-paper-scissors”: each strain both inhibits and is inhibit by other members of the community. Such interactions have been proposed as a prime driver of species diversity, yet experimental realizations thus far remain restricted to bacteriocins or antibiotics, with limited extension to explaining MGE diversity.
We intend to study these dynamics in an experimental system using Escherichia coli strains that differ only in their carriage of two competing antibiotic resistance plasmids: (i) “F0” carries no plasmid and grows fast, (ii) “ML” carries a non-conjugative plasmid with medium cost, and (iii) “SC” carries a costly conjugative plasmid and grows slowest. As a result, F0 outcompetes ML due to growth, ML outcompetes SC due to growth and immunity to superinfection, and SC outcompetes F0 since the conjugative plasmid transforms F0 into SC. We will use pairwise and 3-way competition experiments to study the stable states of this system over multiple growth-dilution cycles. By varying parameters of the experiment, like growth rate, dilution, dispersal, and relative costs, we can probe the conditions for plasmid coexistence over a range of scenarios. Mathematical modelling will help scale these transitivity rules to a broad diversity of co-circulating plasmids and predict their influence on the stability of more complex bacterial communities.
Understanding such plasmid diversity and maintenance is directly relevant for the study of bacterial colonization and infection of human and animal hosts, as well as the spread of antibiotic resistance.
2023
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Grant Awardees - Program Grants
From diffuse to localised signalling: The origin of synaptic neurotransmission in animals
WATANABE Shigeki (United States)
- Johns Hopkins University School of Medicine - Baltimore - United States
IKMI Aissam (MOROCCO)
- Heidelberg European Molecular Biology Laboratory (EMBL - Heidelberg) - Heidelberg - GERMANY
MUSSER Jacob (United States)
- Yale University - New Haven - United States
The evolution of the nervous system is one of the remaining great mysteries of animal evolution. A key step was evolution of the chemical synapse, which enabled the transition from ciliomotor-based movement by diffusive signals to muscle-based locomotion driven by ultrafast localised signals. However, current understanding of this transition is mostly limited to determining the distribution of synaptic genes in early animal genomes, revealing most predate synapses. There are two competing hypotheses for how chemical synapses evolved. The first, termed the “chemical brain hypothesis”, proposes animal behaviour was initially controlled by paracrine cell networks using volume (non-synaptic) signalling. The second, termed the “protosynaptic hypothesis”, proposes that synaptic architecture already existed prior to the origin of true nervous systems, and facilitated some form of directional signalling. To test these hypotheses, we integrate expertise in synaptic dynamics and physiology, functional proteomics, and transgenesis techniques in early animals to uncover how synaptic signalling is achieved in the first animals without synapses (sponges) and those with synapses (cnidarians). To accomplish this, we will reconstruct the ancestral dynamics and localisation of synaptic protein complexes, discover the origins of ultrafast mechanisms for synaptic exo- and endocytosis, and determine the role of electrical potentials in propagating the first synaptic signals. In summary, our study aims to reveal the mechanisms underlying the origin of synaptic transmission with broad implications for the evolution of animal behaviours.
2023
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Long-Term Fellowships - LTF
Mapping the spatiotemporal organization and mechanosensitivity of gamma delta T cell synapses
JUKIC Nebojsa (CROATIA)
Autonomous Matter - Institute for Atomic and Molecular Physics (AMOLF) - Amsterdam - NETHERLANDS
GANZINGER Kristina (Host supervisor)
TANS Sander (Host supervisor)
Background: The spatiotemporal organization of T-cell receptors (TCRs) is critical to target cell recognition that underlies a novel class of cancer therapies. While dynamic receptor reorganization was observed in canonical T-cells, less is known about the recognition mechanisms of gamma delta (gd) T-cells, which are emerging as attractive candidates. Specifically, the spatiotemporal organization of their receptors upon immune synapse (IS) formation, their mechanosensitivity, and possibly crucial membrane deformations remain largely unexplored. While high-resolution fluorescence microscopy of T-cells contacting supported lipid bilayers (SLBs) presenting target proteins has been crucial to dissect canonical T-cell organization and signaling, SLBs containing select antigens and adhesion molecules cannot be used to probe gd T-cells as not all factors involved in antigen presentation are known for gdTCRs.
Aims: Combining my expertise in membrane biophysics and SLB fabrication on non-rigid substrates with the host’s expertise in biophysics, high-resolution fluorescence microscopy and T-cell immunology, we will reveal the spatiotemporal organization of gdTCRs upon immune synapse formation between T-cells and tumor cell-derived SLBs. In brief, we will:
A0. Establish experimental platform - mechanically tunable, tumor cell-derived SLB
A1. Map the spatiotemporal (re)organization of gdTCRs upon IS formation
A2. Assess effect of surface rigidity on organization of gdTCRs and gd T-cell activation
Hypotheses: I conjecture that gd T-cell receptors undergo specific spatiotemporal organization to allow antigen recognition in infection and tumorigenesis. Clustering of TCRs in canonical T-cells and exclusion of phosphatases from the IS amplify the signal from antigen-binding events, but dynamic TCR reorganization in gd T-cells remains unexplored. Intriguingly, receptor organization may interplay with membrane deformation and mechanosensitivity, which may both be critical to T-cell activation. I will study this by modulating support rigidity, with which I have ample experience.
Experimental approach:
E0: Develop polymer-based supports for fluorescence microscopy. Harvest plasma membrane vesicles from tumor cell cultures. Optimize SLB formation.
E1: Total internal reflection fluorescence microscopy - single molecule tracking of synaptic components upon gd T-cell contacting tumor cell-derived SLB.
E2: Measure force of gd T-cell–SLB interaction as a function of SLB rigidity using atomic force microscopy-based single-cell force spectroscopy and acoustic force spectroscopy.
Conclusions: I will observe the spatiotemporal organization of gdTCRs upon immune synapse formation at the molecular level, gaining insight into their activation mechanism – an unresolved question that has stymied progress in gdT-cell application in immunotherapy. I expect my novel, tumor-cell derived experimental platform to open up a range of new avenues in gdTCR research.
2023
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Grant Awardees - Program Grants
Shiny signalling: the production, detection and neurobiological processing of brilliant colours
VAN DER KOOI Casper j. (NETHERLANDS)
- University of Groningen (Rijksuniversiteit Groningen (RUG)) - Groningen - NETHERLANDS
KEMP Darrell (AUSTRALIA)
- Macquarie University - Sydney - AUSTRALIA
KINOSHITA Michiyo (JAPAN)
- The Graduate University for Advanced Studies, SOKENDAI - Kanagawa - JAPAN
Why do some organisms have shiny colours and others do not? Shiny colours are displayed across a suite of plants and animals, including the flowers of buttercups, orchids and tulips, the wings of butterflies, and the surfaces of beetles. The visual appearance of these organisms is dominated by a flash, which entails a bright pulse of polarised light with a strong angular dependence. The dynamic nature of such “flashy” effects presents a paradox in visual ecology, because although flash effects likely enhance long-range signal visibility, they may undermine the ability to locate objects at close range. This may help explain why colours with a matte appearance prevail in nature, yet the repeated independent evolution of shiny colours implies a fundamental, possibly universal adaptive benefit for signal dynamicity per se. Our project will constitute the most integrative cross-taxon approach to understanding the basis of this adaptive benefit conducted to date.
We will achieve an integrative understanding of the ecological significance of flashy colours by: (1) characterising the optical properties of sexually deceptive flowers and relating these to their insect models; (2) quantifying how flower gloss determines the long-distance visibility and short-distance discriminability of flowers to insect pollinators; (3) determining the behavioural significance of flashy colours in insect visual ecology; and (4) elucidating how the insect brain processes bright flashes. Hence, we will trace the full pathway from how such signals are generated to how they ultimately elicit fitness effects in their relevant viewers. This breadth of insight is only possible by integrating our collective expertise in biophysics (van der Kooi), behavioural ecology (Kemp) and neurobiology (Kinoshita), which is precisely why this project promises unprecedented insight into a (literally) brilliant phenomenon that has fascinated researchers for centuries.
2023
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Long-Term Fellowships - LTF
A role for enteric neuroimmune interactions in the development of obesity
KIM Dong-Yoon (KOREA, REPUBLIC OF (SOUTH KOREA))
Mucosal Immunology - The Rockefeller University - New York - United States
MUCIDA Daniel (Host supervisor)
Obesity induces chronic inflammation in the intestine and affects the state of non-immune cells such as gut-associated neurons (e.g., enteric and gut-innervating sensory neurons). For example, the intestinal immune system undergoes proinflammatory shifts during obesity, contributing to metabolic dysfunction; while the sensitivity of sensory neurons to satiety-inducing peripheral signals (e.g., distension and nutrients) are disrupted in obese conditions, which leads to food overconsumption. Furthermore, a growing body of evidence has revealed the importance of neuroimmune crosstalk in several pathological conditions, including obesity. Thus, in this proposal, I hypothesize that enteric neuroimmune interactions underlie the cause of multiple obesity-related pathological symptoms, and manipulation of these interactions may critically modulate those symptoms during the development of obesity. To test this idea, first, I will use diverse techniques to characterize the enteric neuroimmune interactions in multiple aspects during the development of diet-induced obesity (Aim 1, 2). With the Victora lab, the Mucida lab (host lab) has recently developed a murine genetic approach that enables the labeling of cell-cell interactions between specific cell types (universal, or uLIPSTIC). I will apply this tool to label the cells interacting with gut-associated neurons during obesity and use flow cytometry to identify the type of labeled immune cells. Next, I will use live imaging and tissue clearing tools in immune cell/neuron double reporter mice (approaches pioneered by the host lab) in lean and obese conditions. I will also use single-cell or single-nuclei RNA-sequencing from the intestinal immune cells and gut-associated neurons, respectively, in lean and obese mice. These approaches will allow us to define the candidate receptor-ligand molecules and gut-associated neuronal subpopulations involved in these interactions. Second, informed by the characterization performed in Aim 1&2, I will investigate the functional consequences of enteric neuroimmune interactions in developing obesity-related symptoms (Aim 3). I will use genetically engineered mice to target ligand-receptor signaling pathways identified in Aim 1 and manipulate gut-associated neuronal subpopulations while monitoring physiological and behavioral parameters related to obesity-related symptoms using metabolic cages. We can also target immune cells that are found to be changed during the development of obesity by using cell-specific depletion strategies. Collectively, by utilizing state-of-the-art approaches, this project will reveal neuroimmune mechanisms possibly modulating obesity-related pathophysiological and behavioral consequences, which is a poorly understood question in this nascent field.
2023
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Grant Awardees - Program Grants
Intracellular selection and dynamics of mitochondrial ageing
OSMAN Christof (GERMANY)
- Ludwig-Maximilians-Universitaet Muenchen (LMU Munich) - Muenchen - GERMANY
KRIEG Michael (GERMANY)
- ICFO – The Institute of Photonic Sciences - Castelldefels - SPAIN
SHRAIMAN Boris (United States)
- The Regents of the University of California, Santa Barbara - Santa Barbara - United States
Eukaryotic cells contain multiple mitochondrial genome (mtDNA) copies, which encode proteins required for mitochondrial energy production. Maintaining intact mtDNA is critical for cellular and organismal health and its deterioration has been linked to cellular aging. mtDNA is known to mutate at an elevated rate, but extensive evidence also suggests the existence of processes, acting on cellular and subcellular levels, that eliminate damaged mtDNA thus acting to rejuvenate mitochondria. Yet mtDNA integrity declines during ageing, but the timecourse of its decay and the underlying mechanisms remain largely unknown, because of challenges presented by the complex and quantitative nature of involved phenotypes. This project will address these challenges through a multidisciplinary approach that applies yeast as a model organism and combines novel mtDNA-based reporters, special purpose optofluidic devices and advanced mathematical modelling. Our goal is to understand (a) the link between mtDNA decay and physiological changes associated with the ageing process at the single cell level; (b) the mutational events that drive mtDNA decay with single cell sequence resolution and (c) the processes that facilitate intracellular selection against mutant mtDNA and their role in suppressing mtDNA decay during ageing.
Specifically, we will use mtDNA-based fluorescent reporters for mtDNA copy number and expression to infer mtDNA health throughout the ageing process while monitoring the decline of physiological parameters in single cells. To do so, we will develop a novel device that combines optofluidics with advanced fluorescence microscopy to monitor, select and sort single cells during the ageing process and eventually subject them to whole genome amplification and sequencing in a highly parallelized manner to determine mtDNA sequence changes. This will allow us to monitor mitochondrial function and mtDNA variation with cell age and between ancestrally related cell lineages. Resulting data will be analyzed quantitatively with the help of mathematical models of mtDNA propagation within cells, including effects of mutation, selection and random drift, which will enable us to specifically address the role of intracellular purifying selection in extending the mitochondrial healthspan of a cell. Our findings will provide broad fundamental insight into mitochondrial biology.
2023
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Long-Term Fellowships - LTF
Brain remodeling mediated by molecular memory of the social conflict in the ant Harpegnathos
LEE Ching-Han (CHINA, REPUBLIC OF (TAIWAN))
Department of Biolog - New York University - New York - United States
DESPLAN Claude (Host supervisor)
REINBERG Danny (Host supervisor)
Social insects can undergo dramatic changes in their physiology and behavior to support the colony. In the ant Harpegnathos saltator (Hs), when the queen dies, workers can transition into reproductive pseudo-queens (gamergates) to re-establish hierarchy in the colony. In the absence of queen pheromones, the young workers engage into a dueling behavior by trading strikes with their antennae. Most workers rapidly abandon the fight (win-lose) but dueling continues for months among the winners (win-win) who become reproductive and share social dominance. These gamergates show dramatic physiological and behavioral changes, lay eggs and cease to perform workers’ duties. They also have a 5X lifespan extension, and their brain is remodeled and shrinks by 20%. This transformation is fully reversible when gamergates are placed back in a queened colony. The goal of this proposal is to understand how the absence of queen pheromones triggers dueling; what the signals are among winning workers that sustain dueling; what brain circuits are affected by sustained dueling to cause changes in behavior. We hypothesize that the neural circuits responding to queen pheromones and controlling their production regulate dueling and the establishment of queen-like behavior. The pheromones normally repress dueling, so their absence in an orphaned colony releases the inhibition, and multiple workers begin dueling. The winning asymmetry appears to be created and maintained not due to the strongest fighters prevailing but due to a signaling imbalance between the animals engaged in duels. We hypothesize that this is achieved through the action of a negative feedforward loop – duelers quickly start producing queen pheromone to repress other duelers – and a positive feedback loop – duelers are more likely to engage in dueling again, possibly due to lowered sensitivity to the pheromones. Dueling further triggers remodeling of the brain circuits that control queen-like physiology and behavior.
Aim 1: Track the behavior during win-lose and win-win duels, and measure queen pheromones production on the cuticle and in the producing glands.
Aim 2: Generate transgenic lines expressing GCaMP7f or CaMPARI2 in the antennal lobe of the brain to evaluate whether losing and winning workers exhibit different sensitivity to the pheromones.
Aim 3: Perform scRNAseq to determine how the gamergate brain changes and which circuits are affected, focusing on homologs of known (female) aggression and egg laying circuitry in flies.
Experimental system: The host lab has extensive experience in flies and ants, including a deep knowledge of brain genomics as well as metabolomics of the hemolymph. Genetic manipulations in H.s are also possible.
Conclusions: This work will elucidate the molecular underpinning of social conflict that establish a new shared hierarchy in ant colonies, and how molecular memories of social experiences establish long-lasting behavioral traits via brain remodeling.
2023
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Long-Term Fellowships - LTF
Exploring immune-pancreatic progenitor crosstalk during pancreatic development
LEE Christopher (SINGAPORE)
Spagnoli Lab - King's College London - London - United Kingdom
SPAGNOLI Francesca (Host supervisor)
Mammalian development is an intricate process governed by overlapping and often competing cell fate programmes. Although much of the cell intrinsic transcriptomic machinery and pathways responsible for cellular differentiation is well characterised, the contribution and effect of the surrounding tissue niche(s) toward cell identity acquisition remains poorly understood. This is especially the case when we consider that embryonic macrophages and other immune cells infiltrate many organs early on during tissue specification and develop symbiotically alongside the native cells, increasing the complexity of cellular crosstalk within the niche. Furthermore, our understanding of cellular crosstalk has thus far been restricted to extracellular receptor/ligand interactions, despite increasing evidence that cells might be able to communicate directly via gap junctions, tunnelling nanotubes and extracellular vesicles. Consistently, soluble and membrane-bound ligands alone are unable to fully establish and maintain cell identity of ex vivo cultured cells. In this project, I will focus on pancreatic progenitors and their interactions with the surrounding hematopoietic/immune cells during pancreatic development, in the window of time spanning fate specification and differentiation of distinct pancreatic cell types, such as the acinar and hormone-expressing endocrine cells. Although macrophages and other immune cells represent a large fraction of the embryonic pancreatic microenvironment and are key players in diabetes pathogenesis, they are an often-neglected population and understudied in this context. Single-cell transcriptomics have started to unveil the heterogeneity of these populations, but their functional diversity and potential contribution to tissue niche(s) underlying pancreatic lineage decisions remain unexplored. Utilising in vivo mouse models, human induced pluripotent stem cell models and human fetal tissue together with traditional and spatial transcriptomics, we aim to map the cellular communication network between different sets of hematopoietic/immune cells and pancreatic progenitors. Next, we will explore the possibility of cellular crosstalk beyond traditional receptor/ligand interactions, such as direct cytosolic transfer of mRNA and protein subunits via tunneling nanotubes and extracellular vesicles, and validate the functional relevance of these findings in co-culture experimental set ups. By the end of this project, we will not only have a fuller understanding of how cell-cell communication contributes to the pancreatic tissue niches, but also provide evidence towards a novel and alternate form of intercellular communication via direct cytosolic transfer. Finally, beyond the impact on the development and stem cell biology of the pancreas, this study opens new avenues for understanding mechanisms underlying cell-cell communication and how these processes could go awry in diseases.
2023
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Long-Term Fellowships - LTF
Investigation of astrocytic surface molecule-mediated T cell regulation in health and disease
LEE Joon-Hyuk (KOREA, REPUBLIC OF (SOUTH KOREA))
Dept. of Neurology - Brigham and Women's Hospital, Inc. - Boston - United States
QUINTANA Francisco (Host supervisor)
During the central nervous system (CNS) inflammation, substantial number of T cells start to infiltrate into CNS and attack the neurons or myelin in several neurological disorders such as multiple sclerosis, suggesting their potent role during CNS inflammation. For T cells to exhibit their effector function, it is necessary to be re-stimulated and regulated in the inflamed region by tissue-resident cells. However, the CNS-resident cells that regulate the effector T cell (Teff) during CNS inflammation are still unclear.
Interestingly, recent reports suggest that astrocytes are crucial participants in CNS inflammation. Furthermore, infiltrating Teffs are known to physically contact with astrocytes. Since astrocytes express vast range of immune-regulatory surface molecules such as MHC class II (MHCII), co-stimulatory molecules (B7) and immune checkpoints, it is plausible that astrocytes might utilize those molecules to regulate the infiltrating CNS-reactive Teffs.
Based on this idea, we hypothesize that astrocytes contact with Teffs via surface proteins to regulate the Teffs during CNS inflammation.
2023
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Long-Term Fellowships - LTF
Understanding the role of mitochondrial redox sensing in cancer
LIU Shanshan (CHINA, PEOPLE'S REPUBLIC OF)
Birsoy Lab - The Rockefeller University - New York - United States
BIRSOY Kivanc (Host supervisor)
Cells need to maintain metabolic homeostasis to survive and proliferate. Many biochemical systems have evolved to coordinate levels of cellular metabolites in response to changes in extracellular cues. While we know a lot about regulatory processes involved in cellular metabolite homeostasis, how organelles maintain their metabolite availability is poorly understood. This is particularly relevant for mitochondria, as the major oxidative organelle; but whether mitochondria can sense the levels of metabolites and accordingly regulate their availability is unknown. Studying such compartmentalized metabolite sensing mechanisms is challenging due to lack of technologies to measure and modulate organellar metabolite levels.
Recent studies from the host lab discovered SLC25A39 as a mitochondrial transporter for glutathione (GSH), the major antioxidant thiol in mammalian cells. Remarkably, SLC25A39 protein levels are negatively regulated specifically by mitochondrial GSH availability. This observation raises the possibility that mitochondria harbor a sensing system for GSH availability. Building upon these observations, I will identify the mechanism by which mitochondria sense GSH availability and test whether it is required for tumor formation.
My first aim is to determine the precise mechanism and molecular players involved in mitochondrial GSH sensing. Using a combination of biochemical tools and genetic screening approaches, I will identify the molecular players and critical domain(s) and residue(s) of the transporter essential for the GSH sensing. Additionally, my preliminary work shows that SLC25A39 expression is associated with poor prognosis and decreased survival of breast cancer patients, and SLC25A39 protein levels are strongly upregulated in breast cancer cells colonizing to the lung compared to those in mammary tumors. Building upon this, my second aim will determine whether mitochondrial GSH availability and its sensing is necessary for breast cancer progression. To test whether mitochondrial GSH sensing is required for metastatic colonization, I will generate mutant forms of the transporter deficient in GSH sensing. In these mouse models, I will determine the precise molecular pathways impacted by mitochondrial GSH loss, resulting in reduced metastasis. To further test the sufficiency of mitochondrial GSH availability for tumor progression, I will also engineer a mitochondrially-targeted bacterial enzyme called GSHf, which produces GSH in specific compartments, and express it specifically in the breast tumor cells.
Collectively, these studies will provide a unique opportunity to uncover how mitochondria sense and regulate GSH and how compartmentalized redox sensing shapes breast cancer cell function. This will also provide a proof of principle for potential organellar sensing mechanisms for other metabolites.