Project acronym DCRIDDLE
Project A novel physiological role for IRE1 and RIDD..., maintaining the balance between tolerance and immunity?
Researcher (PI) Sophie Janssens
Host Institution (HI) VIB
Call Details Consolidator Grant (CoG), LS3, ERC-2018-COG
Summary Dendritic cells (DCs) play a crucial role as gatekeepers of the immune system, coordinating the balance between protective immunity and tolerance to self antigens. What determines the switch between immunogenic versus tolerogenic antigen presentation remains one of the most puzzling questions in immunology. My team recently discovered an unanticipated link between a conserved stress response in the endoplasmic reticulum (ER) and tolerogenic DC maturation, thereby setting the stage for new insights in this fundamental branch in immunology.
Specifically, we found that one of the branches of the unfolded protein response (UPR), the IRE1/XBP1 signaling axis, is constitutively active in murine dendritic cells (cDC1s), without any signs of an overt UPR gene signature. Based on preliminary data we hypothesize that IRE1 is activated by apoptotic cell uptake, orchestrating a metabolic response from the ER to ensure tolerogenic antigen presentation. This entirely novel physiological function for IRE1 entails a paradigm shift in the UPR field, as it reveals that IRE1’s functions might stretch far from its well-established function induced by chronic ER stress. The aim of my research program is to establish whether IRE1 in DCs is the hitherto illusive switch between tolerogenic and immunogenic maturation. To this end, we will dissect its function in vivo both in steady-state conditions and in conditions of danger (viral infection models). In line with our data, IRE1 has recently been identified as a candidate gene for autoimmune disease based on Genome Wide Association Studies (GWAS). Therefore, I envisage that my research program will not only have a large impact on the field of DC biology and apoptotic cell clearance, but will also yield new insights in diseases like autoimmunity, graft versus host disease or tumor immunology, all associated with disturbed balances between tolerogenic and immunogenic responses.
Summary
Dendritic cells (DCs) play a crucial role as gatekeepers of the immune system, coordinating the balance between protective immunity and tolerance to self antigens. What determines the switch between immunogenic versus tolerogenic antigen presentation remains one of the most puzzling questions in immunology. My team recently discovered an unanticipated link between a conserved stress response in the endoplasmic reticulum (ER) and tolerogenic DC maturation, thereby setting the stage for new insights in this fundamental branch in immunology.
Specifically, we found that one of the branches of the unfolded protein response (UPR), the IRE1/XBP1 signaling axis, is constitutively active in murine dendritic cells (cDC1s), without any signs of an overt UPR gene signature. Based on preliminary data we hypothesize that IRE1 is activated by apoptotic cell uptake, orchestrating a metabolic response from the ER to ensure tolerogenic antigen presentation. This entirely novel physiological function for IRE1 entails a paradigm shift in the UPR field, as it reveals that IRE1’s functions might stretch far from its well-established function induced by chronic ER stress. The aim of my research program is to establish whether IRE1 in DCs is the hitherto illusive switch between tolerogenic and immunogenic maturation. To this end, we will dissect its function in vivo both in steady-state conditions and in conditions of danger (viral infection models). In line with our data, IRE1 has recently been identified as a candidate gene for autoimmune disease based on Genome Wide Association Studies (GWAS). Therefore, I envisage that my research program will not only have a large impact on the field of DC biology and apoptotic cell clearance, but will also yield new insights in diseases like autoimmunity, graft versus host disease or tumor immunology, all associated with disturbed balances between tolerogenic and immunogenic responses.
Max ERC Funding
1 999 196 €
Duration
Start date: 2019-02-01, End date: 2024-01-31
Project acronym DissectPcG
Project Dissecting the Function of Multiple Polycomb Group Complexes in Establishing Transcriptional Identity
Researcher (PI) Diego PASINI
Host Institution (HI) UNIVERSITA DEGLI STUDI DI MILANO
Call Details Consolidator Grant (CoG), LS3, ERC-2016-COG
Summary The activities of the Polycomb group (PcG) of repressive chromatin modifiers are required to maintain correct transcriptional identity during development and differentiation. These activities are altered in a variety of tumours by gain- or loss-of-function mutations, whose mechanistic aspects still remain unclear.
PcGs can be classified in two major repressive complexes (PRC1 and PRC2) with common pathways but distinct biochemical activities. PRC1 catalyses histone H2A ubiquitination of lysine 119, and PRC2 tri-methylation of histone H3 lysine 27. However, PRC1 has a more heterogeneous composition than PRC2, with six mutually exclusive PCGF subunits (PCGF1–6) essential for assembling distinct PRC1 complexes that differ in subunit composition but share the same catalytic core.
While up to six different PRC1 forms can co-exist in a given cell, the molecular mechanisms regulating their activities and their relative contributions to general PRC1 function in any tissue/cell type remain largely unknown. In line with this biochemical heterogeneity, PRC1 retains broader biological functions than PRC2. Critically, however, no molecular analysis has yet been published that dissects the contribution of each PRC1 complex in regulating transcriptional identity.
We will take advantage of newly developed reagents and unpublished genetic models to target each of the six Pcgf genes in either embryonic stem cells or mouse adult tissues. This will systematically dissect the contributions of the different PRC1 complexes to chromatin profiles, gene expression programs, and cellular phenotypes during stem cell self-renewal, differentiation and adult tissue homeostasis. Overall, this will elucidate some of the fundamental mechanisms underlying the establishment and maintenance of cellular identity and will allow us to further determine the molecular links between PcG deregulation and cancer development in a tissue- and/or cell type–specific manner.
Summary
The activities of the Polycomb group (PcG) of repressive chromatin modifiers are required to maintain correct transcriptional identity during development and differentiation. These activities are altered in a variety of tumours by gain- or loss-of-function mutations, whose mechanistic aspects still remain unclear.
PcGs can be classified in two major repressive complexes (PRC1 and PRC2) with common pathways but distinct biochemical activities. PRC1 catalyses histone H2A ubiquitination of lysine 119, and PRC2 tri-methylation of histone H3 lysine 27. However, PRC1 has a more heterogeneous composition than PRC2, with six mutually exclusive PCGF subunits (PCGF1–6) essential for assembling distinct PRC1 complexes that differ in subunit composition but share the same catalytic core.
While up to six different PRC1 forms can co-exist in a given cell, the molecular mechanisms regulating their activities and their relative contributions to general PRC1 function in any tissue/cell type remain largely unknown. In line with this biochemical heterogeneity, PRC1 retains broader biological functions than PRC2. Critically, however, no molecular analysis has yet been published that dissects the contribution of each PRC1 complex in regulating transcriptional identity.
We will take advantage of newly developed reagents and unpublished genetic models to target each of the six Pcgf genes in either embryonic stem cells or mouse adult tissues. This will systematically dissect the contributions of the different PRC1 complexes to chromatin profiles, gene expression programs, and cellular phenotypes during stem cell self-renewal, differentiation and adult tissue homeostasis. Overall, this will elucidate some of the fundamental mechanisms underlying the establishment and maintenance of cellular identity and will allow us to further determine the molecular links between PcG deregulation and cancer development in a tissue- and/or cell type–specific manner.
Max ERC Funding
2 000 000 €
Duration
Start date: 2017-11-01, End date: 2022-10-31
Project acronym EXPAND
Project Defining the cellular dynamics leading to tissue expansion
Researcher (PI) Cedric Blanpain
Host Institution (HI) UNIVERSITE LIBRE DE BRUXELLES
Call Details Consolidator Grant (CoG), LS3, ERC-2013-CoG
Summary Stem cells (SCs) ensure the development of the different tissues during morphogenesis, their physiological turnover during adult life and tissue repair after injuries. .
Our lab has recently developed new methods to study by lineage tracing the cellular hierarchy that sustains homeostasis and repair of the epidermis and to identify distinct populations of SCs and progenitors ensuring mammary gland and prostate postnatal development.
While quantitative clonal analysis combined with mathematical modeling has been used recently to decipher the cellular basis of tissue homeostasis, such experimental approaches have never been used so far in mammals to investigate the cellular hierarchy acting during tissue expansion such as postnatal development and tissue repair.
In this project, we will use a multi-disciplinary approach combining mouse genetic lineage tracing and clonal analysis, mathematical modeling, proliferation kinetics, transcriptional profiling, and functional experiments to investigate the cellular and molecular mechanisms regulating tissue expansion during epithelial development and tissue repair and how the fate of these cells is controlled during this process.
1. We will define the clonal and proliferation dynamics of tissue expansion in the epidermis, the mammary gland and the prostate during postnatal growth and adult tissue regeneration.
2. We will define the clonal and proliferation dynamics of tissue expansion in the adult epidermis following wounding and mechanical force mediated tissue expansion.
3. We will define the mechanisms that regulate the switch from multipotent to unipotent cell fate during development of glandular epithelia.
Defining the cellular and molecular mechanisms underlying tissue growth and expansion during development and how these mechanisms differ from tissue regeneration in adult may have important implications for understanding the causes of certain developmental defects and for regenerative medicine.
Summary
Stem cells (SCs) ensure the development of the different tissues during morphogenesis, their physiological turnover during adult life and tissue repair after injuries. .
Our lab has recently developed new methods to study by lineage tracing the cellular hierarchy that sustains homeostasis and repair of the epidermis and to identify distinct populations of SCs and progenitors ensuring mammary gland and prostate postnatal development.
While quantitative clonal analysis combined with mathematical modeling has been used recently to decipher the cellular basis of tissue homeostasis, such experimental approaches have never been used so far in mammals to investigate the cellular hierarchy acting during tissue expansion such as postnatal development and tissue repair.
In this project, we will use a multi-disciplinary approach combining mouse genetic lineage tracing and clonal analysis, mathematical modeling, proliferation kinetics, transcriptional profiling, and functional experiments to investigate the cellular and molecular mechanisms regulating tissue expansion during epithelial development and tissue repair and how the fate of these cells is controlled during this process.
1. We will define the clonal and proliferation dynamics of tissue expansion in the epidermis, the mammary gland and the prostate during postnatal growth and adult tissue regeneration.
2. We will define the clonal and proliferation dynamics of tissue expansion in the adult epidermis following wounding and mechanical force mediated tissue expansion.
3. We will define the mechanisms that regulate the switch from multipotent to unipotent cell fate during development of glandular epithelia.
Defining the cellular and molecular mechanisms underlying tissue growth and expansion during development and how these mechanisms differ from tissue regeneration in adult may have important implications for understanding the causes of certain developmental defects and for regenerative medicine.
Max ERC Funding
2 400 000 €
Duration
Start date: 2014-06-01, End date: 2019-05-31
Project acronym PyroPop
Project Mechanisms and regulation of inflammasome-associated programmed cell death
Researcher (PI) Mohamed Lamkanfi
Host Institution (HI) JANSSEN PHARMACEUTICA NV
Call Details Consolidator Grant (CoG), LS3, ERC-2015-CoG
Summary Programmed cell death is essential for homeostasis, and its deregulation contributes to human disease. Inflammasome-induced pyroptosis of infected macrophages contributes to host defense against infections, but the concomitant release of inflammatory danger signals and leaderless cytokines is detrimental in chronic inflammatory diseases. The central hypothesis of the PyroPop ERC Consolidator project is that inflammasomes are cytosolic platforms that couple pathogen sensing to multiple programmed cell death modes. This is based on our preliminary data showing that inflammasomes can be triggered to switch from inflammatory pyroptosis to programmed necrosis and non-inflammatory apoptosis. This suggests that the (patho)physiological outcomes of inflammasome activation may be modulated for therapeutic purposes. However, the molecular machinery and effector mechanisms of pyroptosis, inflammasome-induced apoptosis and programmed necrosis are virtually unknown. My objectives are (i) to explore the cleavage events and subcellular dynamics of pyroptosis by proteomics and high-resolution time-lapse microscopy; (ii) to clarify the molecular mechanisms of pyroptosis and inflammasome-controlled cell death switching; and (iii) to address how inflammasome-associated cell death modes impact on anti-bacterial host defense and chronic inflammatory pathology in vivo through the identification of pyroptosis-selective biomarkers and clinical analysis of pyroptosis-deficient mouse models. The central hypothesis in this regard is that inflammasome-mediated secretion of leaderless cytokines (such as IL-1β and IL-18) and danger signals may be mechanistically coupled to pyroptosis, but not apoptosis induction. By clarifying the mechanisms of inflammasome-controlled programmed cell death, this project may set the path for the development of an entirely novel class of inflammation-modulating therapies that are based on converting inflammatory pyroptosis into non-inflammatory apoptosis.
Summary
Programmed cell death is essential for homeostasis, and its deregulation contributes to human disease. Inflammasome-induced pyroptosis of infected macrophages contributes to host defense against infections, but the concomitant release of inflammatory danger signals and leaderless cytokines is detrimental in chronic inflammatory diseases. The central hypothesis of the PyroPop ERC Consolidator project is that inflammasomes are cytosolic platforms that couple pathogen sensing to multiple programmed cell death modes. This is based on our preliminary data showing that inflammasomes can be triggered to switch from inflammatory pyroptosis to programmed necrosis and non-inflammatory apoptosis. This suggests that the (patho)physiological outcomes of inflammasome activation may be modulated for therapeutic purposes. However, the molecular machinery and effector mechanisms of pyroptosis, inflammasome-induced apoptosis and programmed necrosis are virtually unknown. My objectives are (i) to explore the cleavage events and subcellular dynamics of pyroptosis by proteomics and high-resolution time-lapse microscopy; (ii) to clarify the molecular mechanisms of pyroptosis and inflammasome-controlled cell death switching; and (iii) to address how inflammasome-associated cell death modes impact on anti-bacterial host defense and chronic inflammatory pathology in vivo through the identification of pyroptosis-selective biomarkers and clinical analysis of pyroptosis-deficient mouse models. The central hypothesis in this regard is that inflammasome-mediated secretion of leaderless cytokines (such as IL-1β and IL-18) and danger signals may be mechanistically coupled to pyroptosis, but not apoptosis induction. By clarifying the mechanisms of inflammasome-controlled programmed cell death, this project may set the path for the development of an entirely novel class of inflammation-modulating therapies that are based on converting inflammatory pyroptosis into non-inflammatory apoptosis.
Max ERC Funding
1 997 915 €
Duration
Start date: 2017-01-01, End date: 2021-12-31
Project acronym T-Rex
Project Clathrin-mediated endocytosis in plants: mechanistic insight into the TPLATE REcycling compleX and its interplay with AP-2
Researcher (PI) Daniel Joseph G Van Damme
Host Institution (HI) VIB
Call Details Consolidator Grant (CoG), LS3, ERC-2015-CoG
Summary Cells communicate with the outside world through proteins anchored in their plasma membrane and hereto constantly adjust their plasma membrane (PM) proteome. In this adjustment process, removing proteins from the PM mainly occurs through clathrin-mediated endocytosis (CME). Mechanistically however, this process remains poorly understood in plants.
A recent study from my group has shown that, in contrast to other model systems, plant CME involves two early endocytic adaptor protein complexes: the evolutionary conserved Adaptor Protein 2 complex (AP-2) and the newly identified TPLATE complex (TPC). In the same study, we also show that both complexes have overlapping but also independent functions in driving CME in plants, implying that plants use additional ways to recognize membrane proteins (cargo) for internalization.
In this project I will use an integrative approach to unravel the early steps of CME in plants. Specifically, I will address the following biological questions:
- Is the evolutionary retention of the TPC in plants causal to specific cargo recognition? (WP1)
- What are the spatio-temporal dynamics of TPC and CME effectors at the plasma membrane? (WP2)
- How does acute removal of TPC subunits affect complex recruitment and CME? (WP3)
- How is the TPC organized at the structural level? (WP4)
- Which interactions occur and can we couple subunit/domain structures to functionality? (WP5)
To answer these questions, I will combine state-of-the art proteomics with highly dynamic multi-color live cell imaging and structural biology.
The overall objective is to gain a deep mechanistic insight into the developmentally essential process of CME in plants. This will enable me to specifically specifically modulate the abundance of plasma membrane proteins involved in nutrient uptake, toxin avoidance, cell wall formation and hormone and defence responses. Understanding TPC-dependent CME will also provide insight into evolutionary aspects of endocytosis.
Summary
Cells communicate with the outside world through proteins anchored in their plasma membrane and hereto constantly adjust their plasma membrane (PM) proteome. In this adjustment process, removing proteins from the PM mainly occurs through clathrin-mediated endocytosis (CME). Mechanistically however, this process remains poorly understood in plants.
A recent study from my group has shown that, in contrast to other model systems, plant CME involves two early endocytic adaptor protein complexes: the evolutionary conserved Adaptor Protein 2 complex (AP-2) and the newly identified TPLATE complex (TPC). In the same study, we also show that both complexes have overlapping but also independent functions in driving CME in plants, implying that plants use additional ways to recognize membrane proteins (cargo) for internalization.
In this project I will use an integrative approach to unravel the early steps of CME in plants. Specifically, I will address the following biological questions:
- Is the evolutionary retention of the TPC in plants causal to specific cargo recognition? (WP1)
- What are the spatio-temporal dynamics of TPC and CME effectors at the plasma membrane? (WP2)
- How does acute removal of TPC subunits affect complex recruitment and CME? (WP3)
- How is the TPC organized at the structural level? (WP4)
- Which interactions occur and can we couple subunit/domain structures to functionality? (WP5)
To answer these questions, I will combine state-of-the art proteomics with highly dynamic multi-color live cell imaging and structural biology.
The overall objective is to gain a deep mechanistic insight into the developmentally essential process of CME in plants. This will enable me to specifically specifically modulate the abundance of plasma membrane proteins involved in nutrient uptake, toxin avoidance, cell wall formation and hormone and defence responses. Understanding TPC-dependent CME will also provide insight into evolutionary aspects of endocytosis.
Max ERC Funding
1 998 813 €
Duration
Start date: 2016-07-01, End date: 2021-06-30
