Project acronym AsthmaVir
Project The roles of innate lymphoid cells and rhinovirus in asthma exacerbations
Researcher (PI) Hergen Spits
Host Institution (HI) ACADEMISCH MEDISCH CENTRUM BIJ DE UNIVERSITEIT VAN AMSTERDAM
Call Details Advanced Grant (AdG), LS6, ERC-2013-ADG
Summary Asthma exacerbations represent a high unmet medical need in particular in young children. Human Rhinoviruses (HRV) are the main triggers of these exacerbations. Till now Th2 cells were considered the main initiating effector cell type in asthma in general and asthma exacerbations in particular. However, exaggerated Th2 cell activities alone do not explain all aspects of asthma and exacerbations. Building on our recent discovery of type 2 human innate lymphoid cells (ILC2) capable of promptly producing high amounts of IL-5, IL-9 and IL-13 upon activation and on mouse data pointing to an essential role of these cells in asthma and asthma exacerbations, ILC2 may be the main initiating cells in asthma exacerbations in humans. Thus we hypothesize that HRV directly or indirectly stimulate ILC2s to produce cytokines driving the effector functions leading to the end organ effects that characterize this debilitating disease. Targeting ILC2 and HRV in parallel will provide a highly attractive therapeutic option for the treatment of asthma exacerbations. In depth study of the mechanisms of ILC2 differentiation and function will lead to the design effective drugs targeting these cells; thus the first two objectives of this project are: 1) To unravel the lineage relationship of ILC populations and to decipher the signal transduction pathways that regulate the function of ILCs, 2) to test the functions of lung-residing human ILCs and the effects of compounds that affect these functions in mice which harbour a human immune system and human lung epithelium under homeostatic conditions and after infections with respiratory viruses. The third objective of this project is developing reagents that target HRV; to this end we will develop broadly reacting highly neutralizing human monoclonal antibodies that can be used for prophylaxis and therapy of patients at high risk for developing severe asthma exacerbations.
Summary
Asthma exacerbations represent a high unmet medical need in particular in young children. Human Rhinoviruses (HRV) are the main triggers of these exacerbations. Till now Th2 cells were considered the main initiating effector cell type in asthma in general and asthma exacerbations in particular. However, exaggerated Th2 cell activities alone do not explain all aspects of asthma and exacerbations. Building on our recent discovery of type 2 human innate lymphoid cells (ILC2) capable of promptly producing high amounts of IL-5, IL-9 and IL-13 upon activation and on mouse data pointing to an essential role of these cells in asthma and asthma exacerbations, ILC2 may be the main initiating cells in asthma exacerbations in humans. Thus we hypothesize that HRV directly or indirectly stimulate ILC2s to produce cytokines driving the effector functions leading to the end organ effects that characterize this debilitating disease. Targeting ILC2 and HRV in parallel will provide a highly attractive therapeutic option for the treatment of asthma exacerbations. In depth study of the mechanisms of ILC2 differentiation and function will lead to the design effective drugs targeting these cells; thus the first two objectives of this project are: 1) To unravel the lineage relationship of ILC populations and to decipher the signal transduction pathways that regulate the function of ILCs, 2) to test the functions of lung-residing human ILCs and the effects of compounds that affect these functions in mice which harbour a human immune system and human lung epithelium under homeostatic conditions and after infections with respiratory viruses. The third objective of this project is developing reagents that target HRV; to this end we will develop broadly reacting highly neutralizing human monoclonal antibodies that can be used for prophylaxis and therapy of patients at high risk for developing severe asthma exacerbations.
Max ERC Funding
2 499 593 €
Duration
Start date: 2014-03-01, End date: 2019-02-28
Project acronym BABYLON
Project By the Rivers of Babylon: New Perspectives on Second Temple Judaism from Cuneiform Texts
Researcher (PI) Caroline Waerzeggers
Host Institution (HI) UNIVERSITEIT LEIDEN
Call Details Starting Grant (StG), SH6, ERC-2009-StG
Summary This project has the potential to radically change current understanding of cultic and social transformation in the post-exilic temple community of Jerusalem (c. 6th-4th centuries BCE), an important formative phase of ancient Judaism. “BABYLON” draws on recent, ground-breaking advances in the study of cuneiform texts to illuminate the Babylonian environment of the Judean exile, the socio-historical context which gave rise to the transformative era in Second Temple Judaism. In particular, these new data show that the parallels between Babylonian and post-exilic forms of cultic and social organization were substantially more far-reaching than presently recognized in Biblical scholarship. “BABYLON” will study the extent of these similarities and explore the question how Babylonian models could have influenced the restoration effort in Jerusalem.
This goal will be achieved through four sub-projects. P1 will study the social dynamics and intellectual universe of the Babylonian priesthood. P2 will finalize the publication of cuneiform archives of Babylonian priests living in the time of the exile. P3 will identify the exact areas of change in the post-exilic temple community of Jerusalem. P4, the synthesis, will draw from each of these sub-projects to present a comparative study of the Second Temple and contemporary Babylonian models of cultic and social organization, and to propose a strategy of research into the possible routes of transmission between Babylonia and Jerusalem.
The research will be carried out by three team members: the PI (P1 and P4), a PhD in Assyriology (P2) and a post-doctoral researcher in Biblical Studies specialized in the Second Temple period (P3 and P4). The participation of the wider academic community will be invited at two moments in the course of the project, in the form of a workshop and an international conference.
“BABYLON” will adopt an interdisciplinary approach by bringing together Assyriologists and Biblical scholars for a much-needed dialogue, thereby exploding the artificial boundaries that currently exist in the academic landscape between these two fields.
Summary
This project has the potential to radically change current understanding of cultic and social transformation in the post-exilic temple community of Jerusalem (c. 6th-4th centuries BCE), an important formative phase of ancient Judaism. “BABYLON” draws on recent, ground-breaking advances in the study of cuneiform texts to illuminate the Babylonian environment of the Judean exile, the socio-historical context which gave rise to the transformative era in Second Temple Judaism. In particular, these new data show that the parallels between Babylonian and post-exilic forms of cultic and social organization were substantially more far-reaching than presently recognized in Biblical scholarship. “BABYLON” will study the extent of these similarities and explore the question how Babylonian models could have influenced the restoration effort in Jerusalem.
This goal will be achieved through four sub-projects. P1 will study the social dynamics and intellectual universe of the Babylonian priesthood. P2 will finalize the publication of cuneiform archives of Babylonian priests living in the time of the exile. P3 will identify the exact areas of change in the post-exilic temple community of Jerusalem. P4, the synthesis, will draw from each of these sub-projects to present a comparative study of the Second Temple and contemporary Babylonian models of cultic and social organization, and to propose a strategy of research into the possible routes of transmission between Babylonia and Jerusalem.
The research will be carried out by three team members: the PI (P1 and P4), a PhD in Assyriology (P2) and a post-doctoral researcher in Biblical Studies specialized in the Second Temple period (P3 and P4). The participation of the wider academic community will be invited at two moments in the course of the project, in the form of a workshop and an international conference.
“BABYLON” will adopt an interdisciplinary approach by bringing together Assyriologists and Biblical scholars for a much-needed dialogue, thereby exploding the artificial boundaries that currently exist in the academic landscape between these two fields.
Max ERC Funding
1 200 000 €
Duration
Start date: 2009-09-01, End date: 2015-08-31
Project acronym CHINESE EMPIRE
Project China and the Historical Sociology of Empire
Researcher (PI) Hilde Godelieve Dominique Ghislena De Weerdt
Host Institution (HI) UNIVERSITEIT LEIDEN
Call Details Starting Grant (StG), SH6, ERC-2011-StG_20101124
Summary This project revisits a major question in world history: how can we explain the continuity of the Chinese Empire. Moving beyond the comparison of early world empires (China and Rome) to explain the different courses Chinese and European history have taken, this project aims to assess the importance of political communication in the maintenance of empire in the last millennium. The core questions are twofold: 1) How can the continuity of empire in the Chinese case be best explained? 2) Does the nature and extent of political communication networks, measured through the frequency and multiplexity of information exchange ties, play a critical role in the reconstitution and maintenance of empire? Its methodology is based on the conviction that an investigation of the nature and extent of political communication in imperial Chinese society should include a systematic quantitative and qualitative analysis of the rich commentary on current affairs in correspondence and notebooks. By combining multi-faceted digital analyses of relatively large corpora of texts with an intellectually ambitious research agenda, this project will both radically transform our understanding of the history of Chinese political culture and inspire wide-ranging methodological innovation across the humanities.
Summary
This project revisits a major question in world history: how can we explain the continuity of the Chinese Empire. Moving beyond the comparison of early world empires (China and Rome) to explain the different courses Chinese and European history have taken, this project aims to assess the importance of political communication in the maintenance of empire in the last millennium. The core questions are twofold: 1) How can the continuity of empire in the Chinese case be best explained? 2) Does the nature and extent of political communication networks, measured through the frequency and multiplexity of information exchange ties, play a critical role in the reconstitution and maintenance of empire? Its methodology is based on the conviction that an investigation of the nature and extent of political communication in imperial Chinese society should include a systematic quantitative and qualitative analysis of the rich commentary on current affairs in correspondence and notebooks. By combining multi-faceted digital analyses of relatively large corpora of texts with an intellectually ambitious research agenda, this project will both radically transform our understanding of the history of Chinese political culture and inspire wide-ranging methodological innovation across the humanities.
Max ERC Funding
1 432 797 €
Duration
Start date: 2012-04-01, End date: 2017-08-31
Project acronym CIRCUMVENT
Project Closing in on Runx3 and CXCL4 to open novel avenues for therapeutic intervention in systemic sclerosis
Researcher (PI) Timothy Radstake
Host Institution (HI) UNIVERSITAIR MEDISCH CENTRUM UTRECHT
Call Details Starting Grant (StG), LS6, ERC-2011-StG_20101109
Summary Systemic sclerosis (SSc) is an autoimmune disease that culminates in excessive extra-cellular matrix deposition (fibrosis) in skin and internal organs. SSc is a severe disease in which fibrotic events lead to organ failure such as renal failure, deterioration of lung function and development of pulmonary arterial hypertension (PAH). Together, these disease hallmarks culminate in profound disability and premature death.
Over the past three years several crucial observations by my group changed the landscape of our thinking about the ethiopathogenesis of this disease. First, plasmacytoid dendritic (pDCs) cells were found to be extremely frequent in the circulation of SSc patients (1000-fold) compared with healthy individuals. In addition, we observed that pDCs from SSc patients are largely dedicated to synthesize CXCL4 that was proven to be directly implicated in fibroblast biology and endothelial cell activation, two events recapitulating SSc. Finally, research aimed to decipher the underlying cause of this increased pDCs frequency led to the observation that Runx3, a transcription factor that controls the differentiation of DC subsets, was almost not expressed in pDC of SSc patients. Together, these observations led me to pose the “SSc immune postulate” in which the pathogenesis of SSc is explained by a multi-step process in which Runx3 and CXCL4 play a central role.
The project CIRCUMVENT is designed to provide proof of concept for the role of CXCL4 and RUNX3 in SSc. For this aim we will exploit a unique set of patient material (cell subsets, protein and DNA bank), various recently developed in vitro techniques (siRNA for pDCs, viral over expression of CXCL4/RUNX3) and apply three recently optimised experimental models (CXCL4 subcutaneous pump model, DC specific RUNX3 KO and the SCID/NOD/rag2 KO mice).
The project CIRCUMVENT aims to proof the direct role for Runx3 and CXCL4 that could provide the final step towards the development of novel therapeutic targets
Summary
Systemic sclerosis (SSc) is an autoimmune disease that culminates in excessive extra-cellular matrix deposition (fibrosis) in skin and internal organs. SSc is a severe disease in which fibrotic events lead to organ failure such as renal failure, deterioration of lung function and development of pulmonary arterial hypertension (PAH). Together, these disease hallmarks culminate in profound disability and premature death.
Over the past three years several crucial observations by my group changed the landscape of our thinking about the ethiopathogenesis of this disease. First, plasmacytoid dendritic (pDCs) cells were found to be extremely frequent in the circulation of SSc patients (1000-fold) compared with healthy individuals. In addition, we observed that pDCs from SSc patients are largely dedicated to synthesize CXCL4 that was proven to be directly implicated in fibroblast biology and endothelial cell activation, two events recapitulating SSc. Finally, research aimed to decipher the underlying cause of this increased pDCs frequency led to the observation that Runx3, a transcription factor that controls the differentiation of DC subsets, was almost not expressed in pDC of SSc patients. Together, these observations led me to pose the “SSc immune postulate” in which the pathogenesis of SSc is explained by a multi-step process in which Runx3 and CXCL4 play a central role.
The project CIRCUMVENT is designed to provide proof of concept for the role of CXCL4 and RUNX3 in SSc. For this aim we will exploit a unique set of patient material (cell subsets, protein and DNA bank), various recently developed in vitro techniques (siRNA for pDCs, viral over expression of CXCL4/RUNX3) and apply three recently optimised experimental models (CXCL4 subcutaneous pump model, DC specific RUNX3 KO and the SCID/NOD/rag2 KO mice).
The project CIRCUMVENT aims to proof the direct role for Runx3 and CXCL4 that could provide the final step towards the development of novel therapeutic targets
Max ERC Funding
1 500 000 €
Duration
Start date: 2012-08-01, End date: 2017-07-31
Project acronym CONSOLIDATING EMPIRE
Project Consolidating Empire: Reconstructing Hegemonic Practices of the Middle Assyrian Empire at the Late Bronze Age Fortified Estate of Tell Sabi Abyad, Syria, ca. 1230 – 1180 BC
Researcher (PI) Bleda Serge During
Host Institution (HI) UNIVERSITEIT LEIDEN
Call Details Starting Grant (StG), SH6, ERC-2011-StG_20101124
Summary The origins of imperialism, a socio-military system in which hegemony is achieved over alien territories, are poorly investigated. This applies in particular to how imperial strategies affected local communities. This project will investigate the hegemonic practices of one of the earliest stable empires: that of the Assyrians, by focussing on the Late Bronze Age fortified estate at Tell Sabi Abyad, ca. 1230-1180 BC.
The Assyrians created a network of strongholds in conquered territories to consolidate their hegemony. The fortified estate at Tell Sabi Abyad is the only extensively investigated of these Assyrian settlements. This settlement is both small and well preserved and has been completely excavated. The complete plan facilitates a study of the spatial properties of this fortress and how it structured interactions. Further, the estate contained a wealth of in situ finds, which allow for a reconstruction of activity patterns in the settlement. Finally, over 400 cuneiform tablets were found which shed light on the local social and economic situation and the broader imperial context.
This project will provide a bottom up perspective on the Assyrian Empire. Elements of the Tell Sabi Abyad estate that will be investigated include: spatial characteristics; activity areas; the agricultural economy; and the surrounding landscape. Further, data from the Middle Assyrian Empire at large will be reconsidered, in order to achieve a better understanding of how this empire was constituted. This project is innovative because: it investigates a spatial continuum ranging from room to empire; brings together types of data usually investigated in isolation, such as texts and artifacts; will involve the use of novel techniques; and will investigate the short term normally beyond the scope of archaeology. The research will contribute to the cross-cultural issue of how hegemonic control is achieved in alien territories, and add to our understanding of early empires.
Summary
The origins of imperialism, a socio-military system in which hegemony is achieved over alien territories, are poorly investigated. This applies in particular to how imperial strategies affected local communities. This project will investigate the hegemonic practices of one of the earliest stable empires: that of the Assyrians, by focussing on the Late Bronze Age fortified estate at Tell Sabi Abyad, ca. 1230-1180 BC.
The Assyrians created a network of strongholds in conquered territories to consolidate their hegemony. The fortified estate at Tell Sabi Abyad is the only extensively investigated of these Assyrian settlements. This settlement is both small and well preserved and has been completely excavated. The complete plan facilitates a study of the spatial properties of this fortress and how it structured interactions. Further, the estate contained a wealth of in situ finds, which allow for a reconstruction of activity patterns in the settlement. Finally, over 400 cuneiform tablets were found which shed light on the local social and economic situation and the broader imperial context.
This project will provide a bottom up perspective on the Assyrian Empire. Elements of the Tell Sabi Abyad estate that will be investigated include: spatial characteristics; activity areas; the agricultural economy; and the surrounding landscape. Further, data from the Middle Assyrian Empire at large will be reconsidered, in order to achieve a better understanding of how this empire was constituted. This project is innovative because: it investigates a spatial continuum ranging from room to empire; brings together types of data usually investigated in isolation, such as texts and artifacts; will involve the use of novel techniques; and will investigate the short term normally beyond the scope of archaeology. The research will contribute to the cross-cultural issue of how hegemonic control is achieved in alien territories, and add to our understanding of early empires.
Max ERC Funding
1 191 127 €
Duration
Start date: 2012-01-01, End date: 2015-12-31
Project acronym COORDINATINGforLIFE
Project Coordinating for life. Success and failure of Western European societies in coping with rural hazards and disasters, 1300-1800
Researcher (PI) Balthassar Jozef Paul (Bas) Van Bavel
Host Institution (HI) UNIVERSITEIT UTRECHT
Call Details Advanced Grant (AdG), SH6, ERC-2013-ADG
Summary Societies in past and present are regularly confronted with major hazards, which sometimes have disastrous effects. Some societies are successful in preventing these effects and buffering threats, or they recover quickly, while others prove highly vulnerable. Why is this?
Increasingly it is clear that disasters are not merely natural events, and also that wealth and technology alone are not adequate to prevent them. Rather, hazards and disasters are social occurrences as well, and they form a tough test for the organizational capacities of a society, both in mitigation and recovery. This project targets a main element of this capacity, namely: the way societies have organized the exchange, allocation and use of resources. It aims to explain why some societies do well in preventing or remedying disasters through these institutional arrangements and others not.
In order to do so, this project analyses four key variables: the mix of coordination systems available within that society, its degree of autarky, economic equity and political equality. The recent literature on historical and present-day disasters suggests these factors as possible causes of success or failure of institutional arrangements in their confrontation with hazards, but their discussion remains largely descriptive and they have never been systematically analyzed.
This research project offers such a systematic investigation, using rural societies in Western Europe in the period 1300-1800 - with their variety of socio-economic characteristics - as a testing ground. The historical perspective enables us to compare widely differing cases, also over the long run, and to test for the variables chosen, in order to isolate the determining factors in the resilience of different societies. By using the opportunities offered by history in this way, we will increase our insight into the relative performance of societies and gain a better understanding of a critical determinant of human wellbeing.
Summary
Societies in past and present are regularly confronted with major hazards, which sometimes have disastrous effects. Some societies are successful in preventing these effects and buffering threats, or they recover quickly, while others prove highly vulnerable. Why is this?
Increasingly it is clear that disasters are not merely natural events, and also that wealth and technology alone are not adequate to prevent them. Rather, hazards and disasters are social occurrences as well, and they form a tough test for the organizational capacities of a society, both in mitigation and recovery. This project targets a main element of this capacity, namely: the way societies have organized the exchange, allocation and use of resources. It aims to explain why some societies do well in preventing or remedying disasters through these institutional arrangements and others not.
In order to do so, this project analyses four key variables: the mix of coordination systems available within that society, its degree of autarky, economic equity and political equality. The recent literature on historical and present-day disasters suggests these factors as possible causes of success or failure of institutional arrangements in their confrontation with hazards, but their discussion remains largely descriptive and they have never been systematically analyzed.
This research project offers such a systematic investigation, using rural societies in Western Europe in the period 1300-1800 - with their variety of socio-economic characteristics - as a testing ground. The historical perspective enables us to compare widely differing cases, also over the long run, and to test for the variables chosen, in order to isolate the determining factors in the resilience of different societies. By using the opportunities offered by history in this way, we will increase our insight into the relative performance of societies and gain a better understanding of a critical determinant of human wellbeing.
Max ERC Funding
2 227 326 €
Duration
Start date: 2014-03-01, End date: 2019-02-28
Project acronym InflaMet
Project Mechanistic insights into the impact of tumor-associated neutrophils on metastatic breast cancer
Researcher (PI) Karina Elizabeth De Visser
Host Institution (HI) STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Call Details Consolidator Grant (CoG), LS6, ERC-2013-CoG
Summary Metastatic disease is still largely unexplored, poorly understood and incurable. Accumulating evidence indicates that cells and mediators of the immune system can facilitate metastasis. Neutrophil accumulation in cancer patients has been associated with metastasis formation. In mouse tumor models, neutrophils have been reported to be pro- or anti- metastatic, but the underlying mechanisms involved in either function remain largely elusive. This proposal outlines a research program aimed at resolving the pro-metastatic role of neutrophils in breast cancer, as our preliminary data indicate that neutrophils proactively mediate breast cancer metastasis. Using a state-of-the art spontaneous breast cancer metastasis mouse model, we will mechanistically study how neutrophils facilitate metastasis formation and how mammary tumors provoke the metastasis-facilitating function of neutrophils. Building upon my previous studies and our current data, we will focus on the unexplored crosstalk between the adaptive immune system and neutrophils in facilitating spontaneous metastatic disease. These crucial questions will be addressed by undertaking a multidisciplinary approach, involving sophisticated mouse models for metastatic breast cancer, RNA sequencing on tumor-associated neutrophil populations, state-of-the-art mouse engineering, intravital imaging and in vivo neutrophil manipulations. Moreover, we will validate our findings from the mouse metastasis model in human breast cancer samples. We will determine the metastasis predicting power of the identified murine pro-metastatic neutrophil-specific pathways by immunohistochemistry and multi-parameter immunofluorescence on breast cancer samples and blood of untreated patients of which clinical follow-up is available. Thus, we will identify novel molecular pathways that can be targeted to selectively inhibit the pro-metastatic activity of the immune system.
Summary
Metastatic disease is still largely unexplored, poorly understood and incurable. Accumulating evidence indicates that cells and mediators of the immune system can facilitate metastasis. Neutrophil accumulation in cancer patients has been associated with metastasis formation. In mouse tumor models, neutrophils have been reported to be pro- or anti- metastatic, but the underlying mechanisms involved in either function remain largely elusive. This proposal outlines a research program aimed at resolving the pro-metastatic role of neutrophils in breast cancer, as our preliminary data indicate that neutrophils proactively mediate breast cancer metastasis. Using a state-of-the art spontaneous breast cancer metastasis mouse model, we will mechanistically study how neutrophils facilitate metastasis formation and how mammary tumors provoke the metastasis-facilitating function of neutrophils. Building upon my previous studies and our current data, we will focus on the unexplored crosstalk between the adaptive immune system and neutrophils in facilitating spontaneous metastatic disease. These crucial questions will be addressed by undertaking a multidisciplinary approach, involving sophisticated mouse models for metastatic breast cancer, RNA sequencing on tumor-associated neutrophil populations, state-of-the-art mouse engineering, intravital imaging and in vivo neutrophil manipulations. Moreover, we will validate our findings from the mouse metastasis model in human breast cancer samples. We will determine the metastasis predicting power of the identified murine pro-metastatic neutrophil-specific pathways by immunohistochemistry and multi-parameter immunofluorescence on breast cancer samples and blood of untreated patients of which clinical follow-up is available. Thus, we will identify novel molecular pathways that can be targeted to selectively inhibit the pro-metastatic activity of the immune system.
Max ERC Funding
1 999 360 €
Duration
Start date: 2014-03-01, End date: 2019-02-28
Project acronym INTERCOM
Project Communication between immune cells via release of RNA-carrying vesicles: Lessons from viruses
Researcher (PI) Esther Neline Marielle Nolte
Host Institution (HI) UNIVERSITEIT UTRECHT
Call Details Starting Grant (StG), LS6, ERC-2013-StG
Summary "Communication between immune cells is crucial for regulating the magnitude and quality of immune responses. A newly uncovered means of intercellular communication involves transfer of small cell-derived vesicles. I recently discovered that vesicles released by immune cells are enriched for small noncoding RNAs, which may act as regulatory RNAs that can influence gene expression in vesicle-targeted cells. Furthermore, remarkable parallels emerged between RNAs abundantly present in cell-derived vesicles and a group of host RNAs specifically incorporated into retroviruses. These shared RNAs may underlie the formation or function of both cell-derived vesicles and retroviruses. Until now, mechanisms behind selective incorporation of small RNAs into cell-derived vesicles and their function in vesicle-targeted cells are poorly understood.
Aim of INTERCOM: To resolve how the exchange of small RNAs via cell-derived vesicles contributes to intercellular communication between immune cells. Key objectives: 1. To determine the diversity and plasticity of the RNA content of vesicle subpopulations released by immune cells. 2. To explain functional differences between immune cell vesicle populations based on their RNA contents. 3. To determine the function of structural RNAs shared by immune cell-derived vesicles and retroviruses.
Tools in virology research will be used in combination with several high-end technologies, which were uniquely adapted in my lab for vesicle-related research. These include a high-resolution flow cytometric method suited to analyze individual nano-sized vesicles, RNA deep sequencing with previously developed data analysis methods, and super-resolution microscopic imaging.
The proposed work advances our understanding of communication processes in the immune system. This knowledge can be applied in defining vesicle RNA-based biomarkers for immune-related diseases and in designing genetically engineered cell-derived vesicles for therapeutic application."
Summary
"Communication between immune cells is crucial for regulating the magnitude and quality of immune responses. A newly uncovered means of intercellular communication involves transfer of small cell-derived vesicles. I recently discovered that vesicles released by immune cells are enriched for small noncoding RNAs, which may act as regulatory RNAs that can influence gene expression in vesicle-targeted cells. Furthermore, remarkable parallels emerged between RNAs abundantly present in cell-derived vesicles and a group of host RNAs specifically incorporated into retroviruses. These shared RNAs may underlie the formation or function of both cell-derived vesicles and retroviruses. Until now, mechanisms behind selective incorporation of small RNAs into cell-derived vesicles and their function in vesicle-targeted cells are poorly understood.
Aim of INTERCOM: To resolve how the exchange of small RNAs via cell-derived vesicles contributes to intercellular communication between immune cells. Key objectives: 1. To determine the diversity and plasticity of the RNA content of vesicle subpopulations released by immune cells. 2. To explain functional differences between immune cell vesicle populations based on their RNA contents. 3. To determine the function of structural RNAs shared by immune cell-derived vesicles and retroviruses.
Tools in virology research will be used in combination with several high-end technologies, which were uniquely adapted in my lab for vesicle-related research. These include a high-resolution flow cytometric method suited to analyze individual nano-sized vesicles, RNA deep sequencing with previously developed data analysis methods, and super-resolution microscopic imaging.
The proposed work advances our understanding of communication processes in the immune system. This knowledge can be applied in defining vesicle RNA-based biomarkers for immune-related diseases and in designing genetically engineered cell-derived vesicles for therapeutic application."
Max ERC Funding
1 499 806 €
Duration
Start date: 2013-11-01, End date: 2018-10-31
Project acronym MHC CLASS II-OMICS
Project Towards understanding and manipulation of MHC class II antigen presentation
Researcher (PI) Jacobus Jozef Cornelis Neefjes
Host Institution (HI) STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Call Details Advanced Grant (AdG), LS6, ERC-2009-AdG
Summary MHC class II molecules are crucial for specific immune responses. In a complicated series of cell biological events, they catch a peptide in the endosomal route for presentation at the plasma membrane to the immune system. At present some 20 factors have been identified as involved in the process of MHC class II antigen presentation that are potential targets for manipulating these responses as MHC class II molecules are involved in most auto-immune diseases. Defining further targets for manipulating MHC class II responses would have implications for various disease states when these can be inhibited by chemical compounds or biologicals. We have performed a genome-wide FACS-based siRNA screen for molecules affecting MHC class II expression and peptide loading. After 100.000 individual 2-color FACS analyses, we identified 276 proteins that can be functionally sub-clustered for expression and for cell biological effects. We now propose to study the cell biology of these 276 hits to elucidate the molecular and cell biological mechanisms of MHC class II antigen presentation (the MHC class II-ome). As a first step, the 276 hits are sub-clustered for effects on MHC class II transcription or cell biology. These sub-clusters may correspond to networks. We propose to validate and extend these networks by experiments by a team of scientists concentrating on the various aspects of the cell biology of MHC class II antigen presentation. A parallel chemical compound screen will be performed to identify compounds affecting MHC class II antigen presentation. By cross-correlating the biological phenotypes of compounds with those of siRNA silencing, novel target-lead combinations will be defined by reciprocal chemical genetics. Our experiments should result in a global understanding of MHC class II antigen presentation. In addition, it should reveal target-lead combinations for manipulation of MHC class II antigen presentation in infection, auto-immune disease and transplantation.
Summary
MHC class II molecules are crucial for specific immune responses. In a complicated series of cell biological events, they catch a peptide in the endosomal route for presentation at the plasma membrane to the immune system. At present some 20 factors have been identified as involved in the process of MHC class II antigen presentation that are potential targets for manipulating these responses as MHC class II molecules are involved in most auto-immune diseases. Defining further targets for manipulating MHC class II responses would have implications for various disease states when these can be inhibited by chemical compounds or biologicals. We have performed a genome-wide FACS-based siRNA screen for molecules affecting MHC class II expression and peptide loading. After 100.000 individual 2-color FACS analyses, we identified 276 proteins that can be functionally sub-clustered for expression and for cell biological effects. We now propose to study the cell biology of these 276 hits to elucidate the molecular and cell biological mechanisms of MHC class II antigen presentation (the MHC class II-ome). As a first step, the 276 hits are sub-clustered for effects on MHC class II transcription or cell biology. These sub-clusters may correspond to networks. We propose to validate and extend these networks by experiments by a team of scientists concentrating on the various aspects of the cell biology of MHC class II antigen presentation. A parallel chemical compound screen will be performed to identify compounds affecting MHC class II antigen presentation. By cross-correlating the biological phenotypes of compounds with those of siRNA silencing, novel target-lead combinations will be defined by reciprocal chemical genetics. Our experiments should result in a global understanding of MHC class II antigen presentation. In addition, it should reveal target-lead combinations for manipulation of MHC class II antigen presentation in infection, auto-immune disease and transplantation.
Max ERC Funding
2 112 300 €
Duration
Start date: 2010-09-01, End date: 2015-08-31
Project acronym PneumoCell
Project Noise in gene expression as a determinant of virulence of the human pathogen Streptococcus pneumoniae
Researcher (PI) Jan-Willem Veening
Host Institution (HI) RIJKSUNIVERSITEIT GRONINGEN
Call Details Starting Grant (StG), LS6, ERC-2013-StG
Summary Not all cells in bacterial populations exhibit exactly the same phenotype, even though they grow in the same environment and are genetically identical. One of the main driving forces of phenotypic variation is stochasticity, or noise, in gene expression. Possible molecular origins contributing to noise in protein synthesis are stochastic fluctuations in the biochemical reactions of gene expression itself, namely transcription and translation.
The driving hypothesis of this application is that the human pathogen Streptococcus pneumoniae utilizes noisy gene expression to successfully colonize and invade its host. To test this supposition, the total amount of noise in key regulatory networks for virulence factor production will be quantified. Using natural and synthetic bistable switches as highly sensitive probes for noise, in combination with state-of-the-art single-cell imaging, microfluidics and direct transcriptome sequencing, the molecular mechanisms underlying noise generation in S. pneumoniae will be determined. By constructing strains with altered levels of phenotypic variation, the importance of noisy gene expression in S. pneumoniae pathogenesis will be tested.
S. pneumoniae is a leading cause of bacterial pneumoniae, meningitis, and sepsis worldwide. The molecular mechanisms that cause switching of S. pneumoniae to its virulent states are barely understood, although it becomes increasingly clear that noise-driven phenotypic variation plays an important role in pneumococcal pathogenesis. Therefore, understanding the molecular origins of phenotypic variation in S. pneumoniae might not only provide novel fundamental insights in gene expression, but also result in the identification of new anti-pneumococcal targets.
Summary
Not all cells in bacterial populations exhibit exactly the same phenotype, even though they grow in the same environment and are genetically identical. One of the main driving forces of phenotypic variation is stochasticity, or noise, in gene expression. Possible molecular origins contributing to noise in protein synthesis are stochastic fluctuations in the biochemical reactions of gene expression itself, namely transcription and translation.
The driving hypothesis of this application is that the human pathogen Streptococcus pneumoniae utilizes noisy gene expression to successfully colonize and invade its host. To test this supposition, the total amount of noise in key regulatory networks for virulence factor production will be quantified. Using natural and synthetic bistable switches as highly sensitive probes for noise, in combination with state-of-the-art single-cell imaging, microfluidics and direct transcriptome sequencing, the molecular mechanisms underlying noise generation in S. pneumoniae will be determined. By constructing strains with altered levels of phenotypic variation, the importance of noisy gene expression in S. pneumoniae pathogenesis will be tested.
S. pneumoniae is a leading cause of bacterial pneumoniae, meningitis, and sepsis worldwide. The molecular mechanisms that cause switching of S. pneumoniae to its virulent states are barely understood, although it becomes increasingly clear that noise-driven phenotypic variation plays an important role in pneumococcal pathogenesis. Therefore, understanding the molecular origins of phenotypic variation in S. pneumoniae might not only provide novel fundamental insights in gene expression, but also result in the identification of new anti-pneumococcal targets.
Max ERC Funding
1 498 846 €
Duration
Start date: 2013-11-01, End date: 2018-10-31