Project acronym BEEHIVE
Project Bridging the Evolution and Epidemiology of HIV in Europe
Researcher (PI) Christopher Fraser
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Country United Kingdom
Call Details Advanced Grant (AdG), LS2, ERC-2013-ADG
Summary The aim of the BEEHIVE project is to generate novel insight into HIV biology, evolution and epidemiology, leveraging next-generation high-throughput sequencing and bioinformatics to produce and analyse whole-genomes of viruses from approximately 3,000 European HIV-1 infected patients. These patients have known dates of infection spread over the last 25 years, good clinical follow up, and a wide range of clinical prognostic indicators and outcomes. The primary objective is to discover the viral genetic determinants of severity of infection and set-point viral load. This primary objective is high-risk & blue-skies: there is ample indirect evidence of polymorphisms that alter virulence, but they have never been identified, and it is not known how easy they are to discover. However, the project is also high-reward: it could lead to a substantial shift in the understanding of HIV disease.
Technologically, the BEEHIVE project will deliver new approaches for undertaking whole genome association studies on RNA viruses, including delivering an innovative high-throughput bioinformatics pipeline for handling genetically diverse viral quasi-species data (with viral diversity both within and between infected patients).
The project also includes secondary and tertiary objectives that address critical open questions in HIV epidemiology and evolution. The secondary objective is to use viral genetic sequences allied to mathematical epidemic models to better understand the resurgent European epidemic amongst high-risk groups, especially men who have sex with men. The aim will not just be to establish who is at risk of infection, which is known from conventional epidemiological approaches, but also to characterise the risk factors for onwards transmission of the virus. Tertiary objectives involve understanding the relationship between the genetic diversity within viral samples, indicative of on-going evolution or dual infections, to clinical outcomes.
Summary
The aim of the BEEHIVE project is to generate novel insight into HIV biology, evolution and epidemiology, leveraging next-generation high-throughput sequencing and bioinformatics to produce and analyse whole-genomes of viruses from approximately 3,000 European HIV-1 infected patients. These patients have known dates of infection spread over the last 25 years, good clinical follow up, and a wide range of clinical prognostic indicators and outcomes. The primary objective is to discover the viral genetic determinants of severity of infection and set-point viral load. This primary objective is high-risk & blue-skies: there is ample indirect evidence of polymorphisms that alter virulence, but they have never been identified, and it is not known how easy they are to discover. However, the project is also high-reward: it could lead to a substantial shift in the understanding of HIV disease.
Technologically, the BEEHIVE project will deliver new approaches for undertaking whole genome association studies on RNA viruses, including delivering an innovative high-throughput bioinformatics pipeline for handling genetically diverse viral quasi-species data (with viral diversity both within and between infected patients).
The project also includes secondary and tertiary objectives that address critical open questions in HIV epidemiology and evolution. The secondary objective is to use viral genetic sequences allied to mathematical epidemic models to better understand the resurgent European epidemic amongst high-risk groups, especially men who have sex with men. The aim will not just be to establish who is at risk of infection, which is known from conventional epidemiological approaches, but also to characterise the risk factors for onwards transmission of the virus. Tertiary objectives involve understanding the relationship between the genetic diversity within viral samples, indicative of on-going evolution or dual infections, to clinical outcomes.
Max ERC Funding
2 499 739 €
Duration
Start date: 2014-04-01, End date: 2019-03-31
Project acronym DEVOCHROMO
Project Chromosome structure and genome organization in early mammalian development
Researcher (PI) Peter Fraser
Host Institution (HI) THE BABRAHAM INSTITUTE
Country United Kingdom
Call Details Advanced Grant (AdG), LS2, ERC-2013-ADG
Summary "The spatial organization of the genome inside the cell nucleus is tissue-specific and has been linked to several nuclear processes including gene activation, gene silencing, genomic imprinting, gene co-regulation, genome maintenance, DNA replication, DNA repair, chromosomal translocations and X chromosome inactivation. In fact, just about any nuclear/genome function has a spatial component that has been implicated in its control. We know surprisingly little about chromosome conformation and spatial organization or how they are established. The extent to which they are a cause or consequence of genome functions are current topics of considerable debate, however emerging data from my group and many other groups world-wide indicate that nuclear location and organization are drivers of genome functions, which in cooperation with other features including epigenetic marks, non-coding RNAs and trans-factor binding bring about genome control. Thus, genome spatial organization can be considered on a par with other epigenetic features that together contribute to overall genome control. The classical paradigm of early mammalian development arguably represents the most dramatic and yet least understood process of genome reprogramming, where a single cell undergoes a series of divisions to ultimately give rise to the hundreds of different cell types found in a mature organism. Study of pre-implantation embryo development is hindered by the very nature of the life form, composed of extremely low cell numbers at each stage, which severely limits the options for investigation. My lab has recently developed a novel technique called single cell Hi-C, which has the power to detect tens of thousands of simultaneous chromatin contacts from a single cell. In this application I propose to apply this technology to study chromosome structure and genome organization during mouse pre-implantation development along with single cell transcriptome analyses from the same cells."
Summary
"The spatial organization of the genome inside the cell nucleus is tissue-specific and has been linked to several nuclear processes including gene activation, gene silencing, genomic imprinting, gene co-regulation, genome maintenance, DNA replication, DNA repair, chromosomal translocations and X chromosome inactivation. In fact, just about any nuclear/genome function has a spatial component that has been implicated in its control. We know surprisingly little about chromosome conformation and spatial organization or how they are established. The extent to which they are a cause or consequence of genome functions are current topics of considerable debate, however emerging data from my group and many other groups world-wide indicate that nuclear location and organization are drivers of genome functions, which in cooperation with other features including epigenetic marks, non-coding RNAs and trans-factor binding bring about genome control. Thus, genome spatial organization can be considered on a par with other epigenetic features that together contribute to overall genome control. The classical paradigm of early mammalian development arguably represents the most dramatic and yet least understood process of genome reprogramming, where a single cell undergoes a series of divisions to ultimately give rise to the hundreds of different cell types found in a mature organism. Study of pre-implantation embryo development is hindered by the very nature of the life form, composed of extremely low cell numbers at each stage, which severely limits the options for investigation. My lab has recently developed a novel technique called single cell Hi-C, which has the power to detect tens of thousands of simultaneous chromatin contacts from a single cell. In this application I propose to apply this technology to study chromosome structure and genome organization during mouse pre-implantation development along with single cell transcriptome analyses from the same cells."
Max ERC Funding
2 401 393 €
Duration
Start date: 2014-02-01, End date: 2019-01-31
Project acronym EMPSI
Project Receptors, Channels and Transporters:
Development and Application of Novel Technologies for Structure Determination
Researcher (PI) Christopher Gordon Tate
Host Institution (HI) MEDICAL RESEARCH COUNCIL
Country United Kingdom
Call Details Advanced Grant (AdG), LS1, ERC-2013-ADG
Summary Structure determination of G protein-coupled receptors (GPCRs) has been exceedingly successful over the last 5 years due to the development of complimentary generic methodologies that will now allow the structure determination of virtually any GPCR. However, these technologies address only two aspects of the process, namely the stability of the receptors during purification and the ability to form well-diffracting crystals. The strategies also apply only to GPCRs and not transporters or ion channels. The recent successes have been of GPCRs that are expressed in either yeasts or in insect cells using the baculovirus expression system, but many membrane proteins are expressed poorly in these systems or may be expressed in a misfolded non-functional form. A second issue with the future structure determination of GPCRs is the lack of generic technologies to allow the crystallisation of arrestin-GPCR and G protein-GPCR complexes. Although one G protein GPCR complex has been crystallised this was exceedingly diffciult and resulted in poor resolution of the GPCR component of the complex. We believe that it is possible to thermostabilise both arrestin and heterotrimeric G proteins, which will allow a simplified strategy for the crystallisation and structure determination of GPCR complexes. This is based on the development of the strategy of conformational thermostabilisation of GPCRs developed in our lab that has resulted in the structure determination of 3 different GPCRs bound to either antagonists, partial agonists, full agonists and/or biased agonists.
The aims are:
1. The development of generic methodology for the production of eukaryotic membrane proteins in mammalian cells.
2. The development of a thermostable functional arrestin mutant
3. Structures of β1-adrenoceptor, adenosine A2A receptor and angiotensin receptor bound to a G protein and arrestin
4. Understanding the role of each amino acid residue in the activation process of GPCRs through saturation mutagenes
Summary
Structure determination of G protein-coupled receptors (GPCRs) has been exceedingly successful over the last 5 years due to the development of complimentary generic methodologies that will now allow the structure determination of virtually any GPCR. However, these technologies address only two aspects of the process, namely the stability of the receptors during purification and the ability to form well-diffracting crystals. The strategies also apply only to GPCRs and not transporters or ion channels. The recent successes have been of GPCRs that are expressed in either yeasts or in insect cells using the baculovirus expression system, but many membrane proteins are expressed poorly in these systems or may be expressed in a misfolded non-functional form. A second issue with the future structure determination of GPCRs is the lack of generic technologies to allow the crystallisation of arrestin-GPCR and G protein-GPCR complexes. Although one G protein GPCR complex has been crystallised this was exceedingly diffciult and resulted in poor resolution of the GPCR component of the complex. We believe that it is possible to thermostabilise both arrestin and heterotrimeric G proteins, which will allow a simplified strategy for the crystallisation and structure determination of GPCR complexes. This is based on the development of the strategy of conformational thermostabilisation of GPCRs developed in our lab that has resulted in the structure determination of 3 different GPCRs bound to either antagonists, partial agonists, full agonists and/or biased agonists.
The aims are:
1. The development of generic methodology for the production of eukaryotic membrane proteins in mammalian cells.
2. The development of a thermostable functional arrestin mutant
3. Structures of β1-adrenoceptor, adenosine A2A receptor and angiotensin receptor bound to a G protein and arrestin
4. Understanding the role of each amino acid residue in the activation process of GPCRs through saturation mutagenes
Max ERC Funding
2 378 162 €
Duration
Start date: 2014-02-01, End date: 2019-01-31
Project acronym ENABLE
Project Elucidating natural bilayer lipid environments
Researcher (PI) Carol Robinson
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Country United Kingdom
Call Details Advanced Grant (AdG), LS1, ERC-2015-AdG
Summary Excising a membrane protein from its natural environment, preserving the lipid bilayer, and characterising the lipids that surround it is the ‘holy grail’ of membrane protein biophysics. However, with some 40,000 different lipid structures the challenges we face in understanding selective binding arise not just from the complexity and dynamics of the lipidome, but also from the transient nature of protein lipid interactions. To overcome these challenges we will take mass spectrometry (MS) into a new era, allowing, for the first time, the study of proteins in an environment as close as possible to the natural one. To do this we will (i) characterise protein lipid interactions by employing a high resolution Orbitrap mass spectrometer developed in-house, specifically for membrane proteins, (ii) capture the native lipid environment in vehicles suitable for use in conjunction with MS, and (iii) establish a new platform to be known as integral membrane protein desorption electrospray ionization (impDESI). Designed and built in-house impDESI is capable of releasing membrane proteins from surfaces directly into the mass spectrometer (MS). We will develop impDESI for membrane mimetics, and subsequently portions of natural membranes, enabling us to extract proteins with oligomeric state preserved and native lipid binding intact. The development of impDESI, in conjunction with high resolution Orbitrap MS, and coupled with the optimisation of membrane mimetics, has the potential to radically transform our understanding of native lipid binding, not only directly, but also temporally and spatially. Together these advances will answer key questions about how lipids modulate protein interfaces, occupy different binding sites, modulate membrane protein structure and modify function in vivo. Given the importance of membrane proteins as potential drugs targets understanding their modulation by lipids would be a major step towards more effective drug development.
Summary
Excising a membrane protein from its natural environment, preserving the lipid bilayer, and characterising the lipids that surround it is the ‘holy grail’ of membrane protein biophysics. However, with some 40,000 different lipid structures the challenges we face in understanding selective binding arise not just from the complexity and dynamics of the lipidome, but also from the transient nature of protein lipid interactions. To overcome these challenges we will take mass spectrometry (MS) into a new era, allowing, for the first time, the study of proteins in an environment as close as possible to the natural one. To do this we will (i) characterise protein lipid interactions by employing a high resolution Orbitrap mass spectrometer developed in-house, specifically for membrane proteins, (ii) capture the native lipid environment in vehicles suitable for use in conjunction with MS, and (iii) establish a new platform to be known as integral membrane protein desorption electrospray ionization (impDESI). Designed and built in-house impDESI is capable of releasing membrane proteins from surfaces directly into the mass spectrometer (MS). We will develop impDESI for membrane mimetics, and subsequently portions of natural membranes, enabling us to extract proteins with oligomeric state preserved and native lipid binding intact. The development of impDESI, in conjunction with high resolution Orbitrap MS, and coupled with the optimisation of membrane mimetics, has the potential to radically transform our understanding of native lipid binding, not only directly, but also temporally and spatially. Together these advances will answer key questions about how lipids modulate protein interfaces, occupy different binding sites, modulate membrane protein structure and modify function in vivo. Given the importance of membrane proteins as potential drugs targets understanding their modulation by lipids would be a major step towards more effective drug development.
Max ERC Funding
2 481 744 €
Duration
Start date: 2016-06-01, End date: 2021-05-31
Project acronym EVOCAN
Project Why do cancers occur where they do? A genetic and evolutionary approach
Researcher (PI) Ian Phlip Mark Tomlinson
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Country United Kingdom
Call Details Advanced Grant (AdG), LS2, ERC-2013-ADG
Summary "Tumorigenesis is a form of somatic evolution, a topical subject given the advent of cancer genome sequencing. However, we contend that some features of Darwinian evolution have been neglected when cancer is studied, as have some aspects of evolution that are special to cancers. For example, tumours comprise an expanding population of cells, cancers must occur within a normal human lifespan, and genotypes detrimental to growth of the tumour as a whole may be selected. These factors may render invalid the classical model in which successive mutations with large advantages arise and spread through the tumour in selective sweeps. To incorporate these neglected features and to test how tumorigenesis depends on factors such as mutation rate, selection and size constraints, we shall set up a comprehensive model of tumour growth incorporating cell birth, death, division and mutation parameters. We shall examine specific aspects of cancer-as-evolution in mice. By marking mutant clones using fluorescent proteins, we can track them and see how they persist, spread and die. We shall also determine the mutation profiles and genetic diversity of mutant clones and whole tumours in mice and humans using next-generation sequencing. Specific experiments will determine: (i) the fate of new advantageous clones arising in an existing tumour; (ii) whether new disadvantageous clones can persist in tumours; (iii) whether apparently maladaptive traits for tumour growth, such as suppressing the growth of competitors, can be selected; (iv) why do housekeeper gene mutations cause cancer in specific sites; (v) can cancer cells have too much genomic instability; and (vi) whether all cancers develop owing to driver mutations with big effects, or are there “mini-drivers” of tumorigenesis? There will be continual cross-talk between the experimental and modelling work. The results of the project will enhance our basic understanding of tumorigenesis and suggest strategies for anticancer therapy."
Summary
"Tumorigenesis is a form of somatic evolution, a topical subject given the advent of cancer genome sequencing. However, we contend that some features of Darwinian evolution have been neglected when cancer is studied, as have some aspects of evolution that are special to cancers. For example, tumours comprise an expanding population of cells, cancers must occur within a normal human lifespan, and genotypes detrimental to growth of the tumour as a whole may be selected. These factors may render invalid the classical model in which successive mutations with large advantages arise and spread through the tumour in selective sweeps. To incorporate these neglected features and to test how tumorigenesis depends on factors such as mutation rate, selection and size constraints, we shall set up a comprehensive model of tumour growth incorporating cell birth, death, division and mutation parameters. We shall examine specific aspects of cancer-as-evolution in mice. By marking mutant clones using fluorescent proteins, we can track them and see how they persist, spread and die. We shall also determine the mutation profiles and genetic diversity of mutant clones and whole tumours in mice and humans using next-generation sequencing. Specific experiments will determine: (i) the fate of new advantageous clones arising in an existing tumour; (ii) whether new disadvantageous clones can persist in tumours; (iii) whether apparently maladaptive traits for tumour growth, such as suppressing the growth of competitors, can be selected; (iv) why do housekeeper gene mutations cause cancer in specific sites; (v) can cancer cells have too much genomic instability; and (vi) whether all cancers develop owing to driver mutations with big effects, or are there “mini-drivers” of tumorigenesis? There will be continual cross-talk between the experimental and modelling work. The results of the project will enhance our basic understanding of tumorigenesis and suggest strategies for anticancer therapy."
Max ERC Funding
2 500 000 €
Duration
Start date: 2014-09-01, End date: 2019-08-31
Project acronym Gen-Epix
Project Genetic Determinants of the Epigenome
Researcher (PI) Adrian Peter BIRD
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Country United Kingdom
Call Details Advanced Grant (AdG), LS2, ERC-2015-AdG
Summary Decoding of the genome during development and differentiation depends on sequence-specific DNA binding proteins that regulate transcription. The activity of transcription factors is constrained, however, by chromatin structure and by modification of histones and DNA, known collectively as the “epigenome”. Diseased states, particularly cancers, are often accompanied by epigenomic disturbances that contribute to aetiology, but despite much research the molecular determinants of chromatin and DNA marking remain poorly understood. A widespread view is that the epigenome responds to developmental decisions or environmental impacts that are memorised by the epigenetic machinery. Complementary to this “memory” hypothesis, there is evidence that the epigenome can directly reflect the underlying DNA sequence. We aim to explore genetic determinants of the epigenome based on our over-arching hypothesis that chromatin structure is influenced by the interaction of DNA binding proteins with short, frequent base sequence motifs. Prototypes for this scenario are proteins that bind to the two base pair sequence CpG. These proteins accumulate at CpG islands (CGIs), which are platforms for gene regulation, where they recruit multi-protein complexes that lay down epigenetic marks. By identifying and characterising novel DNA-binding proteins that sense global properties of the DNA sequence (e.g. base composition), we will address several major unanswered questions about genome regulation, including the origin of global DNA methylation patterns and the causal basis of higher order chromosome structures. Our research programme will advance genome biology and shed light on the role of epigenetic signalling in development. In particular it will explore the extent to which the epigenome is “hard-wired” by genes, with important implications for health.
Summary
Decoding of the genome during development and differentiation depends on sequence-specific DNA binding proteins that regulate transcription. The activity of transcription factors is constrained, however, by chromatin structure and by modification of histones and DNA, known collectively as the “epigenome”. Diseased states, particularly cancers, are often accompanied by epigenomic disturbances that contribute to aetiology, but despite much research the molecular determinants of chromatin and DNA marking remain poorly understood. A widespread view is that the epigenome responds to developmental decisions or environmental impacts that are memorised by the epigenetic machinery. Complementary to this “memory” hypothesis, there is evidence that the epigenome can directly reflect the underlying DNA sequence. We aim to explore genetic determinants of the epigenome based on our over-arching hypothesis that chromatin structure is influenced by the interaction of DNA binding proteins with short, frequent base sequence motifs. Prototypes for this scenario are proteins that bind to the two base pair sequence CpG. These proteins accumulate at CpG islands (CGIs), which are platforms for gene regulation, where they recruit multi-protein complexes that lay down epigenetic marks. By identifying and characterising novel DNA-binding proteins that sense global properties of the DNA sequence (e.g. base composition), we will address several major unanswered questions about genome regulation, including the origin of global DNA methylation patterns and the causal basis of higher order chromosome structures. Our research programme will advance genome biology and shed light on the role of epigenetic signalling in development. In particular it will explore the extent to which the epigenome is “hard-wired” by genes, with important implications for health.
Max ERC Funding
2 499 717 €
Duration
Start date: 2016-06-01, End date: 2021-12-31
Project acronym HIVINNATE
Project Characterisation and Manipulation of Primate Lentiviral Interactions with Innate Immunity
Researcher (PI) Gregory John Towers
Host Institution (HI) University College London
Country United Kingdom
Call Details Advanced Grant (AdG), LS6, ERC-2013-ADG
Summary Our aim is to seek detailed molecular level understanding of the interactions between HIV-1 and innate immune sensors expressed in myeloid cells. We have demonstrated that HIV-1 replicates in primary human macrophages without triggering interferon production. However, by specific mutation of HIV-1 proteins or by manipulating interaction with host cofactors we can reveal the virus to innate immune receptors and activate an antiviral response leading to secretion of soluble type 1 interferon and cessation of replication. We propose to define the sensors and the details of the antiviral pathways that are activated in macrophages using proven RNA interference techniques reading out activation of innate immune responses by measurement of secreted interferon and induction of gene expression. We have also characterised small molecules that potently inhibit HIV-1 by revealing HIV-1 to innate immune sensors. In collaboration with crystallographers and medicinal chemists we aim to improve the potency and specificity of these drugs and to use them to study the anti-HIV-1 innate immune response. DC are sentinels of innate immunity and their infection induced maturation leads to interferon production and DC dependent T cell maturation that defines the nature and potency of the immune response. We will examine the effect of triggering innate responses in DC using HIV-1 mutants/drug treated wild type virus on allogeneic responses, by measurement of T cell proliferation and function and in an ex vivo CD8 T cell killing assays using peripheral blood CD8 cells from HIV‑1 infected patients. In this way we will uncover the molecular details of HIV-1’s interaction with innate immunity and discover how the virus replicates in primary immune cells without detection. This work will make a significant technical and intellectual contribution to an important emerging scientific field focusing on understanding and manipulating the complex relationship between HIV-1 and innate immunity.
Summary
Our aim is to seek detailed molecular level understanding of the interactions between HIV-1 and innate immune sensors expressed in myeloid cells. We have demonstrated that HIV-1 replicates in primary human macrophages without triggering interferon production. However, by specific mutation of HIV-1 proteins or by manipulating interaction with host cofactors we can reveal the virus to innate immune receptors and activate an antiviral response leading to secretion of soluble type 1 interferon and cessation of replication. We propose to define the sensors and the details of the antiviral pathways that are activated in macrophages using proven RNA interference techniques reading out activation of innate immune responses by measurement of secreted interferon and induction of gene expression. We have also characterised small molecules that potently inhibit HIV-1 by revealing HIV-1 to innate immune sensors. In collaboration with crystallographers and medicinal chemists we aim to improve the potency and specificity of these drugs and to use them to study the anti-HIV-1 innate immune response. DC are sentinels of innate immunity and their infection induced maturation leads to interferon production and DC dependent T cell maturation that defines the nature and potency of the immune response. We will examine the effect of triggering innate responses in DC using HIV-1 mutants/drug treated wild type virus on allogeneic responses, by measurement of T cell proliferation and function and in an ex vivo CD8 T cell killing assays using peripheral blood CD8 cells from HIV‑1 infected patients. In this way we will uncover the molecular details of HIV-1’s interaction with innate immunity and discover how the virus replicates in primary immune cells without detection. This work will make a significant technical and intellectual contribution to an important emerging scientific field focusing on understanding and manipulating the complex relationship between HIV-1 and innate immunity.
Max ERC Funding
2 499 643 €
Duration
Start date: 2014-02-01, End date: 2019-01-31
Project acronym INCA
Project Genetic and environmental factors that control inflammation-driven colon cancer
Researcher (PI) Fiona M Powrie
Host Institution (HI) THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
Country United Kingdom
Call Details Advanced Grant (AdG), LS6, ERC-2013-ADG
Summary "The human gastrointestinal tract is colonized by an abundant and diverse bacterial microbiota that exist in a mutualistic relationship with the host that promotes intestinal health. Maladaptation in this host microbial dialogue leads to a deranged inflammatory response and inflammatory bowel disease (IBD) that can progress to colon cancer. The complex interplay between genetic and environmental factors and their impact on intestinal inflammation are starting to be deciphered in IBD, however little is known about how they influence the transition from colitis to cancer. We recently established a relevant model of bacteria-driven invasive colon cancer and have mapped both genetic and immune pathways that perpetuate disease. Genetic susceptibility maps to a 1.7mb region on chromosome 3 containing the candidate gene Alpk1, an alpha-kinase. This locus mediates its effects through the IL-23 driven innate lymphoid cell response and we have identified the cytokine IL-22 as a key player in driving the tumour cell response. We will use a multi-disciplinary approach to probe the interaction between genetics, microbial drivers and inflammatory pathways that promote colon cancer. BAC transgenics and cell-type specific knock-out mice will be used to establish the function of Alpk1 in bacteria driven colon cancer. In vivo models will be complemented by novel 3D colonic organoid and crypt cultures generated from epithelial stem cells from normal or tumor tissue allowing analysis of microbial and cytokine signals that influence intestinal epithelial cell and stem cell function. Deep sequencing combined with bacterial cell culture will identify changes in the intestinal microbiota that drive tumourigenesis. Results from mouse models will be translated to analysis of human colorectal cancer. These studies will uncover new pathways involved in bacterial interaction, intestinal inflammation and tumour formation that may offer new therapeutic targets in IBD and colon cancer."
Summary
"The human gastrointestinal tract is colonized by an abundant and diverse bacterial microbiota that exist in a mutualistic relationship with the host that promotes intestinal health. Maladaptation in this host microbial dialogue leads to a deranged inflammatory response and inflammatory bowel disease (IBD) that can progress to colon cancer. The complex interplay between genetic and environmental factors and their impact on intestinal inflammation are starting to be deciphered in IBD, however little is known about how they influence the transition from colitis to cancer. We recently established a relevant model of bacteria-driven invasive colon cancer and have mapped both genetic and immune pathways that perpetuate disease. Genetic susceptibility maps to a 1.7mb region on chromosome 3 containing the candidate gene Alpk1, an alpha-kinase. This locus mediates its effects through the IL-23 driven innate lymphoid cell response and we have identified the cytokine IL-22 as a key player in driving the tumour cell response. We will use a multi-disciplinary approach to probe the interaction between genetics, microbial drivers and inflammatory pathways that promote colon cancer. BAC transgenics and cell-type specific knock-out mice will be used to establish the function of Alpk1 in bacteria driven colon cancer. In vivo models will be complemented by novel 3D colonic organoid and crypt cultures generated from epithelial stem cells from normal or tumor tissue allowing analysis of microbial and cytokine signals that influence intestinal epithelial cell and stem cell function. Deep sequencing combined with bacterial cell culture will identify changes in the intestinal microbiota that drive tumourigenesis. Results from mouse models will be translated to analysis of human colorectal cancer. These studies will uncover new pathways involved in bacterial interaction, intestinal inflammation and tumour formation that may offer new therapeutic targets in IBD and colon cancer."
Max ERC Funding
2 484 620 €
Duration
Start date: 2014-03-01, End date: 2019-02-28
Project acronym KIRANDIS
Project NK receptors and disease
Researcher (PI) John Trowsdale
Host Institution (HI) THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
Country United Kingdom
Call Details Advanced Grant (AdG), LS6, ERC-2015-AdG
Summary NK cells are relevant to many kinds of disease, including viral infection, autoimmunity, cancer, transplantation and reproduction. The behavior of NK cells is controlled by a large number of different cell surface receptors, in a region on chromosome 19 called the LRC. Some of these receptors, such as KIR, are highly variable in gene number and allele sequence in different individuals. Many of them interact with HLA class I molecules, which are also highly polymorphic. To understand and exploit NK receptors and disease this project has three aims:
1. To investigate how variation in receptors encoded in the LRC influences viral infection and disease course.
My laboratory is known for high-throughput KIR copy number and allele typing. Highly polymorphic KIR receptors are refractory to analysis by SNP typing and next generation sequencing (NGS) methods, so interrogation of large numbers of samples for accurate disease determination is not feasible. To overcome this problem we propose to develop digital PCR, sequence-based allele typing, imputation and NGS after sequence capture. Once underway, a large number of disease cohorts and matched controls will be investigated, spanning autoimmunity, infection and birth-weight, in collaboration with other laboratories.
2. To investigate mechanisms viruses use to evade NK cells.
To facilitate this we have generated reporter cells that permit weak interaction of receptors with their ligands to be detected by production of Green Fluorescent Protein (GFP). The evasion of NK cells by HCMV, vaccinia and HPV viruses will be studied. This work will be in conjunction with expert virology groups in the UK.
3. To identify novel ligands for LRC-encoded receptors.
We will use the reporter cells to screen for ligands, initially by blocking binding with monoclonal antibodies. We intend to identify ligands for KIR and LILR, where these are unknown, especially focusing on activating receptors.
Summary
NK cells are relevant to many kinds of disease, including viral infection, autoimmunity, cancer, transplantation and reproduction. The behavior of NK cells is controlled by a large number of different cell surface receptors, in a region on chromosome 19 called the LRC. Some of these receptors, such as KIR, are highly variable in gene number and allele sequence in different individuals. Many of them interact with HLA class I molecules, which are also highly polymorphic. To understand and exploit NK receptors and disease this project has three aims:
1. To investigate how variation in receptors encoded in the LRC influences viral infection and disease course.
My laboratory is known for high-throughput KIR copy number and allele typing. Highly polymorphic KIR receptors are refractory to analysis by SNP typing and next generation sequencing (NGS) methods, so interrogation of large numbers of samples for accurate disease determination is not feasible. To overcome this problem we propose to develop digital PCR, sequence-based allele typing, imputation and NGS after sequence capture. Once underway, a large number of disease cohorts and matched controls will be investigated, spanning autoimmunity, infection and birth-weight, in collaboration with other laboratories.
2. To investigate mechanisms viruses use to evade NK cells.
To facilitate this we have generated reporter cells that permit weak interaction of receptors with their ligands to be detected by production of Green Fluorescent Protein (GFP). The evasion of NK cells by HCMV, vaccinia and HPV viruses will be studied. This work will be in conjunction with expert virology groups in the UK.
3. To identify novel ligands for LRC-encoded receptors.
We will use the reporter cells to screen for ligands, initially by blocking binding with monoclonal antibodies. We intend to identify ligands for KIR and LILR, where these are unknown, especially focusing on activating receptors.
Max ERC Funding
1 735 205 €
Duration
Start date: 2016-10-01, End date: 2021-09-30
Project acronym MEXTIM
Project Measurement of temperature exposure and integration over time
Researcher (PI) Caroline Dean
Host Institution (HI) JOHN INNES CENTRE
Country United Kingdom
Call Details Advanced Grant (AdG), LS2, ERC-2013-ADG
Summary "All organisms have to cope with changing temperature and various mechanisms have evolved to protect cellular processes against thermal stresses. Many organisms also use temperature signals to align behaviour and development with certain seasons. How specific temperature cues are extracted from fluctuating temperature levels is unknown but it implies the existence of mechanisms that enable long-term monitoring and integration of the enormously variable temperature levels found in nature. We therefore intend to discover how variable temperature levels are measured and integrated over long timescales in order to provide information used in biological timing. Plants provide an excellent system in which to investigate such thermo-sensory mechanisms. We will exploit our knowledge of the multiple regulatory pathways determining quantitative expression of the plant developmental repressor FLOWERING LOCUS C (FLC). These pathways, which are all independently influenced by temperature, converge to regulate FLC via aspects of a co-transcriptional mechanism involving antisense transcripts and different chromatin pathways. This understanding provides the system to define the primary temperature steps (thermo-sensors) that directly regulate FLC and explore how they combine to record complex temperature profiles. Our hypothesis is that different thermo-sensors monitor distinct aspects of the long-term temperature profile. Their outputs would be integrated via accumulation of chromatin modifications at FLC with feedback and interconnection between the pathways providing reinforcement systems to record previous exposure. Modulation of this mechanism would then provide the basis for adaptation to different climates. Knowledge emerging from this study will provide important concepts in understanding how organisms interact with their environment."
Summary
"All organisms have to cope with changing temperature and various mechanisms have evolved to protect cellular processes against thermal stresses. Many organisms also use temperature signals to align behaviour and development with certain seasons. How specific temperature cues are extracted from fluctuating temperature levels is unknown but it implies the existence of mechanisms that enable long-term monitoring and integration of the enormously variable temperature levels found in nature. We therefore intend to discover how variable temperature levels are measured and integrated over long timescales in order to provide information used in biological timing. Plants provide an excellent system in which to investigate such thermo-sensory mechanisms. We will exploit our knowledge of the multiple regulatory pathways determining quantitative expression of the plant developmental repressor FLOWERING LOCUS C (FLC). These pathways, which are all independently influenced by temperature, converge to regulate FLC via aspects of a co-transcriptional mechanism involving antisense transcripts and different chromatin pathways. This understanding provides the system to define the primary temperature steps (thermo-sensors) that directly regulate FLC and explore how they combine to record complex temperature profiles. Our hypothesis is that different thermo-sensors monitor distinct aspects of the long-term temperature profile. Their outputs would be integrated via accumulation of chromatin modifications at FLC with feedback and interconnection between the pathways providing reinforcement systems to record previous exposure. Modulation of this mechanism would then provide the basis for adaptation to different climates. Knowledge emerging from this study will provide important concepts in understanding how organisms interact with their environment."
Max ERC Funding
2 499 997 €
Duration
Start date: 2014-03-01, End date: 2019-02-28