Project acronym DecodeDiabetes
Project Expanding the genetic etiological and diagnostic spectrum of monogenic diabetes mellitus
Researcher (PI) Jorge FERRER
Host Institution (HI) FUNDACIO CENTRE DE REGULACIO GENOMICA
Call Details Advanced Grant (AdG), LS4, ERC-2017-ADG
Summary Whole genome sequencing is quickly becoming a routine clinical instrument. However, our ability to decipher DNA variants is still largely limited to protein-coding exons, which comprise 1% of the genome. Most known Mendelian mutations are in exons, yet genetic testing still fails to show causal coding mutations in more than 50% of well-characterized Mendelian disorders. This defines a pressing need to interpret noncoding genome sequences, and to establish the role of noncoding mutations in Mendelian disease.
A recent case study harnessed whole genome sequencing, epigenomics, and functional genomics to show that mutations in an enhancer cause most cases of neonatal diabetes due to pancreas agenesis. This example raises major questions: (i) what is the overall impact of penetrant regulatory mutations in human diabetes? (ii) do regulatory mutations cause distinct forms of diabetes? (iii) more generally, can we develop a strategy to systematically tackle regulatory variation in Mendelian disease?
The current project will address these questions with unique resources. First, we have created epigenomic and functional perturbation resources to interpret the regulatory genome in embryonic pancreas and adult pancreatic islets. Second, we have collected an unprecedented international cohort of patients with a phenotype consistent with monogenic diabetes, yet lacking mutations in known gene culprits after genetic testing, and therefore with increased likelihood of harboring noncoding mutations. Third, we have developed a prototype platform to sequence regulatory mutations in a large number of patients.
These resources will be combined with innovative strategies to uncover causal enhancer mutations underlying Mendelian diabetes. If successful, this project will expand the diagnostic spectrum of diabetes, it will discover new genetic regulators of diabetes-relevant networks, and will provide a framework to understand regulatory variation in Mendelian disease.
Summary
Whole genome sequencing is quickly becoming a routine clinical instrument. However, our ability to decipher DNA variants is still largely limited to protein-coding exons, which comprise 1% of the genome. Most known Mendelian mutations are in exons, yet genetic testing still fails to show causal coding mutations in more than 50% of well-characterized Mendelian disorders. This defines a pressing need to interpret noncoding genome sequences, and to establish the role of noncoding mutations in Mendelian disease.
A recent case study harnessed whole genome sequencing, epigenomics, and functional genomics to show that mutations in an enhancer cause most cases of neonatal diabetes due to pancreas agenesis. This example raises major questions: (i) what is the overall impact of penetrant regulatory mutations in human diabetes? (ii) do regulatory mutations cause distinct forms of diabetes? (iii) more generally, can we develop a strategy to systematically tackle regulatory variation in Mendelian disease?
The current project will address these questions with unique resources. First, we have created epigenomic and functional perturbation resources to interpret the regulatory genome in embryonic pancreas and adult pancreatic islets. Second, we have collected an unprecedented international cohort of patients with a phenotype consistent with monogenic diabetes, yet lacking mutations in known gene culprits after genetic testing, and therefore with increased likelihood of harboring noncoding mutations. Third, we have developed a prototype platform to sequence regulatory mutations in a large number of patients.
These resources will be combined with innovative strategies to uncover causal enhancer mutations underlying Mendelian diabetes. If successful, this project will expand the diagnostic spectrum of diabetes, it will discover new genetic regulators of diabetes-relevant networks, and will provide a framework to understand regulatory variation in Mendelian disease.
Max ERC Funding
2 243 746 €
Duration
Start date: 2018-11-01, End date: 2023-10-31
Project acronym DEEPINSIGHT
Project Preclinical micro-endoscopy in tumors: targeting metastatic intravasation and resistance
Researcher (PI) Peter Friedl
Host Institution (HI) STICHTING KATHOLIEKE UNIVERSITEIT
Call Details Consolidator Grant (CoG), LS4, ERC-2013-CoG
Summary Poor prognosis of cancer results from two central progression events, (i) the intravasation of cancer cells into blood vessels which leads to metastasis to distant organs and ultimately lethal tumor overload and (ii) cancer cell survival and adaptation to metabolic stress which causes resistance to anti-cancer therapy and limits life expectancy. Using a novel multiphoton microendoscope device recently developed by myself and collaborators, I here aim to overcome tissue penetration limits and identify important progression events deeply inside tumors. The hard- and software of the microendoscope will be optimized for automated position control and panoramic rotation to sample large tissue volumes and validated for stability and safety. We then will address the locations and mechanisms inside tumors that: (1) enable tumor-cell migration and penetration into blood vessels for distant metastasis and (2) mediate enhanced tumor-cell survival and resistance to experimental radiation- and chemotherapy. This basic inventory will serve to address (3) whether and how the niches for both intravasation and resistance overlap and connected with microenvironmental triggers, including defective blood vessels, signalling pathways of malnutrition and hypoxia, and tissue damage. The strategies include 3D microscopy of live fluorescent multi-color tumors and molecular reporters to record cancer cell migration, proliferation and death in the context with embedding tissue structures and metabolic signals. Once identified and characterized, (4) the niches and signals inducing intravasation and resistance (i.e. integrin adhesion receptors, cytoskeletal regulators, metabolic signalling) will be exploited as targets to enhance experimental radiation and chemotherapy. Preclinical microendoscopy will deliver new insight into cancer progression further contribute impulses to microendoscopy for disease monitoring in patients (“optical biopsy”).
Summary
Poor prognosis of cancer results from two central progression events, (i) the intravasation of cancer cells into blood vessels which leads to metastasis to distant organs and ultimately lethal tumor overload and (ii) cancer cell survival and adaptation to metabolic stress which causes resistance to anti-cancer therapy and limits life expectancy. Using a novel multiphoton microendoscope device recently developed by myself and collaborators, I here aim to overcome tissue penetration limits and identify important progression events deeply inside tumors. The hard- and software of the microendoscope will be optimized for automated position control and panoramic rotation to sample large tissue volumes and validated for stability and safety. We then will address the locations and mechanisms inside tumors that: (1) enable tumor-cell migration and penetration into blood vessels for distant metastasis and (2) mediate enhanced tumor-cell survival and resistance to experimental radiation- and chemotherapy. This basic inventory will serve to address (3) whether and how the niches for both intravasation and resistance overlap and connected with microenvironmental triggers, including defective blood vessels, signalling pathways of malnutrition and hypoxia, and tissue damage. The strategies include 3D microscopy of live fluorescent multi-color tumors and molecular reporters to record cancer cell migration, proliferation and death in the context with embedding tissue structures and metabolic signals. Once identified and characterized, (4) the niches and signals inducing intravasation and resistance (i.e. integrin adhesion receptors, cytoskeletal regulators, metabolic signalling) will be exploited as targets to enhance experimental radiation and chemotherapy. Preclinical microendoscopy will deliver new insight into cancer progression further contribute impulses to microendoscopy for disease monitoring in patients (“optical biopsy”).
Max ERC Funding
2 000 000 €
Duration
Start date: 2014-12-01, End date: 2019-11-30
Project acronym deFIBER
Project Dissecting the cellular and molecular dynamics of bone marrow fibrosis for improved diagnostics and treatment
Researcher (PI) Rebekka SCHNEIDER-KRAMANN
Host Institution (HI) ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM
Call Details Starting Grant (StG), LS4, ERC-2017-STG
Summary Bone marrow (BM) fibrosis is the continuous replacement of blood forming cells in the bone marrow by scar tissue, ultimately leading to failure of the body to produce blood cells. Primary myelofibrosis (PMF), an incurable blood cancer, is the prototypic example of the step-wise development of BM fibrosis. The specific mechanisms that cause BM fibrosis are not understood, in particular as the cells driving fibrosis have remained obscure.
My recent findings demonstrate that Gli1+ cells are fibrosis-driving cells in PMF, that their frequency correlates with fibrosis severity in patients, and that their ablation ameliorates BM fibrosis. These results indicate that Gli1+ cells are the primary effector cells in BM fibrosis and that they represent a highly attractive therapeutic target. This puts me in a unique position to vastly expand our knowledge of the BM fibrosis pathogenesis, improve diagnostics, and discover new therapeutic strategies for this fatal disease. I will do this by: 1) dissecting the molecular and cellular mechanisms of the fibrotic transformation, 2) defining the stepwise disease evolution by genetic fate tracing and analysis of the previously unknown critical effector cells of BM fibrosis , 3) understanding early forms of BM fibrosis for improved diagnostics in patients, all with the ultimate aim to identify novel therapeutic targets to directly block the cellular and molecular changes occuring in BM fibrosis.
I will apply state-of-the-art techniques, including genetic fate tracing experiments, conditional genetic knockout mouse models, tissue engineering of the bone marrow niche and in vivo and in vitro CRISPR/Cas9 gene editing, to unravel the complex molecular and cellular interaction between fibrosis-causing cells and the malignant hematopoietic cells. I will translate these findings into patient samples with the aim to improve the early diagnosis of the disease and to ultimately develop novel targeted therapies with curative intentions.
Summary
Bone marrow (BM) fibrosis is the continuous replacement of blood forming cells in the bone marrow by scar tissue, ultimately leading to failure of the body to produce blood cells. Primary myelofibrosis (PMF), an incurable blood cancer, is the prototypic example of the step-wise development of BM fibrosis. The specific mechanisms that cause BM fibrosis are not understood, in particular as the cells driving fibrosis have remained obscure.
My recent findings demonstrate that Gli1+ cells are fibrosis-driving cells in PMF, that their frequency correlates with fibrosis severity in patients, and that their ablation ameliorates BM fibrosis. These results indicate that Gli1+ cells are the primary effector cells in BM fibrosis and that they represent a highly attractive therapeutic target. This puts me in a unique position to vastly expand our knowledge of the BM fibrosis pathogenesis, improve diagnostics, and discover new therapeutic strategies for this fatal disease. I will do this by: 1) dissecting the molecular and cellular mechanisms of the fibrotic transformation, 2) defining the stepwise disease evolution by genetic fate tracing and analysis of the previously unknown critical effector cells of BM fibrosis , 3) understanding early forms of BM fibrosis for improved diagnostics in patients, all with the ultimate aim to identify novel therapeutic targets to directly block the cellular and molecular changes occuring in BM fibrosis.
I will apply state-of-the-art techniques, including genetic fate tracing experiments, conditional genetic knockout mouse models, tissue engineering of the bone marrow niche and in vivo and in vitro CRISPR/Cas9 gene editing, to unravel the complex molecular and cellular interaction between fibrosis-causing cells and the malignant hematopoietic cells. I will translate these findings into patient samples with the aim to improve the early diagnosis of the disease and to ultimately develop novel targeted therapies with curative intentions.
Max ERC Funding
1 498 544 €
Duration
Start date: 2018-01-01, End date: 2022-12-31
Project acronym DeFiNER
Project Nucleotide Excision Repair: Decoding its Functional Role in Mammals
Researcher (PI) Georgios Garinis
Host Institution (HI) IDRYMA TECHNOLOGIAS KAI EREVNAS
Call Details Consolidator Grant (CoG), LS4, ERC-2014-CoG
Summary Genome maintenance, chromatin remodelling and transcription are tightly linked biological processes that are currently poorly understood and vastly unexplored. Nucleotide excision repair (NER) is a major DNA repair pathway that mammalian cells employ to maintain their genome intact and faithfully transmit it into their progeny. Besides cancer and aging, however, defects in NER give rise to developmental disorders whose clinical heterogeneity and varying severity can only insufficiently be explained by the DNA repair defect. Recent work reveals that NER factors play a role, in addition to DNA repair, in transcription and the three-dimensional organization of our genome. Indeed, NER factors are now known to function in the regulation of gene expression, the transcriptional reprogramming of pluripotent stem cells and the fine-tuning of growth hormones during mammalian development. In this regard, the non-random organization of our genome, chromatin and the process of transcription itself are expected to play paramount roles in how NER factors coordinate, prioritize and execute their distinct tasks during development and disease progression. At present, however, no solid evidence exists as to how NER is functionally involved in such complex processes, what are the NER-associated protein complexes and underlying gene networks or how NER factors operate within the complex chromatin architecture. This is primarily due to our difficulties in dissecting the diverse functional contributions of NER proteins in an intact organism. Here, we propose to use a unique series of knock-in, transgenic and NER progeroid mice to decode the functional role of NER in mammals, thus paving the way for understanding how genome maintenance pathways are connected to developmental defects and disease mechanisms in vivo.
Summary
Genome maintenance, chromatin remodelling and transcription are tightly linked biological processes that are currently poorly understood and vastly unexplored. Nucleotide excision repair (NER) is a major DNA repair pathway that mammalian cells employ to maintain their genome intact and faithfully transmit it into their progeny. Besides cancer and aging, however, defects in NER give rise to developmental disorders whose clinical heterogeneity and varying severity can only insufficiently be explained by the DNA repair defect. Recent work reveals that NER factors play a role, in addition to DNA repair, in transcription and the three-dimensional organization of our genome. Indeed, NER factors are now known to function in the regulation of gene expression, the transcriptional reprogramming of pluripotent stem cells and the fine-tuning of growth hormones during mammalian development. In this regard, the non-random organization of our genome, chromatin and the process of transcription itself are expected to play paramount roles in how NER factors coordinate, prioritize and execute their distinct tasks during development and disease progression. At present, however, no solid evidence exists as to how NER is functionally involved in such complex processes, what are the NER-associated protein complexes and underlying gene networks or how NER factors operate within the complex chromatin architecture. This is primarily due to our difficulties in dissecting the diverse functional contributions of NER proteins in an intact organism. Here, we propose to use a unique series of knock-in, transgenic and NER progeroid mice to decode the functional role of NER in mammals, thus paving the way for understanding how genome maintenance pathways are connected to developmental defects and disease mechanisms in vivo.
Max ERC Funding
1 995 000 €
Duration
Start date: 2016-01-01, End date: 2020-12-31
Project acronym DelCancer
Project The role of loss-of-heterozygosity in cancer development and progression
Researcher (PI) Anna Sablina
Host Institution (HI) VIB VZW
Call Details Starting Grant (StG), LS4, ERC-2012-StG_20111109
Summary Somatically acquired loss-of-heterozygosity (LOH) is extremely common in cancer; deletions of recessive cancer genes, miRNAs, and regulatory elements, can confer selective growth advantage, whereas deletions over fragile sites are thought to reflect an increased local rate of DNA breakage. However, most LOHs in cancer genomes remain unexplained. Here we plan to combine a TALEN technology and the experimental models of cell transformation derived from primary human cells to delete specific chromosomal regions that are frequently lost in cancer samples. The development of novel strategies to introduce large chromosomal rearrangements into the genome of primary human cells will offer new perspectives for studying gene function, for elucidating chromosomal organisation, and for increasing our understanding of the molecular mechanisms and pathways underlying cancer development.Using this technology to genetically engineer cells that model cancer-associated genetic alterations, we will identify LOH regions critical for the development and progression of human cancers, and will investigate the cooperative effect of loss of genes, non-coding RNAs, and regulatory elements located within the deleted regions on cancer-associated phenotypes. We will assess how disruption of the three-dimensional chromosomal network in cells with specific chromosomal deletions contributes to cell transformation. Isogenic cell lines harbouring targeted chromosomal alterations will also serve us as a platform to identify compounds with specificity for particular genetic abnormalities. As a next step, we plan to unravel the mechanisms by which particular homozygous deletions contribute to cancer-associated phenotypes. If successful, the results of these studies will represent an important step towards understanding oncogenesis, and could yield new diagnostic and prognostic markers as well as identify potential therapeutic targets.
Summary
Somatically acquired loss-of-heterozygosity (LOH) is extremely common in cancer; deletions of recessive cancer genes, miRNAs, and regulatory elements, can confer selective growth advantage, whereas deletions over fragile sites are thought to reflect an increased local rate of DNA breakage. However, most LOHs in cancer genomes remain unexplained. Here we plan to combine a TALEN technology and the experimental models of cell transformation derived from primary human cells to delete specific chromosomal regions that are frequently lost in cancer samples. The development of novel strategies to introduce large chromosomal rearrangements into the genome of primary human cells will offer new perspectives for studying gene function, for elucidating chromosomal organisation, and for increasing our understanding of the molecular mechanisms and pathways underlying cancer development.Using this technology to genetically engineer cells that model cancer-associated genetic alterations, we will identify LOH regions critical for the development and progression of human cancers, and will investigate the cooperative effect of loss of genes, non-coding RNAs, and regulatory elements located within the deleted regions on cancer-associated phenotypes. We will assess how disruption of the three-dimensional chromosomal network in cells with specific chromosomal deletions contributes to cell transformation. Isogenic cell lines harbouring targeted chromosomal alterations will also serve us as a platform to identify compounds with specificity for particular genetic abnormalities. As a next step, we plan to unravel the mechanisms by which particular homozygous deletions contribute to cancer-associated phenotypes. If successful, the results of these studies will represent an important step towards understanding oncogenesis, and could yield new diagnostic and prognostic markers as well as identify potential therapeutic targets.
Max ERC Funding
1 498 764 €
Duration
Start date: 2012-10-01, End date: 2017-09-30
Project acronym DEMETINL
Project Decisions in metabolic inflammation of the liver: Adhesive interactions involved in leukocyte retention and resolution of inflammation in metabolic-inflammatory liver disease
Researcher (PI) Triantafyllos Chavakis
Host Institution (HI) TECHNISCHE UNIVERSITAET DRESDEN
Call Details Consolidator Grant (CoG), LS4, ERC-2015-CoG
Summary Resolution of acute inflammation, involving limiting further leukocyte recruitment, apoptosis and clearance
of inflammatory cells via macrophages as well as egress of the inflammatory cells, is operative in acute
inflammation but dysfunctional in chronic inflammatory disease. In the latter scenario, the retention and
activation of leukocytes in the inflamed tissue linked with failure to resolve inflammation contributes to
perpetuation of organ damage and loss of homeostasis. Interestingly, persistent inflammation in insulintarget
organs, such as the adipose tissue and the liver in the context of obesity significantly contributes to
development of insulin resistance (IR), diabetes and non-alcoholic fatty liver disease (NAFLD). So far,
investigations have mainly addressed obesity-related inflammatory mechanisms in the AT and rather less in
other metabolic organs, e.g. the liver. Therefore, the aims of this proposal are: (i) To characterize in the
context of obesity-related metabolic disease novel processes mediating inflammatory cell retention,
especially in the liver. In this context, we will also address the novel hypothesis that adhesive interactions of
inflammatory cells (with e.g. parenchymal cells) in the metabolically challenged environment of obese
organs may activate them via alterations in their cellular metabolism, thereby contributing to perpetuation of
inflammation. (ii) To understand resolution of inflammation including inflammatory cell egress from
metabolic organs, especially from the liver in metabolic-inflammatory disease. To this end, we will also
utilize models of acute inflammation, which is capable to resolve, in order to understand resolution principles
and apply them to non-resolving metabolic-inflammatory disease. In this regard, we will also assess the
therapeutic potential of novel inflammation-modulating factors identified by our lab.
Summary
Resolution of acute inflammation, involving limiting further leukocyte recruitment, apoptosis and clearance
of inflammatory cells via macrophages as well as egress of the inflammatory cells, is operative in acute
inflammation but dysfunctional in chronic inflammatory disease. In the latter scenario, the retention and
activation of leukocytes in the inflamed tissue linked with failure to resolve inflammation contributes to
perpetuation of organ damage and loss of homeostasis. Interestingly, persistent inflammation in insulintarget
organs, such as the adipose tissue and the liver in the context of obesity significantly contributes to
development of insulin resistance (IR), diabetes and non-alcoholic fatty liver disease (NAFLD). So far,
investigations have mainly addressed obesity-related inflammatory mechanisms in the AT and rather less in
other metabolic organs, e.g. the liver. Therefore, the aims of this proposal are: (i) To characterize in the
context of obesity-related metabolic disease novel processes mediating inflammatory cell retention,
especially in the liver. In this context, we will also address the novel hypothesis that adhesive interactions of
inflammatory cells (with e.g. parenchymal cells) in the metabolically challenged environment of obese
organs may activate them via alterations in their cellular metabolism, thereby contributing to perpetuation of
inflammation. (ii) To understand resolution of inflammation including inflammatory cell egress from
metabolic organs, especially from the liver in metabolic-inflammatory disease. To this end, we will also
utilize models of acute inflammation, which is capable to resolve, in order to understand resolution principles
and apply them to non-resolving metabolic-inflammatory disease. In this regard, we will also assess the
therapeutic potential of novel inflammation-modulating factors identified by our lab.
Max ERC Funding
1 953 250 €
Duration
Start date: 2017-01-01, End date: 2021-12-31
Project acronym DENOVOSTEM
Project DE NOVO GENERATION OF SOMATIC STEM CELLS: REGULATION AND MECHANISMS OF CELL PLASTICITY
Researcher (PI) Stefano Piccolo
Host Institution (HI) UNIVERSITA DEGLI STUDI DI PADOVA
Call Details Advanced Grant (AdG), LS4, ERC-2014-ADG
Summary The possibility to artificially induce and expand in vitro tissue-specific stem cells (SCs) is an important goal for regenerative medicine, to understand organ physiology, for in vitro modeling of human diseases and many other applications. Here we found that this goal can be achieved in the culture dish by transiently inducing expression of YAP or TAZ - nuclear effectors of the Hippo and biomechanical pathways - into primary/terminally differentiated cells of distinct tissue origins. Moreover, YAP/TAZ are essential endogenous factors that preserve ex-vivo naturally arising SCs of distinct tissues.
In this grant, we aim to gain insights into YAP/TAZ molecular networks (upstream regulators and downstream targets) involved in somatic SC reprogramming and SC identity. Our studies will entail the identification of the genetic networks and epigenetic changes controlled by YAP/TAZ during cell de-differentiation and the re-acquisition of SC-traits in distinct cell types. We will also investigate upstream inputs establishing YAP/TAZ activity, with particular emphasis on biomechanical and cytoskeletal cues that represent overarching regulators of YAP/TAZ in tissues.
For many tumors, it appears that acquisition of an immature, stem-like state is a prerequisite for tumor progression and an early step in oncogene-mediated transformation. YAP/TAZ activation is widespread in human tumors. However, a connection between YAP/TAZ and oncogene-induced cell plasticity has never been investigated. We will also pursue some intriguing preliminary results and investigate how oncogenes and chromatin remodelers may link to cell mechanics, and the plasticity of the differentiated and SC states by controlling YAP/TAZ.
In sum, this research should advance our understanding of the cellular and molecular basis underpinning organ growth, tissue regeneration and tumor initiation.
Summary
The possibility to artificially induce and expand in vitro tissue-specific stem cells (SCs) is an important goal for regenerative medicine, to understand organ physiology, for in vitro modeling of human diseases and many other applications. Here we found that this goal can be achieved in the culture dish by transiently inducing expression of YAP or TAZ - nuclear effectors of the Hippo and biomechanical pathways - into primary/terminally differentiated cells of distinct tissue origins. Moreover, YAP/TAZ are essential endogenous factors that preserve ex-vivo naturally arising SCs of distinct tissues.
In this grant, we aim to gain insights into YAP/TAZ molecular networks (upstream regulators and downstream targets) involved in somatic SC reprogramming and SC identity. Our studies will entail the identification of the genetic networks and epigenetic changes controlled by YAP/TAZ during cell de-differentiation and the re-acquisition of SC-traits in distinct cell types. We will also investigate upstream inputs establishing YAP/TAZ activity, with particular emphasis on biomechanical and cytoskeletal cues that represent overarching regulators of YAP/TAZ in tissues.
For many tumors, it appears that acquisition of an immature, stem-like state is a prerequisite for tumor progression and an early step in oncogene-mediated transformation. YAP/TAZ activation is widespread in human tumors. However, a connection between YAP/TAZ and oncogene-induced cell plasticity has never been investigated. We will also pursue some intriguing preliminary results and investigate how oncogenes and chromatin remodelers may link to cell mechanics, and the plasticity of the differentiated and SC states by controlling YAP/TAZ.
In sum, this research should advance our understanding of the cellular and molecular basis underpinning organ growth, tissue regeneration and tumor initiation.
Max ERC Funding
2 498 934 €
Duration
Start date: 2015-09-01, End date: 2021-08-31
Project acronym DEPREC
Project The Dependence Receptors notion: from a cell biology paradigm to anti-cancer targeted therapy
Researcher (PI) Patrick Mehlen
Host Institution (HI) UNIVERSITE LYON 1 CLAUDE BERNARD
Call Details Advanced Grant (AdG), LS4, ERC-2011-ADG_20110310
Summary "While it is assumed that transmembrane receptors are active only in the presence of ligand, we have proposed that some receptors may also be active in the absence of ligand stimulation. These receptors, named “dependence receptors” (DRs) share the ability to transmit two opposite signals: in the presence of ligand, these receptors transduce various classical “positive” signals, whereas in the absence of ligand, they trigger apoptosis. The expression of dependence receptors thus creates cellular states of dependence for survival on their respective ligands. To date, more than fifteen such receptors have been identified, including the netrin-1 receptors DCC (Deleted in Colorectal Cancer) and UNC5H1-4, some integrins, RET, EPHA4, TrkA, TrkC and the Sonic Hedgehog receptor Patched (Ptc). Even though the interest in this notion is increasing, two main questions remain poorly understood: (i) how very different receptors, with only modest homology, are able to trigger apoptosis when unengaged by their respective ligand, and (ii) what are the respective biological roles of this pro-apoptotic activity in vivo. We have hypothesized that the DRs pro-apoptotic activity is a mechanism that determines and regulates the territories of migration/localization of cells during embryonic development. We also demonstrated that this may be a mechanism that limits tumor growth and metastasis. The goal of the present project is, based on the study of a relatively small number of these receptors –i.e., DCC, UNC5H, RET, TrkC, Ptc- with a specifically larger emphasis on netrin-1 receptors, to address (i) the common and divergent cell signaling mechanisms triggering apoptosis downstream of these receptors and (ii) the physiological and pathological roles of these DRs on development of neoplasia in vivo. This latter goal will allow us to investigate how this pro-apoptotic activity can be of use to improve and diversify alternative anti-cancer therapeutic approaches."
Summary
"While it is assumed that transmembrane receptors are active only in the presence of ligand, we have proposed that some receptors may also be active in the absence of ligand stimulation. These receptors, named “dependence receptors” (DRs) share the ability to transmit two opposite signals: in the presence of ligand, these receptors transduce various classical “positive” signals, whereas in the absence of ligand, they trigger apoptosis. The expression of dependence receptors thus creates cellular states of dependence for survival on their respective ligands. To date, more than fifteen such receptors have been identified, including the netrin-1 receptors DCC (Deleted in Colorectal Cancer) and UNC5H1-4, some integrins, RET, EPHA4, TrkA, TrkC and the Sonic Hedgehog receptor Patched (Ptc). Even though the interest in this notion is increasing, two main questions remain poorly understood: (i) how very different receptors, with only modest homology, are able to trigger apoptosis when unengaged by their respective ligand, and (ii) what are the respective biological roles of this pro-apoptotic activity in vivo. We have hypothesized that the DRs pro-apoptotic activity is a mechanism that determines and regulates the territories of migration/localization of cells during embryonic development. We also demonstrated that this may be a mechanism that limits tumor growth and metastasis. The goal of the present project is, based on the study of a relatively small number of these receptors –i.e., DCC, UNC5H, RET, TrkC, Ptc- with a specifically larger emphasis on netrin-1 receptors, to address (i) the common and divergent cell signaling mechanisms triggering apoptosis downstream of these receptors and (ii) the physiological and pathological roles of these DRs on development of neoplasia in vivo. This latter goal will allow us to investigate how this pro-apoptotic activity can be of use to improve and diversify alternative anti-cancer therapeutic approaches."
Max ERC Funding
2 485 037 €
Duration
Start date: 2012-05-01, End date: 2017-04-30
Project acronym DiSect
Project The Tumour Stroma as a Driver of Clonal Selection
Researcher (PI) Claus JORGENSEN
Host Institution (HI) THE UNIVERSITY OF MANCHESTER
Call Details Consolidator Grant (CoG), LS4, ERC-2017-COG
Summary Pancreatic ductal adenocarcinomas (PDA) are complex heterocellular tumours characterised by extensive desmoplasia. Tumour and stromal host cells actively engage to establish reciprocal signalling loops, which drive cancer progression, resistance to treatment and evasion of immune surveillance. However, the specificity and directionality of these interactions are incompletely characterised.
We have previously shown that tumour cells expressing the main oncogenic driver (KRASG12D) co-opt stromal fibroblasts to elicit a reciprocal signal, which activate tumour cell IGF-1R and AXL receptor tyrosine kinases. Importantly, these signals enable tumour cells to engage additional signalling pathways not activated when oncogenic KRAS is expressed in homogeneous tumour cell cultures. Therefore, to fully appreciate tumour cell signalling, studies should be undertaken within the context of the tumour stroma.
Early stages of PDA display a gradual accumulation of mutations where activated KRAS is accompanied by loss of tumour suppressors CDKN2A, TP53 and SMAD4. Simultaneously, there is an accumulation of infiltrating stromal cells. To address how PDA cells differ in their interaction with the infiltrating stroma, we will use in vitro co-cultures to study how PDA cells with frequent genetic aberrations recruit and interact with host stromal cells. We will combine our unique methodologies for cell-specific labelling with global proteomics and phosphoproteomics analysis to discern cell-specific signalling between tumour and stroma cells. Following, we will analyse the impact of the tumour stroma on clonal selection and use computational modelling to identify which cell autonomous and non-cell autonomous signals drive progression. Delineating how reciprocal signalling regulates early tumour cell signalling and clonal selection is critical to define pro-tumorigenic from restrictive stromal elements in order to improve combination therapies.
Summary
Pancreatic ductal adenocarcinomas (PDA) are complex heterocellular tumours characterised by extensive desmoplasia. Tumour and stromal host cells actively engage to establish reciprocal signalling loops, which drive cancer progression, resistance to treatment and evasion of immune surveillance. However, the specificity and directionality of these interactions are incompletely characterised.
We have previously shown that tumour cells expressing the main oncogenic driver (KRASG12D) co-opt stromal fibroblasts to elicit a reciprocal signal, which activate tumour cell IGF-1R and AXL receptor tyrosine kinases. Importantly, these signals enable tumour cells to engage additional signalling pathways not activated when oncogenic KRAS is expressed in homogeneous tumour cell cultures. Therefore, to fully appreciate tumour cell signalling, studies should be undertaken within the context of the tumour stroma.
Early stages of PDA display a gradual accumulation of mutations where activated KRAS is accompanied by loss of tumour suppressors CDKN2A, TP53 and SMAD4. Simultaneously, there is an accumulation of infiltrating stromal cells. To address how PDA cells differ in their interaction with the infiltrating stroma, we will use in vitro co-cultures to study how PDA cells with frequent genetic aberrations recruit and interact with host stromal cells. We will combine our unique methodologies for cell-specific labelling with global proteomics and phosphoproteomics analysis to discern cell-specific signalling between tumour and stroma cells. Following, we will analyse the impact of the tumour stroma on clonal selection and use computational modelling to identify which cell autonomous and non-cell autonomous signals drive progression. Delineating how reciprocal signalling regulates early tumour cell signalling and clonal selection is critical to define pro-tumorigenic from restrictive stromal elements in order to improve combination therapies.
Max ERC Funding
1 969 768 €
Duration
Start date: 2018-06-01, End date: 2023-05-31
Project acronym DismantlingNoise
Project Dissecting the (epi)genetic origins of phenotypic variation and metabolic disease susceptibility
Researcher (PI) John Andrew Pospisilik
Host Institution (HI) MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Call Details Consolidator Grant (CoG), LS4, ERC-2015-CoG
Summary Current estimates place the prevalence of obesity beyond 1 billion by the year 2030. As a critical risk factor for heart disease, diabetes and stroke, obesity represents one of the chief socio-economic challenges of our day. While studies have mapped a genetic framework for understanding obesity, the etiological contribution of several regulatory layers, and in particular epigenetic regulation, remain poorly understood. A perfect example, we know that isogenic C57Bl6/J mice can vary by as much as 100% in body weight upon high fat feeding; currently, we have no mechanistic explanation for the emergence of such phenotypic variation. Here, I propose three aims dedicated towards understanding the (epi)genetic control of phenotypic variation and disease susceptibility. First, we will catalogue epigenome and phenome variation to an unprecedented depth and resolution in the isogenic context. Next, we will examine two completely novel models of epigenetically sensitized bi-stable obesity and thus begin a mechanistic dissection of phenotypic variation. Finally, we will map a series of gene-gene and gene-environment epistasis interactions including eight models of developmental plasticity and approximately a dozen chromatin regulator mutants. The latter epistasis matrix will identify the molecular mechanisms that trigger, amplify and buffer phenotypic variation and stochastic obesity in mice. The functional (epi)phenomics approach is unique. It builds the first unbiased framework against which to understand developmental plasticity and phenotypic variation, and at the same time generates powerful resources for disease researchers worldwide.
Summary
Current estimates place the prevalence of obesity beyond 1 billion by the year 2030. As a critical risk factor for heart disease, diabetes and stroke, obesity represents one of the chief socio-economic challenges of our day. While studies have mapped a genetic framework for understanding obesity, the etiological contribution of several regulatory layers, and in particular epigenetic regulation, remain poorly understood. A perfect example, we know that isogenic C57Bl6/J mice can vary by as much as 100% in body weight upon high fat feeding; currently, we have no mechanistic explanation for the emergence of such phenotypic variation. Here, I propose three aims dedicated towards understanding the (epi)genetic control of phenotypic variation and disease susceptibility. First, we will catalogue epigenome and phenome variation to an unprecedented depth and resolution in the isogenic context. Next, we will examine two completely novel models of epigenetically sensitized bi-stable obesity and thus begin a mechanistic dissection of phenotypic variation. Finally, we will map a series of gene-gene and gene-environment epistasis interactions including eight models of developmental plasticity and approximately a dozen chromatin regulator mutants. The latter epistasis matrix will identify the molecular mechanisms that trigger, amplify and buffer phenotypic variation and stochastic obesity in mice. The functional (epi)phenomics approach is unique. It builds the first unbiased framework against which to understand developmental plasticity and phenotypic variation, and at the same time generates powerful resources for disease researchers worldwide.
Max ERC Funding
1 997 853 €
Duration
Start date: 2017-01-01, End date: 2021-12-31
