Objective
Autoimmune and degenerative diseases with an inflammatory component are traditionally studied independently. Particularly for autoimmune diseases, most studies emphasize the role of the immune system rather than the target tissues. This hamper understanding of fundamental mechanisms of diseases and the identification or repurposing of drugs that might be useful for diverse conditions. In the present project our overarching goal is to merge the gene and protein signatures of targeted tissues of highly prevalent inflammatory endocrine and brain diseases – accessible for the first time on a large scale for human tissues – with advanced inducible pluripotent cell (iPSC)-based studies that will allow us to test and validate the novel mechanistic findings, including drug discovery and repurposing, on the relevant human tissues with focus on β-cells in T1D. Against this background, the specific objectives of the project are: 1. To mine available RNA sequencing (RNAseq) data and proteomics from the target cells/tissues of T1D, T2D, MS, AD and RA (whenever available from different early and late stages of the disease) and compare them to our own datasets of in vitro stressed target cells; 2. Use advanced bioinformatics strategies for data integration to identify key gene signatures, networks and pathways that are common or divergent between the five diseases (T1D, T2D, MS, AD, RA) and then mine the information for drug discovery and repurposing, aiming to identify agents that counteract key pathogenic steps and may lead to target tissue protection; 3. Use induced pluripotent stem cells (iPSCs)-derived human β-like cells and primary human islets to study the mechanisms of cell distress identified in Aims 1-2, as well as the impact of candidate genes and the newly identified drugs on β-cell function and survival.
The ultimate objective of the present project is to translate our findings into the discovery of novel drugs for the treatment of T1D, including drugs that may repurposed from RA, MS or AD therapy.
Background Rationale
Autoimmune diseases are diseases of “mistaken identity”, where the immune system – which is supposed to protect us against infectious diseases and neoplasias – mistakenly attacks and destroys components of our own body. There is no cure for autoimmune diseases and their incidence is increasing on a worldwide basis: these conditions - including type 1 diabetes (T1D), rheumatoid arthritis (RA) and multiple sclerosis (MS) - now affect up to 8% of the population in different regions of the globe. While the immune targets of these diseases are distinct, they share several similar features, including up to 50% common genetic risk, chronic local inflammation and mechanisms mediating target tissue damage. Other highly prevalent degenerative diseases, such as type 2 diabetes (T2D) and Alzheimer’s disease (AD), show important inflammatory but not clear autoimmune components. Despite of these common features, autoimmune disorders are traditionally studied independently and with a focus on the immune system rather than on the target tissues. There is, however, increasing evidence that the target tissues of these diseases are not innocent bystanders of the autoimmune attack but participate in a deleterious dialogue with the immune system that contributes to their own demise as shown in recent publications by the Eizirik’s group. Furthermore, in T1D several of the candidate genes that predispose to disease act at the target tissue level (i.e. pancreatic β-cells) regulating the responses to viral infections, the dialogue with the immune system and cell death. We hypothesize that key inflammation-induced mechanisms, potentially shared between T1D, RA and MS, and eventually T2D and AD, may induce similar molecular signatures at the target tissue level. Discovering similar (or, in some cases, divergent) disease-specific signatures may allow us to identify the key regulatory genes that could be targeted for therapy and the repurposing of drugs already in clinical use for other diseases. Indeed, repurposing already FDA-approved drugs whose toxicology, pharmacodynamics, and pharmacokinetic profiles are characterized will facilitate the bench-to-bedside transition. For instance, based on the approach proposed above, we have identified inhibitors of the cytokine interferon-alpha, already in use to treat psoriasis, a skin autoimmune disease, as potential agents to protect pancreatic β-cells in T1D. The rationale for selecting the diseases indicated above includes: 1. The striking gene expression similarity between pancreatic β-cells and neurons; 2. The fact that T1D and MS have several candidate genes in common, and express – at least to some extent – similar up-regulated inflammatory pathways at the target tissue levels; 3. The potential role for inflammation and amyloid deposition in both T2D and AD; 4. The fact that RA, as T1D, is a tissue- targeted autoimmune disease, involving infiltration by T and B lymphocytes and local inflammation.
Description of Project
Autoimmune diseases are diseases of “mistaken identity”, where the immune system – which is supposed to protect us against infectious diseases and neoplasias – mistakenly attacks and destroys components of our own body. There is no cure for autoimmune diseases and their incidence is increasing on a worldwide basis: these conditions - including type 1 diabetes (T1D), rheumatoid arthritis (RA) and multiple sclerosis (MS) - now affect up to 8% of the population in different regions of the globe. While the immune targets of these diseases are distinct, they share several similar features, including up to 50% common genetic risk, chronic local inflammation and mechanisms mediating target tissue damage. Other highly prevalent degenerative diseases, such as type 2 diabetes (T2D) and Alzheimer’s disease (AD), show important inflammatory but not clear autoimmune components. Despite of these common features, autoimmune disorders are traditionally studied independently and with a focus on the immune system rather than on the target tissues. There is, however, increasing evidence that the target tissues of these diseases are not innocent bystanders of the autoimmune attack but participate in a deleterious dialogue with the immune system that contributes to their own demise as shown in recent publications by the Eizirik’s group. Furthermore, in T1D several of the candidate genes that predispose to disease act at the target tissue level (i.e. pancreatic β-cells) regulating the responses to viral infections, the dialogue with the immune system and cell death. We hypothesize that key inflammation-induced mechanisms, potentially shared between T1D, AR and MS, and eventually T2D and AD, may induce similar molecular signatures at the target tissue level. Discovering similar (or, in some cases, divergent) disease-specific signatures may allow us to identify the key regulatory genes that could be targeted for therapy and the repurposing of drugs already in clinical use for other diseases. Indeed, repurposing already FDA-approved drugs whose toxicology, pharmacodynamics, and pharmacokinetic profiles are characterized will facilitate the bench-to-bedside transition. For instance, we have identified inhibitors of the cytokine interferon-alpha, already in use to treat psoriasis, as potential agents to protect pancreatic β-cells in T1D. The rationale for selecting the diseases indicated above includes: 1. The striking gene expression similarity between pancreatic β-cells and neurons; 2. The fact that T1D, RA and MS have several candidate genes in common, and express – at least to some extent – similar up-regulated inflammatory pathways at the target tissue levels; 3. The potential role for inflammation and amyloid deposition in both T2D and AD. Against this background, the aims of the present project are:
1. To mine available RNA sequencing (RNAseq) data and proteomics from the target cells/tissues of T1D, T2D, MS, AD and RA (whenever available from both early and late stages of the disease) and compare them to our own datasets of in vitro stressed β-cells; 2. Use advanced bioinformatics strategies for data integration to identify key gene signatures, networks and pathways that are common or divergent between the five diseases (T1D, T2D, MS, AD, RA) and then mine the information for drug discovery and repurposing, aiming to identify agents that counteract key pathogenic steps and may lead to target tissue protection; 3. Use induced pluripotent stem cells (iPSCs)-derived human β-like cells and primary human islets to study the mechanisms of cell distress identified in Aims 1-2, as well as the impact of candidate genes and the newly identified drugs on β-cell function and survival. The ultimate objective of the present project is to translate our findings into the discovery of novel drugs for the treatment of T1D, including drugs that may repurposed from RA, MS or AD therapy.
Anticipated Outcome
We anticipate the discovery of key gene and protein pathways that mediate tissue damage in pancreatic β-cells and brain tissue during T1D and other autoimmune/degenerative diseases with an inflammatory component. Using advanced bioinformatics approaches, at least in part generated by our group, we will “mine” these disease-mediating pathways to identify drugs that antagonize them and may thus protect β-cells and other target tissues. One of these drug families, namely bromodomain inhibitors (already being tested for AD and some cancers), is already being evaluated to protect human islets against pro-inflammatory cytokines with promising results. We anticipate discovering at least 2-3 additional agents or drug families that will be validated in human islets and then in follow up studies in pre-clinical models of disease as potential therapies to protect β-cells in T1D.
Relevance to T1D
The goal of the present project is to translate our findings into the discovery of novel drugs for the treatment of T1D, including drugs that may repurposed from RA, MS or AD therapy. We have already successfully used this approach to identify potential therapeutic targets and their corresponding drugs for T1D and other autoimmune diseases. Two of these newly identified agents, JAK1/2 and TYK2 inhibitors, have been validated by us and others as protecting β-cells in vitro against cytokine-induced inflammatory responses, dysfunction and death and a third one, a bromodomain inhibitor, will be tested in the course of the present project. In the case of TYK2 inhibitors, we have already promising data that it prevents diabetes in vivo in mouse models (unpublished data; JDRF-supported project in collaboration with Dr Evans-Mollina). A similar approach will be used here, i.e. key findings related to validation of novel drugs will be first tested in human β-cells and then confirmed in follow up projects using mouse models of T1D. Starting with human β-cells and data from actual human diseases, i.e. global gene expression of tissues from relevant diseases, it is crucial to identify key pathogenic pathways that will allow us to mine for drugs that antagonize these deleterious pathways and thus protect β-cells. We propose that this “human-first” approach will decrease the many disappointments generated by following the opposite approach, i.e. starting with mouse models (where hundreds of agents prevent diabetes) and then moving to human T1D. We expect that novel relevant pathways will be discovered and translated into new therapies during the present and future follow up projects.