Inflammatory bowel disease (IBD) is a severe, chronic pathology presenting with progressive intestinal inflammation and fibrosis, whose exact causes and key pathways remain poorly defined. Stromal–immune cell interactions have recently gained momentum in conceptualizing tissue homeostasis and our lab offered solid evidence establishing fibroblast heterogeneity and dominant roles in intestinal pathophysiology. Our recent preliminary evidence, indicated diverse spatial distribution of subsets of activated fibroblasts and revealed synergistic interplays of important inflammatory pathways driving pathogenicity. Detailed insights into such contextual complexities remain obscure. Here, we propose a novel unifying hypothesis that progressive IBD is orchestrated by specific subsets of fibroblasts, becoming causal to pathogenesis, depending on contextual information dictated by origin, topology, and cross-talks with immune or stromal cell types. We propose to use single-cell spatiotemporal phenotyping to deconvolute fibroblast subset-specific functions in disease-staged, fibrotic and non-fibrotic animal models of IBD. We aim to: (1) Map dynamic chromatin and gene expression programs that define cellular heterogeneity and infer cell interactions to build an ‘IBD connectome’ atlas (2) Analyse the origin, spatial distribution, plasticity and lineage trajectories of intestinal fibroblasts and reveal potential functions of pathogenic subsets (3) Perform discovery screens and functional validations on known (TNF, IFNγ, TGFb and interleukins) and novel fibroblast-subset-specific pathways focusing on potential synergistic interplays (4) Employ clinical material to validate involvement of the most prominent new pathways in human. The proposed research should help tackle the complexities of chronic inflammatory and fibrotic disorders in the intestine and beyond, advance mechanistic concepts in immune disease pathophysiology and promote fibroblast-targeting therapeutic discovery.

It is now widely recognized that a variety of major diseases, such as Alzheimer’s disease, Huntington’s disease, systemic amyloidosis, cystic fibrosis, type 2 diabetes etc., are characterized by a common molecular origin: the misfolding of specific proteins. These disorders have been termed protein misfolding diseases (PMDs) and the vast majority of them remain incurable. Here, I propose the development of a unified approach for the discovery of potential therapeutics against PMDs. I will generate engineered bacterial cells that function as a broadly applicable discovery platform for compounds that rescue the misfolding of PMD-associated proteins (MisPs). These compounds will be selected from libraries of drug-like molecules biosynthesized in engineered bacteria using a technology that allows the facile production of billions of different test molecules. These libraries will then be screened in the same bacterial cells that produce them and the rare molecules that rescue MisP misfolding effectively will be selected using an ultrahigh-throughput genetic screen. The effect of the selected compounds on MisP folding will then be evaluated by biochemical and biophysical methods, while their ability to inhibit MisP-induced pathogenicity will be tested in appropriate mammalian cell assays and in established animal models of the associated PMD. The molecules that rescue the misfolding of the target MisPs and antagonize their associated pathogenicity both in vitro and in vivo, will become drug candidates against the corresponding diseases. This procedure will be applied for different MisPs to identify potential therapeutics for four major PMDs: Huntington’s disease, cardiotoxic light chain amyloidosis, dialysis-related amyloidosis and retinitis pigmentosa. Successful realization of ProMiDis will provide invaluable therapeutic leads against major diseases and a unified framework for anti-PMD drug discovery.