Genetic defects and immune dysregulation in patients with early onset inflammatory bowel disease

Project Overview

Model of key intestinal defence functions and cellular immune regulation modules that are impaired ...

Monocyte derived macrophage ingesting Salmonella typhimurium. Different stages of degradation of ...

Inflammatory bowel disease (IBD) encompasses two major diseases Crohn’s disease and ulcerative colitis. A subgroup of children with very early-onset IBD presents with a severe phenotype, is non-responsive to conventional therapy and needs early surgery. Several monogenic disorders can present as very early onset IBD. This includes several forms of immunodeficiency or defects in bacterial handling  as well as defects in immune regulation. We investigate children with very early onset of intestinal inflammation using whole genome or whole exome sequencing to discover novel high impact genes and analyse the involved signaling pathways in vitro, in situ and in vivo. We like to understand the pathogenesis of rare “orphan” diseases to develop better treatment options for those disorders and improve understanding of pathogenic mechanisms of IBD as a whole. 

A common pathomechanism for multiple immune disorders that present with intestinal inflammation is a defect in bacterial handling by macrophages caused by defective autophagy. We therefore study how genetic defects that affect key checkpoints in bacterial recognition and autophagolysosome maturation cause a hyper-inflammatory response. Mapping of the functional checkpoints that are affected by common genetic variants and rare defects will allow to understand basic biology and help to develop novel autophagy inducing therapies. 

Training Opportunities

Training opportunities include both basic immunology and translational research with close link to national and international pediatric gastroenterology departments. The project will have close link to the COLORS in IBD project aiming to understand genetic defects in children with very early onset of inflammatory bowel disease and the 100000 genome project using whole exome and genome sequencing . Laboratory techniques include analysis of next generation sequencing data (exome and genome sequencing), flow cytometric assays, T cell culture and differentiation, macrophage infection models, proteomics, laser scanning and laser microdissection microscopy. We culture primary immune cells assess bacterial recognition and handling pathways. Since patient primary cells can be very difficult to access in particular in very young children or in patients who have undergone stem cell transplantation, we differentiate macrophages from induces pluripotent stem cells. We use CRISPR/Cas9 to produce cells with defined genetic defects. This project will provide a unique insight into translational research from patient genetics towards immunology mechanisms and will allow the graduate student to interact with both basic researchers and clinicians. 


Immunology & Infectious Disease and Genetics & Genomics


Project reference number: 406

Funding and admissions information


Name Department Institution Country Email
Holm Uhlig Experimental Medicine Division Oxford University, John Radcliffe Hospital GBR
Professor Fiona Powrie FRS Experimental Medicine Division Oxford University, John Radcliffe Hospital GBR

Uhlig HH, Powrie F. 2018. Translating Immunology into Therapeutic Concepts for Inflammatory Bowel Disease. Annu. Rev. Immunol., 36 pp. 755-781. Read abstract | Read more

Inflammatory bowel disease (IBD) defines a spectrum of complex disorders. Understanding how environmental risk factors, alterations of the intestinal microbiota, and polygenetic and epigenetic susceptibility impact on immune pathways is key for developing targeted therapies. Mechanistic understanding of polygenic IBD is complemented by Mendelian disorders that present with IBD, pharmacological interventions that cause colitis, autoimmunity, and multiple animal models. Collectively, this multifactorial pathogenesis supports a concept of immune checkpoints that control microbial-host interactions in the gut by modulating innate and adaptive immunity, as well as epithelial and mesenchymal cell responses. In addition to classical immunosuppressive strategies, we discuss how resetting the microbiota and restoring innate immune responses, in particular autophagy and epithelial barrier function, might be key for maintaining remission or preventing IBD. Targeting checkpoints in genetically stratified subgroups of patients with Mendelian disorder-associated IBD increasingly directs treatment strategies as part of personalized medicine. Hide abstract

Uhlig HH, Muise AM. 2017. Clinical Genomics in Inflammatory Bowel Disease. Trends Genet., 33 (9), pp. 629-641. Read abstract | Read more

Genomic technologies inform the complex genetic basis of polygenic inflammatory bowel disease (IBD) as well as Mendelian disease-associated IBD. Aiming to diagnose patients that present with extreme phenotypes due to monogenic forms of IBD, genomics has progressed from 'orphan disease' research towards an integrated standard of clinical care. Advances in diagnostic clinical genomics are increasingly complemented by pathway-specific therapies that aim to correct the consequences of genetic defects. This highlights the exceptional potential for personalized precision medicine. IBD is nevertheless a challenging example for genomic medicine because the overall fraction of patients with Mendelian defects is low, the number of potential candidate genes is high, and interventional evidence is still emerging. We discuss requirements and prospects of explanatory and predictive clinical genomics in IBD. Hide abstract

Schulthess J, Pandey S, Capitani M, Rue-Albrecht KC, Arnold I, Franchini F, Chomka A, Ilott NE, Johnston DGW, Pires E, McCullagh J, Sansom SN, Arancibia-Cárcamo CV, Uhlig HH, Powrie F. 2019. The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages. Immunity, 50 (2), pp. 432-445.e7. Read abstract | Read more

Host microbial cross-talk is essential to maintain intestinal homeostasis. However, maladaptation of this response through microbial dysbiosis or defective host defense toward invasive intestinal bacteria can result in chronic inflammation. We have shown that macrophages differentiated in the presence of the bacterial metabolite butyrate display enhanced antimicrobial activity. Butyrate-induced antimicrobial activity was associated with a shift in macrophage metabolism, a reduction in mTOR kinase activity, increased LC3-associated host defense and anti-microbial peptide production in the absence of an increased inflammatory cytokine response. Butyrate drove this monocyte to macrophage differentiation program through histone deacetylase 3 (HDAC3) inhibition. Administration of butyrate induced antimicrobial activity in intestinal macrophages in vivo and increased resistance to enteropathogens. Our data suggest that (1) increased intestinal butyrate might represent a strategy to bolster host defense without tissue damaging inflammation and (2) that pharmacological HDAC3 inhibition might drive selective macrophage functions toward antimicrobial host defense. Hide abstract

Schwerd T, Pandey S, Yang HT, Bagola K, Jameson E, Jung J, Lachmann RH, Shah N, Patel SY, Booth C, Runz H, Düker G, Bettels R, Rohrbach M, Kugathasan S, Chapel H, Keshav S, Elkadri A, Platt N, Muise AM, Koletzko S, Xavier RJ, Marquardt T, Powrie F, Wraith JE, Gyrd-Hansen M, Platt FM, Uhlig HH. 2016. Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn's disease. Gut, Read abstract | Read more

OBJECTIVE: Patients with Niemann-Pick disease type C1 (NPC1), a lysosomal lipid storage disorder that causes neurodegeneration and liver damage, can present with IBD, but neither the significance nor the functional mechanism of this association is clear. We studied bacterial handling and antibacterial autophagy in patients with NPC1. DESIGN: We characterised intestinal inflammation in 14 patients with NPC1 who developed IBD. We investigated bacterial handling and cytokine production of NPC1 monocytes or macrophages in vitro and compared NPC1-associated functional defects to those caused by IBD-associated nucleotide-binding oligomerization domain-containing protein 2 (NOD2) variants or mutations in X-linked inhibitor of apoptosis (XIAP). RESULTS: Patients with the lysosomal lipid storage disorder NPC1 have increased susceptibility to early-onset fistulising colitis with granuloma formation, reminiscent of Crohn's disease (CD). Mutations in NPC1 cause impaired autophagy due to defective autophagosome function that abolishes NOD2-mediated bacterial handling in vitro similar to variants in NOD2 or XIAP deficiency. In contrast to genetic NOD2 and XIAP variants, NPC1 mutations do not impair NOD2-receptor-interacting kinase 2 (RIPK2)-XIAP-dependent cytokine production. Pharmacological activation of autophagy can rescue bacterial clearance in macrophages in vitro by increasing the autophagic flux and bypassing defects in NPC1. CONCLUSIONS: NPC1 confers increased risk of early-onset severe CD. Our data support the concept that genetic defects at different checkpoints of selective autophagy cause a shared outcome of CD-like immunopathology linking monogenic and polygenic forms of IBD. Muramyl dipeptide-driven cytokine responses and antibacterial autophagy induction are parallel and independent signalling cascades downstream of the NOD2-RIPK2-XIAP complex. Hide abstract