Search

Single-cell and spatial transcriptomics analysis of stricturing Crohn’s disease highlights cellular heterogeneity in fibrotic tissue and identifies neighborhoods of fibroblasts and immune cells contributing to this severe disease complication.

Currently, gut microbiome profiling largely relies on next-generation sequencing, which is slow and expensive. Here, the authors develop a low-cost, paper-based synthetic biology platform that allows species-specific quantification of bacterial mRNAs and clinically relevant host biomarkers.

In this Review, Iliev, Ananthakrishnan and Guo explore the gut microbiota in inflammatory bowel disease, highlighting bacterial and fungal components, immune mechanisms, metabolites, links between the microbiota and enteric nervous system, as well as therapeutic and diagnostic opportunities.

A novel multi-omics workflow, combining gut microbiome metagenomics, metatranscriptomics and metabolomics, enabled the identification of the microbial pathways responsible for the degradation of the immunomodulatory drug 5-ASA in the gut of patients with inflammatory bowel disease.

PINNACLE is a context-specific geometric deep learning model for generating protein representations. Leveraging single-cell transcriptomics combined with networks of protein–protein interactions, cell type-to-cell type interactions and a tissue hierarchy, PINNACLE generates high-resolution protein representations tailored to each cell type.

A new discovery strategy, ‘reverse metabolomics’, facilitates high-throughput matching of mass spectrometry spectra in public untargeted metabolomics datasets, and a proof-of-concept experiment identified an association between microbial bile amidates and inflammatory bowel disease.

Polygenic Priority Score (PoPS) prioritizes candidate effector genes at complex trait loci by integrating genome-wide association summary statistics with other data types. Combining PoPS with methods that leverage local genetic signals further improves the performance.

Large-scale sequence-based analyses identify novel risk variants and susceptibility genes for Crohn’s disease, and implicate mesenchymal cell-mediated intestinal homeostasis in disease etiology.

While hundreds of loci are linked with inflammatory bowel diseases (IBDs), the functional consequences of the associated variants remain unclear. Here, the authors screened in ulcerative colitis (UC) patients’ genomes for protein-truncating variants near IBD loci, and identify a protein truncating variant in RNF186to be protective against UC.

scHLApers is an analysis pipeline that quantifies single-cell expression of HLA genes using a personalized genomic reference. Mapping of HLA expression quantitative trait loci at single-cell resolution identifies dynamic effects across cell states.

The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

Analysis of paired metagenomes and metatranscriptomes associated with patients with inflammatory bowel disease (IBD) and non-IBD controls over time provides some insights into microbial community variation and potential pathways influencing IBD symptoms.

A wide variety of environmental triggers have been associated with IBD pathogenesis, including the gut microbiota, diet, pollution and early-life factors. This Review discusses the latest evidence and progress towards better understanding the environmental factors associated with IBD.

The incidence and prevalence of IBD is changing, in both established and emerging populations. Here, the epidemiological trends of IBD are described, as are the risk factors (such as genetics, microbiota and lifestyle) that might contribute to disease development. How these risk factors, particularly the environmental ones, can be modified as a means of intervention for disease management are also discussed.

Inflammatory bowel disease (IBD) has emerged as a global disease, yet identifying those at higher risk of developing IBD remains challenging. A new study highlights the use of a multi-ethnic polygenic risk score to determine risk of inflammatory bowel disease in a large primary care population.

Important studies published in 2018 highlight novel therapeutic strategies along the disease course of IBD, including potential specific dietary modifications at early stages and treatment with adipose-derived stem cells in perianal Crohn’s disease. A treat-to-target approach that involves proactive serial monitoring of inflammatory biomarkers can assist in timely treatment escalation and promises improved patient outcomes.

PheCAP takes structured data and narrative notes from electronic medical records and enables patients with a particular clinical phenotype to be identified.

Most of the more than 200 known genetic risk loci for inflammatory bowel disease (IBD) reside in regulatory regions. Here, the authors provide eQTL datasets for six circulating immune cell types and ileal, colonic and rectal biopsies to map regulatory modules and identify potential causative genes for IBD.

A meta-analysis of previous genome-wide association studies of Crohn’s disease and ulcerative colitis, the two most common forms of inflammatory bowel disease, with a combined total of more than 75,000 cases and controls, finds that most loci contribute to both phenotypes and other immune-mediated disorders.

In this Review, Jess and colleagues describe the prevalence of depression and anxiety in patients with inflammatory bowel disease, the mechanisms underlying the bidirectional association between these diseases and the effect of treatment on their co-occurrence.

Clostridium difficileis as an important health-care-associated pathogen and is linked to significant morbidity, economic burden, and even mortality. A dramatic rise in the incidence ofC. difficileinfections has occurred over the past decade and new at-risk populations are emerging. This Review discusses recent changes in the epidemiology of CDI and its risk factors, examines the evidence behind various treatment regimens and management strategies and suggests measures for infection control.

Emerging data implicate diet as a crucial factor in the development and progression of IBD. Here, the authors discuss epidemiological, animal, gene–environment interaction and gut microbiome studies that have investigated the role of diet in the aetiopathogenesis of IBD.

Fatigue is an important problem for patients with IBD, but little is known about its pathophysiology. In this Review, the authors explore the epidemiology, putative mechanisms and optimal management of this symptom.

In an inter-laboratory study, the authors compare the accuracy and performance of three optical density calibration protocols (colloidal silica, serial dilution of silica microspheres, and colony-forming unit (CFU) assay). They demonstrate that serial dilution of silica microspheres is the best of these tested protocols, allowing precise and robust calibration that is easily assessed for quality control and can also evaluate the effective linear range of an instrument.

John Rioux, Andre Franke, Tom Karlsen and colleagues perform a fine-mapping study of the HLA region in Crohn's disease and ulcerative colitis. They identify a primary role for HLA-DRB1*01:03 in both diseases and find evidence of heterozygous advantage in protection against ulcerative colitis.