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Modern medicine keeps unraveling new ways to investigate autoimmunity, leading to the production of boundless amounts of genetic, cellular and imaging data. Although the precision with which this information can define the etiology and mechanisms of a particular autoimmune disease is encouraging, much work lies ahead until all the knowledge acquired can be translated into the clinic. In 'Bedside to Bench', Calliope A. Dendrou, John I. Bell and Lars Fugger discuss the promises and limitations of genome-wide and next-generation genetic studies to provide further understanding of mechanisms driving autoimmune disorders and the role of experimental medicine in the new era of integrative clinical practice and personalized medicine. In 'Bench to Bedside', Lawrence Steinman argues the concept of a 'hub and spoke' pattern of T cell activation and organ targeting in multiple sclerosis, inflammatory bowel disease and type 1 diabetes. This paradigm suggests new ways to develop drugs to keep autoreactive T cells in the organ where activation occurs and preclude them from reaching the target organ and cause disease.

Technological advances have given valuable insight into the molecular mechanisms that underpin the association between HLA genetics and disease. Dendrou and colleagues review mechanisms of HLA–peptide–T cell receptor binding in health and disease and discuss how this knowledge may be translated into clinical benefit.

In this Resource, Buckley and colleagues profile patients with Crohn’s disease and ulcerative colitis before and after adalimumab therapy. Specific pretreatment differences in the epithelial and myeloid compartments were associated with remission outcomes in both diseases. The authors also describe the cellular circuitry in nonremission patients following treatment.

This Review provides an insightful discussion on the current concepts in multiple sclerosis research, including genetic predisposition and environmental triggers, and explores the evolving link between inflammation and neurodegeneration. The authors highlight the clinical challenges and key questions that remain to be addressed.

Genome-wide association studies in combination with functional analyses identify a genetic variant that explains why anti-tumour necrosis factor therapy, used in several autoimmune diseases, exacerbates multiple sclerosis.

Gil McVean and colleagues present a new Bayesian analysis framework that exploits the hierarchical structure of diagnosis classifications to analyze genetic variants against UK Biobank disease phenotypes derived from self-reporting and hospital episode statistics. Their method displays increased power to detect genetic effects over other approaches and identifies novel associations between classical HLA alleles and common immune-mediated diseases.

Peng et al. find that immunodominant cytotoxic T lymphocytes (CTLs) specific for NP_105–113-B*07:02 are associated with reduced COVID-19 severity. Mechanistically, NP_105–113-B*07:02-specific CTLs show potent antiviral functionality and may represent rational T cell vaccine targets.

Gilean McVean and colleagues report the results of a large-scale clinical genome sequencing project spanning a broad spectrum of disorders. They identify factors influencing successful genetic diagnosis and highlight the challenges of interpreting findings for genetically heterogeneous disorders.

HLA-C expression levels correlate with immune responses to pathogens and autoimmunity, and vary in an allele-specific manner across individuals. Here the authors identify factors that drive differential expression of HLA-C allomorphs at the cell surface, and influence the structure of the peptide-binding cleft and diversity of peptides bound by HLA-C molecules.

FitzPatrick et al. use single-cell RNA and spatial transcriptomics to dissect the immune microenvironments within the small bowel mucosa in celiac disease.

Neuroinflammation is central in many neurological conditions, and 'big data' have the potential to elucidate the complexity of inflammatory processes. This Review considers how the drive to collect and analyse big data is increasing our understanding of neuroinflammation in disease, and how these data can be used to improve clinical management.

A method to cluster genetic risk profiles applied to 3,025 loci across 19,155 disease codes from over 300,000 individuals in the UK Biobank identifies 339 distinct disease association profiles and links clusters to biological pathways.

By complementing spatial transcriptomics with high-resolution proteomics, Kaufmann et al. tracked a gradient of disease severity across the brains of patients with progressive multiple sclerosis, uncovering new therapeutic opportunities to slow disease.

Linda Wicker and colleagues examine the effect of SNPs in the IL2RA region, previously associated to type 1 diabetes, on CD25 protein expression on the cell surface of primary immune cells from donors within the Cambridge BioResource. They demonstrate the value of using fresh primary cells from a large bioresource of genotype-selectable healthy volunteers.

Gil McVean and colleagues report a meta-analysis of Immunochip studies including over 17,000 multiple sclerosis cases and 30,000 controls, with imputation of classical HLA alleles. They find two interactions involving class II HLA alleles but no evidence for significant epistatic interactions or interactions between HLA and non-HLA risk variants.