Soumya Raychaudhuri

Oct 22, 2024 | nature.com | Maria Kiourlappou |Lisa Gartner |Nicholas E. Ilott |Fadi Issa |Joanna Hester |Jason Turner | +12 more

AbstractPrecision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular understanding of treatment response. We describe a therapeutic atlas for Crohn’s disease (CD) and ulcerative colitis (UC) following adalimumab, an anti-tumour necrosis factor (anti-TNF) treatment. We generated ~1 million single-cell transcriptomes, organised into 109 cell states, from 216 gut biopsies (41 subjects), revealing disease-specific differences.

Jul 30, 2024 | nature.com | Joshua Chiou |Saori Sakaue |Stephen Christensen |Soumya Raychaudhuri

AbstractGenetic variation in the human leukocyte antigen (HLA) loci is associated with risk of immune-mediated diseases, but the molecular effects of HLA polymorphism are unclear. Here we examined the effects of HLA genetic variation on the expression of 2940 plasma proteins across 45,330 Europeans in the UK Biobank, with replication analyses across multiple ancestry groups.

Jun 11, 2024 | nature.com | Garrett S. Dunlap |Nida Meednu |Ruoqiao Wang |fan zhang |Anna Jonsson |Kevin H-C Wei | +11 more

AbstractRheumatoid arthritis (RA) is an autoimmune disease involving antigen-specific T and B cells. Here, we perform single-cell RNA and repertoire sequencing on paired synovial tissue and blood samples from 12 seropositive RA patients. We identify clonally expanded CD4 + T cells, including CCL5+ cells and T peripheral helper (Tph) cells, which show a prominent transcriptomic signature of recent activation and effector function.

Mar 26, 2024 | nature.com | Vanessa L Kronzer |Jeffrey A Sparks |Soumya Raychaudhuri

AbstractRheumatoid arthritis (RA) has an estimated heritability of nearly 50%, which is particularly high in seropositive RA. HLA alleles account for a large proportion of this heritability, in addition to many common single-nucleotide polymorphisms with smaller individual effects. Low-frequency and rare variants, such as those captured by next-generation sequencing, can also have a large role in heritability in some individuals.

Feb 22, 2024 | biorxiv.org | Soumya Raychaudhuri |Cristian Valencia |Aparna Nathan |Joyce B Kang

AbstractIdentifying response expression quantitative trait loci (reQTLs) can help to elucidate mechanisms of disease associations. Typically, such studies model the effect of perturbation as discrete conditions. However, perturbation experiments usually affect perturbed cells heterogeneously.