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Precisely defining disease variant effects in CRISPR-edited single cells

A plate-based assay called CRAFTseq has been developed that uses ‘multi-omic’ single-cell RNA sequencing and direct genotyping of CRISPR edits to test the functional effects of genetic variants on cell state and function.

Yuriy Baglaenko
Zepeng Mu
Soumya Raychaudhuri
ResearchOpen Access23 Jul 2025
Nature

Volume: 646, P: 117-125
Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions

TCAT is a pipeline that can simultaneously capture gene expression programs related to T cell subsets and activation states for accurate T cell characterization.

Dylan Kotliar
Michelle Curtis
Soumya Raychaudhuri
ResearchOpen Access03 Sept 2025
Nature Methods

Volume: 22, P: 1964-1980
Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development

Fine-mapping has previously implicated the non-coding single nucleotide polymorphism rs117701653 as a risk variant for rheumatoid arthritis and type 1 diabetes, however its function remained unclear. Here the authors show that this variant decreases binding of the inhibitory factor SMCHD1 to enhance expression of ICOS, promoting development of potentially pathogenic T peripheral helper cells.

Taehyeung Kim
Marta Martínez-Bonet
Peter A. Nigrovic
ResearchOpen Access09 Mar 2024
Nature Communications

Volume: 15, P: 1-14
Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci

Deep mRNA sequencing at eight time points during memory CD4⁺ T cell activation identifies widespread dynamic allele-specific expression events that are enriched in HLA and other autoimmune disease loci.

Maria Gutierrez-Arcelus
Yuriy Baglaenko
Soumya Raychaudhuri
Research17 Feb 2020
Nature Genetics

Volume: 52, P: 247-253
Single-cell eQTL models reveal dynamic T cell state dependence of disease loci

A single-cell Poisson model is used to analyse eQTLs in memory T cells across continuous, dynamic cell states, revealing that the cell context is critical to understanding variation in eQTLs and their association with disease.

Aparna Nathan
Samira Asgari
Soumya Raychaudhuri
Research11 May 2022
Nature

Volume: 606, P: 120-128
The liver and muscle secreted HFE2-protein maintains central nervous system blood vessel integrity

Blood vessel integrity is critical to maintain brain health. Here, the authors show that both the liver and the muscles secrete HFE2, a protein that promotes blood vessel integrity in healthy animals and in an animal model for multiple sclerosis.

Xue Fan Wang
Robin Vigouroux
Philippe P. Monnier
ResearchOpen Access03 Feb 2024
Nature Communications

Volume: 15, P: 1-16
Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin

Psoriasis is a chronic, systemic inflammatory condition primarily affecting skin. Here, the authors investigate the genetic basis of gene expression in skin biopsies from psoriasis patients and interactions with inflammation to better understand mechanisms of the disease.

Qian Xiao
Joseph Mears
Soumya Raychaudhuri
ResearchOpen Access07 Oct 2023
Nature Communications

Volume: 14, P: 1-17
Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians

Between 5 and 15% of latent Mycobacterium tuberculosis infections develop into active tuberculosis (TB). Here, Luo et al. report a genome-wide association study for early TB progression in a total of 4002 active TB cases and their household contacts in Peru and they identify a locus on 3q23 in which ATP1B3 is mapped as the likely causal gene.

Yang Luo
Sara Suliman
Soumya Raychaudhuri
ResearchOpen Access21 Aug 2019
Nature Communications

Volume: 10, P: 1-10
Fast, sensitive and accurate integration of single-cell data with Harmony

Harmony, for the integration of single-cell transcriptomic data, identifies broad and fine-grained populations, scales to large datasets, and can integrate sequencing- and imaging-based data.

Ilya Korsunsky
Nghia Millard
Soumya Raychaudhuri
Research18 Nov 2019
Nature Methods

Volume: 16, P: 1289-1296
Apoptotic cell–induced AhR activity is required for immunological tolerance and suppression of systemic lupus erythematosus in mice and humans

McGaha and colleagues show that phagocytosis of apoptotic cells leads to activation of the transcription factor AhR and production of the cytokine IL-10 in phagocytes, in a manner dependent on the recognition of DNA.

Rahul Shinde
Kebria Hezaveh
Tracy L. McGaha
Research14 May 2018
Nature Immunology

Volume: 19, P: 571-582
Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease

Raychaudhuri and colleagues use high-dimensional single-cell analysis of T cells from a human tuberculosis progression cohort. They identify a T_H17–like cluster reactive to Mycobacterium tuberculosis peptides that is reduced in people who previously progressed to active disease.

Aparna Nathan
Jessica I. Beynor
Soumya Raychaudhuri
Research24 May 2021
Nature Immunology

Volume: 22, P: 781-793
Genome editing to define the function of risk loci and variants in rheumatic disease

Genome editing technology, such as CRISPR–Cas, has great potential in the study of rheumatic disease genetics, including in discovering disease-associated genes and regulatory regions, in validating causal variants and in characterizing important cell types and cell states.

Yuriy Baglaenko
Dana Macfarlane
Soumya Raychaudhuri
Reviews29 Jun 2021
Nature Reviews Rheumatology

Volume: 17, P: 462-474

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