The regulation and differentiation of regulatory T cells and their dysfunction in autoimmune diseases

TS Sumida, NT Cheru, DA Hafler - Nature Reviews Immunology, 2024 - nature.com
The discovery of FOXP3+ regulatory T (Treg) cells as a distinct cell lineage with a central
role in regulating immune responses provided a deeper understanding of self-tolerance …

Single-cell eQTL models reveal dynamic T cell state dependence of disease loci

A Nathan, S Asgari, K Ishigaki, C Valencia, T Amariuta… - Nature, 2022 - nature.com
Non-coding genetic variants may cause disease by modulating gene expression. However,
identifying these expression quantitative trait loci (eQTLs) is complicated by differences in …

Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis

K Ishigaki, S Sakaue, C Terao, Y Luo, K Sonehara… - Nature …, 2022 - nature.com
Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-
ancestry genetic research of RA promises to improve power to detect genetic signals, fine …

The genetic basis of autoimmunity seen through the lens of T cell functional traits

KA Lagattuta, HL Park, L Rumker, K Ishigaki… - Nature …, 2024 - nature.com
Autoimmune disease heritability is enriched in T cell-specific regulatory regions of the
genome. Modern-day T cell datasets now enable association studies between single …

The UCSC Genome Browser database: 2025 update

G Perez, GP Barber, A Benet-Pages… - Nucleic Acids …, 2025 - academic.oup.com
Abstract The UCSC Genome Browser (https://genome. ucsc. edu) is a widely utilized web-
based tool for visualization and analysis of genomic data, encompassing over 4000 …

Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements

T Amariuta, K Ishigaki, H Sugishita, T Ohta, M Koido… - Nature …, 2020 - nature.com
Poor trans-ancestry portability of polygenic risk scores is a consequence of Eurocentric
genetic studies and limited knowledge of shared causal variants. Leveraging regulatory …

Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability

A Gupta, K Weinand, A Nathan, S Sakaue, MJ Zhang… - Nature …, 2023 - nature.com
In autoimmune diseases such as rheumatoid arthritis, the immune system attacks the body's
own cells. Developing a precise understanding of the cell states where noncoding …

Deep neural networks identify sequence context features predictive of transcription factor binding

A Zheng, M Lamkin, H Zhao, C Wu, H Su… - Nature machine …, 2021 - nature.com
Transcription factors bind DNA by recognizing specific sequence motifs, which are typically
6–12 bp long. A motif can occur many thousands of times in the human genome, but only a …

Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers

J He, W Wen, A Beeghly, Z Chen, C Cao… - Nature …, 2022 - nature.com
Transcriptome-wide association studies (TWAS) have successfully discovered many
putative disease susceptibility genes. However, TWAS may suffer from inaccuracy of gene …

Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians

Y Luo, S Suliman, S Asgari, T Amariuta… - Nature …, 2019 - nature.com
Of the 1.8 billion people worldwide infected with Mycobacterium tuberculosis, 5–15% will
develop active tuberculosis (TB). Approximately half will progress to active TB within the first …