Shimon Sakaguchi

The paper introduces a framework for multimodal chemical screens combining RNA, protein, and epigenomic readouts, revealing compound-specific mechanisms and off-target effects in T cells.

The paper identifies SATB1's role in genome organization through direct binding to BURs, linking chromatin structure to cell type-specific gene expression.

This study shows that loss of PI3Kδ activity impairs extrathymic Treg differentiation in the colon, leading to autoimmune colitis.

This study converts effector/memory T cells into antigen-specific, functionally stable Tregs for immunological disease treatment.

This study shows that thymic imprinting causes naive CD4 T cells to have different cytokine responses, leading to varied Treg induction and effector function.

This study shows that oral antigen exposure with co-stimulation blockade generates stable regulatory T cells in antigen-sensitized mice, establishing long-term immune tolerance.

This paper introduces icCITE-seq, a method that simultaneously measures surface and intracellular proteins and gene expression in single cells, validated in primary human T cells.

This study shows that Ikzf1 associates with Foxp3 to repress genes in Treg cells, and disrupting this association leads to autoimmunity and enhanced tumor immunity.

The paper shows that ZAP-70 mutations in mice lead to a shift in T cell repertoires, with pathogenic Th17 cells resembling Tregs and contributing to autoimmune arthritis.

VIRTUS detects and quantifies viral transcripts in RNA-seq data, enabling identification of infected cells and viral composition.

This paper introduces ASAP-seq, a method to simultaneously profile chromatin accessibility, protein levels, and mtDNA in single cells, demonstrating its application in hematopoietic differentiation and T cell perturbations.