W141 - Mapping Critical Regulators of Tissue-resident Memory T Cell Temporal Development Across Skin and Intestinal Niches

Yu Yan – Brigham and Women’s Hospital; Youdong Pan – Brigham and Women’s Hospital; Kasidet Manakongtreecheep – Massachusetts General Hospital; Alexandra-Chloe Villani – Massachusetts General Hospital; Thomas Kupper – Brigham and Women’s Hospital

Abstract Text: Tissue-resident memory T cells (Trm) play a critical role in peripheral immune-responses to pathogens upon infection, but the understanding of their development remains incomplete. To investigate this process, OT-I cells were adoptively-transferred to mice followed by intradermal VACV infection. Single-cell-RNAseq (scRNAseq) was performed on OT-I cells from skin and draining-lymph node across 10 timepoints (day 0 – 60) post-infection. Additionally, we obtained a publicly available scRNAseq dataset capturing adoptively-transferred P14 cells from the small-intestine intraepithelial-lymphocyte (IEL) compartment post-LCMV infection (8 timepoints: day 4 – 90). Linear modelling of each dataset captured genes significantly associated with Trm development whose expression steadily increased with their temporal trajectory. There were 166 Trm-associated genes unique to skin, including transcription factor Ikzf2/Helios and immune mediators Ccr1 and Gzmc. There were 270 Trm-associated genes unique to the IEL compartment, including transcription factors (Zeb2, Klf3, and Tox) and heat-shock proteins (Hspa1a, Hspa1b, Hsph1). We defined a consensus signature of 71 Trm genes found at both sites that included genes associated with hypoxia (Klf6, Tiparp, Rora) and those canonically associated with immediate-early responses (Fos, Fosl2, Nr4a2). Additionally, SCENIC regulon analysis demonstrated an up-regulation of genes with Fos/Jun transcription factor binding motifs in the Trm from skin and IEL compartments. ATAC-seq performed on OT-I cells 30 days post-infection confirmed open chromatin at known Fos/Jun binding sites. In conclusion, we find that while there are important distinct features at disparate sites, there is a consensus regulatory program driven by Fos/Jun transcription factors that is critical to Trm development across niches.