Resident memory T cell development is gradual and shows AP-1 gene expression in mature cells
JCI Insight. 2025;10(12):e187381. DOI 10.1172/jci.insight.187381.
How to cite
AMA
Smith NP, Yan Y, Pan Y, Williams JB, Manakongtreecheep K, Pant SM, et al. Resident memory T cell development is gradual and shows AP-1 gene expression in mature cells. JCI Insight. 2025;10(12):e187381. doi:10.1172/jci.insight.187381APA
Smith, N. P., Yan, Y., Pan, Y., Williams, J. B., Manakongtreecheep, K., Pant, S. M., et al. (2025). Resident memory T cell development is gradual and shows AP-1 gene expression in mature cells. JCI Insight, 10(12), e187381. https://doi.org/10.1172/jci.insight.187381BibTeX
@article{smith2025resident,
title = {Resident memory T cell development is gradual and shows AP-1 gene expression in mature cells},
author = {Smith, Neal P. and Yan, Yu and Pan, Youdong and Williams, Jason B. and Manakongtreecheep, Kasidet and Pant, Shishir M. and others},
journal = {JCI Insight},
volume = {10},
number = {12},
pages = {e187381},
year = {2025},
doi = {10.1172/jci.insight.187381}
}Some immune cells stay behind in the skin and gut long after an infection clears, standing guard so the body responds faster if the same microbe returns. How these resident memory T cells settle into that on-call state has been hard to pin down, because maturation happens over weeks and cannot easily be caught in the act.
This team followed the cells across ten time points with single-cell sequencing and found the change is gradual rather than switch-like, sharpening as the weeks pass. As the cells matured, a family of transcription factors called AP-1 came on, a pattern the sequencing and chromatin data agreed on.
To check that this held in real tissue, the authors imaged intact mouse skin more than one hundred days after infection and found the AP-1 proteins gathered in the nuclei of the resident cells.
Key findings
- Skin and gut CD8 T cell memory forms gradually, not in a single step. Single-cell RNA-seq across 10 developmental time points traced the effector-to-memory transition as a continuum, and linear modeling defined a temporal resident-memory signature that separates these cells from circulating T cells.
- The maturation signature converges on the AP-1 transcription factor family. Four AP-1 members — Fos, Fosb, Fosl2 and Junb — rose with maturation, and ATAC-seq found AP-1-specific motifs at open chromatin sites in mature resident-memory T cells.
- Cyclic imaging placed AP-1 proteins in the nuclei of long-lived resident cells in intact skin. Among 159 CD8+CD103+ T cells profiled more than 100 days after infection, 36.5% stained for JunB and 35.2% for cFos, and where either appeared the signal sat in the nucleus alongside the Hoechst stain.
CyteFinder II HT in the methods
“Images were acquired using the CyteFinder II HT Instrument (RareCyte Inc. Seattle WA) with a 20x/0.75 NA objective. ASHLAR (Alignment by Simultaneous Harmonization of Layer/Adjacency Registration) software was used to stitch the image tiles and register each immunofluorescence cycle together into a single OME-TIFF file.”
— Smith et al., JCI Insight (2025), Methods, “T-CyCIF imaging”
Disclosure: RareCyte is named in the competing-interests statement of the publication cited above.
Why it matters for CyteFinder II HT users
If you are weighing the CyteFinder II HT for a tissue study, look at the specific job it did here. The paper's central claim came from sequencing and chromatin data: a family of transcription factors, AP-1, switches on as resident memory T cells mature. Sequencing tells you which genes are active, but not where the protein ends up or in which cells — and for a transcription factor, the nucleus is the point. That is the question the CyteFinder II HT answered. The authors ran cyclic immunofluorescence on intact FFPE mouse skin, staining CD8, CD103, CD11c and the AP-1 proteins JunB and cFos across successive rounds, then scanned each cycle on the instrument and registered them into a single image. In that tissue they could point to individual CD8+CD103+ resident cells more than a hundred days after infection and show JunB and cFos sitting in the nucleus, next to the counterstain. For your own work the lesson is that whole-slide cyclic imaging places several markers on one section, so you can confirm a molecular signature in place rather than infer it from dissociated cells.
