This work is a wonderful collaboration led by amazing Sarah Walker, with Joris van der Veeken and Sasha Rudensky.
More details in the preprint: doi.org/10.1101/2025...

Looking forward to any feedback! 🙌

In sum, we provide:
– A resource and framework for high-resolution T cell regulatory analysis.
– Archetypal regulatory decomposition of core T cell functions across lineages and infection contexts.
– Insights into shared regulatory logic of CD8 progenitors and CD4 Tfh cells.

A key challenge is to decompose regulatory programs driving overlapping core T cell functions e.g. self-renewal, expansion, cytotoxicity, cytokine production.
For this, we did archetypal analysis.
It revealed that CD8 progenitors combine CD8 exhaustion & CD4 Tfh archetypes.

Surprisingly, these progenitor CD8 T cells were transcriptionally & epigenomically most similar to CD4 Tfh (follicular helper) cells.
Despite distinct lineages, they shared activity of CXCR5, BCL6, TOX, TCF1, ID3 and PD-1.
This suggests converging cellular phenotypes.

Notably, fundamentally and translationally important Tcf1⁺ progenitor CD8 T cells formed a shared population across acute & chronic infection.
These results help reconcile recent studies of several related populations.

We profiled 31k+ T cells with scATAC+RNA-seq during acute & chronic viral infection and built a 285-sample ATAC-seq atlas.
This enabled robust identification of all major T cell states: naive, effector, memory, Treg, Tfh, exhausted & progenitor, shared across infection conditions.

Thanks Lee! In short, I think it's possible, and Drosophila is a good system for this, but the outcome depends on the loop. We described several classes, now working on a more detailed classification.
Some perturbations have already been reported, e.g. for tethering elements etc. but not at scale

A wonderful collaboration with the Mike Levine &
Olga Troyanskaya labs!

More papers and preprints from the lab coming soon — stay tuned!

pritykinlab.github.io

We find 3D chromatin structures earlier than previously thought — before zygotic genome activation — and persisting through mitosis. Developmental elements linked to GAF/Zelda act as conserved bookmarks for gene regulation.

Come talk to me at #ISMBECCB2025 this week if interested in this opportunity

For CSI COSI, I am very thankful to my co-chair Jishnu Das and steering committee @yuripritykin.bsky.social, Hatice Ulku Osmanbeyoglu, Aly Azeem Khan. And everyone who submitted their for consideration for this session www.iscb.org/ismbeccb2025...