Prostate cancer is common, yet immunotherapy has been difficult to apply effectively.

New research maps how tissue‑resident memory T cells are organized inside the prostate, revealing location‑specific roles in immune defense and memory.

In collaboration with @lji.org & @ucsandiego.bsky.social

Pain-sensing neurons in the intestines play an important role in defending the body from threats.

New study led by the Artis Lab at @weillcornell.bsky.social shows TRPV1+ nociceptors in the gut activate tuft cells, leading to expulsion of parasites.

🔗 https://go.nature.com/4jTvO7k

So glad to see this finally being published. Congrats to Wen Zhang, Elizabeth Emanuel, David Artis, and all the co-authors on “Neuro-epithelial circuits promote sensory convergence and intestinal immunity” in Nature! #immunology

#ICYMI: T cells rise up to fight infections in the gut. Fascinating research led by AAI members Ananda Goldrath, Maximilian Heeg and Miguel Reina-Campos show how a special group of T cells travels through the small intestine to combat pathogens. https://ow.ly/M4rQ50ULWSJ

I just completed "Secret Entrance" - Day 1 - Advent of Code 2025 #AdventOfCode adventofcode.com/2025/day/1

Susan Kaech, Ph.D., named next leader of Allen Institute’s Immunology moonshot Leader in immunology to advance the Institute’s next frontier in understanding the immune system’s role across health and disease

Susan Kaech, PhD, has been selected to be the new EVP of our Immunology moonshot.

She currently leads the @salkinstitute.bsky.social NOMIS Center for Immunobiology & Microbial Pathogenesis.

🔗 alleninstitute.org/news/susan-k...

#Immunology #CellBio #ImmunoBio

So proud to be a co-author on this study and absolutely loved the beautiful thread by @marionpepper.bsky.social — high recommended 👇

@biorxivpreprint.bsky.social Tertiary lymphoid structures support the development of allergen-specific progenitor CD4+ T cells @marionpepper.bsky.social
www.biorxiv.org/content/10.1...

More coming on what this means but this was one of those stories that took almost a decade to come together but was well worth the time. Also check out a companion piece on @biorxiv by Patrick Brennan!

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted - Nature Profiling of the location and transcriptome of tissue-resident memory CD8 T cell formation at single-transcript resolution finds regionalized signalling as the basis of immune diversity in t...

Very impressive paper by the Heeg and Goldrath labs using spatial transcriptomics to define CD8 Trm biology in the intestine in mice and humans. Congrats to @reinacampos.bsky.social and co-authors. #ImmunoSky

Jobs We are working to solve the biggest mysteries in bioscience.

📢 Join our team at @alleninstitute.bsky.social! We're hiring a Bioinformatics Scientist II for spatial transcriptomics in immunology.
Our latest work in Nature shows how tissue architecture shapes immune cell diversity. Now we're expanding our team!
Learn more: alleninstitute.org/careers/jobs...

Yes. The colors in the final row are unrelated. This shows Leiden Cluster and not cell types.

The first three rows of Fig 1d are colored as indicated in the legend. Row 4 highlights the antigen specific T cells and row 5 is coloured by leiden clustering. If you want to explore the cell types I recommend having a look at the anndata object: www.ncbi.nlm.nih.gov/geo/query/ac...

Thanks. Are you going to be in asilomar this weekend?

I cannot believe you still have that picture! That's when all the fun started almost two years ago....

Spatial omics rides again, this time determining how immune CD8 T cells by location in the gut have different roles, such as killing function in the villus and backup reinforcements in the crypts
www.nature.com/articles/s41...
Good Explainer www.lji.org/news-events/...
@alleninstitute.bsky.social

New: Amir Ferry, Ananda Goldrath and colleagues @ucsdhealthsci.bsky.social show that differentiation of tissue-resident memory T cells (TRM) is accompanied by the upregulation of the conventional DC1 (cDC1) chemoattractant, Xcl1. https://buff.ly/4hrKCYe

#MucosalImmunology #TumorImmunology

When your gut is under attack, the immune system is activated. Like any good army, the roles of each cellular soldier depends on their location. 🧵

📸 Elena Lin/ @ucsdhealthsci.bsky.social

#ImmunoSky

Beautiful thread on how tissue-resident T cells organize in the gut post-infection from my co-conspirator @reinacampos.bsky.social. Our spatial multi-omics work revealed unexpected complexity in immune system architecture. Think less checkers, more 4D chess 🧬🔬

T cells rise up to fight infections in the gut Scientists show how a special group of T cells travels through the small intestine to combat pathogens

New in @nature.com — LJI's @reinacampos.bsky.social and colleagues at @ucsdhealthsci.bsky.social and @alleninstitute.bsky.social track the amazing journey of T cells in the gut.

“For the first time, we were able to capture the formation of immunological memory in space and time."

bit.ly/40Tnlt7

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted - Nature Profiling of the location and transcriptome of tissue-resident memory CD8 T cell formation at single-transcript resolution finds regionalized signalling as the basis of immune diversity in t...

🧵 10/10 This work establishes a framework for studying tissue immune networks and reveals how cellular positioning shapes immune cell identity and function. Full paper: www.nature.com/articles/s41...
Big thanks again to all the authors for their incredible work! ❤️

🧵 9/10 Technical innovation: We developed a strategy for pooled optically encoded gene perturbations compatible with spatial transcriptomics, enabling mechanistic studies in situ

🧵 8/10 Our spatial framework reveals that T cell location and functional state are fundamentally intertwined - establishing a new paradigm for understanding tissue immunity

🧵 7/10 Importantly, we validated these findings in human tissue. Analysis of healthy human terminal ileum revealed similar spatial organization of CD8 T cell states

🧵 6/10 TGFβ signaling proved essential for proper TRM positioning. TGFβRII KO cells showed impaired migration to the villus tip and reduced acquisition of tissue-residency programs

🧵 5/10 Using CRISPR-based perturbations with spatial readout, we demonstrated that CXCR3 signaling is crucial for early positioning of effector cells. Loss of CXCR3 altered cellular positioning and subsequent differentiation fate

Specialized cellular contacts create a complex molecular landscape that guides TRM differentiation. Cells in the small intestine are colored by cell type and connected to their neighboring cells.

🧵 4/10 This diversity is regulated by:
1. Distinct ligand-receptor activities
2. Spatial cytokine gradients
3. Specialized cellular contacts creating a complex molecular landscape that guides TRM differentiation

🧵 3/10 Key finding: We identified two distinct TRM states defined by their location:
• Differentiated TRM cells (Gzma+, Gzmb+, Itgae+) in upper villus
• Progenitor-like TRM cells (Tcf7+, Slamf6+) in lower villus/crypt

Each cell is colored according to its positions along the 3 main axes (crypt to villus, epithelial distance and longitudinal).

🧵 2/10 Using spatial transcriptomics (Xenium & MERSCOPE), we discovered that intestinal TRM cells occupy distinct niches that shape their phenotype and function. We developed computational approaches to map cells along three anatomical axes 📊

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted - Nature Profiling of the location and transcriptome of tissue-resident memory CD8 T cell formation at single-transcript resolution finds regionalized signalling as the basis of immune diversity in t...

Today in @nature.com. We mapped the spatial and temporal dynamics of intestinal tissue-resident memory CD8 T (TRM) cell differentiation.
🔗 www.nature.com/articles/s41....
@ucsandiego.bsky.social @lji.org @alleninstitute.bsky.social @amonell.bsky.social @reinacampos.bsky.social @GoldrathLab 🧵 1/10