This vibrant video by our Immunology team shows how similar millions of cells are to one another. Each tiny dot represents a single cell; and their color, the cell type: cyan for intestinal cells, red for T cells, white for liver cells, orange for smooth muscle cells.

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

Nature@nature.com · 7mo ago

Nature research paper: Neuro-epithelial circuits promote sensory convergence and intestinal immunity go.nature.com/4qeRjlt

#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, 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

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

alleninstitute.org

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

Marion Pepper@marionpepper.bsky.social · 10mo ago

Asthma is a chronic disease characterized by acute, intermittent, recurrent episodes of airway inflammation. A decade of work developing the tools, techniques and collaborations needed to figure out how CD4+ T cells in the lungs propagate disease can be found here: www.biorxiv.org/content/10.1...

@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!

Waggoner Lab@labwaggoner.bsky.social · 10mo ago

@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...

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

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...

nature.com

📢 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...

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We are working to solve the biggest mysteries in bioscience.

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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 🧬🔬

Miguel Reina-Campos@reinacampos.bsky.social · 2y ago

It turns out the immune system is playing 4D chess while we thought it was just playing checkers. Using #spatialtranscriptomics from @10xgenomics.bsky.social and @vizgen.bsky.social we were able to peek into the secret lives of tissue resident T cells in the gut as they form after infection 1/n

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

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

lji.org

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

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...

nature.com