1/ Keen to share the story of my postdoc research in @TheXavierLab! We built a massive resource characterizing the spatial landscape of the gut, and yes, we dug deep into the biology too. If you’ve got a minute, let me walk you through the story. 🧵👇.

RT @ericmichbrown: Our most recent work on sphingolipids is now published in @cellhostmicrobe! Here we discovered a….

RT @TrendsImmuno: Mouse gut blueprint: regionality and resilience #immunology

RT @RossjohnLab: Latest paper from lab, where Awad et al describe how cigarette smoke impacts that MAIT-MR1 axis and implications for lung….

RT @Y_Gilad: My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you coul….

RT @Lo_Zanzi: #WeekendRead! #LocationLocationLocation! @TouficMayassi @TheXavierLab &co show @Nature the regional specialization of the gut….

RT @broadinstitute: The intestine maintains a delicate balance in the body. This equilibrium is disrupted in parts of the organ in some dis….

RT @ericmichbrown: Huge congrats to Toufic and all! Been fortunate to witness this incredible piece of work come together over the years an….

RT @TheXavierLab: 1/3 Thrilled to share exciting new work in @Nature by @TouficMayassi, @li_chenhao, Åsa Segerstolpe, et al. Spatial profil….

RT @li_chenhao: It was such an experience working on this large-scale dataset and most importantly in the team with diverse backgrounds. I….

RT @threadreaderapp: @li_chenhao @TouficMayassi @li_chenhao Hi, please find the unroll here: Talk to you soon. 🤖.

22/ Processed data and scripts can be found at Data can also be viewed on the Single Cell Portal Read more about the story here:

21/ This work represents years of effort shaped by the guidance of mentors, support of colleagues, and encouragement from family and friends. Grateful to everyone who contributed, directly or indirectly. Excited to keep exploring the mysteries of the gut! Until next time. .

20/ Our results demonstrate that intestinal regionalization is characterized by robust and resilient structural cell states and that the intestine can adapt to environmental stress in a spatially controlled manner via the crosstalk between immunity and structural cell homeostasis.

19/ Remarkably, we turned off ANG4 expression in the middle colon. Using our Xenium panel, we showed the loss of the middle colon-adapted goblet cell population, demonstrating that ILC2s are essential for actively maintaining this adaptation.

18/ Intrigued by these results, we reached out to David Artis and his group @WeillCornell to test if ILC2s drive the middle colon’s microbiota adaptation. I drove down to NYC with my tools and together with the talented @HiroTheHero_PhD we turned the lights off on the mid colon.

17/ Together with my officemate of 4yrs and close friend @ericmichbrown we were then able to show ILC2 derived signals could induce the middle colon signature in ex vivo explants.

16/ We leveraged our sc data to compare all immune cell types across regions between SPF and GF mice and found only ILC2s showed a unique microbiota driven signature in the middle colon (B) which we could also validate with flow cytometry for a variety of markers.

15/ By now, you’re probably wondering what’s up with the middle colon? So were we. Mid colon genes like Ang4, Pla2g4c and Spta1 are linked to type II immunity tissue responses (helminth/protozoa colonization), yet we observed them in steady state and in absence of those drivers.

14/ Using our data to design a customized 480 gene panel we then leveraged high resolution Xenium technology to map all our cell states in space and validated the regional association of cell states as well as the middle colon adapted cells.

13/ We found unique structural cells defined each region (enterocytes, fibroblasts, and goblet cells) and strikingly the middle colon associated region (B) had unique subsets only found in the presence of the microbiota.