Toufic Mayassi
@touficmayassi.bsky.social
Mucosal immunologist drawn to the computational world | Bana Jabri lab graduate | Postdoc in @thexavierlab.bsky.social at the @broadinstitute.bsky.social
Thank you Liam!
November 24, 2024 at 11:11 AM
Thank you Liam!
22/ Processed data and scripts can be found at tinyurl.com/4fsxwcc6
Data can also be viewed on the Single Cell Portal tinyurl.com/ykmajssf
tinyurl.com/56wh3x9t
tinyurl.com/2mjftsc3
Read more about the story here: tinyurl.com/5epdfrma
Data can also be viewed on the Single Cell Portal tinyurl.com/ykmajssf
tinyurl.com/56wh3x9t
tinyurl.com/2mjftsc3
Read more about the story here: tinyurl.com/5epdfrma
Files · main · Xavier Lab Computation / public / molecular cartography of mouse gut · GitLab
GitLab.com
tinyurl.com
November 21, 2024 at 10:21 PM
22/ Processed data and scripts can be found at tinyurl.com/4fsxwcc6
Data can also be viewed on the Single Cell Portal tinyurl.com/ykmajssf
tinyurl.com/56wh3x9t
tinyurl.com/2mjftsc3
Read more about the story here: tinyurl.com/5epdfrma
Data can also be viewed on the Single Cell Portal tinyurl.com/ykmajssf
tinyurl.com/56wh3x9t
tinyurl.com/2mjftsc3
Read more about the story here: tinyurl.com/5epdfrma
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...
November 21, 2024 at 10:21 PM
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
November 21, 2024 at 10:21 PM
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.
November 21, 2024 at 10:21 PM
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.bsky.social we turned the lights off on the mid colon.
November 21, 2024 at 10:21 PM
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.bsky.social we turned the lights off on the mid colon.
17/ Together with my officemate of 4yrs and close friend Eric Brown we were then able to show ILC2 derived signals could induce the middle colon signature in ex vivo explants.
November 21, 2024 at 10:21 PM
17/ Together with my officemate of 4yrs and close friend Eric Brown 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.
November 21, 2024 at 10:21 PM
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.
November 21, 2024 at 10:21 PM
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.
November 21, 2024 at 10:21 PM
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.
November 21, 2024 at 10:21 PM
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.
12/ To uncover the cellular drivers of the gut’s spatial landscape and the middle colon adaptation we used scRNA-seq. Using a customized extraction protocol we profiled 99 cell states of epithelial, stromal and immune cells in one go from four distinct regions of the colon.
November 21, 2024 at 10:21 PM
12/ To uncover the cellular drivers of the gut’s spatial landscape and the middle colon adaptation we used scRNA-seq. Using a customized extraction protocol we profiled 99 cell states of epithelial, stromal and immune cells in one go from four distinct regions of the colon.
11/ We then tested if spatial gut circuits were resilient to inflammation using a spatiotemporal model of acute colonic inflammation. Both robust and adaptable landscapes were disrupted at peak inflammation but recovered over time, showcasing their resilience.
November 21, 2024 at 10:21 PM
11/ We then tested if spatial gut circuits were resilient to inflammation using a spatiotemporal model of acute colonic inflammation. Both robust and adaptable landscapes were disrupted at peak inflammation but recovered over time, showcasing their resilience.
10/ We did find an exception tho: the middle colon adapts! Its identity depended on the microbiota, marked by genes like Ang4, Retnlb, Itln1, Pnliprp2, Aqp4, and Slc9a3. ANG4 protein staining showed exquisite specificity for the middle colon, serving as a biomarker in later exps.
November 21, 2024 at 10:21 PM
10/ We did find an exception tho: the middle colon adapts! Its identity depended on the microbiota, marked by genes like Ang4, Retnlb, Itln1, Pnliprp2, Aqp4, and Slc9a3. ANG4 protein staining showed exquisite specificity for the middle colon, serving as a biomarker in later exps.
9/ Ok, so how does the landscape respond to the microbiota? We found in germ-free mice, most genes maintained regional expression bias, even classical antimicrobial genes—suggesting a surprisingly robust and microbiota-independent landscape (the same applied to circadian rhythm).
November 21, 2024 at 10:21 PM
9/ Ok, so how does the landscape respond to the microbiota? We found in germ-free mice, most genes maintained regional expression bias, even classical antimicrobial genes—suggesting a surprisingly robust and microbiota-independent landscape (the same applied to circadian rhythm).
8/ First surprise: distal gut regions shared unique expression patterns! Quantifying this revealed the duodenum shares many unique genes with the colon, hinting at unexpected redundancy in biological processes—highlighted again for SLC transporters.
November 21, 2024 at 10:21 PM
8/ First surprise: distal gut regions shared unique expression patterns! Quantifying this revealed the duodenum shares many unique genes with the colon, hinting at unexpected redundancy in biological processes—highlighted again for SLC transporters.
7/ With these tools we were then able to map the continuous spatial transcriptome in both the X-axis (duodenum to colon) and Y-axis (serosa to epithelium) allowing us to interrogate the distribution of gene expression for any biological theme of interest (SLCs example).
November 21, 2024 at 10:21 PM
7/ With these tools we were then able to map the continuous spatial transcriptome in both the X-axis (duodenum to colon) and Y-axis (serosa to epithelium) allowing us to interrogate the distribution of gene expression for any biological theme of interest (SLCs example).
6/ Next challenge - reconstruct the tissue to its native state and unify segments within and across mice to facilitate downstream analysis and visualization. Enter the room @lichenhao.bsky.social, a brilliant scientist that helped me supercharge the study along with my computational skills.
November 21, 2024 at 10:21 PM
6/ Next challenge - reconstruct the tissue to its native state and unify segments within and across mice to facilitate downstream analysis and visualization. Enter the room @lichenhao.bsky.social, a brilliant scientist that helped me supercharge the study along with my computational skills.
5/ The idea: use the gut swiss roll (before you started to see them everywhere) and ideally with fresh frozen tissue. With Toru Nakata (best hands I worked with), we figured it out and with Asa Segerstolpe, profiled 40+ rolls using 10xGenomics Visium. #SpatialBiology
November 21, 2024 at 10:21 PM
5/ The idea: use the gut swiss roll (before you started to see them everywhere) and ideally with fresh frozen tissue. With Toru Nakata (best hands I worked with), we figured it out and with Asa Segerstolpe, profiled 40+ rolls using 10xGenomics Visium. #SpatialBiology
4/ I set out to map the spatial transcriptome of the entire gut with the goal to then use it to ask if the landscape was robust to homeostatic drivers (microbiota circadian diet etc), if/how the landscape was adaptable in space and finally if it was resilient to insults.
November 21, 2024 at 10:21 PM
4/ I set out to map the spatial transcriptome of the entire gut with the goal to then use it to ask if the landscape was robust to homeostatic drivers (microbiota circadian diet etc), if/how the landscape was adaptable in space and finally if it was resilient to insults.
3/ I felt the best place to do that would be @broadinstitute.org in Ramnik's lab. Spatial transcriptomics was just taking off in 2020 and I felt if I asked the right questions and designed the right experiment I could generate a dataset to mine for ideas for the rest of my career.
November 21, 2024 at 10:21 PM
3/ I felt the best place to do that would be @broadinstitute.org in Ramnik's lab. Spatial transcriptomics was just taking off in 2020 and I felt if I asked the right questions and designed the right experiment I could generate a dataset to mine for ideas for the rest of my career.
2/ I trained as an immunologist in Bana Jabri's lab @UChicagoCOI and studied the unconventional gd T cell in the context of celiac disease. I have always been fascinated by gut biology and expanded my expertise during my postdoc by taking a systems approach to my next question.
November 21, 2024 at 10:21 PM
2/ I trained as an immunologist in Bana Jabri's lab @UChicagoCOI and studied the unconventional gd T cell in the context of celiac disease. I have always been fascinated by gut biology and expanded my expertise during my postdoc by taking a systems approach to my next question.