Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis
Authors: Julia Waldman
Gabriella Velonias
Daniel B Graham
Adam L Haber
Matan Hofree
Lan T Nguyen
Michal Slyper
Malika Sud
Orit Rozenblatt-Rosen
John J Garber
Christopher S Smillie
Noga Rogel
Moshe Biton
Karthik Jagadeesh
Elizabeth A Creasey
Junmei Yao
Grace Burgin
Ashwin N Ananthakrishnan
Alex K Shalek
Jose Ordovas-Montanes
Mark J Daly
Elizabeth Andrews
Christine Stevens
Ramnik J Xavier
Keri M Sullivan
Hamed Khalili
Danielle Dionne
A Nicole Desch
Aviv Regev
Hailiang Huang
Sanja Vickovic
Alexandra-Chloé Villani
Rebecca H Herbst
Journal: Cell (2019)
Discipline: MOLECULAR BIOLOGY & GENETICS
Keywords: anti-TNF resistance; cell-cell interactions; colon; genome-wide association studies; inflammation
Affiliations: Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA., Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Department of Molecular Biology, MGH, Boston, MA, USA., Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, USA; Department of Chemistry, MIT, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA., Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA., Department of Molecular Biology, MGH, Boston, MA, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA., Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA., Center for Computational and Integrative Biology, MGH, Boston, MA, USA., Broad Institute, Cambridge, MA, USA., Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Center for Immunology and Inflammatory Diseases, Department of Medicine, MGH, Boston, MA, USA., Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Analytical and Translational Genetics Unit, MGH, Boston, MA, USA., Broad Institute, Cambridge, MA, USA; Center for Computational and Integrative Biology, MGH, Boston, MA, USA., Medical and Population Genetics, Broad Institute, Cambridge, MA, USA; Analytical and Translational Genetics Unit, MGH, Boston, MA, USA; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland., Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA. Electronic address: ., Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, USA; Department of Chemistry, MIT, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. Electronic address: ., Department of Molecular Biology, MGH, Boston, MA, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA; Broad Institute, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA; Center for Computational and Integrative Biology, MGH, Boston, MA, USA. Electronic address: ., Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA, USA. Electronic address: .

Abstract:  Genome-wide association studies (GWAS) have revealed risk alleles for ulcerative colitis (UC). To understand their cell type specificities and pathways of action, we generate an atlas of 366,650 cells from the colon mucosa of 18 UC patients and 12 healthy individuals, revealing 51 epithelial, stromal, and immune cell subsets, including BEST4+ enterocytes, microfold-like cells, and IL13RA2+IL11+ inflammatory fibroblasts, which we associate with resistance to anti-TNF treatment. Inflammatory fibroblasts, inflammatory monocytes, microfold-like cells, and T cells that co-express CD8 and IL-17 expand with disease, forming intercellular interaction hubs. Many UC risk genes are cell type specific and co-regulated within relatively few gene modules, suggesting convergence onto limited sets of cell types and pathways. Using this observation, we nominate and infer functions for specific risk genes across GWAS loci. Our work provides a framework for interrogating complex human diseases and mapping risk variants to cell types and pathways. 

Retracted: No

PubPeer comments:
 Hi, interesting study! I was wondering about the FOXP3 staining in Figure 5B. It does not look specific to me. The staining should be nuclear, which it is clearly not. It is staining the cytoplasm membrane. Could the authors please provide more images? Thank you.![file] , 
 #1 ![file] , 
 #2 ![file] ![file] , 
 I thank the authors for their reply and appreciate their time in putting together the response. Unfortunately, it is quite hard to assess the images due to the low quality provided, but in my opinion the cell the authors point out as regulatory T cell with  cytoplasmic FOXP3 staining is in fact morphologically consistent with a polymorphonuclear granulocyte (see the figure in point 3. by the authors, bottom row, second to left, yellow arrow). It clearly has a bilobed (or trilobed) nucleus and therefore is not a lymphocyte. Unfortunately, these PMNs are very sticky to all kinds of staining reagents, therefore they often unspecifically bind antibodies (and possibly also oligonucleotides) and are therefore very bright in all channels (hence the positivity for all the markers). Could the authors please provide additional images with higher resolution in order to examine the cellular morphology better, including nuclear stain (DAPI Hoechst) to examine the nuclear morphology? I assume DAPI Hoechst was stained with all microscopy experiments in order to correctly allocate signal to a nucleus? Furthermore, it would be very interesting to see the numbers for  cytoplasmic FOXP3+ Tregs vs. nuclear FOXP3+ Tregs, if the authors could provide these. , 
 We are sorry for the low quality of the images. Here is the same image in higher resolution. The cytoplasmic stain shown in the upper panel (yellow arrow) is clearly not of polymorphonuclear granulocytes. In addition, you can also appreciate the nuclear stain of Foxp3 in the cells labeled by the red arrows in both panels. ![file] , 
 Thank you for the better image. Do you have DAPI Hoechst nuclear stain to prove that the  nuclear staining in the top row is in fact a nucleus and not just an aggregate of some sort? To me, it looks like an aggregate. In addition, the  cytoplasmic staining in the lower panel is clearly a granulocyte morphologically, and certainly not a lymphocyte. So far, the claim that these are regulatory T cells is not convincing at all - see my annotation and interpretation below in the image. Again, if the authors could provide some numeric on how many of these  regulatory T cells with cytoplasmic vs. nuclear FOXP3 staining were found in the paper, that would be interesting and important. 90% cytoplasmic vs. 10% nuclear would be weird, no? ![file] ,