Two distinct colonic CD14+ subsets characterized by single-cell RNA profiling in Crohn's disease

Abstract

Inflammatory bowel diseases are associated with dysregulated immune responses in the intestinal tissue. Four molecularly identified macrophage subsets control immune homeostasis in healthy gut. However, the specific roles and transcriptomic profiles of the phenotypically heterogeneous CD14 + macrophage-like population in inflamed gut remain to be investigated in Crohn's disease (CD). Here we identified two phenotypically, morphologically and functionally distinct colonic HLADR + SIRPα + CD14 + subpopulations that were further characterized using single-cell RNA-sequencing (scRNAseq) in CD. Frequencies of CD64 hi CD163 −/dim cells selectively augmented in inflamed colon and correlated with endoscopic score of disease severity. IL-1β and IL-23-producing CD64 hi CD163 −/dim cells predominated over TNF-α-producing CD64 hi CD163 hi cells in lesions. Purified "inflammatory monocyte-like" CD163 − , but not "macrophage-like" CD163 hi cells, through IL-1β, promoted Th17/Th1 but not Th1 responses in tissue memory CD4 + T cells. Unsupervised scRNAseq analysis that captures the entire HLADR + SIRPα + population revealed six clusters, two of which were enriched in either CD163 − or CD163 hi cells, and best defined by TREM1/FCAR/FCN1/IL1RN or CD209/MERTK/MRCI/CD163L1 genes, respectively. Selected newly identified discriminating markers were used beyond CD163 to isolate cells that shared pro-Th17/Th1 function with CD163 − cells. In conclusion, a molecularly distinct pro-inflammatory CD14 + subpopulation accumulates in inflamed colon, drives intestinal inflammatory T-cell responses, and thus, might contribute to CD disease severity.

Human Intestinal Mononuclear Phagocytes in Health and Inflammatory Bowel Disease

“…It is now clear that the frequency and number of Mfs among intestinal LP cells is increased in IBD patients compared to controls, especially in active lesion areas (132,221,223,225,226,228,246,263,(267)(268)(269)(270)(271)(272) (Figure 5E). More specifically, the augmentation of intestinal Mfs is due to an increase in the frequency of immature Mfs among LP cells, despite that somewhat different surface markers and combinations thereof have been used to characterized them (i.e., HLA-DR or CD11c levels; scRNA-seq) (132,221,223,225,226,228,256,263,270,(272)(273)(274)(275) (Figure 5F). This accumulation seems to be due to the inflammatory intestinal microenvironment of IBD patients, which boosts the recruitment of classical monocytes through mechanisms involving CCL2, IL-8, and TGF-β signaling (223,276).…”

“…These newly recruited monocytes are maintained in the immature pro-inflammatory state, which in turn amplify intestinal chronic inflammation (11,277). Chapuy et al showed that the frequency of immature Mfs, but not mature Mfs, is positively correlated with endoscopic score of disease severity in Crohn's patients (228). To note, age, gender, age at diagnosis, disease location and disease behavior, as well treatment history, did not influence the increased frequency of immature Mfs in Crohn's patients (228).…”

“…In addition to their accumulation, intestinal Mfs produced more pro-inflammatory cytokines, such as TNF, IL-23, IL-1β and IL-6, in basal conditions as well as after TLR stimulation, in UC patients and even more in Crohn's patients compared to controls (226,228,246,256,271,287). These pro-inflammatory cytokines can promote and/or perpetuate a pathologic environment (11).…”

“…This seems to be due to immature Mf accumulation within the total Mf population in Crohn's patients. Indeed, Chapuy et al have recently shown that immature Mfs from IBD patients, but seemingly not mature Mfs, induce Th17 cells, as well pathologic IFN-y + IL-17 + T cells (303), from autologous colonic CD4 + T cells mainly through their production of IL-1β (228,272). Corroborating this, Martin et al have shown that, while initial steps of lymphocyte aggregate formation depend on DCs, immature Mfs likely participate in T cell activation in situ (263).…”

Combinatorial prediction of marker panels from single-cell transcriptomic data

“…Single-cell transcriptomic technologies have enabled the exciting discovery of novel cell populations within various in vivo contexts (Baron et al, 2016;Chapuy et al, 2019;Jia et al, 2018;Kernfeld et al, 2018;Kurtulus et al, 2019;Paul et al, 2015;Satija et al, 2015;Shekhar et al, 2016;Singer et al, 2016;Spallanzani et al, 2019;Vento-Tormo et al, 2018;Villani et al, 2017). Following the discovery of a new cell population of interest based on full transcriptome analysis (of typically a few thousand genes), follow-up studies require succinct gene-marker panels by which the cells of interest can be distinguished from the general cell population ( Figure 1).…”