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Review
. 2020 Mar 27;9(4):813.
doi: 10.3390/cells9040813.

Single-Cell Protein and RNA Expression Analysis of Mononuclear Phagocytes in Intestinal Mucosa and Mesenteric Lymph Nodes of Ulcerative Colitis and Crohn's Disease Patients

Laurence Chapuy  1 , Marika Sarfati  1
Affiliations
Review

Single-Cell Protein and RNA Expression Analysis of Mononuclear Phagocytes in Intestinal Mucosa and Mesenteric Lymph Nodes of Ulcerative Colitis and Crohn's Disease Patients

Laurence Chapuy et al. Cells. .

Abstract

Inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative colitis (UC), are driven by an abnormal immune response to commensal microbiota in genetically susceptible hosts. In addition to epithelial and stromal cells, innate and adaptive immune systems are both involved in IBD immunopathogenesis. Given the advances driven by single-cell technologies, we here reviewed the immune landscape and function of mononuclear phagocytes in inflamed non-lymphoid and lymphoid tissues of CD and UC patients. Immune cell profiling of IBD tissues using scRNA sequencing combined with multi-color cytometry analysis identifies unique clusters of monocyte-like cells, macrophages, and dendritic cells. These clusters reflect either distinct cell lineages (nature), or distinct or intermediate cell types with identical ontogeny, adapting their phenotype and function to the surrounding milieu (nurture and tissue imprinting). These advanced technologies will provide an unprecedented view of immune cell networks in health and disease, and thus may offer a personalized medicine approach to patients with IBD.

Keywords: Crohn’s disease; flow cytometry; inflammatory bowel disease; mononuclear phagocytes; single cell RNA sequencing; ulcerative colitis.

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Conflict of interest statement

The authors have no conflict of interest to declare.

Figures

Figure 1
Figure 1
Ontogeny of macrophages, monocyte-derived cells and dendritic cells. Macrophage (Mɸ) can be derived from embryonic precursor or monocyte. Monocyte can differentiate into Mɸ, dendritic cell (Mo-DC) or tissue inflammatory monocyte-like cell. Conventional dendritic cells (cDC1 and cDC2 that is further subdivided into DC2 and DC3 subsets) originate from a dedicated precursor (pre-cDC).
Figure 2
Figure 2
Distribution and function of intestinal conventional DCs. SIRPα−CD103+ cDC1, SIRPα+CD103+ cDC2, SIRPα+CD103− cDC2 are relatively conserved between mice and humans. Human jejunal cDCs prime allogenic naive CD4+ T cells and promote differential T cell responses. The proportion of human cDC subsets according to their gut location is depicted in the pie charts (Literature cited in blue).
Figure 3
Figure 3
Intestinal monocyte/macrophage populations at steady state in mice and humans. In mice (left panel), the majority of Mɸ derive from circulating monocytes. Once recruited in tissue, monocytes undergo a maturation process into anergic Mɸ (P1 to P4), producing and responding to IL-10 and ensuring diverse functions in the lamina propria. Embryonic Mɸ are located in the submucosa. In humans (right panel), monocyte derived-Mɸ (M1 to M4), the potential counterparts of murine mononuclear phagocytes (MNPs) and several anergic Mɸ subsets have been reported in the lamina propria. (Literature cited in blue along with gut location).
Figure 4
Figure 4
Proposed schematic model for mononuclear phagocytes diversity in inflamed colon of inflammatory bowel disease (IBD) patients. In inflamed IBD gut mucosa, the accumulation of HLADRdimCD14+CD163−CD89+TREM+ inflammatory monocyte-like subset (Inf Mo-like) (in red) secreting pro-inflammatory cytokines, could result from the increase recruitment of circulating CD14hi monocytes (in gold) that differentiate into Inf Mo-like cells in concert with the potential arrest in the maturation program towards HLADRhiCD14hiCD209+MERTK+ post-inflammatory Mɸ (in green) that likely contribute to tissue repair. Transitioning cells (in orange) are generated during this maturation process. Post-inflammatory Mɸ coexist with resident Mɸ (in yellow–green) that represent the predominant Mɸ population at steady state. Mɸ expressing TIM-4+ and CD4+ (in mint green), like embryonic Mɸ reported in mice, have been identified in the inflamed colon of IBD patients. Besides Inf Mo-like cells and Mɸ, conventional dendritic cells that include cDC1 (in khaki), DC2 (in blue), and plasmacytoid DC (in black) are seeded in the inflamed mucosa. Inflammatory monocyte-derived DC (in gold) and inflamed DC3 (in dark pink) may infiltrate inflamed lamina propria in IBD patients.
Figure 5
Figure 5
MNPs in human mesenteric lymph nodes in Crohn’s disease and ulcerative colitis. Rare SIRPα− cDC1 (in khaki) and four CD14−CD64−CD163− DCs subsets: (1) pDCs (in black), the major DC subset found at higher frequency in CD compared to UC; (2) resident CD11chiCD1c+CD33+ DC2 (in light blue); (3) rare migratory HLADRhiCDR7+ DC2 (in dark blue) and (4) CD163intCD11b+CD36+CD1c− cDCs (in pink), reported in similar proportion in CD and UC. A higher proportion of HLADRdimCD68dimCD169+ monocyte-like cells (in purple) and HLADRhiCD68+MERTK+CD169− Mɸ (in dark green) contributes to increased frequency of CD14+CD64+CD163+ cells in UC compared to CD. The former (purple) could derive from circulating monocytes (in gold) directly entering MLN, or mucosal monocyte-like cells (in red) that have acquired CD163 and migratory capacities. CD169+ Mɸ (2 subsets depicted in light green) display a sinusoidal-like Mɸ phenotype. HLADRdimCD14+CD64+CD163− monocyte/monocyte-like cells (brown, burgundy and navy blue).
Figure 6
Figure 6
Complementary axis for personalized medicine in IBD. Different translation axis of data (patients characteristics, investigation techniques combined with molecular and functional analysis of biological samples) can potentially establish a comprehensive score that might ultimately offer clinicians therapeutic perspectives for individual IBD patient.
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