Transcriptomic Analysis and High-dimensional Phenotypic Mapping of Mononuclear Phagocytes in Mesenteric Lymph Nodes Reveal Differences Between Ulcerative Colitis and Crohn’s Disease

Abstract

Background and Aims Crohn’s disease [CD] and ulcerative colitis [UC] are distinct forms of inflammatory bowel disease. Heterogeneity of HLA-DR+SIRPα + mononuclear phagocytes [MNPs], including macrophages [MΦ], monocyte-derived [Mono] cells, and dendritic cells [DCs], was reported in gut tissue but not yet investigated in mesenteric lymph nodes [MLNs] of IBD patients. We here compared the phenotype, function, and molecular profile of HLA-DR+SIRPα + MNPs in CD and UC MLNs. Methods Cell distribution, morphology, immune function, and transcriptomic [bulk RNAseq] and high-dimensional protein expression profiles [CyTOF] of HLA-DR+SIRPα + MNPs were examined in MLNs of UC [n = 14], CD [n = 35], and non-IBD [n = 12] patients. Results Elevated frequencies of CD14+CD64+CD163+ [Mono/MΦ-like] MNPs displaying monocyte/MΦ morphology and phagocytic function were a distinct feature of UC MLNs. In CD, the proportion of CD14-CD64-CD163- [DC-like] cells was augmented relative to Mono/MΦ-like cells; DC-like cells drove naïve T cell proliferation, Th1 polarisation, and Th17 TCM plasticity. Gene expression profile corroborated the nature of DC-like cells, best represented by BTLA, SERPINF, IGJ and, of Mono/MΦ-like cells, defined by CD163, MARCO, MAFB, CD300E, S100A9 expression. CyTOF analysis showed that CD123+ plasmacytoid cells predominated over conventional DCs in DC-like cells. Four CD163+ clusters were revealed in Mono/MΦ-like cells, two of which were enriched in MARCO-CD68dimHLA-DRdim monocyte-like cells and MARCOhiCD68hiHLA-DRhi Mɸ, whose proportion increased in UC relative to CD. Conclusions Defining the landscape of MNPs in MLNs provided evidence for expansion of CD163+ Mono/MΦ-like cells in UC only, highlighting a distinction between UC and CD, and thus the potential contribution of monocyte-like cells in driving colitis.

Human Intestinal Mononuclear Phagocytes in Health and Inflammatory Bowel Disease

“…These data corroborated with those from mice, where it has been shown that mLN Mfs poorly activate naïve T cells and were involved in clearing apoptotic cells and promoting B cell activation (314,315). To note, using CyTOF, Chapuy et al described 7 mLN Mf subsets in IBD patients (313), but their location, function and disease involvement remain to be deciphered.…”

“…However, these mLN Mfs poorly activated naïve T cells and did not contribute to Th17 plasticity toward Th1 and Th1/Th17 profiles compared to mLN SIRPα + DCs (313). Finally, mLN Mfs highly expressed genes involved in phagocytosis and in leucocyte chemotaxis (313). These data corroborated with those from mice, where it has been shown that mLN Mfs poorly activate naïve T cells and were involved in clearing apoptotic cells and promoting B cell activation (314,315).…”

“…Granot et al showed that the Mf population represents 0.8% of CD45 + cells in mLNs from control individuals (135). In IBD patients, the frequency of Mfs in mLNs increases and they produced more IL-1β and TNF compared to those from controls (268,312,313). Chapuy et al recently showed that mLN Mfs had high frequency of cells positive for inflammatory cytokines compared to mLN SIRPα + DCs, which contain a mix of cDC2 and pDCs (313).…”

“…In IBD patients, the frequency of Mfs in mLNs increases and they produced more IL-1β and TNF compared to those from controls (268,312,313). Chapuy et al recently showed that mLN Mfs had high frequency of cells positive for inflammatory cytokines compared to mLN SIRPα + DCs, which contain a mix of cDC2 and pDCs (313). However, these mLN Mfs poorly activated naïve T cells and did not contribute to Th17 plasticity toward Th1 and Th1/Th17 profiles compared to mLN SIRPα + DCs (313).…”

“…Chapuy et al recently showed that mLN Mfs had high frequency of cells positive for inflammatory cytokines compared to mLN SIRPα + DCs, which contain a mix of cDC2 and pDCs (313). However, these mLN Mfs poorly activated naïve T cells and did not contribute to Th17 plasticity toward Th1 and Th1/Th17 profiles compared to mLN SIRPα + DCs (313). Finally, mLN Mfs highly expressed genes involved in phagocytosis and in leucocyte chemotaxis (313).…”