A Myeloid Lineage Signifying Anti-tumor Necrosis Factor Resistance in Crohn's Disease

Although anti-tumor necrosis factor (TNF) therapy has improved Crohn's disease (CD) management, the development of a refractory phenotype having resistance to the drug is not uncommon. The mechanisms behind this anti-TNF nonresponse are unknown but are likely multifactorial. Here, we examined myeloid cells expressing signal regulatory protein α (SIRPα) for their potential role in refractory CD.

Response to anti-TNF was defined as having reached endoscopic and histological healing, whereas nonresponders did not. Isolated cells from peripheral blood and mucosal biopsies were analyzed by high dimensional flow cytometry, single-cell and bulk RNA sequencing, and Luminex. Ileal organoids were also challenged with secretomes from stimulated SIRPα⁺ cells.

Among the CD phenotypes, patients with anti-TNF refractory CD had the highest levels of CD33⁺HLA-DR⁺CD11c⁺SIRPα⁺ cells in their intestinal mucosa, but the levels in peripheral blood were unchanged. SIRPα⁺ cells from the gut displayed a higher proinflammatory transcriptome, with increased levels of interleukin (IL)-6, TNFα, p40, and IL-1β expression. When isolated and stimulated in vitro with flagellin, these SIRPα⁺ cells showed a more pro-inflammatory transcriptome during CD47 ligation than with an IgG control. Moreover, the secretomes of flagellin/CD47-stimulated SIRPα⁺ cells from patients with refractory CD increased cell death and promoted gene expression associated with Rho GTPase and innate immune responses in epithelial cells, while downregulating their gene expression involved in RNA, lipid metabolism, and adaptive response signaling.

Increased levels of myeloid lineage expressing CD33⁺HLA-DR⁺CD11c⁺SIRPα⁺ cells in the intestinal mucosa negatively impact epithelial cell function, possibly explaining one mechanism for anti-TNF resistance. The abundance of mucosal SIRPα⁺ cells should be further explored as a biomarker and therapeutic target.