Background Immune cell populations in the intestinal muscularis propria during colitis
are poorly resolved. Maintaining homeostasis in this niche is critical, highlighted
by the poorer prognosis of inflammatory bowel disease associated with muscularis propria
inflammation.Methods This study utilizes single-cell RNA sequencing to survey the
immune cell populations within the muscularis propria of normal colon and dextran
sodium sulfate-induced colitis. Findings are validated by immunohistochemistry, flow
cytometry and cell-lineage tracing in vivo, and in vitro assays with muscularis macrophages
(MM phi).Results In na & iuml;ve conditions, transcriptional duality is observed in
MM phi s with 2 major subpopulations: conventional resident Cx3cr1+ MM phi s and Lyve1+
MM phi s. The Lyve1+ population is phagocytic and expresses several known MM phi markers
in mouse and human, confirming their identity as a bona fide MM phi subset. Single-cell
transcriptomics indicate that resident MM phi s are retained during colitis and exhibit
plasticity toward an inflammatory profile. Lyve1+ MM phi s, which express anti-inflammatory
marker CD163, are absent during colitis, as confirmed by flow cytometry. In contrast,
lineage tracing finds that resident Cx3cr1+ MM phi s remain during colitis and are
not completely replaced by the inflammatory infiltrating monocytes. In vitro studies
provide biological evidence of the plasticity of resident Cx3cr1+ MM phi s in response
to lipopolysaccharide (LPS), mirroring transcriptional observations in vivo of their
inflammatory plasticity. Potential markers for colitic MM phi s, validated in animal
models and in individuals with ulcerative colitis, are identified.Conclusions Our
findings contribute to the understanding of the immune system in the muscularis propria
niche during colitis by resolving the heterogeneity and origins of colitic MM phi
s. Involvement of the muscularis propria accompanies a poorer prognosis in IBD. This
study characterizes muscularis macrophage subpopulations during colitis, highlighting
the loss of anti-inflammatory LYVE-1+ macrophages and inflammatory plasticity in resident
CX3CR1+ macrophages, providing insights into prognostic and therapeutic targets.
