Background/Purpose: Our group has made important contributions to an emerging understanding of monocytes and macrophages as central to SSc pathogenesis. There are numerous studies that relate transcriptional signatures from PBMC or whole skin of SSc patients to disease activity. As these studies combine multiple cell types in their analysis, they are limited in their ability to detect transcriptional changes and heterogeneity in specific cell populations. In particular, tissue macrophages exhibit heterogeneity in health and disease and several subpopulations coexist depending on the tissue- and disease-specific context. Here, we evaluate the transcriptional heterogeneity of macrophages isolated from the esophagus and lungs of SSc patients.

Methods: CD45⁺ immune cells were sorted from distal and proximal esophageal biopsies as well as from Bronchoalveolar Lavage (BAL) using fluorescence-activated cell sorting (FACS) from diffuse cutaneous (dc) SSc patients (six patients). Single-cell RNA sequencing (scRNA-seq), as well as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), was performed, and samples were processed using the 10X Genomics 3′ v3.0 pipeline and analyzed in R using the Seurat package.

Results: We collected an average of 10,000 and 500 immune cells from BAL and esophageal biopsy samples, respectively. Of the former, approximately 60% were annotated as monocytes or macrophages based on their transcriptional profile, and these comprised subpopulations exhibiting monocyte-derived vs. alveolar macrophage phenotypes. In the esophagus, approximately 30% were annotated as macrophages or monocytes, much less than in the lungs. We observed variability in macrophage composition across patients in each tissue. Moreover, macrophage subpopulations demonstrated heterogeneity in their gene and surface marker expression of CD11b, CD11c, and CCR2 among other key identifying features, that directly relate to their functional capabilities. These macrophage subsets also displayed differences in their expression of HLA proteins, indicating distinct antigen presentation capabilities. Finally, we identified similarities in the transcriptional landscape between the lung and esophagus macrophages from the same patients.

Conclusion: These data are the first to analyze lung and esophageal cells from the same SSc patients. These results enable the comparison of macrophages from different end organs to provide a systems-level understanding of disease. By precisely annotating immune cells within an affected organ, we can define the role of specific cell populations that drive pathogenesis and may identify novel therapeutic targets. Future studies with larger cohorts will interrogate the clinical relevance of macrophage subpopulations and have the potential to inform clinical decision-making at the patient level.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/investigating-macrophage-heterogeneity-in-the-esophagus-and-lungs-of-ssc-patients/