Implantation in mares occurs approximately between days 35 when the chorionic girdle starts to invade endometrium and day 45 when the allantochorion is more firmly attached to endometrium. Immune cells are known to be present in the endometrium over this period but their phenotype and role in implantation in the mare is poorly understood. The aim of this study was to phenotypically characterize subpopulations of immune cells in the endometrium around the time of implantation using single cell RNAseq. Clinically healthy mares were monitored via transrectal ultrasonography. Ovulation was induced with hCG when the follicle diameter was ≥35mm and uterine edema was present. Mares were inseminated with cooled semen. Morphologically normal embryos were flushed by non-surgical lavage at day 33 (n=2) and day 42 (n=2) post ovulation, endometrial biopsies obtained, and serum samples collected for progesterone assays. Biopsies were digested to obtain single cell suspensions, PBMC enriched over Ficoll and then 10 000 cells per sample were processed for scRNA-Seq on the 10X Genomics Chromium platform (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1; Dual Index). Sequencing was performed at the initial depth of ∼20 000 reads/cell. Data was analyzed with Seurat R package v4.0 and the EquCab 3.0 as the reference. Clusters were annotated using established markers of immune cells . (Patel et al. BMC biology. 2021;19:1-13).Unsupervised graph-based clustering of 53909 cells detected 17 clusters of cells that expressed 17667 genes. Cluster 3 was annotated as NK-like cells based on expression of LY49F, LY49C, GNLY, GZMA, CTSW and CD96. Cluster 4 was annotated as heterogenous T cell populations based on the expression of CD3 genes, CCL5, CD2 and CD5. Cluster 7 was assigned to macrophages due to expression of C1Q transcripts, CD68, APOE, DQ and DR transcripts, CXCL10 and CCL8. Both cluster 12 and 16 showed transcripts characteristic for neutrophils including CXCL8, IL1RW, IL1B, IL1BP, TG, RGS2, CCRL2 and PLEK. Cells in cluster 15 expressed genes characteristic both for γδT cells like CCL3, IL2RB, GLNY, GZMA, CTSW, but also Tregs as IL2R and CD80. Cells in cluster 17 expressed markers characteristic for plasma cells and B cells such as ENSECAG00000039599, TP53INP1, CD79A, MEF2C, PRDX4. Some clusters could not be annotated (cluster 1, 2, 5, 6, 8, 9, 10, 11) and are currently being screened for markers for endometrial cells and fibroblasts. In conclusion, these results indicate scRNAseq is a viable approach to simultaneously identify a large number of immune populations present in the endometrium. Deeper sequencing is needed to further differentiate and annotate subpopulations of cells within the clusters and to compare these subpopulations prior to and after chorionic girdle invasion.
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