Single Cell Rna-Seq Analysis Of The Human Fallopian Tube.

Single cell RNA-seq analysis has provided a novel way to characterize cell types through whole transcriptome analysis on the level of the individual cell and has been used to effectively analyze many human organs. Here we use single cell RNA-seq to define major and rare cell types of the human fallopian tube. Characterizing cellular composition and heterogeneity of human fallopian tube using single cell RNA-seq analysis A fallopian tube sample was collected from a perimenopausal female undergoing surgery for a benign indication and was dissected into 3 anatomic segments (isthmus, ampulla, fimbria). Fresh samples from these three anatomic areas were dissociated using our in-house protocols (allowing for > 95 % viability) and analyzed separately. Single cell RNA-seq data were generated using the 10X Genomics Chromium platform. Data analysis was performed using R package Seurat, following our pipeline previously described (Green et al. 2018). After data processing and QC, we analyzed a high-quality set of 2,338 cells in the isthmus, 5,918 cells in the ampulla, and 4,252 cells in the fimbria. Analysis of the three fallopian tube samples separately identified 11 distinct cell clusters in each. Cluster-cluster correlation across the three segments demonstrated a high degree of correlation of the cell clusters, suggesting that most of the cell types are present over the length of the fallopian tube. We merged the data from the 3 segments (n=12,508 cells) and analyzed together to generate a final cell atlas with 15 recognizable clusters. Using marker gene analysis we annotated the 15 cell clusters as the following cell types: ciliated, secretory (3 sub types), myofibroblast, smooth muscle, pericyte, endothelial, vascular smooth muscle, micro vessel, cytotoxic T/natural killer (two subtypes), mast, and monocyte/macrophage (2 subtypes). The diversity of observed cell types confirms the reliability of our dissociation method and collectively represent a deep census of cell heterogeneity from the fallopian tube. Well known molecular markers based on published literature were used to confirm cell identification. Here we present the first comprehensive catalogue of transcriptome-defined cell types of the human fallopian tube. We annotate them to known major cell types and present a foundational reference of functional states and molecular markers for this complex organ. These data provide a new knowledge resource for studies of female reproduction and its disorders, including infertility and ovarian cancer.