Single Cell Transcriptomics identifies a WNT7A-FZD5 Signaling Axis that maintains Fallopian Tube Stem Cells in Patient-derived Organoids [scRNA-seq]
Despite its significance to reproduction, fertility, sexually transmitted infections and various pathologies, the fallopian tube (FT) is relatively understudied. Strong evidence points to the FT as the tissue-of-origin of high grade serous ovarian cancer (HGSOC), the most fatal gynaecological malignancy. HGSOC precursor lesions arise specifically in the distal FT (fimbria) which is reported to be enriched in stem-like cells. Investigation of the role of FT stem cells in health and disease has been hampered by a lack of characterization of FT stem cells and lack of models that recapitulate stem cell renewal and differentiation in vitro. Using optimized organoid culture conditions to address these limitations, we found that FT stem cell renewal is highly dependent on WNT/ß-catenin signaling and engineered endogenous WNT/ß-catenin signaling reporter organoids to biomark, isolate and characterize putative FT stem cells. Using functional approaches as well as bulk and single cell transcriptomic analyses, we show that an endogenous hormonally-regulated WNT7A-FZD5 signaling axis is critical for self-renewal of human FT stem cells, and that WNT/ß-catenin pathway-activated cells form a distinct transcriptomic cluster of FT cells enriched in ECM remodelling and integrin signaling pathways. In addition, we find that the WNT7A-FZD5 signaling axis is dispensable for mouse oviduct regeneration. Overall, we provide a deep characterization of FT stem cells and their molecular requirements for self-renewal, paving the way for mechanistic work investigating the role of stem cells in FT health and disease. Overall design: SMART-seq2 based scRNA-seq of patient-derived Fallopian tube Wnt/ß-catenin signalling reporter organoids Please note that in both the processed data files (counts_batch1.csv and counts_batch2.csv) every data column represents one cell (respectively 768 and 384 total). However, while for the Batch1, there are raw data file for each (barcoded) sample (768 pairs of FASTQ files), only one pair of FASTQ files are provided for the Batch2  (represented as one sample records). As two batches were sequenced at two different times, the first one was demultiplexed per index while the second one received whole lane demultiplexing. The cell_info_batch*.csv files contain all the barcodes information, together with the indication of the WNT status and the patient provenience for each cell.