Single-cell analysis of the tubal transcriptome in germline BRCA1 mutation carriers: Exploring early events in carcinogenesis (123)

Objectives: Loss of ciliated cells in the fallopian tube has been proposed to be a primary step in tumor initiation in high-grade serous ovarian cancer (HGSOC). Our objective was to identify single-cell transcriptional networks related to ciliated cell function in the fallopian tubes of women with germline BRCA1 mutations who are at high risk of developing HGSOC. Methods: Four women aged 38-44 years with pathogenic germline BRCA1 mutations underwent risk-reducing surgery at an urban, academic tertiary care center. Under the supervision of a pathologist, fallopian tube ampullae were collected, digested and primary cells were reconstituted in a single-cell suspension. Single-cell RNA-sequencing libraries were prepared using the Chromium Next GEM Single Cell 3’ kit with a cell recovery target of 2000-8000 cells. Libraries were sequenced on an Illumina NovaSeq 6000. Seurat v3 and Harmony were used for data dimensionality reduction, cell cluster identification, and classification. Ancestry-based cluster analysis and pseudo-time trajectory analysis were performed using Harmony and Monocle 3. Results: Integrated analysis of 6015 cells from four BRCA1 tubal epithelia samples identified ten cell clusters with unique transcriptional profiles. Of these, clusters 4 and 10 had features of ciliated cells. Cluster 4 cells expressed PAX8, RFX2, RFX3, and FOXJ1 associated with an intermediate phase ciliated and secretory cell phenotype. Gene ontology analysis showed upregulation of cilia-related genes and stemness pathways, including an upregulation of the gene, SNAI2, belonging to stem-cell development pathway (Enrichment score [ES]: 6.30, p=1.83 x 10-3). Cluster 10 cells expressed RFX2 and RFX3 associated with early progenitor ciliated cells, and gene ontology analysis showed upregulation of stemness pathways, with SOX17, SOX18, and NOTCH1 regulating stem-cell proliferation (ES: 7.45, p=5.79 x10-4). Trajectory analysis identified an early progenitor ciliated cell population and a late-stage ciliated cell population with stem-cell populations intermediate to the two populations. Cells belonging to Cluster 4 showed transitionary features and are identified at all branch points along the trajectory. Conclusions: Single-cell RNA sequencing analysis of the tubal epithelia from BRCA1 mutation carriers identified select clusters having progenitor and stem-like transcriptional profiles of secretory and ciliated cells, with the SOX18, PAX8, RFX2, and RFX3 genes defining these cell populations. Trajectory analysis indicated the differential potential of the ciliated cells to be involved in malignant transformation. The implications of these findings will be further explored by comparison to wild-type and HGSOC transcriptomes. Objectives: Loss of ciliated cells in the fallopian tube has been proposed to be a primary step in tumor initiation in high-grade serous ovarian cancer (HGSOC). Our objective was to identify single-cell transcriptional networks related to ciliated cell function in the fallopian tubes of women with germline BRCA1 mutations who are at high risk of developing HGSOC. Methods: Four women aged 38-44 years with pathogenic germline BRCA1 mutations underwent risk-reducing surgery at an urban, academic tertiary care center. Under the supervision of a pathologist, fallopian tube ampullae were collected, digested and primary cells were reconstituted in a single-cell suspension. Single-cell RNA-sequencing libraries were prepared using the Chromium Next GEM Single Cell 3’ kit with a cell recovery target of 2000-8000 cells. Libraries were sequenced on an Illumina NovaSeq 6000. Seurat v3 and Harmony were used for data dimensionality reduction, cell cluster identification, and classification. Ancestry-based cluster analysis and pseudo-time trajectory analysis were performed using Harmony and Monocle 3. Results: Integrated analysis of 6015 cells from four BRCA1 tubal epithelia samples identified ten cell clusters with unique transcriptional profiles. Of these, clusters 4 and 10 had features of ciliated cells. Cluster 4 cells expressed PAX8, RFX2, RFX3, and FOXJ1 associated with an intermediate phase ciliated and secretory cell phenotype. Gene ontology analysis showed upregulation of cilia-related genes and stemness pathways, including an upregulation of the gene, SNAI2, belonging to stem-cell development pathway (Enrichment score [ES]: 6.30, p=1.83 x 10-3). Cluster 10 cells expressed RFX2 and RFX3 associated with early progenitor ciliated cells, and gene ontology analysis showed upregulation of stemness pathways, with SOX17, SOX18, and NOTCH1 regulating stem-cell proliferation (ES: 7.45, p=5.79 x10-4). Trajectory analysis identified an early progenitor ciliated cell population and a late-stage ciliated cell population with stem-cell populations intermediate to the two populations. Cells belonging to Cluster 4 showed transitionary features and are identified at all branch points along the trajectory. Conclusions: Single-cell RNA sequencing analysis of the tubal epithelia from BRCA1 mutation carriers identified select clusters having progenitor and stem-like transcriptional profiles of secretory and ciliated cells, with the SOX18, PAX8, RFX2, and RFX3 genes defining these cell populations. Trajectory analysis indicated the differential potential of the ciliated cells to be involved in malignant transformation. The implications of these findings will be further explored by comparison to wild-type and HGSOC transcriptomes.