Dissection of transcriptome dysregulation and immune characterization in women with germline BRCA1 mutation at single-cell resolution

Abstract

Background High-grade serous carcinoma (HGSC) is the most frequent and lethal type of ovarian cancer. It has been proposed that tubal secretory cells are the origin of ovarian HGSC in women with familial BRCA1/2 mutations. However, the molecular changes underlying malignant transformation remain unknown. Method We performed single-cell RNA and T cell receptor sequencing of tubal fimbriated ends from 3 BRCA1 germline mutation carriers (BRCA1 carriers) and 3 normal controls with no high-risk history (non-BRCA1 carriers). Results Exploring the transcriptomes of 19,008 cells, predominantly from BRCA1+ samples, we identified 5 major cell populations in the fallopian tubal mucosae. The secretory cells of BRCA1+ samples had differentially expressed genes involved in tumor growth and regulation, chemokine signaling, and antigen presentation compared to the wild-type BRCA1 controls. There are several novel findings in this study. First, a subset of the fallopian tubal secretory cells from one BRCA1 carrier exhibited an epithelial-to-mesenchymal transition (EMT) phenotype, which was also present in the mucosal fibroblasts. Second, we identified a previously unreported phenotypic split of the EMT secretory cells with distinct evolutionary endpoints. Third, we observed increased clonal expansion among the CD8+ T cell population from BRCA1+ carriers. Among those clonally expanded CD8+ T cells, PD-1 was significantly increased in tubal mucosae of BRCA1+ patients compared with that of normal controls, indicating that T cell exhaustion may occur before the development of any premalignant or malignant lesions. Conclusion These results indicate that EMT and immune evasion in normal-looking tubal mucosae may represent early events leading to the development of HGSC in women with BRCA1 germline mutation. Our findings provide a probable molecular mechanism explaining why some, but not all, women with BRCA1 germline mutation present with early development and rapid dissemination of HGSC.

A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast

“…4a and 5 ). A similar phenotype was reported in the Fallopian tube of BRCA1 mutation carriers, suggesting commonalities across tissues 37 . Interestingly, when considering transcriptional shifts in HR donors compared with AR donors, we observe an increase in PDL1 expression, mainly in LASPs and macrophages but also across some of the LHS cells (Fig.…”

Fallopian tube single cell analysis reveals myeloid cell alterations in high-grade serous ovarian cancer

“…We identified the macrophage-to-monocyte ratio changes as potentially linked with disease progression. Next, we wanted to evaluate this ratio using FT scRNA-Seq from patients with BRCA1 germline mutations, 25 who are high risk of developing HGSCs. We used marker genes consistent with our 12 sample FT reference to identify myeloid cell types ( Figures S6 A and S6B) using representative genes (LYZ for pan-myeloid cells, FCN1 for monocytes, and C1QB for macrophages, consistent with our FT data).…”

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Figure 5 Macrophage and monocyte heterogeneity analysis show the altered gene expression in high-risk patients with germline BRCA mutations and response to chemotherapy (A) The log2 macrophage-to-monocyte ratio in benign FT compared with FT in germlin e BRCA1 carriers (Yu et al. 2022 25 ) (N = 3 patients, each). (B) Examples of monocytic genes defined in human FTs are differentially expressed in FTs of BRCA 1 carriers.

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“… (A) The log2 macrophage-to-monocyte ratio in benign FT compared with FT in germlin e BRCA1 carriers (Yu et al. 2022 25 ) (N = 3 patients, each). …”

“…The heterogeneity of T/NK, myeloid, and stromal cells and their cell-cell interactions in FT remain incomplete in published scRNA-Seq analyses. 24 We therefore analyzed immune and stromal cell heterogeneity from scRNA-Seq of benign human FTs 24 and HGSC tumors and adjacent normal samples from >80 in-house and publicly available sources, 14 , 15 , 16 , 18 , 24 , 25 , 26 identifying 7 fibroblast/stromal, 6 T/NK, and 7 myeloid cell subsets with distinct gene, pathway, and regulatory network signatures. Further examination of single-cell derived transcriptomic signatures reveals associations with molecular subtypes in bulk transcriptome data from The Cancer Genome Atlas (TCGA).…”