High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification
Abstract:Background
High-grade serous tubo-ovarian cancer (HGSTOC) is characterised by extensive inter- and intratumour heterogeneity, resulting in persistent therapeutic resistance and poor disease outcome. Molecular subtype classification based on bulk RNA sequencing facilitates a more accurate characterisation of this heterogeneity, but the lack of strong prognostic or predictive correlations with these subtypes currently hinders their clinical implementation. Stromal admixture profoundly affects the… Show more
“…Our study describes the first comprehensive analysis of paired methylation landscapes generated by WGBS in HGSOCs and their recurrences after chemotherapy, and the first such comparison in patients with and without germline BRCA1 and BRCA2 mutations. This study highlights the molecular heterogeneity that exists in HGSOCs between patients, consistent with single-cell analyses [ 80 , 81 ], and provides evidence that this heterogeneity extends to chemoresistant, recurrent disease. We have shown that there is an absence of common methylation signatures or specific methylation biomarkers that would indicate common mechanisms and underlying biology associated with disease recurrence or chemoresistance.…”
Background
Little is known about the role of global DNA methylation in recurrence and chemoresistance of high grade serous ovarian cancer (HGSOC).
Methods
We performed whole genome bisulfite sequencing and transcriptome sequencing in 62 primary and recurrent tumors from 28 patients with stage III/IV HGSOC, of which 11 patients carried germline, pathogenic BRCA1 and/or BRCA2 mutations.
Results
Landscapes of genome-wide methylation (on average 24.2 million CpGs per tumor) and transcriptomes in primary and recurrent tumors showed extensive heterogeneity between patients but were highly preserved in tumors from the same patient. We identified significant differences in the burden of differentially methylated regions (DMRs) in tumors from BRCA1/2 compared to non-BRCA1/2 carriers (mean 659 DMRs and 388 DMRs in paired comparisons respectively). We identified overexpression of immune pathways in BRCA1/2 carriers compared to non-carriers, implicating an increased immune response in improved survival (P = 0.006) in these BRCA1/2 carriers.
Conclusion
These findings indicate methylome and gene expression programs established in the primary tumor are conserved throughout disease progression, even after extensive chemotherapy treatment, and that changes in methylation and gene expression are unlikely to serve as drivers for chemoresistance in HGSOC.
“…Our study describes the first comprehensive analysis of paired methylation landscapes generated by WGBS in HGSOCs and their recurrences after chemotherapy, and the first such comparison in patients with and without germline BRCA1 and BRCA2 mutations. This study highlights the molecular heterogeneity that exists in HGSOCs between patients, consistent with single-cell analyses [ 80 , 81 ], and provides evidence that this heterogeneity extends to chemoresistant, recurrent disease. We have shown that there is an absence of common methylation signatures or specific methylation biomarkers that would indicate common mechanisms and underlying biology associated with disease recurrence or chemoresistance.…”
Background
Little is known about the role of global DNA methylation in recurrence and chemoresistance of high grade serous ovarian cancer (HGSOC).
Methods
We performed whole genome bisulfite sequencing and transcriptome sequencing in 62 primary and recurrent tumors from 28 patients with stage III/IV HGSOC, of which 11 patients carried germline, pathogenic BRCA1 and/or BRCA2 mutations.
Results
Landscapes of genome-wide methylation (on average 24.2 million CpGs per tumor) and transcriptomes in primary and recurrent tumors showed extensive heterogeneity between patients but were highly preserved in tumors from the same patient. We identified significant differences in the burden of differentially methylated regions (DMRs) in tumors from BRCA1/2 compared to non-BRCA1/2 carriers (mean 659 DMRs and 388 DMRs in paired comparisons respectively). We identified overexpression of immune pathways in BRCA1/2 carriers compared to non-carriers, implicating an increased immune response in improved survival (P = 0.006) in these BRCA1/2 carriers.
Conclusion
These findings indicate methylome and gene expression programs established in the primary tumor are conserved throughout disease progression, even after extensive chemotherapy treatment, and that changes in methylation and gene expression are unlikely to serve as drivers for chemoresistance in HGSOC.
“…Very recently, data for cells from seven untreated HGSC tumours were published, and for each cluster of tumour and host cells, specific transcriptomic markers were identified. 26 We could verify in the scRNA‐Seq dataset the cell‐type specificity of the majority of TU‐selective (7/12), immune‐cell‐selective (32/43) and CAF‐selective (8/13) cytokine genes identified in the present study (Figure S16 ), supporting the conclusions drawn from our data.…”
Section: Discussionsupporting
confidence: 89%
“…Despite considerable progress over the past years, our knowledge of the intercellular signalling network operating in HGSC metastases remains fragmentary. Published systematic transcriptomic studies suitable for the development of signalling networks are limited to ascites cells, 17 , 25 and were partly performed by scRNA‐Seq, 19 , 22 , 23 , 26 which is not informative for a subset of weakly expressed genes and possesses a limited power for differential expression studies compared to bulk analyses. 27 , 28 , 29 , 30 , 31 , 32 It is also currently unclear, to which extent ascites‐derived cell types resemble their counterparts in solid tumour lesions, since unbiased omics analysis have not been described for tumour‐associated non‐immune cells from HGSC patients.…”
BackgroundTranscoelomic spread is the major route of metastasis of ovarian high‐grade serous carcinoma (HGSC) with the omentum as the major metastatic site. Its unique tumour microenvironment with its large populations of adipocytes, mesothelial cells and immune cells establishes an intercellular signaling network that is instrumental for metastatic growth yet poorly understood.MethodsBased on transcriptomic analysis of tumour cells, tumour‐associated immune and stroma cells we defined intercellular signaling pathways for 284 cytokines and growth factors and their cognate receptors after bioinformatic adjustment for contaminating cell types. The significance of individual components of this network was validated by analysing clinical correlations and potentially pro‐metastatic functions, including tumour cell migration, pro‐inflammatory signal transduction and TAM expansion.ResultsThe data show an unexpected prominent role of host cells, and in particular of omental adipocytes, mesothelial cells and fibroblasts (CAF), in sustaining this signaling network. These cells, rather than tumour cells, are the major source of most cytokines and growth factors in the omental microenvironment (n = 176 vs. n = 13). Many of these factors target tumour cells, are linked to metastasis and are associated with a short survival. Likewise, tumour stroma cells play a major role in extracellular‐matrix‐triggered signaling. We have verified the functional significance of our observations for three exemplary instances. We show that the omental microenvironment (i) stimulates tumour cell migration and adhesion via WNT4 which is highly expressed by CAF; (ii) induces pro‐tumourigenic TAM proliferation in conjunction with high CSF1 expression by omental stroma cells and (iii) triggers pro‐inflammatory signaling, at least in part via a HSP70–NF‐κB pathway.ConclusionsThe intercellular signaling network of omental metastases is majorly dependent on factors secreted by immune and stroma cells to provide an environment that supports ovarian HGSC progression. Clinically relevant pathways within this network represent novel options for therapeutic intervention.
“…We used marker genes CD45 and EPCAM to separate the epithelial cells from stromal cells. Cells were negative for CD45 and strongly expressed EPCAM were identified as epithelial cells [ 34 , 35 ]. Cells were filtered through a seventy-millimeter cell-Strainer (BD Biosciences, San Jose, CA, USA) and centrifuged at 1200 rpm for five minutes.…”
Background
Stanniocalcin 1 (STC1) plays an integral role in ovarian cancer (OC). However, the functional role of STC1 in metastasis, lipid metabolism and cisplatin (DDP) chemoresistance in OC is not fully understood.
Methods
Single-cell sequencing and IHC analysis were performed to reveal STC1 expression profiles in patient tissues. Metastasis, lipid metabolism and DDP chemoresistance were subsequently assessed. Cell-based in vitro and in vivo assays were subsequently conducted to gain insight into the underlying mechanism of STC1 in OC.
Results
Single-cell sequencing assays and IHC analysis verified that STC1 expression was significantly enhanced in OC tissues compared with para-carcinoma tissues, and it was further up-regulated in peritoneal metastasis tissues compared with OC tissues. In vitro and in vivo experiments demonstrated that STC1 promoted metastasis, lipid metabolism and DDP chemoresistance in OC. Simultaneously, STC1 promoted lipid metabolism by up-regulating lipid-related genes such as UCP1, TOM20 and perilipin1. Mechanistically, STC1 directly bound to integrin β6 (ITGB6) to activate the PI3K signaling pathway. Moreover, STC1 was directly regulated by Forkhead box C2 (FOXC2) in OC. Notably, targeting STC1 and the FOXC2/ITGB6 signaling axis was related to DDP chemoresistance in vitro.
Conclusions
Overall, these findings revealed that STC1 promoted metastasis, lipid metabolism and DDP chemoresistance via the FOXC2/ITGB6 signaling axis in OC. Thus, STC1 may be used as a prognostic indicator in patients with metastatic OC. Meanwhile, STC1 could be a therapeutic target in OC patients, especially those who have developed chemoresistance to DDP.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.