The human fallopian tube harbors the cell of origin for the majority of high-grade serous “ovarian” cancers (HGSCs), but its cellular composition, particularly the epithelial component, is poorly ...characterized. We perform single-cell transcriptomic profiling of around 53,000 individual cells from 12 primary fallopian specimens to map their major cell types. We identify 10 epithelial subpopulations with diverse transcriptional programs. Based on transcriptional signatures, we reconstruct a trajectory whereby secretory cells differentiate into ciliated cells via a RUNX3high intermediate. Computational deconvolution of advanced HGSCs identifies the “early secretory” population as a likely precursor state for the majority of HGSCs. Its signature comprises both epithelial and mesenchymal features and is enriched in mesenchymal-type HGSCs (p = 6.7 × 10−27), a group known to have particularly poor prognoses. This cellular and molecular compendium of the human fallopian tube in cancer-free women is expected to advance our understanding of the earliest stages of fallopian epithelial neoplasia.
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•Single-cell transcriptomics create a cellular atlas for benign fallopian tubes•A secretory-intermediate-ciliated path is projected for epithelial differentiation•PAX8, SOX17, and RUNX3 potentially drive fallopian epithelial differentiation•“Early secretory” epithelial cells are likely precursors for the majority of HGSCs
Using single-cell transcriptomic profiling of around 53,000 cells from human fallopian tubes, Dinh et al. identify SOX17 as a critical factor in fallopian epithelia and construct a differentiation trajectory involving a RUNX3+ intermediate. Early secretory epithelial cells are revealed to be a likely cell of origin for high-grade serous “ovarian” carcinomas.
Transcription factors (TFs) are major contributors to cancer risk and somatic development. In preclinical and clinical studies, direct or indirect inhibition of TF-mediated oncogenic gene expression ...profiles have proven to be effective in many tumor types, highlighting this group of proteins as valuable therapeutic targets. In spite of this, our understanding of TFs in epithelial ovarian cancer (EOC) is relatively limited. EOC is a heterogeneous disease composed of five major histologic subtypes; high-grade serous, low-grade serous, endometrioid, clear cell and mucinous. Each histology is associated with unique clinical etiologies, sensitivity to therapies, and molecular signatures - including diverse transcriptional regulatory programs. While some TFs are shared across EOC subtypes, a set of TFs are expressed in a histotype-specific manner and likely explain part of the histologic diversity of EOC subtypes. Targeting TFs present with unique opportunities for development of novel precision medicine strategies for ovarian cancer. This article reviews the critical TFs in EOC subtypes and highlights the potential of exploiting TFs as biomarkers and therapeutic targets.
General transcription inhibitors are being evaluated as novel agents to treat various malignancies in isolation and combination with other agents. Cancer cells have been demonstrated to have ...‘transcriptional oncogene addiction’ due to their reliance on master transcription factors (MTFs) for survival. General transcription inhibitors have been shown to inhibit these master transcription factors leading to cell death, making them ideal drug targets. Our goal was to see if general transcription inhibitors had activity within clear cell ovarian cancer (CCOC) cell line models, to identify novel therapeutic options that warrant further evaluation in a disease that is frequently chemoresistant.
We performed integrated multi-omic analyses of genome-wide transcriptomic, epigenomic and knock-out screen data to prioritize candidate MTFs for CCOC. Three prototypic human CCOC cell lines: RMGII, JHOC5 and OVMANA were used to study responses to general transcription inhibitors. 3000-5000 cells were seeded in 96-well plates and then were treated with serial dilutions of transcription inhibitors: THZ1, THZ531 and JQ1; inhibitors of CDK7, CDK12/13 and BRD1/2/4 respectively with three technical replicates for 72 hours. Cell viability was quantified using the Cell-titer Glo reagent and results were analyzed using GraphPad Prism Software preforming non-linear regression to obtain dose response curves and IC50 values.
Using integrated analyses of gene expression, landscapes of active chromatin, and functional dependencies prioritized HNF1B and PAX8 as candidate master regulators for CCOC. All three transcription inhibitors showed activity in the three CCOC lines studied. CCOC models were the most sensitive to THZ1 with IC50 values for THZ1 at 11nM, 14nM and 22nM in RMGII, OVMANA and JHOC5 respectively (SD: 8,12,12nM). IC50 for THZ531 was 51nM, 157nM and 361nM for RMGII, OVMANA and JHOC5 (SD: 35,32,12nM) and JQ1 demonstrated the least activity overall with IC50 of 39nM, 105nM and 294nM for the respective cell lines (RMGII, OVMANA, JHOC5, (SD:23, 47, 107nM)).
General transcription inhibitors have activity in clear cell ovarian cancer cell lines. Mechanistic studies are exploring the role of PAX8 and HNF1B in determining CCOC sensitivity to these drugs. Further exploration of synergy with agents such as PARP inhibitors and standard chemotherapeutics is underway in in vitro models to identify potential actionable drug combinations for clinical trial development.
PAX8 is a master transcription factor that is essential during embryogenesis and promotes neoplastic growth. It is expressed by the secretory cells lining the female reproductive tract, and its ...deletion during development results in atresia of reproductive tract organs. Nearly all ovarian carcinomas express PAX8, and its knockdown results in apoptosis of ovarian cancer cells. To explore the role of PAX8 in these tissues, we purified the PAX8 protein complex from nonmalignant fallopian tube cells and high-grade serous ovarian carcinoma cell lines. We found that PAX8 was a member of a large chromatin remodeling complex and preferentially interacted with SOX17, another developmental transcription factor. Depleting either PAX8 or SOX17 from cancer cells altered the expression of factors involved in angiogenesis and functionally disrupted tubule and capillary formation in cell culture and mouse models. PAX8 and SOX17 in ovarian cancer cells promoted the secretion of angiogenic factors by suppressing the expression of
, which encodes a proteinase inhibitor with antiangiogenic effects. The findings reveal a non-cell-autonomous function of these transcription factors in regulating angiogenesis in ovarian cancer.
Candidate causal risk variants from genome-wide association studies reside almost exclusively in noncoding regions of the genome and innovative approaches are necessary to understand their biological ...function. Multi-marker analysis of genomic annotation (MAGMA) is a widely used program that nominates candidate risk genes by mapping single-nucleotide polymorphism summary statistics from genome-wide association studies to gene bodies. We augmented MAGMA to create chromatin-MAGMA (chromMAGMA), a method to nominate candidate risk genes based on the presence of risk variants within noncoding regulatory elements (REs). We applied chromMAGMA to a genetic susceptibility dataset for epithelial ovarian cancer (EOC), a rare gynecologic malignancy characterized by high mortality. This identified 155 unique candidate EOC risk genes across five EOC histotypes; 83% (105/127) of high-grade serous ovarian cancer risk genes had not previously been implicated in this EOC histotype. Risk genes nominated by chromMAGMA converged on mRNA splicing and transcriptional dysregulation pathways. chromMAGMA is a pipeline that nominates candidate risk genes through a gene regulation-focused approach and helps interpret the biological mechanism of noncoding risk variants for complex diseases.
Critical developmental “master transcription factors” (MTFs) can be subverted during tumorigenesis to control oncogenic transcriptional programs. Current approaches to identifying MTFs rely on ...ChIP-seq data, which is unavailable for many cancers. We developed the CaCTS (Cancer Core Transcription factor Specificity) algorithm to prioritize candidate MTFs using pan-cancer RNA sequencing data. CaCTS identified candidate MTFs across 34 tumor types and 140 subtypes including predictions for cancer types/subtypes for which MTFs are unknown, including e.g. PAX8, SOX17, and MECOM as candidates in ovarian cancer (OvCa). In OvCa cells, consistent with known MTF properties, these factors are required for viability, lie proximal to superenhancers, co-occupy regulatory elements globally, co-bind loci encoding OvCa biomarkers, and are sensitive to pharmacologic inhibition of transcription. Our predictions of MTFs, especially for tumor types with limited understanding of transcriptional drivers, pave the way to therapeutic targeting of MTFs in a broad spectrum of cancers.
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