Transforming ovarian cancer care by targeting minimal residual disease

Frontline treatment and resultant cure rates in patients with advanced ovarian cancer have changed little over the past several decades. Here, we outline a multidisciplinary approach aimed at gaining novel therapeutic insights by focusing on the poorly understood minimal residual disease phase of ovarian cancer that leads to eventual incurable recurrences.

Mutation and methylation profiles of ectopic and eutopic endometrial tissues

Adenomyosis and peritoneal endometriosis are common gynecologic lesions; they are characterized by aberrant locations of normal-appearing endometrium in myometrium and peritoneal surface, respectively. Both ectopic lesions are speculated to originate from uterine eutopic endometrium, which is composed of epithelium and stroma, but how these two different tissue types co-evolve in ectopic locations remains unclear. Here, we analyzed exome-wide mutations and global methylation in microdissected epithelium and stroma separately in paired adenomyosis, peritoneal endometriosis, and endometrium to investigate their relationship. Analyses of somatic mutations and their allele frequencies indicate monoclonal development not only in epithelium but also in the stroma of adenomyosis and peritoneal endometriosis. Our preliminary phylogenetic study suggests a plausible clonal derivation in epithelium and stroma of both ectopic and eutopic endometrium from the same founder epithelium-stroma progenitor cells. While a patient-specific methylation landscape is evident, adenomyosis epithelium and stroma can be distinguished from normal-appearing eutopic endometrium epigenetically. In summary, endometrial stroma, like its epithelial counterpart, could be clonal and both ectopic and eutopic endometrium following divergent evolutionary trajectories. Our data also warrant future investigations into the role of endometrial stroma in the pathobiology of endometrium-related disorders. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Ligation-Enabled Fluorescence-Coding PCR for High-Dimensional Fluorescence-Based Nucleic Acid Detection

Polymerase chain reaction (PCR) is by far the most commonly used method of nucleic acid amplification and has likewise been employed for a plethora of diagnostic purposes. Nonetheless, multiplexed PCR-based detection schemes have hitherto been largely limited by technical challenges associated with nonspecific interactions and other limitations inherent to traditional fluorescence-based assays. Here, we describe a novel strategy for multiplexed PCR-based analysis called Ligation-eNabled fluorescence-Coding PCR (LiNC PCR) that exponentially enhances the multiplexing capability of standard fluorescence-based PCR assays. The technique relies upon a simple, preliminary ligation reaction in which target DNA sequences are converted to PCR template molecules with distinct endpoint fluorescence signatures. Universal TaqMan probes are used to create target-specific multicolor fluorescence signals that can be readily decoded to identify amplified targets of interest. We demonstrate the LiNC PCR technique by implementing a two-color-based assay for detection of 10 ovarian cancer epigenetic biomarkers at analytical sensitivities as low as 60 template molecules with no detectable target cross-talk. Overall, LiNC PCR provides a simple and inexpensive method for achieving high-dimensional multiplexing that can be implemented in manifold molecular diagnostic applications.

Abstract B55: Epigenetic reprogramming of mesenchymal stem cells by ovarian carcinoma to facilitate metastasis

Ovarian cancer, the most deadly gynecologic cancer, resides within a complex tumor microenvironment that supports cancer growth, survival, and spread. Carcinoma-associated mesenchymal stem cells (CA-MSCs) are stromal stem cells within the ovarian TME that strongly support tumor growth promoting cancer initiation, increasing the cancer stem cell pool and enhancing chemotherapy resistance. We recently demonstrated that ovarian cancer stimulation converts normal tissue-derived MSCs into CA-MSCs. The goal of this work is to investigate the mechanism of cancer-mediated CA-MSC formation. We hypothesize that ovarian cancer stimulation induces the epigenetic reprogramming of MSCs creating CA-MSCs. EPIC array DNA methylation analysis, histone mass spectrometry, and Assay for Transposase-Accessible Chromatin using sequencing (ATACseq) were performed on CA-MSCs derived from ovarian cancer patient samples and normal MSCs derived from benign fallopian tube and omentum. We demonstrate that CA-MSCs have large-scale DNA methylation differences vs. normal tissue MSCs. This DNA methylation pattern is distinct from cancer cells; however, the CA-MSC methylation pattern is represented in the DNA methylation pattern of bulk tumor from clear-cell, endometrioid, and high-grade serous cancers, indicating the importance of stromal contribution to bulk tumor analysis. DNA methylation changes were acquired during the conversion of a normal MSC into a CA-MSC and retained after CA-MSC adipocyte and fibroblast differentiation. Histone mass spectrometry and ATACseq demonstrated enrichment in repressive histone marks and overall decreased ATACseq peaks consistent with altered chromosome accessibility. Integration of DNA methylation, ATACseq, and RNAseq data demonstrates strong correlation between epigenetic changes and transcriptomic changes. Interestingly, cell:cell adhesion pathways were consistently upregulated consistent with a partial mesenchymal-to-epithelial transition (MET). This partial MET engenders CA-MSCs with enhanced tumor cell-binding capacity. Direct tumor cell:CA-MSC binding enhanced ovarian cancer migration, extravasation, and nonadherent survival in vitro and increased ovarian cancer metastasis in vivo. This partial MET may be mediated via WT1, a mediator of MET during development, as knockdown of WT1 prevented the formation of a CA-MSCs while overexpression of WT1 enhances the formation of a CA-MSC. Collectively, we demonstrate ovarian cancer stimulates the epigenetic reprogramming of normal MSCs into CA-MSCs, thus enhancing direct tumor cell binding, which facilitates ovarian cancer metastasis. Further investigation is needed to identify the molecular drivers of this reprogramming to allow the disruption of the protumorigenic TME, which may represent a powerful approach to the treatment of ovarian cancer.

Citation Format: Leonard Frisbie, HuiHui Fan, Thomas Pisanic, Hui Shen, Lan Coffman. Epigenetic reprogramming of mesenchymal stem cells by ovarian carcinoma to facilitate metastasis [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B55.

A parallelized microfluidic DNA bisulfite conversion module for streamlined methylation analysis

Aberrant methylation of DNA has been identified as an epigenetic biomarker for numerous cancer types. The vast majority of techniques aimed at detecting methylation require bisulfite conversion of the DNA sample prior to analysis, which until now has been a benchtop process. Although microfluidics has potential benefits of simplified operation, sample and reagent economy, and scalability, bisulfite conversion has yet to be implemented in this format. Here, we present a novel droplet microfluidic design that facilitates rapid bisulfite conversion by reducing the necessary processing steps while retaining comparable performance to existing methods. This new format has a reduced overall processing time and is readily scalable for use in high throughput DNA methylation analysis.