High-grade Serous Carcinoma Tumor Research Articles

VISTA/CTLA4/PD1 coexpression on tumor cells confers a favorable immune microenvironment and better prognosis in high-grade serous ovarian carcinoma.

Immunotherapy by blocking immune checkpoints programmed death/ligand (PD1/PDL1) and cytotoxic T-lymphocyte-associated protein 4(CTLA4) has emerged as new therapeutic targets in cancer. However, their efficacy has been limited due to resistance. A new- checkpoint V-domain Ig-containing suppressor of T cell activation (VISTA) has appeared, but the use of its inhibition effect in combination with antibodies targeting PDL1/PD1and CTLA4 has not been reported in ovarian cancer. In this study, we investigated the expressions of VISTA, CTLA4, and PDL1 using immunohistochemistry (IHC)on 135 Formalin-Fixed Paraffin-Embedded (FFPE)tissue samples of High-grade serous carcinoma (HGSOC). VISTA, CTLA4, PDL1, PD1, CD8, CD4, and FOXP3 mRNA extracted from 429 patients with ovarian cancer in the Cancer Genome Atlas (TCGA) database was included as a validation cohort. Correlations between these checkpoints, tumor-infiltrating- lymphocytes (TILs), and survival were analyzed. CTLA4 was detectable in 87.3% of samples, VISTA in 64.7%, PD1 in 56.7%, and PDL1 in 48.1%. PDL1 was the only tested protein associated with an advanced stage (p=0.05). VISTA was associated with PDL1, PD1, and CTLA4 expressions (p=0.005, p=0.001, p=0.008, respectively), consistent with mRNA level analysis from the TCGA database. Univariate analyses showed only VISTA expression (p=0.04) correlated with overall survival (OS). Multivariate analyses showed that VISTA expression (p=0.01) and the coexpression of VISTA+/CTLA4+/PD1+ (p=0.05) were associated with better OS independently of the clinicopathological features. Kaplan-Meier analysis showed that the coexpression of the VISTA+/CTLA4+/PDL1+ and VISTA+/CTLA4+/PD1+ checkpoints on tumor cells (TCs)were associated with OS (p=0.02 and p<0.001; respectively). VISTA+/CTLA4+/PD1+ in TCs and CD4+/CD8+TILswere associated with better 2-yer OS. This correlation may refer to the role of VISTA as a receptor in the TCs and not in the immune cells. Thus, targeting combination therapy blocking VISTA, CTLA4, and PD1 could be a novel and attractive strategy for HGSOC treatment, considering the ambivalent role of VISTA in the HGSOC tumor cells.

Abstract 1617: Tumor evolution during therapy in ovarian cancer

Abstract The evolution of tumors from diagnosis to relapse in ovarian high-grade serous carcinoma (HGSC) patients is poorly understood. Consequently, it is unknown whether diagnostic samples are representative enough to guide treatment directions at relapse, or whether acquired changes during therapy provide targets in patients with relapses. To answer these questions and characterize tumor evolution during treatment, we used data from &amp;gt;700 tissue and plasma samples from 200 HGSC patients belonging to the observational, longitudinal DECIDER trial (NCT04846933). Mutations from whole-genome sequencing data from tissue samples (2-12 per patient) were used to construct phylogenetic trees. The trees were corrected by the copy-number alterations and curated to integrate circulating tumor DNA (ctDNA) exome- and targeted-sequencing data from plasma samples. Evolutionary states presenting within and between sample heterogeneity were evaluated through clonal complexity and divergence. Additionally, genetic differences between persistent and non-persistent subclones were studied to identify features affecting treatment resistance. Our results indicate that the majority of subclones survive chemotherapy treatment and major subclonal replacement takes place in only a few patients. Within-sample heterogeneity was higher in plasma samples than in ascites, highlighting the importance of ctDNA samples to estimate persistent subclones. Additionally, our recently reported evolutionary states (Lahtinen et al. Cancer Cell 2023) were often altered by the treatment induced selection pressure. At late relapses, subclone compositions typical of maintaining evolutionary state tumors were less common, and a higher number of acquired subclones were detected, suggesting further evolution of the persisting clones. In summary, chemotherapy does not suppress heterogeneity in HGSC tumors. Interestingly, patients with the worst prognosis have a stable composition of multiple clones in their tumors, and tumors with low heterogeneity responded better to primary treatment. Relapse samples show lower within-sample heterogeneity and further evolution. Furthermore, we detected several evolutionary trajectories from stable, persistent cancer subclone populations to highly dynamic subclone structures. This renders diagnostic samples suitable to guide relapse treatment decisions in a subset of patients with HGSC but not for all. Our characterization of the dynamics of tumor clonal heterogeneity during treatment allows to define better therapeutic interventions for HGSC patients with relapsed disease. Citation Format: Sampsa Kalervo Hautaniemi, Jaana Oikkonen, Alexandra Lahtinen, Mai T.N. Nguyen, Giovanni Marchi, Kari Lavikka, Anna Rajavuori, Sakari Hietanen, Anni Virtanen, Johanna Hynninen. Tumor evolution during therapy in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1617.

Abstract B069: Bone marrow-derived adipocytes promote ovarian cancer progression and metastasis

Abstract B069: Bone marrow-derived adipocytes promote ovarian cancer progression and metastasis

118. Single-cell RNA sequencing and co-occurring cellular state analysis of high-grade serous ovarian cancer

High-grade serous carcinoma (HGSC) is the most lethal subtype of ovarian cancer, and a majority of patients are diagnosed at advanced stages. One standard-of-care is neoadjuvant chemotherapy followed by cytoreductive surgery, however up to 80% of HGSC patients develop recurrent disease. There exists a critical need to better understand the features of this tumor microenvironment that may highlight potential therapeutic targets, help stratify chemotherapy responders from non-responders, and uncover novel cell states that may serve as prognostic or predictive biomarkers. We obtained multiple biopsies from five patients with advanced-stage HGSC, both pre- and post-treatment, and analyzed these samples using single-cell RNAseq. We identified 20 distinct transcriptional clusters of cells, including a well-defined tumor subset enriched for EPCAM and KRT8. We annotated each cluster using known marker genes, and additionally validated these data through genome-wide copy number and developmental maturity analyses. We then performed transcriptome deconvolution to identify co-occurring transcriptional states using EcoTyper. We then performed bulk RNAseq on paired pre- and post-treatment tumor biopsies from 23 HGSC patients. Applying our fingerprints of ecotypes from the scRNA-seq data, we identified multiple distinct transcriptional states within the pre- and post-treatment HGSC tumor microenvironment, which were enriched for distinct co-occurring states comprised of multiple immunologic lineages, including CD4 T and NK cell states. We plan to validate these ecotypes using spatial transcriptomics and compare clinical outcomes across transcriptional states to determine the potential prognostic or predictive implications of our discoveries.

Changes in focal adhesion protein Talin-1 expression during malignant transformation leading to ovarian high-grade serous carcinoma.

e17586 Background: Ovarian high-grade serous carcinoma (HGSC), the most lethal form of ovarian cancer, is often detected at late stages due to the lack of an early detection test resulting in low 5-year survival rates. Information on factors associated with malignant transformation and early metastasis is critical in developing interventional strategies to reduce the incidence and death due to HGSC. Talin-1, a focal adhesion protein, regulates cell–cell adhesion, and induces cytoskeletal remodeling leading to tumor cell migration and adhesion. Destabilization of the cell membrane during malignant development may shed Talin-1 in circulation which may be a potential early marker of progression of HGSC. Objective: The goal of this study was to examine the changes in Talin-1 expression during malignant transformation in ovaries and fimbria of the fallopian tube and its prevalence in serum. Difficulty in accessing patients with early-stage HGSC is a significant barrier to study malignant transformation and progression. Laying hen model of spontaneous ovarian HGSC was used together with clinical specimens. Methods: Two experiments were conducted. Exploratory study:Archived normal ovaries (n = 10), ovaries with HGSC at early (n = 10) and late (n = 10) stages from patients and their serum samples were used. Prospective study: Laying hens with no detectable abnormalities were selected and monitored using transvaginal ultrasound (TVUS) imaging at 10 week intervals for 10 months and sera were collected at each scan. Hens were euthanized at diagnosis of solid mass during scanning or at the end of the study; ovaries, fimbria and serum samples were collected. Normal hens (n = 10), hens with early (n = 7) and late-stage (n = 8) tumors were selected. Talin-1 expression in tissues and serum was determined by immunohistochemistry (IHC), Western blotting (WB), gene expression (qPCR), and immunoassay (ELISA). Significant differences in Talin-1 expression among all groups were determined by ANOVA and/or paired/unpaired t-tests, significance was taken when P&lt; 0.05. Results: Expression of Talin-1was detected in all tissues with various intensities. Compared with normal, ovarian HGSC tissues showed intense expression of Talin-1 in IHC, WB and qPCRs ( P&lt; 0.05). Similar patterns were observed in serum levels in ELISA ( P&lt; 0.01) in the exploratory study. Prospective study in hens showed significant increase in serum Talin-1 levels even before the formation of a solid tumor mass in the ovary or fimbria detectable by TVUS. Conclusions: Elevated Talin-1 expression in early-stage ovarian HGSC tumors suggests its association with malignant development. Serum prevalence of Talin-1 during malignant transformation makes it a potential marker for early detection of HGSC and its progression. These results will serve as foundation for a clinical study with larger cohorts. Support: NIH R01 CA210370 (AB)

High-grade serous ovarian tumor cells modulate NK cell function to create an immune-tolerant microenvironment.

SUMMARYTubo-ovarian high-grade serous carcinoma (HGSC) is unresponsive to immune checkpoint blockade despite significant frequencies of exhausted T cells. Here we apply mass cytometry and uncover decidual-like natural killer (dl-NK) cell subpopulations (CD56+CD9+CXCR3+KIR+CD3−CD16−) in newly diagnosed HGSC samples that correlate with both tumor and transitioning epithelial-mesenchymal cell abundance. We show different combinatorial expression patterns of ligands for activating and inhibitory NK receptors within three HGSC tumor compartments: epithelial (E), transitioning epithelial-mesenchymal (EV), and mesenchymal (vimentin expressing [V]), with a more inhibitory ligand phenotype in V cells. In cocultures, NK-92 natural killer cells acquire CD9 from HGSC tumor cells by trogocytosis, resulting in reduced anti-tumor cytokine production and cytotoxicity. Cytotoxicity in these cocultures is restored with a CD9-blocking antibody or CD9 CRISPR knockout, thereby identifying mechanisms of immune suppression in HGSC. CD9 is widely expressed in HGSC tumors and so represents an important new therapeutic target with immediate relevance for NK immunotherapy.

A randomized phase III, two-arm trial of paclitaxel, carboplatin, and maintenance letrozole versus letrozole monotherapy in patients with stage II-IV, primary low-grade serous carcinoma of the ovary or peritoneum.

TPS5601 Background: Low-grade serous carcinoma of the ovary or peritoneum (LGSOC) is a rare subtype of epithelial carcinoma. Differences in epidemiology, pathogenesis, disease presentation, and clinical outcomes have been characterized between women diagnosed with LGSOC and those with the p53-driven high-grade serous carcinoma (HGSOC). Ultimately, patients with LGSOC should be treated differently than those with HGSOC. Several studies suggest that LGSOC is relatively chemoresistant and that most tumors robustly express estrogen and progesterone receptors. Recently, retrospective reports suggest that utilization of the aromatase inhibitor, letrozole, as monotherapy or in addition to platinum/taxane-based chemotherapy in those with primary advanced-stage LGSOC results in preliminarily promising survival outcomes. Methods: This study is a two-arm, randomized, open-label, Phase III clinical trial. The primary objective is to assess whether letrozole monotherapy (2.5 mg po daily) is non-inferior to carboplatin (AUC 5-6) and paclitaxel (175 mg/m2) followed by letrozole maintenance therapy with respect to progression free survival in women with primary, Stage II-IV LGSOC who have undergone an attempt at maximal surgical cytoreduction. Secondary endpoints include incidence of adverse events, objective response rate in those with measurable disease after surgery, response duration, overall survival, and adherence to letrozole maintenance therapy. Study subjects must have undergone a bilateral salpingo-oophorectomy, and p53 IHC testing of tumors is required to rule out those with aberrant p53 expression commonly observed in HGSOC tumors. Study strata include residual disease status and country of enrollment. Four hundred and fifty patients will be enrolled in the United States, Canada and South Korea through the NRG Oncology trials network. Correlative aims include analyzing the association of ER/PR tumoral expression with aromatase inhibitor therapy response and determining ESR1 mutational status in those who develop letrozole resistance. The study includes two interim analyses; at 20% information time, a futility analysis will be conducted, and at 40% information time, both efficacy and futility will be assessed. This is one of the first randomized trials performed in women with primary, advanced LGSOC, and the study is open with 71 patients enrolled at the time of abstract submission. Clinical trial information: NCT04095364.

Characterization of immunoreactivity with whole-slide imaging and digital analysis in high-grade serous ovarian cancer.

Ovarian cancer is the most lethal of gynecological cancers with 5-year survival rate of ca. 45%. The most common histologic subtype is high-grade serous carcinoma, which typically is presented with advanced stage and development of chemoresistance. Therefore, new treatment options, including immunotherapies, are needed. Understanding the features of the immune cell populations in the tumor microenvironment is essential for developing personalized treatments and finding predictive biomarkers. Digital image analysis may enhance the accuracy and reliability of immune cell infiltration assessment in the tumor microenvironment. The aim of this study was to characterize tumor microenvironment in a retrospective cohort of high-grade serous carcinoma samples with whole-slide imaging and digital image analysis. Formalin-fixed paraffin-embedded high-grade serous carcinoma tumor tissue samples (n = 67) were analyzed for six immunohistochemical stainings: CD4, CD8, FoxP3, granzyme B, CD68, and CD163. The stained sample slides were scanned into a digital format and assessed using QuPath 0.1.2 and ImageJ software. Staining patterns were associated with clinicopathological data. The higher numbers of intraepithelial CD8+, CD163+, and granzyme B+ immune cells were associated with survival benefit when analyzed individually, while high levels of both CD8+ and granzyme B+ tumor-infiltrating lymphocytes were an independent prognostic factor in the Cox multivariate regression analysis (median progression-free survival; hazard ratio = 0.287, p = 0.002). Specimens taken after administration of neoadjuvant chemotherapy presented with lower FoxP3+ tumor-infiltrating lymphocyte density (Fisher's exact test, p = 0.013). However, none of the studied immunomarkers was associated with overall survival or clinical factors. Tumors having high amount of both intraepithelial CD8+ and granzyme B+ tumor-infiltrating lymphocytes showed better progression-free survival, possibly reflecting an activated immune state in the tumor microenvironment. The combined positivity of CD8 and granzyme B warrants further investigation with respect to predicting response to immune therapy. Neoadjuvant chemotherapy may have an effect on the tumor microenvironment and therefore on the response to immuno-oncologic or chemotherapy treatments.

Targeting IDH1 as a Prosenescent Therapy in High-grade Serous Ovarian Cancer.

Epithelial ovarian cancer (EOC) is the deadliest gynecologic cancer. High-grade serous carcinoma (HGSC) is the most frequently diagnosed and lethal histosubtype of EOC. A significant proportion of patients with HGSC relapse with chemoresistant disease. Therefore, there is an urgent need for novel therapeutic strategies for HGSC. Metabolic reprogramming is a hallmark of cancer cells, and targeting metabolism for cancer therapy may be beneficial. Here, we found that in comparison with normal fallopian tube epithelial cells, HGSC cells preferentially utilize glucose in the TCA cycle and not for aerobic glycolysis. This correlated with universally increased TCA cycle enzyme expression in HGSC cells under adherent conditions. HGSC disseminates as tumor cell spheroids within the peritoneal cavity. We found that wild-type isocitrate dehydrogenase I (IDH1) is the only TCA cycle enzyme upregulated in both adherent and spheroid conditions and is associated with reduced progression-free survival. IDH1 protein expression is also increased in patients with primary HGSC tumors. Pharmacologic inhibition or knockdown of IDH1 decreased proliferation of multiple HGSC cell lines by inducing senescence. Mechanistically, suppression of IDH1 increased the repressive histone mark H3K9me2 at multiple E2F target gene loci, which led to decreased expression of these genes. Altogether, these data suggest that increased IDH1 activity is an important metabolic adaptation in HGSC and that targeting wild-type IDH1 in HGSC alters the repressive histone epigenetic landscape to induce senescence. IMPLICATIONS: Inhibition of IDH1 may act as a novel therapeutic approach to alter both the metabolism and epigenetics of HGSC as a prosenescent therapy.

Insights into Impact of DNA Copy Number Alteration and Methylation on the Proteogenomic Landscape of Human Ovarian Cancer via a Multi-omics Integrative Analysis

In this work, we propose iProFun, an integrative analysis tool to screen for proteogenomic functional traits perturbed by DNA copy number alterations (CNAs) and DNA methylations. The goal is to characterize functional consequences of DNA copy number and methylation alterations in tumors and to facilitate screening for cancer drivers contributing to tumor initiation and progression. Specifically, we consider three functional molecular quantitative traits: mRNA expression levels, global protein abundances, and phosphoprotein abundances. We aim to identify those genes whose CNAs and/or DNA methylations have cis-associations with either some or all three types of molecular traits. Compared with analyzing each molecular trait separately, the joint modeling of multi-omics data enjoys several benefits: iProFun experienced enhanced power for detecting significant cis-associations shared across different omics data types, and it also achieved better accuracy in inferring cis-associations unique to certain type(s) of molecular trait(s). For example, unique associations of CNAs/methylations to global/phospho protein abundances may imply posttranslational regulations.We applied iProFun to ovarian high-grade serous carcinoma tumor data from The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium and identified CNAs and methylations of 500 and 121 genes, respectively, affecting the cis-functional molecular quantitative traits of the corresponding genes. We observed substantial power gain via the joint analysis of iProFun. For example, iProFun identified 117 genes whose CNAs were associated with phosphoprotein abundances by leveraging mRNA expression levels and global protein abundances. By comparison, analyses based on phosphoprotein data alone identified none. A network analysis of these 117 genes revealed the known oncogene AKT1 as a key hub node interacting with many of the rest. In addition, iProFun identified one gene, BIN2, whose DNA methylation has cis-associations with its mRNA expression, global protein, and phosphoprotein abundances. These and other genes identified by iProFun could serve as potential drug targets for ovarian cancer.

Changes in the Management and Prognosis of Ovarian Cancer Due to the New FIGO and WHO Classifications: A Case Series Observational Descriptive Study. Seven Years of Follow-up.

Ovarian cancer is the deadliest of gynecologic cancers. In recent years, International Federation of Gynecology and Obstetrics (FIGO) and the World Health Organization (WHO) classifications were revised. We compared the major changes between the classifications and examined the effects on the therapy and prognosis of the ovarian, fallopian tubes, and peritoneum cancer in our series according to both classifications. We performed an observational descriptive study of 210 patients who were diagnosed with a malignant ovarian tumor from 2010 to 2016. The accepted FIGO and WHO classifications at each point in time were registered. We reclassified both data, obtaining both classifications for each patient. The changes in the therapeutic management and prognosis were examined. In both FIGO classifications of our case series, most patients with ovarian cancer were in FIGO stage III. We found that 4.2% of the previous stage IIIC patients have changed to stage IIIA2 or stage IIIB, with better prognosis and survival rate. In the new WHO classification, the main change, in our case series, was the increase in the high-grade serous carcinoma percentage. According to the current recommendations, we observed 7.56% more patients in early ovarian cancer stages treated with platinum and taxane. In both early and advanced ovarian cancer group, high-grade serous carcinoma tumors were predominant. The newly created WHO and FIGO classifications have improved the ability to predict the prognosis and consequently to change the therapeutic managements of patients with ovarian cancer.

Abstract A63: Estrogen receptor signaling in fallopian tube epithelia of BRCA mutation carriers

Abstract Background: The most common and aggressive type of epithelial ovarian cancers (EOC) is high-grade serous carcinoma (HGSC), which accounts for 90% of ovarian cancer deaths. HGSC is the predominant histotype associated with BRCA1 and BRCA2 mutations. Prophylactic surgery in BRCA mutation carriers has implicated the fallopian tube epithelium (FTE), a hormonal responsive tissue, as the etiologic site of origin for HGSC. Estrogen and its receptors are major regulators of growth and differentiation in normal ovaries and fallopian tubes, and its mutagenic properties have been linked to ovarian carcinogenesis. Estrogen receptors (ER) are rarely mutated, amplified, or deleted in HGSC, yet only 10% of patients respond to antiestrogen treatment. TP53 mutations in the form of the p53 signature have been found in serous tubal intraepithelial carcinomas (STIC) and are ubiquitously present in patients with HGSC. We hypothesized that in the presence of dysfunctional p53, subsequent promiscuous binding of ER will yield aberrant signaling, contributing to cellular transformation. Methods: We used our previously published gene expression profiles to generate a candidate gene list, which was chosen based on the presence of known estrogen-responsive elements. We analyzed expression of 6 ER responsive genes using data collected from laser capture microdissection in normal FTE tissues. Tissue microarray analysis (TMA) was also performed on a subset of HGSC tumor samples from this cohort, staining for PR, ER, and p53, and expression was analyzed alongside their respective outcome and overall survival Finally, to mimic the in vivo environment of early carcinogenesis, FTE-normal and FTE-p53 mutant cell lines were established and treated with 100nM estradiol, an estrogen analog, to observe changes in response. Results: Preliminary data showed that FTE-BRCA and FTE-nonBRCA seemingly look and express ER and PR proteins similarly. Underlying these morphologic similarities is a potential haploinsufficiency predisposing FTE-BRCA to cytotoxic stresses. Microarray gene expression of laser captured FTE-BRCA and FTE-nonBRCA showed varied levels of ER mRNA expression across samples (n=25) while PR transcript levels change dynamically. The data generated have facilitated the development of gene signatures and biomarkers that will predict response to antiestrogen therapy and identify patients who will benefit from hormonal therapies. Citation Format: Leah V. Dodds, Omar Nelson, Patricia Shaw, Anca Milea, Ramlogan Sowamber, Sophia HL George. Estrogen receptor signaling in fallopian tube epithelia of BRCA mutation carriers. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr A63.

Altered expression of different GalNAc‑transferases is associated with disease progression and poor prognosis in women with high-grade serous ovarian cancer.

Protein glycosylation perturbations are implicated in a variety of diseases, including cancer. Aberrant glycosylation in cancer is frequently attributed to altered expression of polypeptide GalNAc transferases (GalNAc‑Ts) - enzymes initiating mucin-type O-glycosylation. A previous study from our group demonstrated that one member of this family (GALNT3) is overexpressed in epithelial ovarian cancer (EOC), and GALNT3 expression correlated with shorter progression-free survival (PFS) in EOC patients with advanced disease. As considerable degree of redundancy between members of the GalNAc‑Ts gene family has been frequently observed, we decided to investigate whether other members of this family are essential in EOC progression. Insilico analysis based on publically available data was indicative for altered expression of five GalNAc‑Ts (GALNT2, T4, T6, T9 and T14) in ovarian high-grade serous carcinoma (HGSC) samples compared to non-tumoral (control) ovarian tissue. We analyzed protein expression of these GalNAc‑Ts in EOC cells and tumors by western blotting, followed by immunohistochemical (IHC) evaluation of their expression in EOC tumor and control samples using tissue microarrays (TMAs). Western blot analyses were indicative for low expression of GALNT2 and strong expression of GALNT6, T9 and T14 in both EOC cells and tumors. These observations were confirmed by IHC. GALNT2 displayed significantly lower expression, while GALNT6, GALNT9 and GALNT14 showed significantly higher expression in HGSC tumors compared to control tissue. Importantly, GALNT6 and GALNT14 expression correlated with poor prognosis of serous EOC patients. Moreover, our results suggest for overlapping functions of some GalNAc‑Ts, more specifically GALNT3 and GALNT6, in directing EOC progression. Our results are indicative for a possible implication of different members of the GalNAc‑T gene family in modulating EOC progression, and the potential use of GALNT6 and GALNT14 as novel prognostic EOC biomarkers. These data warrant future studies on the role of members of the GalNAc‑Ts gene family in ovarian tumorigenesis.

Abstract 821: Loss and retention of mutations in cell culture model systems

Abstract Although relevant, the genomic and proteomic alterations between original tumor tissue and newly established cell lines are frequently uncharacterized. In developing a novel cell model (Powder) of high grade serous carcinoma (HGSC), we followed the status of clinically relevant biomarkers to identify changes taking place between the tissue and cultured cell population. Understanding these changes enables proper utilization of new models and continued model optimization. Using a validated panel, we analyzed 592 genes in the Powder cell model and tumor from which it was derived, detecting several classes of genomic alterations. This included point mutations, indels, copy number variations, fusions, and variant transcripts. p53 mutation status of Powder was matched to a panel of previously reported HGSC cell lines. We further subdivided the panel by p53 protein expression level by reanalyzing previously published reverse phase protein array (RPPA) data. Significance of differential expression between groups was determined with a Welch's t-test. A majority (14/21 or 67%) of the mutations detected in the HGSC tumor were conserved in the Powder cell model. Two additional mutations, undetected in the tumor, were found in the cell model. The tumor exhibited moderate to strong diffuse positive p53 immunostaining, and p53 mutations were measured in 79% of alleles. While the p53 mutation did not carry to the cell model, the cells were positive for CK7 and PAX8, consistent with ovarian cancer cells. In the panel of HGSC cell lines, we examined p53 mutation status and protein level, identifying 3 groups: (1) p53-mut/high protein, (2) p53-mut/low protein and (3) p53-WT/low protein. Powder identified with the p53-WT/low protein group. Previous work identifies the p53-WT/low protein group of cell models as part of a larger set of novel ovarian cell models with a stem-like molecular profile and higher drug resistance. Analysis of differential protein expression revealed upregulation in the p53 low protein group of both normal cell cycle genes and of notable cancer-related proteins. This included p21 and BAD, which are upregulated in cells with functional p53, eIF4E, a candidate cancer therapeutic target, and BOP1, which is disregulated in multiple solid cancers, including ovarian. These results underscore the need for further characterization of the Powder cell model to clarify its applications to specific research questions. Continued examination of Powder and other p53-WT cell models derived from HGSC tumors may uncover independent pathways driving disease. Additionally, understanding which mutations are underrepresented by cell models is necessary for ongoing methods development. Citation Format: Pamela S. Shaw, Rick Nicoletti, Naghmeh Salimi, Helen L. Yang, Abigail E. Witt, Agoston T. Agoston, Elin S. Agoston. Loss and retention of mutations in cell culture model systems [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 821. doi:10.1158/1538-7445.AM2017-821

Loss of PAX8 in high-grade serous ovarian cancer reduces cell survival despite unique modes of action in the fallopian tube and ovarian surface epithelium.

High-grade serous carcinoma (HGSC) is the most common and lethal form of ovarian cancer. PAX8 is a transcription factor expressed in fallopian tube epithelial cells and in 80–96% of HGSC tumors. The ovarian surface epithelium (OSE) only acquires PAX8 expression after malignant transformation. In this study, forced PAX8 expression in OSE cells increased proliferation and migration through upregulation of EMT factors such as N-cadherin and Fibronectin. OSE cells expressing PAX8 also had an increase in the FOXM1 pathway, but PAX8 alone was not sufficient to drive tumorigenesis. PAX8 knockdown in the oviductal epithelium cells did not decrease expression of the FOXM1 pathway and induced only a slight decrease in cell proliferation. No changes in migration, cell cycle, or apoptosis were detected after PAX8 knockdown in oviductal cells. Finally, PAX8 knockdown in HGSC cell lines resulted in increased apoptosis and decreased FOXM1 levels. The results presented here suggest that PAX8 has a cell specific role in governing proliferation and migration in nontransformed ovarian surface epithelium cells compared to the oviductal cells, but its reduction in serous cancer cell lines provides a common mechanism for reducing cell survival.

Abstract 4246: Comparison of pathology versus IHC-based ovarian carcinoma histology assignment using gene expression, DNA methylation, and clinical outcome data

Abstract Background: Epithelial ovarian cancer (EOC) is composed of five major histologic types: 1) high-grade serous carcinoma (HGSC), accounting for most cases (∼70%); and the rarer 2) clear cell, 3) endometrioid, 4) mucinous, and 5) low- grade serous carcinoma (LGSC). As EOC risk factors are histology specific, as are the site of precursor lesions, accurate subtyping is critical to understanding EOC prognostic factors and etiology. Our aim was to compare two currently employed histology assignment strategies using gene expression, DNA methylation, and clinical outcome data Methods: Histology assignment based on: a) pathologist, and b) an integrated pathologist and IHC prediction algorithm (pathIHC) (using ARID1A, CDKN2A, DKK1, HNF1B, MDM2, PGR, TP53, TFF3, VIM, and WT1 staining patterns), was compared for tumors of all histologies at the Mayo Clinic, Rochester. The 500 most variable probes from Illumina Methylation450 BeadChips (N = 259) and Agilent 4×44K expression arrays (N = 245) were used to perform unsupervised hierarchical clustering. Fisher's Exact test was used to test the association of clusters with histology. Cox proportional hazards regression analysis was used to test the association of clusters and histology with time to progression (TTP) and time to death (TTD). Results: Eighty-two percent of tumors were concordant between histology assignment strategies. Clustering based on methylation data produced two distinct clusters. PathIHC produced more homogenous clusters (p-value = 2.8×10-16) than pathology alone (p = 1.3×10-9). Cluster M1, characterized by high levels of methylation across almost all probes, was enriched for the rarer EOC subtypes; cluster M2, characterized by moderate levels of methylation across 50%-75% of probes, was predominantly HGSC. These patterns were observed irrespective of histology assignment strategy; however, when using histology by pathologist, cluster M2 had more endometrioid and LGSC tumors interspersed with HGSC tumors. Clustering based on expression data also produced two clusters. PathIHC produced slightly more homogenous clusters (p = 9.0×10-11, pathology alone, p = 2.3×10-10). Cluster E1 was enriched for the rarer EOC subtypes; cluster E2 was primarily serous lineage tumours (HGSC and LGSC), particularly when using histology by pathIHC. Considering only clinical outcomes, histologies by pathology were more significantly different in terms of TTP (p = 1.1×10-6) and TTD (p = 1.7×10-3) than histologies by pathIHC (TTP, p = 5.4×10-6; TTD, p = 5.7×10-3). Conclusions: Histology by pathIHC produced more homogeneous clusters in both the methylation and expression data; thus, molecular data supports this strategy. Differences in clinical outcomes (TTP and TTD) between histology groups were more pronounced when using assignment by pathologist; thus, clinical data supports this strategy. Citation Format: M A. Earp, S J. Winham, S M. Armasu, B L. Fridley, M C. Larson, Z C. Fogarty, K R. Kalli, C Wang, G L. Keeney, J M. Cunningham, S Ramus, M Kobel, E L. Goode. Comparison of pathology versus IHC-based ovarian carcinoma histology assignment using gene expression, DNA methylation, and clinical outcome data. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4246. doi:10.1158/1538-7445.AM2015-4246

Abstract SY44-03: Proteogenomic and phosphoproteomic analysis of ovarian cancer

Abstract A comprehensive molecular level view of cancer is desirable for understanding the underlying causes of disease, for predicting prognosis, and ultimately guiding treatment. The Cancer Genome Atlas (TCGA) conducted an extensive genomic and transcriptomic characterization of ovarian high-grade serous carcinoma (HGSC) with the objective of informing prognosis and the development of targeted therapies for this highly lethal gynecologic malignancy1. However, proteins are likely closer to biological and disease phenotypes, often not well correlated with their transcripts, and their characterization is expected to provide insights not evident from genomic studies. Therefore, to obtain a more comprehensive assessment of the complex HGSC phenotype, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) conducted an extensive proteomic and phosphoproteomic characterization of the HGSC tumors previously characterized by TCGA, providing quantitative measurements for 10,030 proteins across 174 tumors, and 25,598 phosphosites from 6,769 phosphoproteins. Novel insights into ovarian cancer biology arising from these proteogenomic studies include: 1) a substantial trans-regulation of protein abundances by copy number alterations (CNAs), which when analyzed at a pathway level converged on the cancer-associated processes of proliferation, cell motility/invasion, and immune regulation; 2) identification of five proteomic subtypes in the TCGA cohort, with two subtypes showing robust concordance with the mesenchymal and proliferative subtypes, and tumors from transcript assigned differentiated and immunoreactive subtypes not robustly segregating into distinct clusters, demonstrating their proteomic heterogeneity; 3) identification of specific post-translational modifications associated with homologous repair deficiency; and 4) phosphoproteomic data revealing a consistent novel set of activated pathways associated with patient survival, including up-regulation of VEGFR signaling in patients with poor outcomes, and suggesting a strategy for selecting anti-angiogenesis therapies. This study will inform future use of protein markers to stratify patients who may benefit from anti-angiogenesis or PARP inhibitor therapy, predicting development of platinum resistant disease, identifying immunoregulatory networks that can be exploited for cancer immunotherapy, and determining the clinical phenotypes based upon proteomic ovarian cancer subtypes. Citation Format: Karin D. Rodland. Proteogenomic and phosphoproteomic analysis of ovarian cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr SY44-03. doi:10.1158/1538-7445.AM2015-SY44-03