Abstract PS18-01: Glucocorticoid receptor expression in early-stage triple-negative breast cancer is associated with a high level of tumor immune cell infiltrates

Background: Triple-negative breast cancer (TNBC) with high glucocorticoid receptor activity (GR-high) is associated with a high risk of relapse and chemotherapy resistance. Glucocorticoids (GC) are essential for the regulation of immune and inflammatory responses. Multiple mechanisms of GC-induced immunosuppression have been proposed, including suppression of T cell proliferation and dendritic cell antigen presentation and function. The importance of intact immune surveillance in controlling neoplastic transformation is well-established, and accumulating evidence demonstates a correlation between tumor-infiltrating lymphocytes (TILs) in cancer tissue and favorable prognosis. In particular, the presence of CD8+ T-cells and the ratio of CD8+ effector T-cells / Foxp3+ regulatory T-cells (Tregs) appears to correlate with improved prognosis and long-term survival. We hypothesized that tumor GR activity would modulate the tumor immune microenvironment (TME), thereby suppressing anti-tumor immunity in TNBC.

Methods: We identified 46 patients with TNBC who received neoadjuvant chemotherapy at The University of Chicago between 2002-2014, and had pretreatment tissue available for study. Tumors were stained for GR expression using the anti-GR rabbit monoclonal XP antibody (Cell Signaling, 1:200 dilution). GR expression was determined independently by two pathologists. Using multiplex immunohistochemistry, six phenotypes for immune cell markers (BATF3+ dendritic cells, CD8+ T-cells, Foxp3+ Tregs, PD-L1+tumor, PD-L1-tumor, PD-L1+immune cells) were identified in the tumor and stroma of the pretreatment biopsy specimens. Absolute counts of each type of immune cell as well as ratios between immune cell types were compared in GR-low, GR-moderate, and GR-high expressing TNBC specimens using the Kruskal-Wallis test.

Results: There were 8 GR-low, 23 GR-moderate, and 15 GR-high expressing tumors in our cohort. When comparing GR-low to GR-moderate or GR-moderate to GR-high expressing tumors, there were no significant difference observed in immune cell types. However, when comparing GR-high to GR-low expressing TNBCs, there were significantly higher levels of CD8+ T-cells, Foxp3+ Treg cells, and BATF3+ dendritic cells in GR-high vs GR-low TNBC tumors (p=0.0004, p=0.011, and p=0.0072, respectively). When comparing the ratio of CD8+ T-cells to Foxp3+ Treg cells, PD-L1+ tumor or immune cells, no significant differences were observed by level of GR expression (p=ns for all comparisons).

Conclusions: We report for the first time that GR-high, treatment-naïve, primary TNBCs have significantly higher CD8+ T cells, Foxp3+ T cells, and BATF3+ dendritic cells compared to GR-low TNBCs, consistent with an inflamed TME. While historically a robust immune infiltrate in the TME in early TNBC has been associated with a better response to chemotherapy and a more favorable long-term outcome, high GR activity in early TNBC has been associated with a worse outcome. Our observation that GR-high tumors have an inflamed TME, suggests that checkpoint blockade to either suppress Foxp3+ Tregs or activate CD8+ T cells may be able to restore anti-tumor immunity.

Citation Format: Deniz N Dolcen, Marie Dreyer, Aaron Miller, Anna Biernacka, Ken Hatogai, Randy Sweis, Rita Nanda, Suzanne D Conzen. Glucocorticoid receptor expression in early-stage triple-negative breast cancer is associated with a high level of tumor immune cell infiltrates [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-01.

Abstract 1290: Role of NNMT-regulated m6A mRNA modification in triple-negative breast cancer oncogenic gene expression

Background: Post-transcriptional RNA methylation is implicated as a mechanism regulating gene expression associated with stem cell differentiation and malignant transformation. N6-methyladenosine (m6A) is the most abundant eukaryotic mRNA methylation modification. Proteins that selectively bind m6A alter m6A-modifed mRNA stability and translational efficiency. One mechanism regulating nucleic acid methylation is methyl donor availability and nicotinamide N-methyltransferase (NNMT) removes the methyl moiety from S-adenosyl methionine (SAM) and uses it to methylate nicotinamide, reducing methyl donor availability. Therefore, high NNMT activity depletes SAM; as a result, SAM-dependent methyltransferase targets such as mRNA become hypomethylated. NNMT-induced DNA and histone hypomethylation have been shown to result in oncogenic gene expression in cancer cells, although m6A hypomethylation of mRNA is less well understood. We found consistently high NNMT protein expression in triple-negative breast cancer (TNBC) cell lines relative to estrogen receptor (ER)+ lines. We also discovered the glucocorticoid receptor (GR) activation, which is associated with aggressive TNBC, further increased NNMT expression in MDA-MB-231 and HCC1937 cells. We therefore hypothesized that NNMT overexpression/activity might increase oncogenic gene expression(by reducing m6A modification)of mRNA transcripts involved in TNBC biology.

Methods and Results: We found that TNBC cells upregulate NNMT expression following GR activation and therefore asked whether GR activation (and concomitant NNMT induction) significantly decrease global m6A mRNA modification as measured by mass spectrometry. Furthermore, either GR or NNMT antagonism restored m6A mRNA modification, suggesting that high NNMT activity may decrease m6A mRNA methylation. We then performed m6A immunoprecipitation-coupled RNAseq to determine m6A-modification levels on transcripts of individual genes before and after GR activation. We identified ~7000 m6A-modified transcripts among ~9000 expressed transcripts. Importantly, GR activation and concomitant NNMT induction significantly reduced the m6A modification of a subset of ~3000 transcripts that were found to be relatively enriched with cancer-promoting pathways (e.g. RAF signaling).

Conclusions: NNMT overexpression is implicated in the biology of several epithelial cancers; however, its mechanism of action is not fully understood. Our ongoing work will determine whether reduced m6A modification of selective TNBC mRNAs contribute to the oncogenic phenotype via increased half-life and protein production. We are using inducible NNMT-knockdown to determine whether reduced NNMT expression results in increased m6A modification of pro-oncogenic mRNAs and thereby inhibits oncogenic phenotypes such as invasion and cell survival.

Citation Format: Deniz N. Dolcen, Bryan Harada, Chuan He, Suzanne D. Conzen. Role of NNMT-regulated m6A mRNA modification in triple-negative breast cancer oncogenic gene expression [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1290.

Abstract 2812: Triple-negative breast cancer cell-intrinsic glucocorticoid receptor activity and modulation of the immune microenvironment

Background: Variation in the infiltration of TNBC immune microenvironment is not well understood. Our lab previously demonstrated that high glucocorticoid receptor (GR; nuclear hormone receptor) activity in TNBC models is associated with tumor cell-intrinsic anti-inflammatory gene expression pathways. In addition, high GR expression in early-stage TNBC is associated with a significantly lower rate of recurrence-free survival suggesting a role for GR-associated mechanisms in TNBC progression. GR activation in lymphocytes is well known to result in their apoptosis; however, a current gap in knowledge regarding GR biology is whether tumor-cell intrinsic GR activity modulates immune cells in the microenvironment. We hypothesized that TNBC cell-intrinsic GR activity may inhibit antitumor T cell activity in the tumor microenvironment.

Methods and Results: We divided TCGA primary TNBC RNAseq expression data based on GR expression and determined enrichment for immune cells using two transcriptome parsing algorithms. We found that TNBCs with high GR expression are significantly enriched for the T cell-inflamed gene expression signature, suggesting the presence of T cells in the microenvironment. The xCell algorithm found that TNBCs with high GR expression are significantly enriched for the CD4+ naïve T cell transcriptome, which is absent in TNBCs with low GR-expression. To begin to determine whether GR activation in TNBC cells induces the secretion of cytokines and/or growth factors that result in the chemotaxis of CD4+ naïve T cells, we collected conditioned cell culture media from control versus GR-active TNBC cells and performed multiplex cytokine ELISA. We found that G-CSF secretion by TNBC cells was significantly increased following GR activation; G-CSF has been shown to promote immunosupressive Treg cell differentiation.

Conclusions: Prior data suggest that breast tumor-infiltrating immunosuppressive Tregs arise from chemotaxis of circulating naive CD4+ T cells that differentiate into Tregs in situ. Thus targeting GR in TNBC may be an important therapeutic approach to potentiate antitumor T cell responses and suppress the Treg population in the tumor microenvironment. Ongoing work is aimed at further delineating a mechanism by which GR can modulate the immune tumor microenvironment.

Citation Format: Deniz N. Dolcen, Diana West Szymanski, Ananth Panchamukhi, Xiaomeng Wang, Randy F. Sweis, Rita Nanda, Suzanne Conzen. Triple-negative breast cancer cell-intrinsic glucocorticoid receptor activity and modulation of the immune microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2812.

Abstract 2541: Combined androgen and glucocorticoid receptor (AR/GR) activity drives TNBC progression

Background: A recent effort to distinguish early-stage TNBC based on outcome and to expose driver pathways using gene profiling/cluster analysis divided TNBC into four subtypes- basal-like, mesenchymal, immunomodulatory, and luminal androgen receptor (LAR). The clinical AR+ TNBC subtype (>10% AR by IHC) comprises up to 35% of metastatic disease. The discovery of this TNBC subtype and the concomitant development of potent new anti-androgens for prostate cancer have led to several clinical trials evaluating AR antagonists in TNBC. In parallel, glucocorticoid receptor (GR) expression and activation have been shown to mediate anti-apoptotic gene expression in TNBC. However, to our knowledge, no one has examined the coordinate expression of GR and AR activity and the potential crosstalk downstream of dual GR and AR activation. We hypothesized that AR/GR cooperative gene expression pathways may induce TNBC therapy resistance and tumor progression. Methods and Results: We analyzed GR+ TNBC primary tumor gene expression from TCGA samples and found a wide range of AR expression. To examine whether GR-associated gene expression differed in high versus low AR+ TNBC, we divided TCGA TNBC primary tumors (N=123) at the AR median into “high” versus “low” AR expression. We then identified relative GR target gene expression levels in those genes identified from a previous TNBC meta-analysis. Invasion, motility and proliferation pathways were found to be most significantly expressed among GR-associated genes in AR high TNBC (top 5 significant pathways). Similarly, we found that GR and AR co-activation in AR+ MDA-MB-453 TNBC cells significantly increased cell migration compared to GR or AR activation alone. In addition, when MDA-MB-453 cells were exposed to the AR antagonist enzalutamide (enza) for more than 30 days (long-term, LT), the magnitude of increase in cell migration following GR activation increased, suggesting that increased GR activity may compensate for long-term AR blockade. Furthermore, long-term enza exposure (LTenza) in AR+ MFM-223 and MDA-MB-453 cells resulted in increased GR mRNA and protein levels. The magnitude of GR-mediated target gene expression was also significantly increased in LTEnza versus control-treated cells. In vivo, LTenza-treated MDA-MB-453 xenografts were relatively insensitive to paclitaxel chemotherapy treatment, consistent with increased GR activity compared to control cells. Conclusions: We conclude that coordinate GR and AR expression in TNBC contributes to a particularly poor outcome in TNBC. Downstream AR/GR gene expression favoring cell survival and invasive phenotypes may contribute to this outcome. Consideration of dual AR/GR inhibition in TNBC may increase the effectiveness of anti-androgen therapy.

Citation Format: Deniz N. Dolcen, Eva Tonsing-Carter, Ryan Harkless, Caroline Kim, Kathleen Bowie, Gini Fleming, Suzanne Conzen. Combined androgen and glucocorticoid receptor (AR/GR) activity drives TNBC progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2541.

Abstract 4867: Comparative analysis of RNA sequencing methods for characterization of cancer transcriptomics

RNA sequencing (RNASeq) provides the ability to comprehensively assay the transcriptome in a high-throughput manner. Current there are a variety of library preparation methodologies for measuring and sequencing the transcriptome depending on (a) the sample source and (b) outcomes of interest. Beyond protocol selection, the requisite computational tools and resources are significant considerations in processing, analyzing and reporting the experimental results. While there are many resources readily available to effectively perform RNA-seq experiments, optimal protocols and analysis tools for the cancer domain remain to be developed.

We have developed and characterized a set of protocols and analysis procedures that comprise an RNA-seq pipeline that can effectively be used in a cancer research setting. The analysis pipeline consists of a sequence of functions and tools to process and clean the raw data, generate quality control and summary metrics, and perform secondary analyses that include expression quantification, fusion detection and somatic mutation calling. We applied this pipeline to three different RNAseq strategies (whole-transcriptome, exome, and targeted RNA-seq) and performed an in-depth comparative analysis to investigate the implications of the choice of strategy on the downstream analysis and results. More specifically, we investigated the impact of library preparation methods on the dynamic range and expression profiles, variant calling and fusion detection. While the data indicated that capture-based protocols provided efficient methods for sampling transcripts as compared to whole-transcriptome RNA-seq, there are considerations in its use, particularly for duplicate reads and uncaptured transcripts. We illustrate the implications of these issues on downstream analysis, such as somatic mutation and fusion calling and differential expression.

In summary, we have described a RNA-seq analysis platform that provides a varied set of library preparations and analytical components for large-scale clinical or research transcriptomics. Our analysis has characterized the technical features of the different library preparations, providing a necessary understanding of the costs and benefits of each method and the potential effects on the downstream analyses.

Citation Format: Ryan P. Abo, Ling Lin, Samuel S. Hunter, Deniz N. Dolcen, Rachel R. Paquette, Angelica Laing, Luc de Waal, Aaron R. Thorner, Matthew D. Ducar, Liuda Ziaugra, William C. Hahn, Matthew L. Meyerson, Laura E. MacConaill, Paul Van Hummelen. Comparative analysis of RNA sequencing methods for characterization of cancer transcriptomics. [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 4867. doi:10.1158/1538-7445.AM2015-4867