Abstract A56: A SOX10-associated epigenetic program linking primitive differentiation state with reduced immunogenicity in triple-negative breast cancer
Authors: Saunus Jodi 
Published: August 2018

Triple-negative breast cancer (TNBC) is arguably the most heterogeneous breast cancer subtype, with diverse histologic features and clinical behavior, yet limited therapeutic options. TNBCs exhibit impressive early responses to chemotherapy, but this is not a reliable predictor of long-term outcome. Additional molecular and biologic insights are needed in order to stratify this disease into clinically meaningful groups and identify new therapeutic approaches.

We originally began studying the SRY (sex determining region Y)-box 10 (SOX10) transcription factor because it was implicated in regulating differentiation in embryonic neural crest and melanocytes, and exhibited bimodal expression in TNBC, so may feasibly discriminate subgroups with distinct biology. Using immunohistochemistry (IHC) and analysis of RNA expression data from human reduction mammoplasty samples (n=20 and n=3 respectively), we observed highest SOX10 expression in the luminal progenitor compartment, and heterogeneity among mature luminal cells of lobules compared with ducts. Analysis of published breast cancer genomic datasets showed that SOX10 mRNA levels correlate strongly with promoter methylation (r-0.82; p&lt;1E-15), with hypomethylation and copy-number gains far more frequent in TNBC than non-TNBCs (p&lt;1E-15 and p=2.67E-05). IHC and Kaplan Meier analysis of two independent tumor cohorts (n=1500 total) showed that nuclear SOX10 is associated with poor outcome in TNBC (p=7.0E-04; HR 1.90 (95% CI 1.25-2.89); n=288), while cytoplasmic expression is associated with better outcome than SOX10 negativity (p = 0.027; HR 0.55 (0.35-0.86)). To understand the biologic context of SOX10 function in breast cancer, we interrogated published expression datasets to identify genes coexpressed with SOX10, and gene ontologies enriched in SOX10-high tumors. These systems approaches suggest that SOX10 is a “hub” gene in one of several networks expressed at different ratios in TNBC. Expression of this “SOX-module” has a dose-dependent relationship with survival, is associated with a DNA methylation program underpinning expression of embryonic development and neural differentiation genes, and is inversely associated with expression of an antigen-specific immune response module.

shRNA-mediated depletion of SOX10 resulted in decreased expression of stem cell and proliferation genes in vitro (e.g., CD133, MYC, LIN28B, ALDH1A1), and interestingly, marked induction of interferon-gamma (IFNg) targets (p&lt;1.0E-60), including MHC-II HLA genes involved in antigen presentation (confirmed by IHC analysis of HLA-DP/DQ/DR protein levels in cells, mammary fat pad xenografts, and SOX10-high human TNBCs). Consistent with this, SOX10-depleted cells exhibited altered IFNg responses in vitro, suggesting the SOX-module could be causally associated with immunosuppression in TNBC. Current work is focusing on investigating the effects of the SOX-module in patient-derived xenograft and syngeneic models of breast cancer, and the potential clinical utility of cancer-testis antigens in the SOX-module.

Citation Format: Jodi Saunus. A SOX10-associated epigenetic program linking primitive differentiation state with reduced immunogenicity in triple-negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr A56.