Abstract P3-09-14: Regulation of gene expression and DNA methylation with cytotoxic T lymphocytes evaluation in subtypes of breast cancers
Authors: Shen Yuanyuan(Daisy) , Shyu Chi-Ren , Mitchem Jonathan B. , Shi Yifeng , Shajahan-Haq Ayesha N. 
Published: March 2020

Introduction: Low cytotoxic T lymphocyte (CTLs) infiltration and poor immunogenicity in the breast cancer (BC) microenvironment is a challenge to treatment with immune checkpoint (ICK) inhibitors. However, ICK inhibitors were recently approved by the FDA in triple-negative breast cancer (TNBC), which are characterized by high levels of tumor infiltrating CTL. DNA methylation is a component of epigenetic modification involved in gene expression programming that can promote the progression of cancers, including BC. However, the association between transcriptional and methylation changes that modulate CTL infiltration in the tumor microenvironment in specific subtypes of breast cancer is still unclear. In this study, we compare transcriptional and methylation profile data in patients with different BC subtypes to identify targetable genes to improve CTL infiltration and ICK inhibitor efficacy in BC patients.

Methods: We included The Cancer Genome Atlas (TCGA) RNA sequencing (n=1,212) and DNA methylation (Illumina Human Methylation 450K; n=783) databases to detect the gene expression and methylation profiles based on molecular subtypes: LumA vs TNBC, LumB vs TNBC, Her2+ vs TNBC. To be consistent with clinical diagnosis, our TNBC patients included all ER-, PR-, Her2 -/1+/2+ patients (n=192). Microenvironment Cell Populations-counter (MCPcounter) were used to determine CTL infiltration in BC subtypes. Genes with significantly different expression (p&lt;0.01, LogFC≥|1.5|) and difference of mean methylation β value ≥|0.25| were integrated for Pearson correlation coefficient analysis with CTL MCPcounter score (r&gt;|0.7|).

Results: Comparing LumA and TNBC patients, hypermethylation was associated with 113 upregulated genes and 309 downregulated genes. Hypomethylation was associated with 156 upregulated genes and 104 downregulated genes. Additionally, in LumA tumors, 7 genes were differentially methylated and associated with CTL scores: 3 genes were downregulated and hypomethylated (AIM2, SEL1L3, TOX), and 4 genes were downregulated and hypermethylated (CD38, HLA-DOB, LAMP3, RUNX3). Comparing LumB and TNBC tumors, hypermethylation was associated with 158 upregulated genes and 525 downregulated genes. In these tumors, hypomethylation was associated with 178 upregulated genes and 168 downregulated genes. In this group, three genes (AIM2, GPR55, UBD) were downregulated, hypomethylated, and highly correlated with CTL scores. Finally, comparison of Her2+ BC with TNBC tumors showed that hypermethylation was associated with 39 upregulated genes and 223 downregulated genes. In this group, hypomethylation was associated with 54 upregulated genes and 31 downregulated genes. Among these genes, CHST2 gene was the only gene found downregulated with hypermethylated and associated with CTL score in Her2+ tumors.

Conclusion: We found eleven genes that were differentially expressed, differentially methylated, and highly correlated with CTL infiltration were identified in LumA, LumB and Her2+ subtypes compared with TNBC. Specifically, interferon-inducible protein AIM2 is a gene that was altered in both LumA and LumB, is associated with response to ICK in murine models and may be a potential target to improve response to immune based therapy in these subtypes of BC patients.

Citation Format: Yuanyuan(Daisy) Shen, Chi-Ren Shyu, Jonathan B. Mitchem, Yifeng Shi, Ayesha N. Shajahan-Haq. Regulation of gene expression and DNA methylation with cytotoxic T lymphocytes evaluation in subtypes of breast cancers [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-09-14.