MicroRNAs (miRNAs) perform their functions through targeting messenger RNAs (mRNAs). X chromosome-located (X-linked) miRNAs have a broad role in cell lineage determination, immune regulation, and oncogenesis. The regulating roles of miRNAs in cancer and immunity are often altered when aberrant expression happens. Sex-biased genes could contribute to cancer sex bias in the context of their expression change due to targeting miRNAs. How biological roles and associations with immune cell abundance levels for sex-biased gene-miRNA pairs in gender-related cancer (e.g., breast cancer) change due to the alteration of their expression pattern to identify candidate therapeutic markers has not been investigated thoroughly. Upon analyzing anti-correlated genes and miRNAs within significant clusters of 12 The Cancer Genome Atlas (TCGA) cancer types and the list of sex-biased genes and miRNAs reported from previous studies, 125 sex-biased genes (11 male-biased and 114 female-biased) were identified in breast cancer (BC). Seventy-three sex-biased miRNAs (40 male-biased and 33 female-biased) were identified across 5 out of 12 cancers (head and neck squamous cell carcinoma (HNSC), kidney chromophobe (KICH), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), and lung adenocarcinoma (LUAD)). Correlation between the BC sex-biased genes and tumor infiltrating immune cell types was further evaluated. We found eight genes having high correlation with immune infiltration. Fifteen candidate female-biased BC genes targeted by 3 X-linked miRNAs (has-mir-18hashsa-mir-221, and hsa-mir-224) were pinpointed in this study. Our computational result indicates that many identified female-biased genes which have positive associations with immune cell abundance levels could serve as alternative therapeutic markers. Our analysis suggests that female-biased expression of BC candidate genes is likely influenced by their targeting miRNA(s).

Introduction: Breast Cancer (BC) occurrence, especially triple-negative BC (TNBC), is relatively high among African American women. In addition, Caucasian BC mortality has decreased much faster than African American BC mortality even with advancing medicines over the last few years. Researchers have reported socioeconomic and biological factors that may contribute to African American BC disparity, but concrete genetic biomarkers have not been elucidated. In this study, we conducted a systematic bioinformatics analysis to compare the gene expression pattern and examine the immunological differences in Black and White patients for different breast cancer subtypes. Methods: Using the public portal of The Cancer Genome Atlas (TCGA), Level 3 RNA-Seq expression data and corresponding clinical data for 183 African American and 764 Caucasian BC patients were downloaded. These patients were then categorized by four subtypes (luminal A, luminal B, HER2-enriched, and TNBC) and subsequently analyzed for gene expression and immune infiltration association. The average expression in RPKM (reads per kilobase of transcript per million mapped reads) of transcribed genes for each race and subtype was calculated using a custom R script. For each subtype, the top 30 genes with the highest expression in each race were selected and cross-checked for any overlap. Association between their expression and tumor infiltrates for six immune cell types (B cell, Dendritic cell, Macrophage, Neutrophil, T-cell CD4, T-cell CD8) was assessed using TIMER2.0. Results: For all subtypes, the majority of the top 30 genes overlapped between both races. In particular, 24 out of the top 30 genes (80%) were common between both races for TNBC. Five genes (ADAM6, CD74, LOC96610, B2M, HLA-B) were reported to show strong positive correlation between their expression and immune infiltration. Interestingly, out of the unique gene set for both races in the TNBC subtype, none of them showed strong positive correlation. ADAM6, a transcribed pseudogene, was identified to be positively correlated to immune infiltration in African American BC patients uniquely across all subtypes excluding TNBC in our study. Conclusion: Our computation result provides a candidate list of unique and common genes having high expression for four BC subtypes in African American and Caucasian patients. Our work also suggests that expressed pseudogenes could serve as potential biomarkers for BC patients. We plan to continue to investigate biomarkers in BC subtypes and immune response over post-transcriptional regulatory network in the context of breast cancer etiology. Citation Format: Eric W. Li, Yongsheng Bai. Characterization of pseudogene expression and immune infiltration in breast cancer subtypes for African American and Caucasian patients [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PR-02.