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April 5, 2026Cancer Research0 citations

Abstract 1513: Gene signatures and infiltration patterns of mast cells in breast cancer revealed by integrated bulk and single-cell RNA sequencing Analyses

Key Points

This study aims to investigate mast cell infiltration and gene expression profiles across different breast cancer subtypes.
Utilized publicly available transcriptomic datasets for analysis.
Performed comprehensive reanalysis of bulk RNA-seq and single-cell RNA-seq data.
Identified differentially expressed genes using specific statistical criteria.
Conducted Gene Ontology enrichment analysis to determine biological pathways involved.
Significant upregulation of mast cell marker genes in ER+, HER2+, and TN breast cancers compared to benign lesions.
Bulk RNA-seq showed the highest expression of specific mast cell genes in ER+, intermediate in HER2+, and minimal in benign lesions.
Mast cell proportion was higher in tumor tissue (4.59%) versus normal tissue (2.89%).
Identified 13 distinct cell clusters in single-cell RNA-seq analysis, including a specialized mast cell cluster associated with breast cancer.

Abstract

Abstract Background: Breast cancer is one of the leading cancers in women, caused by uncontrolledcell growth in breast tissue. Mast cells, a type of immune cell generally responsible forinflammation and allergic reactions, have emerged as key immune players within the tumormicroenvironment. However, the functions of these cells in breast cancer remain incompletelyunderstood and sometimes controversial. This study investigated mast cell infiltration and geneexpression profiles across three breast cancer subtypes by using integrated bulk and single-cellRNA-seq analyses. Methods: Publicly available transcriptomic datasets GSE45419, GSE254991 were downloadedfrom NCBI and reanalyzed with standard pipelines. Differentially expressed genes (DEGs) wereidentified with |logFC| 0.2 and FDR 0.05. UMAPs and Heatmaps were generated tovisualize the data. Gene Ontology (GO) enrichment analysis was subsequently performed toidentify significantly enriched biological pathways. Results: Bulk RNA-seq data analysis of GSE45419 revealed significant upregulations of mastcell marker genes (KIT, FCER1A, MS4A2, CPA3, HDC and TPSAB1) in ER+, HER2+, TN+(triple negative) breast cancers compared with benign breast lesions (Figure 1). Expressions ofthese genes were the highest in ER+, intermediate in HER2+, lower in TN+, and minimal inbenign breast lesions. Reanalysis of single-cell RNA-seq dataset GSE254991 identified 13clusters of cells in both cancer and adjacent tissues, including a distinct mast cell clusterexpressing canonical markers (KIT, FCER1A, MS4A2, CPA3, HDC and TPSAB1). Theproportion of mast cells is higher in tumor tissue (4.59%) than in paired normal breast tissue(2.89%) from the same patient. Cross-comparison of mast cell gene expression profilesbetween cancerous and adjacent regions identified the core DEGs enriched in mast cellsassociated with breast cancer. GO analysis indicated the significantly up-regulated pathways inbreast cancer including antigen processing and presentation of peptide antigen, antigen binding,MHC Class I and II protein complex assembly, leukocyte mediated immunity and cell-celladhesion, response to type II interferon. Conclusion: Integrated bulk and single-cell transcriptomic data analysis revealed increasedmast cell infiltration and distinct transcriptional reprogramming in three subtypes of breastcancer. These findings provide new insights into potential immunoregulatory roles of mast cellsin tumor progression and may inform the development of novel therapies targeting mast cells tofight for breast cancer. Citation Format: Eva Liu, Benjamin Jin, Cindy Hu, Qian Wang, . Gene signatures and infiltration patterns of mast cells in breast cancer revealed by integrated bulk and single-cell RNA sequencing Analyses abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1513.

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