Genomic mapping of copy number variations influencing immune response in breast cancer

Abstract

Identification of genomic alterations that influence the immune response within the tumor microenvironment is mandatory in order to identify druggable vulnerabilities. In this article, by interrogating public genomic datasets we describe copy number variations (CNV) present in breast cancer (BC) tumors and corresponding subtypes, associated with different immune populations. We identified regulatory T-cells associated with the Basal-like subtype, and type 2 T-helper cells with HER2 positive and the luminal subtype. Using gene set enrichment analysis (GSEA) for the Type 2 T-helper cells, the most relevant processes included the ERBB2 signaling pathway and the Fibroblast Growth Factor Receptor (FGFR) signaling pathway, and for CD8+ T-cells, cellular response to growth hormone stimulus or the JAK-STAT signaling pathway. Amplification of ERBB2, GRB2, GRB7, and FGF receptor genes strongly correlated with the presence of type 2 T helper cells. Finally, only 8 genes were highly upregulated and present in the cellular membrane: MILR1, ACE, DCSTAMP, SLAMF8, CD160, IL2RA, ICAM2, and SLAMF6. In summary, we described immune populations associated with genomic alterations with different BC subtypes. We observed a clear presence of inhibitory cells, like Tregs or Th2 when specific chromosomic regions were amplified in basal-like or HER2 and luminal groups. Our data support further evaluation of specific therapeutic strategies in specific BC subtypes, like those targeting Tregs in the basal-like subtype.

Keywords: CNVs; Gene Amplification; breast cancer; immune response; new surface targets.

Figure 1

Identification of CNV in human breast tumors. Workflow chart displaying dataset sources and selection criteria of CNV in BC including 1070 patients, and the statistical association with different immune cell populations using TCGA database. Cells were created with BioRender.com.

Figure 2

Association between amplified genes and chromosomic location stratified by BC molecular subtype. (A): Chromatogram with amplified gene locations by BC molecular subtype. Created with BioRender.com. (B): Bar graph with the number of gain CNV-related genes by chromosome location and stratified by BC molecular subtype. C: Bar graph with the number of gain CNV-related genes by BC molecular subtype.

Figure 3

Volcano plot of altered (deleted or amplified) genes with its immune score relationship. The highlighted area corresponds with the thresholds selected parameters for p-values lower than 0.01 and FC higher than 1.74. (A): Basal molecular subtype with loss CNV genes; (B-E): Basal, HER2 +, Luminal A, and Luminal B molecular subtype with gain genes. Emphasizing those amplified genes associated with relevant immunological function.

Figure 4

The overall distribution of amplified genes and their association to immune populations. From inside to outside, BC molecular subtype, related immune cell population, and chromosomic location of the genes are colored following a gradient according to the number of amplified genes selected as statistically significant.

Figure 5

Gene locations and biological processes associated. (A): Number of gain CNV-related genes selected by chromosome location and stratified by BC molecular subtype using gene set enrichment analysis. (Created with BioRender.com). (B-G): Horizontal bar charts with the top 5 Gene Ontology Biological Processes, the genes implicated are located inside the bar plot.

Figure 6

Differential expression in tumoral and normal breast tissue. Gene expression of Tumor (red) vs Normal (gray) samples of (A): SLAMF6, (B): IL2RA, (C): ICAM2, and (D): SLAMF8.