Case-Case Genome-Wide Analyses Identify Subtype-Informative Variants That Confer Risk for Breast Cancer

Abstract

Breast cancer includes several subtypes with distinct characteristic biological, pathologic, and clinical features. Elucidating subtype-specific genetic etiology could provide insights into the heterogeneity of breast cancer to facilitate the development of improved prevention and treatment approaches. In this study, we conducted pairwise case-case comparisons among five breast cancer subtypes by applying a case-case genome-wide association study (CC-GWAS) approach to summary statistics data of the Breast Cancer Association Consortium. The approach identified 13 statistically significant loci and eight suggestive loci, the majority of which were identified from comparisons between triple-negative breast cancer (TNBC) and luminal A breast cancer. Associations of lead variants in 12 loci remained statistically significant after accounting for previously reported breast cancer susceptibility variants, among which, two were genome-wide significant. Fine mapping implicated putative functional/causal variants and risk genes at several loci, e.g., 3q26.31/TNFSF10, 8q22.3/NACAP1/GRHL2, and 8q23.3/LINC00536/TRPS1, for TNBC as compared with luminal cancer. Functional investigation further identified rs16867605 at 8q22.3 as a SNP that modulates the enhancer activity of GRHL2. Subtype-informative polygenic risk scores (PRS) were derived, and patients with a high subtype-informative PRS had an up to two-fold increased risk of being diagnosed with TNBC instead of luminal cancers. The CC-GWAS PRS remained statistically significant after adjusting for TNBC PRS derived from traditional case-control GWAS in The Cancer Genome Atlas and the African Ancestry Breast Cancer Genetic Consortium. The CC-GWAS PRS was also associated with overall survival and disease-specific survival among patients with breast cancer. Overall, these findings have advanced our understanding of the genetic etiology of breast cancer subtypes, particularly for TNBC. Significance: The discovery of subtype-informative genetic risk variants for breast cancer advances our understanding of the etiologic heterogeneity of breast cancer, which could accelerate the identification of targets and personalized strategies for prevention and treatment.

Figure 1.. The workflow of main analysis in the present study.

Abbreviations: CC-GWAS, case-case genome-wide association study; HER2, HER2-enriched-like breast cancer; LumA, luminal A-like breast cancer; LumB, luminal B-like breast cancer; LumBHN, luminal B/HER2-negative breast cancer; TNBC, triple-negative breast cancer; PRS, polygenic risk score

Figure 2.. Manhattan plots of results from CC-GWAS analysis, restricting to SNPs associated with both indicated subtypes in the original case-control data after the filtering.

Abbreviations: HER2, HER2-enriched-like breast cancer; LumA, luminal A-like breast cancer; LumB, luminal B-like breast cancer; LumBHN, luminal B/HER2-negative breast cancer; TNBC, triple-negative breast cancer.

Figure 3.. UCSC Genome Browser plots for FPS-prioritized credible sets (SusieR) at (A) 3q26.31/rs2270418, (B) 8q22.3/rs13258434, and (C) 8q23.3/rs6982226.

At each locus, high-FPS (>100) variants are shown in red, the lead SNP from CC-GWAS is shown in blue (if not designated high-FPS), and previously reported breast cancer risk variants are shown in gray. ATAC-seq track is derived from TCGA_BRCA (Corces et al. 2018). Enhancer/superenhancer (Enh/SE) tracks are derived from predictions based on H3K27ac profiling (Hnisz et al. 2013); light green=HCC1954, dark green=MCF-7, brown=HMEC. ChIP-seq track displays binding peaks located within 50 bp of high-FPS variants, reported in female breast tumor tissues (ReMap2022)

Figure 4.. Validation of a candidate functional variant at risk locus 8q22.3.

(A) UCSC Genome Browser plot highlighting a minimal candidate enhancer region (CER) selected for testing the prioritized variant rs16867605. (B) Luciferase reporter enhancer activity assays. CER genomic fragments cloned in the forward (FOR) or reverse (REV) orientation and bearing the “G” or “A” allele at rs16867605 were assessed for allele-specific activity. Two independent experiments were performed in triplicate in MCF-7 cells, as indicated (Exp1: red, Exp2: black). Differences in luciferase activity between fragments bearing the “G” or “A” allele were assessed using generalized estimating equations (GEE).