VEGFA Gene Expression in Breast Cancer Is Associated With Worse Prognosis, but Better Response to Chemotherapy and Immunotherapy

Abstract

Background: Vascular endothelial growth factor-A (VEGFA) is a key inducer of angiogenesis, responsible for generating new blood vessels in the tumor microenvironment (TME) and facilitating metastasis. Notably, Avastin, which targets VEGFA, failed to demonstrate any significant benefit in clinical trials for breast cancer (BC). This study aimed to investigate the clinical relevance of VEGFA gene expression in BC.

Methods: A total of 7,336 BC patients across eight independent cohorts: ISPY2 (GSE173839), Sweden Cancerome Analysis Network-Breast (SCAN-B) (GSE96058), Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), GSE25066, GSE163882, GSE34138, GSE20194, and The Cancer Genome Atlas (TCGA), were analyzed. The calculated median VEGFA expression level was used to stratify these cohorts into high and low groups.

Results: High VEGFA was associated with worse disease-free, disease-specific, and overall survival in the METABRIC cohort, with findings supported by the SCAN-B cohort, which also showed worse overall survival (all P < 0.02). High VEGFA expression was seen in triple-negative breast cancer (TNBC) but not in BC with lymph node metastasis. Additionally, there was a significant correlation between high VEGFA expression and higher silent and non-silent mutations, single-nucleotide variant (SNV) neoantigens, homologous recombination defect, intratumoral heterogeneity, in the TCGA cohort. In the TCGA, METABRIC, and SCAN-B cohorts, high VEGFA BC was also associated with higher cell proliferation: higher Ki67 gene expression, higher Nottingham histological grade, and consistent enrichment of all the Hallmark cell proliferation-related gene sets. Unexpectedly, the angiogenesis gene set was not enriched in any of the cohorts and showed no association with infiltrations of lymphatic or blood vascular endothelial cells besides pericytes. High VEGFA BC had significantly less infiltration of anti-cancer immune cells but higher infiltration of pro-cancer immune cells in TCGA, METABRIC, and SCAN-B cohorts. Interestingly, BC, which had a pathological complete response (pCR) after anthracycline- and taxane-based neoadjuvant therapy, was associated with significantly heightened VEGFA expression in both estrogen receptor (ER)+/human epidermal growth factor receptor 2 (HER2)- and TNBC subtypes in the GSE25066 cohort and after immunotherapy in ER+/ HER2- subtype, but not TNBC in the ISPY2 cohort.

Conclusions: Our research indicates that high VEGFA BC confers high cell proliferation, reduced immune cell infiltration, and poorer survival, but allows better response to anthracycline- and taxane-based chemotherapy, and immunotherapy.

Keywords: Angiogenesis; Breast cancer; Chemotherapy; Gene expression; Immunotherapy; VEGFA.

Figure 1

Survival relevance for VEGFA expression. Kaplan-Meier curve with log-rank P value of disease-free survival (DFS), disease-specific survival (DSS), and overall survival (OS) in TCGA and METABRIC and OS in SCAN-B. The median value was used as a cutoff for two VEGFA expression groups, low (blue) and high (red). VEGFA: vascular endothelial growth factor-A; SCAN-B: Sweden Cancerome Analysis Network-Breast; METABRIC: Molecular Taxonomy of Breast Cancer International Consortium; TCGA: The Cancer Genome Atlas.

Figure 2

The association between VEGFA expression and clinical parameters. Boxplots of clinical factors: subtype, stage, lymph node metastasis, and distant metastasis in TCGA, METABRIC and SCAN-B cohorts by VEGFA expression. ER: estrogen receptor; HER2: human epidermal growth factor receptor 2; VEGFA: vascular endothelial growth factor-A; SCAN-B: Sweden Cancerome Analysis Network-Breast; METABRIC: Molecular Taxonomy of Breast Cancer International Consortium; TCGA: The Cancer Genome Atlas.

Figure 3

Association of VEGFA with pathological grade, mutation rates, neoantigens, and cell proliferation-related gene sets. (a) Boxplots of pathological grade and Ki67 gene (MKI67) expression in TCGA, METABRIC, and SCAN-B cohorts. (b) Enrichment score plots of cell proliferation-related gene sets: mitotic spindle, G2M checkpoint, E2F targets, MYC targets v1 and v2, and MTORC1 signaling in TCGA, METABRIC, and SCAN-B cohorts by GSEA using NES (normalized enrichment score) and FDR (false discovery rate). As recommended by GSEA software, FDR < 0.25 defined statistical significance. (c) Boxplots of homologous recombination defects (HRD), intratumor heterogeneity, and the mutation-related scores: silent and non-silent mutation rate, single nucleotide variation (SNV) and indel neoantigens in TCGA cohort. High and low VEGFA expression groups were determined by median cutoff. VEGFA: vascular endothelial growth factor-A; SCAN-B: Sweden Cancerome Analysis Network-Breast; METABRIC: Molecular Taxonomy of Breast Cancer International Consortium; TCGA: The Cancer Genome Atlas; GSEA: gene set enrichment analysis; ITH: intratumor heterogeneity.

Figure 4

Infiltration fractions of immune cells in the tumor microenvironment by VEGFA expression. Box plots show infiltration fractions for immune cells: CD8⁺ T cells, CD8⁺ Tcm cells, CD4⁺ T cells, CD4⁺ naive T cells, helper T type 1 (Th1 cells), dendric cells (DC), regulatory T cells (Tregs), helper T type 2 (Th2) cells, B cells, naive B cells, and plasma cells in TCGA, METABRIC, and SCAN-B cohorts by low and high VEGFA expression groups determined by median cutoff. VEGFA: vascular endothelial growth factor-A; SCAN-B: Sweden Cancerome Analysis Network-Breast; METABRIC: Molecular Taxonomy of Breast Cancer International Consortium; TCGA: The Cancer Genome Atlas.

Figure 5

VEGFA association with angiogenesis and angiogenesis-related data. (a) Boxplots of infiltration fractions for angiogenesis-related cells: pericytes, endothelial cells, microvascular endothelial (MVE) cells, and lymphatic endothelial cells (LECs) in in TCGA, METABRIC, and SCAN-B cohorts. (b) Enrichment score plots of angiogenesis gene set by VEGFA high and low groups by GSEA in TCGA, METABRIC, and SCAN-B cohorts. VEGFA: vascular endothelial growth factor-A; SCAN-B: Sweden Cancerome Analysis Network-Breast; METABRIC: Molecular Taxonomy of Breast Cancer International Consortium; TCGA: The Cancer Genome Atlas.

Figure 6

VEGFA association with neoadjuvant therapy patients with pCR. (a) Boxplots for VEGFA expression versus pathological complete response (pCR) and residual disease (RD) response for the immunotherapy treatment (durvalumab/olaparib) group and standard chemotherapy group determined from the ISPY2 cohort. (b) Boxplots for VEGFA expression versus pCR and RD response for anthracycline- and taxane-based chemotherapy in neoadjuvant cohorts GSE25066, GSE20194, GSE163882, and GSE34138. VEGFA: vascular endothelial growth factor-A; ER: estrogen receptor; HER2: human epidermal growth factor receptor 2; TNBC: triple-negative breast cancer; NS: not significant.