Figure 1.
ECM3 gene pattern in breast carcinomas.
(A) Expression profile of LAS biclustering in breast tumors from the Van't Veer dataset [15]. (B) Frequency distribution of most influential ECM3 genes in 6 datasets ([15]–[20]), tumor clustering and gene importance estimation.
Table 1.
Frequency of clinico-pathological characteristic in patients according to ECM3 classification.
Figure 2.
ECM3 classification of breast carcinomas by qRT-PCR.
(A) qPCR analysis of ECM3 score derived from the average expression levels of COL1A1, COL5A2, SPARC and LAMA4 genes on FFPE specimens of 24 breast tumors of the ITA cohort [13] classified as ECM3 or non-ECM3 by unsupervised clustering. ** p<0.01 in unpaired t-test. (B) Receiver-operator characteristics (ROC) curve for expression of ECM3 genes in the ECM3 tumor subgroup.
Figure 3.
ECM3 gene expression in tumor cells.
(A) Representative immunohistochemical staining for Collagen VI and SPARC in ECM3 and non-ECM3 breast tumors. Magnification: ×400. (B,C) Fold-increase in ECM3 score expression as assessed by qRT-PCR after treatment with TGFβ (B) and 17β-estradiol (C) in breast carcinoma and fibroblast cell lines. Dotted line indicates average ECM3 expression in untreated cell lines. *p<0.05 in unpaired t-test vs untreated cells.
Figure 4.
ECM3 prognostic significance in relation to differentiation status.
(A) Association between ECM3 grade III (ECM3 GIII, solid black line), non-ECM3 grade III (non-ECM3 GIII, dotted black line), ECM3 grade I–II (ECM3 GI-II, solid grey line) and non-ECM3 grade I–II (non-ECM3 GI-II, dotted grey line) with DMFS in untreated patient joined datasets. (B–E) Association between ECM3 (black line) and non-ECM3 (grey line) with DMFS in ER-negative grade I–II (B), ER-positive grade I–II (C), ER-negative grade III (D) and ER-positive grade III (E) subgroups. p-values by log rank test.
Table 2.
Multivariate proportional hazards analysis of metastasis-free survival in untreated patients.
Figure 5.
Molecular characteristics of breast carcinomas according to ECM and grade classification by Gene Set Enrichment Analysis (GSEA).
Heatmap shows the normalized enrichment scores (NES) of gene sets significantly enriched at p<0.05 and FDR<25% in ECM3 grade III (A) and grade I–II (B) tumors of Desmedt [19] and Chin [16] datasets.