Phyllodes tumors with and without fibroadenoma-like areas display distinct genomic features and may evolve through distinct pathways

Abstract

Breast fibroepithelial lesions (fibroadenomas and phyllodes tumors) are underpinned by recurrent MED12 exon 2 mutations, which are more common in fibroadenomas and benign phyllodes tumors. TERT promoter hotspot mutations have been documented in phyllodes tumors, and found to be more frequent in borderline and malignant lesions. Several lines of evidence suggest that a subset of phyllodes tumors might arise from fibroadenomas. Here we sought to investigate the genetic differences between phyllodes tumors with fibroadenoma-like areas vs. those without. We retrieved data for 16 borderline/ malignant phyllodes tumors, including seven phyllodes tumors with fibroadenoma-like areas and nine phyllodes tumors without fibroadenoma-like areas, which had been previously subjected to targeted capture massively parallel sequencing. Whilst MED12 exon 2 mutations were significantly more frequent in tumors with fibroadenoma-like areas (71 vs. 11%), an enrichment in genetic alterations targeting bona fide cancer genes was found in those without fibroadenoma-like areas, in particular in EGFR mutations and amplifications (78 vs. 14%). No significant difference in the frequency of TERT genetic alterations was observed (71% in cases with fibroadenoma-like areas vs 56% in those without fibroadenoma-like areas). Our data suggest that the development of phyllodes tumors might follow two different evolutionary pathways: a MED12-mutant pathway that involves the progression from a fibroadenoma to a malignant phyllodes tumor; and a MED12-wild-type pathway, where malignant phyllodes tumors arise de novo through the acquisition of genetic alterations targeting cancer genes. Additional studies are warranted to confirm our observations and define whether the outcome differs between both pathways.

Fig. 1

Histologic features of phyllodes tumors (PTs) with and without fibroadenoma (FA)-like areas included in this study. Representative micrographs of a malignant PT with FA-like areas a, displaying areas of marked stromal cellularity and cytologic atypia b intermingled with FA-like areas showing intracanalicular growth pattern, low stromal cellularity and no cytologic atypia c. Representative micrographs of a malignant PT without FA-like areas d, displaying infiltrative borders, prominent stromal cellularity e, marked cellular atypia and numerous mitoses f. Scale bars in a and d, 100 μm, b, c, and f, 20 μm, and e, 50 μm

Fig. 2

Repertoire of somatic genetic alterations identified in phyllodes tumors (PTs) with fibroadenoma (FA)-like areas and PTs without FA-like areas. Heatmap illustrating non-synonymous somatic mutations, gene amplifications and homozygous deletions in PTs with FA-like areas (n = 7) and PTs without FA-like areas (n = 9), identified by targeted capture massively parallel sequencing (MSK-IMPACT). Cases are shown in columns and genes are represented in rows. Only genetic alterations affecting the 227 genes present in both targeted capture panels used in this study are shown. The different genetic alterations are color-coded according to the legend. Loss of heterozygosity of a mutated gene is indicated by a diagonal bar. Promoter SNVs are shown with a triangle. MED12 exon 2 mutations are indicated by an asterix; BOPT3 harbored a MED12 mutation in exon 4. OncoKB level 3A (breast cancer) is indicated by a circle

Fig. 3

Histologic features of a phyllodes tumor (PT) with myxoid fibroadenoma (FA)-like areas. Representative micrographs of a malignant PT with myxoid FA-like areas a, displaying regions with marked stromal atypia and frequent mitoses b immediately adjacent to FA-like areas with myxoid hypocellular stroma c. Scale bar in a 100 μm, and b and c, 50 μm

Fig. 4

Proposed model of the evolutionary origin of borderline and malignant phyllodes tumors. Phyllodes tumors might follow two different evolutionary pathways. (i) In the MED12-mutant pathway, MED12 exon 2 mutations are posited to lead to the development of a benign fibroepithelial lesion, which upon the occurrence of additional genetic alterations affecting TERT and/ or other cancer genes may progress to a borderline or malignant phyllodes tumor. (ii) In the MED12-independent pathway, borderline or malignant phyllodes tumors might arise de novo, through the acquisition of genetic alterations targeting cancer genes, such as TERT and/ or EGFR. TSG tumor suppresor genes