Genomic Landscape of Malignant Phyllodes Tumors Identifies Subsets for Targeted Therapy

Abstract

Purpose: Malignant phyllodes tumors (MPTs) are rare fibroepithelial tumors of the breast with aggressive biologic behavior and high recurrence rates. Surgery remains the primary treatment modality for these tumors; however, initial investigations suggest a potential for targeted therapies in managing this disease. Therefore, we aimed to assess the molecular landscape of MPTs to reveal possible treatment opportunities.

Methods: MPTs (n = 57) from primary and metastatic sites underwent genomic sequencing (592-gene panel or whole exome), whole-transcriptome sequencing, and immunohistochemistry (PD-L1, human epidermal growth factor receptor 2 [HER2]) at Caris Life Sciences (Phoenix, AZ). Immune cell fractions in the tumor microenvironment were estimated using quanTIseq. Mann-Whitney U, chi-square, and Fisher's exact tests were used to determine significance (P < .05).

Results: MPTs had low ERBB2 expression, comparable with the HER2-negative subset of a large cohort of breast adenocarcinoma samples (N = 9,926). Frequent alterations included TERT promoter; MED12, TP53, and NF1 mutations; and less frequently EGFR, PIK3CA, and BRAF. Differences in mutation prevalences were observed between primary sites, lung metastases, and nonlung metastases. One MPT specimen harbored a pathogenic TPM4:NTRK1 fusion, and treatment with larotrectinib for over 16 months suggested a clinical response to therapy. PD-L1+ status was observed in 15.2% of MPTs overall, with similar prevalence in primary sites and lung metastases. B cells, M2 macrophages, neutrophils, and natural killer cells had the highest median cell fractions in MPTs.

Conclusion: Considering the occurrence of several actionable alterations including a TPM4:NTRK1 fusion reported herein, these results support the use of next-generation sequencing (NGS) including RNA analysis for fusion detection to identify such alterations in patients with MPTs. These findings highlight the importance of comprehensive NGS in MPT research to uncover potential targeted treatment options for these patients.

FIG 1.

Extrapolating HER2 (ERBB2) status for phyllodes tumors. ERBB2 expression (log₂ TPM) was determined for HER2-positive, HER2-low, and HER2-negative subsets of a cohort of breast adenocarcinomas (N = 9,926) and compared with ERBB2 expression in MPT. ****P < .00005. HER2, human epidermal growth factor receptor 2; MPT, malignant phyllodes tumor; TPM, transcripts per million.

FIG 2.

Genomic landscape of phyllodes tumors. Oncoplot shows prevalence of pathogenic gene aberrations in primary MPT, MPT lung metastases, and MPT NLM. ERBB2 expression (log₂ TPM) is shown at the top for each tumor. Bars at the right indicate the total percentage per group. *P < .05 (Fisher's exact test). Amp, copy number amplification; IHC, immunohistochemistry; mets, metastases; MPT, malignant phyllodes tumor; NLM, nonlung metastases; TPM, transcripts per million.

FIG 3.

Immune-oncology biomarkers in phyllodes tumors. (A) Percentages of tumors that were PD-L1–positive (SP142 antibody), MMRd/MSI-H, and TMB-H in primary MPT, MPT lung metastases, and MPT NLM. (B) Heat map showing quanTIseq-inferred immune cell infiltration (top) and relative expression of indicated immune genes (bottom) in primary MPT, MPT lung metastases, and MPT NLM. *P < .05; **P < .005. mets, metastases; MMRd, mismatch repair deficiency; MPT, malignant phyllodes tumor; MSI-H, microsatellite instability-high; NK, natural killer cells; NLM, nonlung metastases; TMB-H, tumor mutational burden-high.

FIG 4.

TPM4:NTRK1 fusion event in phyllodes tumor. One patient presented with an NTRK1 pathogenic fusion and was treated for 16 months with larotrectinib. The diagram shows the representative structure of TPM4:NTRK1 fusion with amino acid residues noted. Ig_2, immunoglobulin-like domain; LRR_8, leucine-rich repeat.