Molecular determinants of post-mastectomy breast cancer recurrence

Abstract

Breast cancer (BC) adjuvant therapy after mastectomy in the setting of 1–3 positive lymph nodes has been controversial. This retrospective Translational Breast Cancer Research Consortium study evaluated molecular aberrations in primary cancers associated with locoregional recurrence (LRR) or distant metastasis (DM) compared to non-recurrent controls. We identified 115 HER2 negative, therapy naïve, T 1–3 and N 0-1 BC patients treated with mastectomy but no post-mastectomy radiotherapy. This included 32 LRR, 34 DM, and 49 controls. RNAseq was performed on primary tumors in 110 patients; with no difference in RNA profiles between patients with LRR, DM, or controls. DNA analysis on 57 primary tumors (17 LRR, 15 DM, and 25 controls) identified significantly more NF1 mutations and mitogen-activated protein kinase (MAPK) pathway gene mutations in patients with LRR (24%, 47%) and DM (27%, 40%) compared to controls (0%, 0%; p < 0.0001 and p = 0.0070, respectively). Three patients had matched primary vs. LRR samples, one patient had a gain of a NF1 mutation in the LRR. There was no significant difference between the groups for PTEN loss or cleaved caspase 3 expression. The mean percentage Ki 67 labeling index was higher in patients with LRR (29.2%) and DM (26%) vs. controls (14%, p = 0.0045). In summary, mutations in the MAPK pathway, specifically NF1, were associated with both LRR and DM, suggesting that alterations in MAPK signaling are associated with a more aggressive tumor phenotype. Validation of these associations in tissues from randomized trials may support targeted therapy to reduce breast cancer recurrence.

Genomic, Transcriptomic, and Proteomic Profiling of Metastatic Breast Cancer

“…Notably, 1 patient in the matched series had a complete mismatch of genomic alterations, with a match of polymorphisms (not shown) confirming the same donor. We had reported such a case in a prior breast cancer study as well (23). Such cases emphasize that patients with DM could have another primary (same tumor type or other), emphasizing importance of pathologic confirmation of metastatic disease.…”

“…We had identified NF1 loss in patients with both HR þ MBC and TNBC, and found that NF1 deletions noted on NGS on the T200 platform are indeed lost on SNP arrays. We had also reported NF1 as a gene of interest in a multicenter study of patients with breast cancer who had modified radical mastectomy for clinical node positive disease with 1-3 positive nodes (23). DNA analysis on primary tumors of patients who developed a LRR or DM versus patients who did not recur identified significantly more NF1 mutations in patients with LRR or DM, respectively.…”

“…For cases with limited yield, RNA sequencing (RNA-seq) was prioritized over DNA sequencing. RNA extraction, cDNA and library preparation, target enrichment, and sequencing were performed on all samples following a validated protocol as described previously (23).…”

“…ESR1 mutations are almost exclusively detected in patients with metastatic disease after endocrine therapy in the adjuvant or metastatic setting (21), and may differentially benefit from different endocrine therapies (22). We have reported an enrichment of NF1 mutations in patients with breast cancer with LRR and DM, with acquisition of NF1 mutations in some patients (23). Recently, somatic NF1 loss was shown to activate Ras/MAPK pathway and confer resistance to endocrine therapy.…”

Identification of a Modified HOXB9 mRNA in Breast Cancer

“…HOXB9v was commonly detected from clinical breast cancer samples (Figure 3(a)), regardless of their hormone receptor and HER2 status. However, HOXB9v was not detected in normal mammary gland samples (Figure 3(b) us, to further confirm the presence of HOXB9v in human breast cancer samples, we reanalyzed a publicly available breast cancer RNA sequence data set (GSE119937) [18] and mapped the reads onto the HOXB9 gene sequence. We identified a region in exon 1 where the number of mapped reads was low in numerous samples; this region matched the deletion region of HOXB9v (Figure 4).…”