Profiling molecular regulators of recurrence in chemorefractory triple-negative breast cancers

Abstract

Background Approximately two thirds of patients with localized triple-negative breast cancer (TNBC) harbor residual disease (RD) after neoadjuvant chemotherapy (NAC) and have a high risk-of-recurrence. Targeted therapeutic development for TNBC is of primary significance as no targeted therapies are clinically indicated for this aggressive subset. In view of this, we conducted a comprehensive molecular analysis and correlated molecular features of chemorefractory RD tumors with recurrence for the purpose of guiding downstream therapeutic development. Methods We assembled DNA and RNA sequencing data from RD tumors as well as pre-operative biopsies, lymphocytic infiltrate, and survival data as part of a molecular correlative to a phase II post-neoadjuvant clinical trial. Matched somatic mutation, gene expression, and lymphocytic infiltrate were assessed before and after chemotherapy to understand how tumors evolve during chemotherapy. Kaplan-Meier survival analyses were conducted categorizing cancers with TP53 mutations by the degree of loss as well as by the copy number of a locus of 18q corresponding to the SMAD2, SMAD4, and SMAD7 genes. Results Analysis of matched somatic genomes pre-/post-NAC revealed chaotic acquisition of copy gains and losses including amplification of prominent oncogenes. In contrast, significant gains in deleterious point mutations and insertion/deletions were not observed. No trends between clonal evolution and recurrence were identified. Gene expression data from paired biopsies revealed enrichment of actionable regulators of stem cell-like behavior and depletion of immune signaling, which was corroborated by total lymphocytic infiltrate, but was not associated with recurrence. Novel characterization of TP53 mutation revealed prognostically relevant subgroups, which were linked to MYC-driven transcriptional amplification. Finally, somatic gains in 18q were associated with poor prognosis, likely driven by putative upregulation of TGFß signaling through the signal transducer SMAD2. Conclusions We conclude TNBCs are dynamic during chemotherapy, demonstrating complex plasticity in subclonal diversity, stem-like qualities, and immune depletion, but somatic alterations of TP53/MYC and TGFß signaling in RD samples are prominent drivers of recurrence, representing high-yield targets for additional interrogation. Electronic supplementary material The online version of this article (10.1186/s13058-019-1171-7) contains supplementary material, which is available to authorized users.

ADAM12 is A Potential Therapeutic Target Regulated by Hypomethylation in Triple-Negative Breast Cancer

“…Accordingly, several studies have shown ADAM12 mRNA overexpression in chemo-resistant ER-negative breast tumours [40,41]. In addition, ADAM12 re-expression in the non-malignant breast epithelial MCF 10A cell line has been reported to induce resistance to cisplatin [42], while ADAM12 silencing facilitates 5-fluorouacil sensitivity in a TNBC xenograft model [39]. Consistent with these findings, paclitaxel administration has been shown to increase ADAM12 protein levels in the SUM159PT TNBC cell line [37].…”

Resistance to Neoadjuvant Treatment in Breast Cancer: Clinicopathological and Molecular Predictors

“…The tested expression variants allow the generation of two tumor categories; one includes tumors with higher differentiation, high Ki67, and low TGFß and MEK activity, while the second agglutinates those tumors enriched in genes related to invasive pathways and poor differentiation. Consistent with the stem-like phenotype typically induced by the latter and already related to residual disease [ 83 ], this group is characterized by enhanced MEK and TGFß activation, together with the deletion of DUSP4 [ 80 , 84 , 85 , 86 ]. In line with this, additional studies focused on the TN subtype reported the reduction in DUSP4 expression in RD as related to poor RFS ( p < 0.0004) [ 84 ].…”

“…In the analysis of 75 TN RD arising from a phase II trial (BRE09-146), it was observed that the most abundant mutations were also in TP53 (88%), followed by PIK3CA mutations (11%). Regarding the CNA profile of RD, they identified gains in MCL1 , MYC , and GATA3 , and losses in BRCA2 , FLT3 and RB1 , with the most frequently amplified gene being MYC (24% of cases) and the most frequently depleted gene BRCA2 (68% of cases) [ 83 ]. In addition, the analysis of 18 matched pre-NAC vs. post-NAC matched samples showed a mutational homogeneity between both scenarios, given that 13 out of the 18 matched samples had identical mutational profiles.…”

“…However, this is not the case for the CNA behavior. The NAC modulated the CNA pattern with chaotic acquisition of copy gains and losses, including amplifications in known genes, such as MCL1 , MYC , KRAS , BCL9 , EGFR , CDKN2A , BIRC2 , and BIRC3 , found in the post-NAC scenario compared with the one before treatment [ 83 ]. In this study, among the molecular perturbations induced by NAC that predicted recurrence, the loss of TP53 was associated with a significant DFS and OS decrease ( p < 0.02 and p < 0.03, respectively), highlighting the importance of the loss of locus 17p for TN aggressiveness.…”

“…Interestingly, TP53 mutations and MYC signaling upregulation also tend to be concomitant ( p < 0.05), and related to MYC amplification, although only TP53 mutations correlate with worse DFS and OS ( p < 0.007 and p < 0.007, respectively). Finally, the copy gain of regions in close proximity of SMAD4 (chromosome 18q) is also associated with poor DFS ( p < 0.01) [ 83 ]. Another comprehensive study by Balko et al reported the characterization of the gene expression and genetic variants associated with the residual disease phenotype in the TN subtype after NAC using a panel of 450 transcripts that include the signatures of PAM50, MEK and TGFß activation, and post-NAC Ki67 index related genes [ 80 ].…”