Actionable gene alterations in an Asian population with triple-negative breast cancer

EGFR-to-Src family tyrosine kinase switching in proliferating-DTP TNBC cells creates a hyperphosphorylation-dependent vulnerability to EGFR TKI

Triple-Negative Breast Cancer (TNBC) is the most aggressive type of breast malignancy, with chemotherapy as the only mainstay treatment. TNBC patients have the worst prognoses as a large fraction of them do not achieve complete pathological response post-treatment and develop drug-resistant residual disease. Molecular mechanisms that trigger proliferation in drug-resistant chemo-residual TNBC cells are poorly understood due to the lack of investigations using clinically relevant cellular models. In this study, we have established TNBC subtype-specific cellular models of proliferating drug-tolerant persister (PDTP) cells using different classes of chemotherapeutic agents that recapitulate clinical residual disease with molecular heterogeneity. Analysis of total phospho-tyrosine signals in TNBC PDTPs showed an enhanced phospho-tyrosine content compared to the parental cells (PC). Interestingly, using mass-spectrometry analysis, we identified a dramatic decrease in epidermal growth factor receptor (EGFR) expression in the PDTPs, while the presence of hyper-activated tyrosine phosphorylation of EGFR compared to PC. Further, we show that EGFR has enhanced lysosomal trafficking in PDTPs with a concomitant increase in N-Myc Downstream Regulated-1 (NDRG1) expression that co-localizes with EGFR to mediate receptor degradation. More surprisingly, we found that reduced protein levels of EGFR are coupled with a robust increase in Src family kinases, including Lyn and Fyn kinases, that creates a hyper-phosphorylation state of EGFR-Src tyrosine kinases axis in PDTPs and mediates downstream over-activation of STAT3, AKT and MAP kinases. Moreover, paclitaxel-derived PDTPs show increased sensitivity to EGFR TKI Gefitinib and its combination with paclitaxel selectively induced cell death in Paclitaxel-derived PDTP (PDTP-P) TNBC cells and 3D spheroids by strongly downregulating phosphorylation of EGFR-Src with concomitant downregulation of Lyn and Fyn tyrosine kinases. Collectively, this study identifies a unique hyper-phosphorylation cellular state of TNBC PDTPs established by switching of EGFR-Src family tyrosine kinases, creating a vulnerability to EGFR TKI.

Germline variants detected by multigene panel testing in patients with suspected hereditary breast cancer

PURPOSE

To clarify the status of multigene panel testing for suspected hereditary breast cancer in our institute, and disclose the characteristics of the variants detected.

METHODS

This was a retrospective study of individuals who underwent next-generation sequencing-based multigene panel testing at our institute to investigate hereditary genetic variants for suspected hereditary breast cancer.

RESULTS

We identified 36 women who underwent multigene panel testing: 8 (22.2%) had a pathogenic variant, with or without other variants of uncertain significance (VUSs); 15 (41.7%) had VUSs only; and 13 (36.1%) had negative genetic test results. Of the eight pathogenic variants, five were BRCA2 variants and one each were BRCA1, MLH1, and RINT1 variants. The VUSs included BRCA1 and BRCA2, as well as other breast cancer-associated genes, such as ATM, CDH1, CHEK2, and PALB2. Referring to the latest ClinVar database, one of the variants identified as a VUS at diagnosis was re-determined as likely pathogenic, and three of the variants identified as VUSs at diagnosis were re-determined as benign.

CONCLUSION

VUSs are frequently identified during testing and it is important to monitor these individuals because VUS evaluations can change over time.

Results from the randomized KEYNOTE-355 study of pembrolizumab plus chemotherapy for Asian patients with advanced TNBC

In the phase 3 KEYNOTE-355 study (NCT02819518), pembrolizumab plus chemotherapy demonstrated statistically significant and clinically meaningful improvements in progression-free survival (PFS) and overall survival (OS) versus placebo plus chemotherapy among patients with previously untreated locally recurrent inoperable or metastatic triple-negative breast cancer (TNBC) and programmed cell death ligand 1 (PD-L1) combined positive score (CPS) ≥ 10 tumors. We analyzed outcomes for the subgroup of patients enrolled in Asia in KEYNOTE-355. Patients received pembrolizumab 200 mg or placebo (2:1 randomization) every 3 weeks for 35 cycles plus investigator's choice chemotherapy. Primary endpoints were PFS per Response Evaluation Criteria in Solid Tumors version 1.1 and OS. Among patients enrolled in Hong Kong, Japan, Korea, Malaysia and Taiwan (pembrolizumab plus chemotherapy, n = 113; placebo plus chemotherapy, n = 47), 117 (73.1%) had PD-L1 CPS ≥ 1 and 56 (35.0%) had PD-L1 CPS ≥ 10. Median time from randomization to data cutoff (June 15, 2021) was 43.8 (range, 36.8‒53.2) months (intent-to-treat [ITT] population). Hazard ratios (HRs [95% CI]) for PFS in the CPS ≥ 10, CPS ≥ 1, and ITT populations were 0.48 (0.24‒0.98), 0.58 (0.37‒0.91), and 0.66 (0.44‒0.99), respectively. Corresponding HRs (95% CI) for OS were 0.54 (0.28‒1.04), 0.62 (0.40‒0.97), and 0.57 (0.39‒0.84). Grade 3/4 treatment-related adverse events (AEs) occurred in 77.9% versus 78.7% of patients with pembrolizumab plus chemotherapy versus placebo plus chemotherapy. No grade 5 AEs occurred. Clinically meaningful improvement in PFS and OS with manageable toxicity were observed with pembrolizumab plus chemotherapy versus placebo plus chemotherapy in patients enrolled in Asia with previously untreated, inoperable or metastatic TNBC.Trial registration: ClinicalTrials.gov, NCT02819518.

Functional exploration of copy number alterations in a Drosophila model of triple-negative breast cancer

Accounting for 10-20% of breast cancer cases, triple-negative breast cancer (TNBC) is associated with a disproportionate number of breast cancer deaths. One challenge in studying TNBC is its genomic profile: with the exception of TP53 loss, most breast cancer tumors are characterized by a high number of copy number alterations (CNAs), making modeling the disease in whole animals challenging. We computationally analyzed 186 CNA regions previously identified in breast cancer tumors to rank genes within each region by likelihood of acting as a tumor driver. We then used a Drosophila p53-Myc TNBC model to identify 48 genes as functional drivers. To demonstrate the utility of this functional database, we established six 3-hit models; altering candidate genes led to increased aspects of transformation as well as resistance to the chemotherapeutic drug fluorouracil. Our work provides a functional database of CNA-associated TNBC drivers, and a template for an integrated computational/whole-animal approach to identify functional drivers of transformation and drug resistance within CNAs in other tumor types.

Landmark Series: The Cancer Genome Atlas and the Study of Breast Cancer Disparities

Race-related variation in breast cancer incidence and mortality are well-documented in the United States. The effect of genetic ancestry on disparities in tumor genomics, risk factors, treatment, and outcomes of breast cancer is less understood. The Cancer Genome Atlas (TCGA) is a publicly available resource that has allowed for the recent emergence of genome analysis research seeking to characterize tumor DNA and protein expression by ancestry as well as the social construction of race and ethnicity. Results from TCGA based studies support previous clinical evidence that demonstrates that American women with African ancestry are more likely to be afflicted with breast cancers featuring aggressive biology and poorer outcomes compared with women with other backgrounds. Data from TCGA based studies suggest that Asian women have tumors with favorable immune microenvironments and may experience better disease-free survival compared with white Americans. TCGA contains limited data on Hispanic/Latinx patients due to small sample size. Overall, TCGA provides important opportunities to define the molecular, biologic, and germline genetic factors that contribute to breast cancer disparities.

Copy number alteration is an independent prognostic biomarker in triple-negative breast cancer patients

BACKGROUND

Next-generation sequencing (NGS) has enabled comprehensive genomic profiling to identify gene alterations that play important roles in cancer biology. However, the clinical significance of these genomic alterations in triple-negative breast cancer (TNBC) patients has not yet been fully elucidated. The aim of this study was to clarify the clinical significance of genomic profiling data, including copy number alterations (CNA) and tumor mutation burden (TMB), in TNBC patients.

METHODS

A total of 47 patients with Stage I-III TNBC with genomic profiling of 435 known cancer genes by NGS were enrolled in this study. Disease-free survival (DFS) and overall survival (OS) were evaluated for their association to gene profiling data.

RESULTS

CNA-high patients showed significantly worse DFS and OS than CNA-low patients (p = 0.0009, p = 0.0041, respectively). TMB was not associated with DFS or OS in TNBC patients. Patients with TP53 alterations showed a tendency of worse DFS (p = 0.0953) and significantly worse OS (p = 0.0338) compared with patients without TP53 alterations. Multivariable analysis including CNA and other clinicopathological parameters revealed that CNA was an independent prognostic factor for DFS (p = 0.0104) and OS (p = 0.0306). Finally, multivariable analysis also revealed the combination of CNA-high and TP53 alterations is an independent prognostic factor for DFS (p = 0.0005) and OS (p = 0.0023).

CONCLUSIONS

We revealed that CNA, but not TMB, is significantly associated with DFS and OS in TNBC patients. The combination of CNA-high and TP53 alterations may be a promising biomarker that can inform beyond standard clinicopathologic factors to identify a subgroup of TNBC patients with significantly worse prognosis.

Cost-effectiveness of BRCA1/2 mutation profiling to target olaparib use in patients with metastatic breast cancer

Aim: Olaparib monotherapy improves progression-free survival in patients with metastatic breast cancer and BRCA1/2 mutations. We evaluated the cost-effectiveness of BRCA1/2 mutation profiling to target olaparib use. Methods: A Markov cohort model was generated to compare the 5-year cost-effectiveness of BRCA1/2 mutation profiling to target olaparib use. Results: The incremental cost-effectiveness ratio of BRCA1/2 mutation profiling plus olaparib monotherapy was JPY14,677,259/quality-adjusted life year (QALY) (US$131,047/QALY), compared with standard chemotherapy alone. Conclusion: BRCA1/2 mutation profiling to target olaparib use is not a cost-effective strategy for metastatic breast cancer. The strategy provides minimal incremental benefit at a high incremental cost per QALY. Hence, further cost reductions in the cost of both BRCA1/2 mutation profiling and olaparib are required.