Genomic characterization of breast cancer in high risk subsets of breast cancer

Division Of Basic Sciences - Nci

Investigators

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Abstract

1) In the first aim we have looked at the clinical outcomes and interrogated the proteogenomic features of women under the age of 40 with breast cancer. Women under the age of 40 account for approximately 5-7% percent of breast cancer patients but numerous studies have shown that they have a worse prognosis and poorer outcome than women diagnosed at older ages. Breast tumors from young women are often ER-negative, from African-American patients and have other indicators of high risk: yet, multivariate analyses demonstrated that young age, in and of itself, is an independent predictor of poor outcome. At least partially due to the unique nature of the patient population served by DOD, a disproportionate number of breast cancer cases in young women are seen at Walter Reed National Military Medical Center and within the DOD system. We have previously characterized the clinical features and outcomes in breast cancer patients <40 in the DOD databases (Zimmer et al., Breast Cancer Res and Treat. 168(2), 501-511, 2018 finding that women under the age of 40 was more often seen in African American and Hispanic women, had adverse clinical features (e.g., higher stage and grade, ER negative), and higher frequency of recurrence. Utilizing the tissue bank for the CBCP, 34 tumors from women under the age of 40 were compared to those of women 60 years old or older matched for histologic subtype and race were subjected to an integrated proteogenomic analysis (whole exome sequencing, RNAseq, and proteomic analysis). In this cohort tumors from women <40 had were enriched for more aggressive molecular subtypes (e.g. basal tumors) and women <40 had a shorter progression free interval than older women. Our multi-omic analysis identified distinct clusters in luminal, but not basal-like cancers between age groups. Notably, GATA3 mutations were enriched in luminal tumors from young women, while TP53 and PIK3CA mutations more common in luminal tumors from older women. Young women's tumors exhibited lower estrogen receptor (ER) expression yet paradoxically enhanced ER response pathways and increased expression of tamoxifen-resistance-associated genes (IRS1, FERMT1). Immune pathway activity and immune scores were lower in tumors from young women, whereas proliferative and MYC pathways were notably elevated, identifying potential therapeutic targets. Transcriptomic data from TCGA and METABRIC confirmed our findings, with 10 of 11 observed pathways corroborated. Finally, differential expression of four immune-related surface proteins also suggested potential age-specific responses of immune-based therapies. Together, these findings may contribute to the understanding of the molecular mechanisms underlying worse outcomes in young women, and offer new insight to therapeutic strategies. This work is currently in press at NPJ Breast Cancer. 2) In the second aim, the phase I portion of the clinical trial for the metaplastic patients has been completed at Methodist Hospital and has identified the recommended phase II dose. In the phase I study treating 9 patients, the ORR was 44% and the CBR was 78% (presented at the SABCS in 2024). The phase II study is approved by the central IRB and we are in the process opening the phase II study at the NIH Clinical Center. 3) In the third aim we are examining the clinical impact and the biological features of Epidermal Growth Factor Receptor (EGFR) amplification in breast cancer patients. EGFR amplification occurs in approximately 1-2.5% of breast cancer patients, more frequently in TNBC (2.45-6.7%) and ER-/HER2+ (1.3-6.5%) breast cancers, and in the molecular basal (2.33-8.1%) and HER2 enriched (1.87-5.4%) subtypes. EGFR amplified patients in cBioPortal and in the Caris datasets had worse median OS compared to those with non-amplified EGFR (mOS: 111.1 m vs 164.6 m, p=0.0269, and 21.6 m vs 32.9 m, HR 0.69, 95% CI 0.58 - 0.82, p <0.0001 for the cBioPortal and Caris data, respectively). cBioPortal and Caris databases showed that 54-71% of EGFR amplified tumors have activating mutations in the PI3K pathway. Our in vitro studies showed combination EGFR and PI3K inhibitors more dramatically reduced MAPK, mTOR and AKT signaling in the BT20 and MDA-MB-468 cells, whereas the inhibition of downstream signaling was less significant in MDA-MB-231 cells. Combination of EGFR and PI3K inhibitors reduced cell viability in these three cell lines, but inhibition was greater, statistically significant, and synergistic in MDA-MB-468 and BT20 compared to MDA-MB-231. Only MDA-MB-468 and BT20 cells had an increased fraction of apoptotic cells with combined pathway inhibition. EGFR or PI3K inhibition alone in a BT20 xenograft model reduced tumor volume, however the combination induced the only statistically significant reduction in tumor volume when compared to vehicle control. EGFR/PI3K inhibitor combination causes apoptosis and reduction in tumor growth in cells with EGFR amplification and PI3K alteration. EGFR amplification with coincident PI3K pathway mutations are drivers in a subset of breast cancers and identify a subgroup of breast cancers that are more likely to respond to dual targeted therapy. This work is currently under review for publication.