Abstract Cancer treatment options including small molecules, antibody-drug conjugates (ADCs), CAR T-cells, and combination therapies are rapidly expanding to improve cancer patient survival. However, efficacy of targeted therapies is limited by interpatient and intratumoral heterogeneity in breast cancer, and may be further exacerbated by dysregulated tumor microenvironments. For example, studies suggested that changes in tumor and breast tissue microenvironment in obesity (e.g. inflammation, increased growth factors) could lead to worsened prognosis that could be related to therapy resistance. Systematic characterization of the cellular effects of emerging drug candidates, particularly across different tumor microenvironments, is challenging, as it needs to be surveyed in diverse cancer contexts beyond just a handful of cancer cell lines. To overcome this challenge, we created PRISM (Profiling Relative Inhibition Simultaneously in Mixtures), an effective drug discovery screening platform with over 900 genetically distinct cancer cell lines of diverse lineages, to rapidly test therapeutics in a high-throughput manner. These cell lines, including 33 different breast cancer cell lines covering diverse cell types and subgroups, carry a specific 24 nucleotide “barcode” tag and have rich baseline genomic and functional characterization. They are first pooled into 20-25 cell pools of different lineages with similar growth rates, then subsequently cultured together with or without drugs. The relative barcode quantity read out by NextGen sequencing determines cell line responses to drugs. This pooled approach significantly reduces the time and the resources required for drug screening. Importantly, utilizing the rich cell line characterization to interpret viability profiles enables the identification of drivers of differential sensitivity and potential biomarkers of compound response. Furthermore, we created a breast cancer cell specific pool to investigate how media conditions mirroring different tumor microenvironments [e.g. media filtration, addition of insulin (0.01 mg/mL) or EGF (0.01 ug/mL)] can impact drug effects on breast cancer cells. In the PRISM 900+ cell panel treated with ADCs conjugated to different payloads that target HER2, there was a clear association between cell line sensitivity and ERBB2 (encoding HER2) gene expression, with the strongest effects on viability observed in a subset of cell lines overexpressing ERBB2. Upon further comparison of biomarker profiles across different ADCs, we established relationships between payload resistance and ABCB1 efflux pumps emerged for a subset of ADC payloads. Using the breast cancer cell specific pool, our data showed that estrogen receptor (ER) degraders fulvestrant and vepdegestrant (ARV-471) had significantly greater effects in reducing viability of ER+ versus ER- breast cancer cell lines. Media filtering reduced the drug effects of fulvestrant but not ARV-471, suggesting that ARV-471 efficacy may be less sensitive to the tumor microenvironment than fulvestrant. Lapatinib (HER2/neu and EGF receptor inhibitor) was more effective in killing HER2+ than HER2- negative breast cancer cells, with cells cultured in EGF-spiked media being more sensitive to lapatinib, whereas media filtration diminished its effects. We did not observe breast cancer subgroup specific killing by alpelisib (PI3K inhibitor) or olaparib (PARP inhibitor), but breast cancer cells became less sensitive to alpelisib when cultured in either insulin- or EGF-spiked media, and less sensitive to olaparib in EGF-spiked media. Overall, our study highlights how the PRISM 900+ cell panel can provide insights into drug specificity, cancer subtype selectivity, and to uncover clinically relevant targets. The breast cancer specific pool can further increase the throughput of understanding how drug responses may be altered in different tumor microenvironments in breast cancer. Citation Format: Blanche C. Ip, Jillian N. Eskra, Tenzin Sangpo, Ashish Bino George, Melissa Ronan, Matthew G. Rees, Jennifer A. Roth. PRISM high-throughput screening to elucidate how tumor microenvironments modulate drug responses of breast cancer cells [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P4-10-26.
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