Cross-study analysis identifies estrogen depletion and exposure duration as key determinants of bisphenol A transcriptomic potency in MCF-7 cells.

High-throughput transcriptomics (HTTr) is increasingly used to derive transcriptomic points of departure (tPODs) for chemical screening and prioritization, yet the robustness of these estimates across studies with differing experimental designs remains unclear. Here, we compared tPODs for bisphenol A (BPA) across multiple HTTr studies conducted in MCF-7 breast cancer cells, including datasets from our laboratory and others. Although these studies employed broadly similar approaches, they differed in key methodological features, including estrogen-depletion protocols, exposure duration, and maximum test concentration. Using a standardized downstream bioinformatic workflow, we evaluated the consistency of BPA transcriptomic potency estimates and assessed factors contributing to variability across studies. Overall, five of seven studies yielded BPA potency estimates within a similar concentration range, supporting the utility of HTTr for comparative potency assessment despite some inter-study variability. Notably, studies conducted under estrogen-depleted conditions yielded higher potency estimates relative to those performed under standard culture conditions. Similarly, longer exposure durations were associated with higher potency estimates. These findings indicate that, while tPODs are generally reproducible across HTTr studies, experimental conditions, particularly estrogen depletion and exposure duration, can influence potency estimates in MCF-7 cells. However, these factors were not systematically varied or independently controlled across datasets, and therefore their individual contributions cannot be definitively disentangled in the present analysis. This work highlights the importance of standardizing hormone conditions and exposure durations when applying HTTr to screen estrogenic chemicals. Collectively, these results support the use of HTTr for chemical prioritization while underscoring the need for harmonized experimental design in endocrine-relevant in vitro models.