Drug Responses in Plexiform Neurofibroma Type I (PNF1) Cell Lines Using High-Throughput Data and Combined Effectiveness and Potency

Paul O Zamora; Gabriel Altay; Ulisses Santamaria; Nathan Dwarshuis; Hari Donthi; Chang In Moon; Dana Bakalar; Matthew Zamora

doi:10.3390/cancers15245811

Drug Responses in Plexiform Neurofibroma Type I (PNF1) Cell Lines Using High-Throughput Data and Combined Effectiveness and Potency

Cancers (Basel). 2023 Dec 12;15(24):5811. doi: 10.3390/cancers15245811.

Authors

Paul O Zamora¹, Gabriel Altay², Ulisses Santamaria³, Nathan Dwarshuis¹, Hari Donthi¹, Chang In Moon^{4

5}, Dana Bakalar⁶, Matthew Zamora¹

Affiliations

¹ MoCo Makers, Gaithersburg, MD 20879, USA.
² HacDC, Washington, DC 20010, USA.
³ DMV Petri Dish, Rockville, MD 20850, USA.
⁴ Dan L. Duncan Comprehensive Cancer Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
⁵ Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
⁶ National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.

Abstract

Background: Neurofibromatosis type 1 (NF1) is a genetic disorder characterized by heterozygous germline NF1 gene mutations that predispose patients to developing plexiform neurofibromas, which are benign but often disfiguring tumors of the peripheral nerve sheath induced by loss of heterozygosity at the NF1 locus. These can progress to malignant peripheral nerve sheath tumors (MPNSTs). There are no approved drug treatments for adults with NF1-related inoperable plexiform neurofibromas, and only one drug (selumetinib), which is an FDA-approved targeted therapy for the treatment of symptomatic pediatric plexiform neurofibromas, highlighting the need for additional drug screening and development. In high-throughput screening, the effectiveness of drugs against cell lines is often assessed by measuring in vitro potency (AC50) or the area under the curve (AUC). However, the variability of dose-response curves across drugs and cell lines and the frequency of partial effectiveness suggest that these measures alone fail to provide a full picture of overall efficacy. Methods: Using concentration-response data, we combined response effectiveness (EFF) and potency (AC50) into (a) a score characterizing the effect of a compound on a single cell line, S = log[EFF/AC50], and (b) a relative score, ΔS, characterizing the relative difference between a reference (e.g., non-tumor) and test (tumor) cell line. ΔS was applied to data from high-throughput screening (HTS) of a drug panel tested on NF1-/- tumor cells, using immortalized non-tumor NF1+/- cells as a reference. Results: We identified drugs with sensitivity, targeting expected pathways, such as MAPK-ERK and PI3K-AKT, as well as serotonin-related targets, among others. The ΔS technique used here, in tandem with a supplemental ΔS web tool, simplifies HTS analysis and may provide a springboard for further investigations into drug response in NF1-related cancers. The tool may also prove useful for drug development in a variety of other cancers.

Keywords: NF1; concentration–response; drug evaluation; high-throughput; in vitro; neurofibromatosis; plexiform; web tool.

Grants and funding

N/A/Children's Tumor Foundation