Abstract 5720: Combination therapies in matched 3D in vitro and in vivo preclinical models of rare and recalcitrant cancers from the National Cancer Institute’s Patient-Derived Models Repository

There is a major need in oncology drug development to establish predictive preclinical assays with high translational relevance to patient responses. The National Cancer Institute’s Patient-Derived Models Repository (https://pdmr.cancer.gov) offers a collection of highly characterized models from a variety of cancer types including rare and recalcitrant malignancies and tumors from patients of diverse ancestry. This collection includes matched sets of patient-derived cell lines, organoids, and xenografts (PDXs), which allows comparisons of drug responses from in vitro and in vivo assays performed with the same patient-derived tumor model. A high-throughput screen was conducted using matched sets of patient-derived organoids and cell lines. Patient-derived cell lines were grown as 3D multicellular spheroids mixed with endothelial cells and mesenchymal stem cells. The patient-derived organoids were 100% tumor cells and were plated in 5% basement membrane extract supplemented with growth factors and cytokines. All drugs were tested at concentrations up to their reported clinical Cmax values and cell viability for individual drug treatments and drug combinations were assayed using CellTiter-Glo 3D after seven days drug exposure. Prior to the endpoint viability measurements, growth curves for spheroid median volume and organoid median surface area were calculated from a series of non-invasive brightfield images collected every 12 hours. For some drug combinations, differential responses were observed between the matched organoids and multicellular spheroids, potentially reflecting the contribution of the stromal component in the spheroids. Overall, the drug-dependent growth responses observed from the two 3D in vitro models (i.e., multicellular spheroids and organoids) were frequently comparable to those observed in vivo from PDXs. For example, the in vitro activities of several drug combinations including: BAY1895344 + temozolomide, erlotinib + cediranib, entinostat + talazoparib, and selumetinib + abemaciclib, demonstrated good agreement with the responses observed in vivo. However, among the drug combinations tested ixazomib + panobinostat showed the greatest cytotoxicity in vitro but had no activity in the matched PDX models. The availability of matched patent-derived cell lines, organoids and PDXs provides an opportunity to learn about the features of assay methodologies and data analyses that influence the successful translation of preclinical results between in vitro and in vivo systems. The results of this study are encouraging, but also highlight discrepancies that will be important to investigate, understand and address in order to improve translational capacity of future assays. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261201500003I.

Citation Format: Thomas S. Dexheimer, Thomas Silvers, Rene Delosh, Russell Reinhart, Chad Ogle, Zahra Davoudi, Eric Jones, Debbie Trail, John Carter, Justine Mills, Kyle Georgius, Howard Stotler, Michelle Norris, Shannon Uzelac, Suzanne Borgel, Tiffanie Minor, Luke Stockwin, Michael Mullendore, Kevin Plater, Keegan Kalmbach, Jessica Steed, Matthew Murphy, Gareth Bliss, Carrie Bonomi, Kelly Dougherty, Marion Gibson, Kevin Cooper, Dianne Newton, Cindy R. Timme, Yvonne A. Evrard, Melinda G. Hollingshead, Nathan P. Coussens, Ralph E. Parchment, James H. Doroshow, Beverly A. Teicher. Combination therapies in matched 3D in vitro and in vivo preclinical models of rare and recalcitrant cancers from the National Cancer Institute’s Patient-Derived Models Repository. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5720.

Abstract 1054: RAS-pathway inhibitors (Sotorasib, MRTX-1257, TNO-155, BI-3406) in a Complex Spheroid Combination Screen with PDMR Cell Lines

The KRAS G12C selective inhibitors, sotorasib and MRTX-1257, as well as the SHP-2 inhibitor TNO-155 and the SOS-1 inhibitor were assayed alone and in combination with approved and investigational anticancer agents in complex spheroids including tumor cells, endothelial cells (HUVEC) and mesenchymal stem cells (MSCs). The cell lines were from the PDMR collection (https://pdmr.cancer.gov/models/database.htm). The Ras mutation status of each line was known and included KRAS G12C (5 lines), KRAS G12D (7 lines) and 8 lines which were RAS WT or harbored other RAS mutations. The high concentration range of each agent was near the clinical Cmax for the drug or was 10 μM and decreased in half-logs covering a 3-log range. The complex spheroids were established for 3 days before drug(s) were added. Seven days after drug exposure the experiment was terminated with CellTiter-Glo 3D. Cell viability was determined relative to a vehicle treated control and IC50 values were calculated from concentration response curves. The concentration response for sotorasib and MRTX-1257 (except for concentrations 3 μM or higher) inhibitors were shallow to flat. The 4 KRAS G12C mutant line were most sensitive to sotorasib and MRTX-1257 with the KRAS G12C mutant pancreatic cancer line being the next most sensitive. A similar pattern was observed with the SHP-2 inhibitor TNO-155; however, there was no selectivity for the KRAS G12C mutant lines in response to the SOS-1 inhibitor BI-3406. There was heterogeneity in the occurrence of additivity/synergy amongst the KRAS G12C mutant lines in the combination studies likely indicating that factors in addition to KRAS mutations influenced response. The most successful combination was TNO-155 plus ipatasertib which resulted in more than 1-log of cell kill in 9 of 20 lines including the 5 KRAS G12C mutant lines. Venetoclax in combination with the RAS pathway inhibitors was active in 4 of the 5 KRAS G12C lines as was the combination of sapanisertib and TNO-155. TNO-155 in combination with sotorasib, MRTX-1257 or BI-3406 was highly active in the LG0567-F671 NSCLC harboring KRAS G12C. The response of the RAS mutant lines to the combinations was compared with the response of RAS WT lines to the same combinations. Often at the higher concentrations of the drugs/investigational agents, lines without RAS mutations are responsive. Next steps include PDX studies with the same tumor models. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261200800001E.

Citation Format: Naoko Takebe, Thomas Dexheimer, Thomas Silvers, Rene Delosh, Julie Laudeman, Siddhartha Paul, Russell Reinhardt, Chad Ogle, Joel Morris, Nathan Coussens, James H. Doroshow, Beverly A. Teicher. RAS-pathway inhibitors (Sotorasib, MRTX-1257, TNO-155, BI-3406) in a Complex Spheroid Combination Screen with PDMR Cell Lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1054.

Abstract 1881: Drug combination screening of Ipatasertib and Abemaciclib with other targeted agents in complex multicellular tumor spheroids from the NCI-60 and the National Cancer Institute’s Patient-Derived Models Repository

Drug combinations are frequently used to improve clinical efficacy, to minimize toxicity, and to reduce the development of drug resistance. Here, we investigated the growth inhibitory activities of the pan-Akt inhibitor ipatasertib and the CDK4/6 inhibitor abemaciclib in combination with other targeted agents. Twelve well-characterized patient-derived cancer cell lines from the National Cancer Institute’s Patient-Derived Models Repository (https://pdmr.cancer.gov/models/database.htm) and seven established cell lines from the NCI-60 tumor cell line panel (https://dtp.cancer.gov/discovery_development/nci-60/cell_list.htm) were grown as multicellular 3D complex spheroids. The complex spheroids, a mixture of tumor cells (60%), endothelial cells (25%), and mesenchymal stem cells (15%), were grown for 3 days before drug(s) were added. All agents were tested both alone and in combinations at multiple concentrations up to their reported clinical Cmax value and cell viability was assayed using CellTiter-Glo 3D seven days after drug exposure. While abemaciclib had minimal activity as a single agent, ipatasertib was noticeably selective for tumor cells harboring activating PI3K/AKT/mTOR pathway variants. Dual inhibition of the PI3K/AKT/mTOR and RAS/MEK/ERK pathways was one of the most effective combinations. For example, the combination of ipatasertib with the MEK inhibitor selumetinib or the ERK inhibitor ravoxertinib resulted in additive and/or synergistic cytotoxicity in over half the complex spheroid models screened. The V600E variant-specific BRAF inhibitor vemurafenib and the KRAS G12C selective inhibitor sotorasib in combination with ipatasertib showed activity in the one BRAF V600E and two KRAS G12C variant containing complex spheroid models, respectively. Another effective ipatasertib combination was vertical inhibition of the PI3K/AKT/mTOR pathway with the mTORC1/2 kinase inhibitor sapanisertib, which demonstrated additive and/or synergistic responses across multiple complex spheroid models. For abemaciclib, the most successful combination was with the CDK2/7/9 inhibitor BMS-387032, which achieved greater than one log of cytotoxicity in the majority of the complex spheroid models. For the combination of abemaciclib and selumetinib, there was a high correlation between the responses of two patient-derived cell lines grown as complex spheroids and their corresponding patient-derived xenografts (PDX). Additional PDX studies are planned for promising drug combinations from this in vitro screen. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261201500003I.

Citation Format: Thomas Steven Dexheimer, Thomas Silvers, Rene Delosh, Julie Laudeman, Russell Reinhart, Chad Ogle, Siddhartha Paul, Nathan P. Coussens, Ralph E. Parchment, Joel Morris, John Wright, Naoko Takebe, Beverly A. Teicher, James H. Doroshow. Drug combination screening of Ipatasertib and Abemaciclib with other targeted agents in complex multicellular tumor spheroids from the NCI-60 and the National Cancer Institute’s Patient-Derived Models Repository [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1881.

Abstract P222: Combinations of receptor tyrosine kinase inhibitors targeting the tumor and stromal cells of complex spheroids from the National Cancer Institute’s Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov/)

Tumor stroma is critical in shaping the tumor microenvironment and promoting tumor growth and metastasis. Six stroma-targeted kinase inhibitors (cediranib, vandetanib, axitinib, pazopanib, cabozantinib, and lenvatinib) were tested both as single agents and in combination with five tumor cell-targeted kinase inhibitors (erlotinib, gefitinib, osimertinib, rociletinib, and erdafitinib)using a complex spheroid cell culture model. Complex spheroids, containing 60% tumor cells, 25% endothelial cells (HUVEC) and 15% mesenchymal stem cells (MSC), serve as a cell culture model of human solid tumors incorporating both malignant and stromal cells. Seventeen tumor cell lines were grown as complex spheroids, including varied sarcoma and non-small cell lung cancer types. Drug sensitivities of the HUVEC and MSC were also evaluated, both individually as monolayers and mixed as monolayers and spheroids. Overall, the HUVEC and MSC were more sensitive to the VEGFR inhibitors than to the EGFR inhibitors. Growth as complex spheroids reduced the sensitivity of HUVEC and MSC to several kinase inhibitors compared to each cell type alone or in mixed monolayer culture. A significant correlation was observed between the EGFR mRNA expression in patient-derived tumor lines and their sensitivity to the EGFR inhibitors. In combination regimens, Erlotinib was most effective when combined with the VEGFR inhibitors pazopanib, vandetanib and cediranib, which produced more than one log of cell killing at concentrations less than the clinical Cmax of each drug. Osimertinib and rociletinib, which irreversibly target EGFR variants, were more cytotoxic towards complex spheroids of NCI-H1975 NSCLC (EGFR L858R, T790M) than NCI-H522 NSCLC (EGFR wildtype). Combinations of the mutant-selective EGFR inhibitors with a VEGFR inhibitor (especially, vandetanib, lenvatinib or cediranib) increased the cytotoxicity in complex spheroids containing EGFR mutant and wildtype tumor lines. Highly effective combinations included erdafitinib with vandetanib and erlotinib with cediranib. The combination of cediranib and erlotinib was also evaluated in nine patient-derived xenograft (PDX) models and resulted in two partial responses in a penile squamous carcinoma and uterine sarcoma, while the remainder showed stable, slowed, or progressive disease. Using >1 log of cell kill at drug concentrations less than the mouse Cmax concentration for each drug as a predictor for in vivo responsiveness, the complex spheroid assay was 88% accurate in predicting response or progressive disease in the PDX models. This criteria for predicting in vivo activity from in vitro model results will be further explored. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261200800001E.

Citation Format: Thomas S. Dexheimer, Julie Laudeman, Thomas Silvers, Rene Delosh, Russell Reinhart, Chad Ogle, Eric Jones, Nathan P. Coussens, Beverly A. Teicher, Naoko Takebe, Alice Chen, James H. Doroshow. Combinations of receptor tyrosine kinase inhibitors targeting the tumor and stromal cells of complex spheroids from the National Cancer Institute’s Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov/) [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P222.

Abstract 2644: Comparison of PDMR cell line complex spheroid response and PDX response to trametinib

The NCI is engaged in developing a large resource of well-characterized patient-derived xenografts and corresponding cell lines and organoid cultures which are available to the global cancer research community (https://pdmr.cancer.gov/models/database.htm). The current study explored trametinib in PDMR models including cell lines and PDX tumors. Trametinib is a selective reversible allosteric inhibitor of MEK1 and MEK2 activity. The RAS-RAF-MEK-ERK pathway is important in cell proliferation and differentiation and is active in many cancers. Twenty-one PDMR lines were grown as complex spheroids, tumor cells mixed with HUVEC and MSC, to model human solid tumors. Complex spheroids were established for 3 days before drug was added. Seven days after drug addition the experiment was terminated with CellTiter-Glo 3D. Cell viability was determined relative to vehicle treated control and IC50 values calculated from concentration response data. Response to trametinib was assessed over a concentration range (0.0001 - 0.03 μM) achievable in patients. The clinical Cmax concentration for trametinib is 0.021 μM. 3 cell lines did not reach an IC50 at 0.02 μM. PDX studies were performed in 5 PDMR models. Three lines were derived from one pancreatic cancer patient: 521955-158-R2-J5 was from a liver metastasis; 521955-158-R6-J3 was from a myometrium metastasis; and 521955-158-R7-J2 was from a colon metastasis. The trametinib IC50 values for the 521955-158-R2, 521955-158-R7 and 128128-338-R lines ranged from 0.001 - 0.0015 μM. The 521955-158-R6 line was resistant with an IC50 of 0.03 μM. The 349418-098-R NSCLC line, which harbors a BRAF V600E mutation, was sensitive to trametinib with an IC50 value of 0.0002 μM. PDX studies had 8-15 mice in control groups and 6-15 mice in treated groups. The PDX models, 128128-338-R, 521955-158-R6, 521955-158-R7, 877537-175-T-J1 and 349418-098-R, responded rapidly to trametinib but had modest to moderate responses with all 5 tumors reaching maximal responses ranging between 25 and 50% of control tumor volume. The PDX tumors had a range of growth rates taking between 14 and 45 days to reach volumes of 150-200 mm3, to begin treatment. Trametinib was administered, in 10% DMSO/5% Cremophor orally once daily for 28 days. During the treatment period tumor quadrupling times were 128128-338-R, controls 21days and treated 36 days; 521955-158-R6, controls 15 days and treated 40 days; 521955-158-R7, controls 17 days and treated 35 days; 977537-175-T-J1, controls 6 days and treated 18 days and 349418-098-R, controls 19 days and treated 32 days. The differences in tumor response were not sufficient to find a correlation with spheroid response, although the 128128-338-R model which had the lowest IC50 value also had the greatest tumor response as determined by T/C volume ratio. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261200800001E.

Citation Format: Beverly A. Teicher, Nathan P. Coussens, Melinda Hollingshead, John Wright, Thomas Silvers, Rene Delosh, Julie Laudeman, Russell Reinhart, Chad Ogle, James Doroshow. Comparison of PDMR cell line complex spheroid response and PDX response to trametinib [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2644.

Exposure time versus cytotoxicity for anticancer agents

PURPOSE

Time is a critical factor in drug action. The duration of inhibition of the target or residence time of the drug molecule on the target often guides drug scheduling.

METHODS

The effects of time on the concentration-dependent cytotoxicity of approved and investigational agents [300 compounds] were examined in the NCI60 cell line panel in 2D at 2, 3, 7 and in 3D 11 days.

RESULTS

There was a moderate positive linear relationship between data from the 2-day NCI60 screen and the 3-, 7- and 11-day and a strong positive linear relationship between 3-, 7- and 11-day luminescence screen IC50s by Pearson correlation analysis. Cell growth inhibition by agents selective for a specific cell cycle phase plateaued when susceptible cells were growth inhibited or killed. As time increased the depth of cell growth inhibition increased without change in the IC50. DNA interactive agents had decreasing IC50s with increasing exposure time. Epigenetic agents required longer exposure times; several were only cytotoxic after 11 days' exposure. For HDAC inhibitors, time had little or no effect on concentration response. There were potency differences amongst the three BET bromodomain inhibitors tested, and an exposure duration effect. The PARP inhibitors, rucaparib, niraparib, and veliparib reached IC50s < 10 μM in some cell lines after 11 days.

CONCLUSIONS

The results suggest that variations in compound exposure time may reflect either mechanism of action or compound chemical half-life. The activity of slow-acting compounds may optimally be assessed in spheroid models that can be monitored over prolonged incubation times.

Small cell lung carcinoma cell line screen of etoposide/carboplatin plus a third agent

The SCLC combination screen examined a 9-point concentration response of 180 third agents, alone and in combination with etoposide/carboplatin. The predominant effect of adding a third agent to etoposide/carboplatin was additivity. Less than additive effects occurred frequently in SCLC lines sensitive to etoposide/carboplatin. In SCLC lines with little or no response to etoposide/carboplatin, greater than additive SCLC killing occurred over the entire spectrum of SCLC lines but never occurred in all SCLC lines. Exposing SCLC lines to tubulin-targeted agents (paclitaxel or vinorelbine) simultaneously with etoposide/carboplatin resulted primarily in less than additive cell killing. As single agents, nuclear kinase inhibitors including Aurora kinase inhibitors, Kinesin Spindle Protein/EG5 inhibitors, and Polo-like kinase-1 inhibitors were potent cytotoxic agents in SCLC lines; however, simultaneous exposure of the SCLC lines to these agents along with etoposide/carboplatin, generally, resulted in less than additive cell killing. Several classes of agents enhanced the cytotoxicity of etoposide/carboplatin toward the SCLC lines. Exposure of the SCLC lines to the MDM2 inhibitor JNJ-27291199 produced enhanced killing in 80% of the SCLC lines. Chk-1 inhibitors such as rabusertib increased the cytotoxicity of etoposide/carboplatin to the SCLC lines in an additive to greater than additive manner. The combination of GSK-3β inhibitor LY-2090314 with etoposide/carboplatin increased killing in approximately 40% of the SCLC lines. Exposure to the BET bromodomain inhibitor MK-8628 increased the SCLC cell killing by etoposide/carboplatin in 20-25% of the SCLC lines. Only 10-15% of the SCLC lines had an increased response to etoposide/carboplatin when simultaneously exposed to the PARP inhibitor talazoparib.

Abstract 4831: Small cell lung carcinoma (SCLC) cell line screen of standard of care (etoposide/carboplatin) plus a third agent

The standard-of-care for limited stage and extensive stage SCLC has remained etoposide and a platinum complex for more than 30 years because 60-80% of patients respond; however, SCLC inevitably recurs. Recurrent SCLC has proven to be resistant to many therapeutics administered as second- or third-line treatments; therefore, combining therapies in the first instance may be a critically useful strategy. A high throughput screen was performed where 62 SCLC lines were exposed to etoposide (0.3uM)/carboplatin (3.7 uM) (E/C) with or without simultaneous exposure to a third agent (n = 220). Viability of the cells was measured using CellTiter-Glo after 96 hr exposure to 9 concentrations of each individual compound or combination with E/C. The test concentrations encompassed the clinical Cmax for each third agent, and the concentrations of E/C selected for the screen were systematically determined to produce SCLC kill that would allow observation of additivity/synergy upon addition of a third agent. IC50s were determined from the concentration response data and showed that the predominant effect of adding a third agent to E/C was additive. Less than additive effects occurred more frequently in SCLC lines that were sensitive to etoposide/carboplatin. Antagonism with E/C occurred in combination with taxanes and tubulin fragmenters such as vinorelbine. Effective single agents such as the nuclear kinase inhibitors (aurora kinase inhibitors, KSP/EG5 inhibitors and polo-like kinase inhibitors) were antagonistic in combination with E/C but were effective single agents. Greater than additive SCLC killing occurred with E/C in combination with several classes of agents. The combination of the Chk1 inhibitor rabusertib with E/C resulted in an IC50 that was &gt;1 log lower than that of rabusertib alone in several SCLC lines. The GSK-3β inhibitor LY-2090314 produced greater than additive SCLC killing in combination with E/C. LY-2090314 had little effect on the SCLC lines alone but the simultaneous combination with E/C resulted in multi-log killing in selected SCLC lines. The BET bromodomain inhibitor MK-8628 was highly effective when combined with E/C as was the PARP1 inhibitor talazoparib in a small subset of the SCLC lines. While many agents have been tested in combination with E/C in SCLC and failed to improve patients’ survival, the findings of this study identified third agents that may represent new leads for the treatment of this recalcitrant disease. Distinct patterns of response in select subsets of the 62 SCLC lines tested may allow identification of biomarkers predictive of the responders to certain 3-drug regimens. This project has been funded in whole or in part with federal funds from the National Cancer Institute, NIH, under contract no. HHSN261200800001E.

Note: This abstract was not presented at the meeting.

Citation Format: Beverly A. Teicher, Michael Selby, Thomas Silvers, Julie Laudeman, Russell Reinhart, Rene Delosh, Chad Ogle, Ralph Parchment, Julia Krushkal, Dmitriy Sonkin, Joel Morris, Mark Kunkel, David Evans. Small cell lung carcinoma (SCLC) cell line screen of standard of care (etoposide/carboplatin) plus a third agent [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4831. doi:10.1158/1538-7445.AM2017-4831

Abstract 348: Comparison of the response of the NCI60 NSCLC panel with the response of patient-derived NSCLC lines to approved and investigational agents

An 800 compound screen with the NCI60 cell lines and 5 patient-derived NSCLC lines (PD NSCLC), was conducted at 9 concentrations and included the FDA approved oncology agents and an investigational agents library. The screen was conducted using 384-well monolayer cultures, an exposure time of 72 hrs and compound concentrations from 1 nM to 10 uM. CellTiter-Glo was used to measure viability as an endpoint. The NCI60 NSCLC panel consists of 9 cell lines: A549, EKVX, HOP-62, HOP-92, NCI-H226, NCI-H23, NCI-H322M, NCI-H460 and NCI-H522. The response of these lines was compared with the response of 5 PD NSCLC lines and 60 SCLC lines. While both sets of NSCLC lines had similar responses to the majority of compounds, there were some marked differences. Differences in response of the NCI60 NSCLC lines and the PD NSCLC lines were notable upon exposure to tubulin fragmenters, KSP/EG5 inhibitors, GAR transformylase inhibitors, Polo-like kinase-1 inhibitors (PLK1), MEK inhibitors, and IAP inhibitors. The NCI60 NSCLC lines were more sensitive to the tubulin fragmenters than were the PD NSCLC and the SCLC lines. Verubulin had a mean GI50 in NCI60 NSCLC of 0.0037 uM and 0.0042 uM in SCLC versus 0.047uM in the PD NSCLC lines. The NCI60 NSCLC lines were more sensitive to the KSP inhibitor, ARRY-520 (mean GI50 0.0049 uM) than the SCLC lines (0.028 uM) and the PD NSCLC lines (0.26 uM). The NCI60 NSCLC lines (mean GI50 0.019 uM) and the SCLC lines (mean GI50 0.04 uM) were more sensitive to PLK1 inhibitors such as BI-2536 than the PD NSCLC lines (0.13 uM). However, the NCI60 NSCLC lines (mean GI50 0.8 uM) and the SCLC lines (mean GI50 0.134 uM) were less sensitive than the PD NSCLC lines (mean GI50 0.025uM) to GAR transformylase inhibitors such as pelitrexol. The NCI60 NSCLC lines (mean GI50 6.3 uM) and SCLC lines (mean GI50 10 uM) were also less responsive to IAP inhibitors, than were PD NSCLC lines (mean GI50 1.6 uM). A heterogeneous response to the MEK inhibitors such as cobimetinib (GDC-0973) was observed with the SCLC lines (mean GI50 8.9 uM) versus 1.15 uM in the NCI60 NSCLC lines and 0.56 uM in the PD NSCLC lines. PD NSCLC lines exhibit some interesting differences in response from established lung cancer lines upon in vitro exposure to anticancer agents and thus add to our knowledge and understanding of NSCLC and help inform discovery efforts and/or clinical development of therapeutics in this disease. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261200800001E.

Citation Format: Beverly A. Teicher, David Evans, Thomas Silvers, Michael Selby, Rene Delosh, Julie Laudeman, Chad Ogle, Russell Reinhart, Joel Morris, Gurmeet Kaur, James Doroshow. Comparison of the response of the NCI60 NSCLC panel with the response of patient-derived NSCLC lines to approved and investigational agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 348. doi:10.1158/1538-7445.AM2017-348

3D Models of the NCI60 Cell Lines for Screening Oncology Compounds

The NCI60 cell line panel screen includes 60 human tumor cell lines derived from nine tumor types that has been used over the past 20+ years to screen small molecules, biologics, and natural products for activity. Cells in monolayer culture in 96-well plates are exposed to compounds for 48 h, and Sulforhodamine B is used to determine cell viability. Data analysis tools such as COMPARE allow classification of compounds based on the pattern of cell line response. However, many compounds highly active in monolayer cell culture fail to show efficacy in vivo. Therefore, we explored 3D culture of the NCI60 panel as a strategy to improve the predictive accuracy of the screen. 3D cultures more closely resemble tumors than monolayer cultures with tighter cell-cell contact and nutrient and oxygen gradients between the periphery and the center. We optimized the NCI60 cell line panel for generating 3D spheroids of a prespecified diameter (300-500 µm) in ultra-low attachment (ULA) plates. Spheroids were classified into four categories based on imaging, and concentration response of select agents in 2D and 3D models is presented.

Small Cell Lung Cancer Screen of Oncology Drugs, Investigational Agents, and Gene and microRNA Expression

BACKGROUND

Small cell lung carcinoma (SCLC) is an aggressive, recalcitrant cancer, often metastatic at diagnosis and unresponsive to chemotherapy upon recurrence, thus it is challenging to treat.

METHODS

Sixty-three human SCLC lines and three NSCLC lines were screened for response to 103 US Food and Drug Administration-approved oncology agents and 423 investigational agents. The investigational agents library was a diverse set of small molecules that included multiple compounds targeting the same molecular entity. The compounds were screened in triplicate at nine concentrations with a 96-hour exposure time using an ATP Lite endpoint. Gene expression was assessed by exon array, and microRNA expression was derived by direct digital detection. Activity across the SCLC lines was associated with molecular characteristics using pair-wise Pearson correlations.

RESULTS

Results are presented for inhibitors of targets: BCL2, PARP1, mTOR, IGF1R, KSP/Eg5, PLK-1, AURK, and FGFR1. A relational map identified compounds with similar patterns of response. Unsupervised microRNA clustering resulted in three distinct SCLC subgroups. Associating drug response with micro-RNA expression indicated that lines most sensitive to etoposide and topotecan expressed high miR-200c-3p and low miR-140-5p and miR-9-5p. The BCL-2/BCL-XL inhibitors produced similar response patterns. Sensitivity to ABT-737 correlated with higher ASCL1 and BCL2. Several classes of compounds targeting nuclear proteins regulating mitosis produced a response pattern distinct from the etoposide response pattern.

CONCLUSIONS

Agents targeting nuclear kinases appear to be effective in SCLC lines. Confirmation of SCLC line findings in xenografts is needed. The drug and compound response, gene expression, and microRNA expression data are publicly available at http://sclccelllines.cancer.gov.

Abstract 605: Building better cell models for screening oncology compounds

The NCI60 screen is a valuable compound screening service offered to researchers for 20+ years. The screen allows the submission of small molecules, biologics and natural products for testing in the NCI60 cell line panel (60 cell lines covering 9 major tumor types). Sophisticated tools such as COMPARE allow stratification of compounds based on pattern of cell line response and these tools elucidated several compounds with differential specificity for a disease type (e.g. breast cancer over melanoma).

Since inception the NCI60 screen has been performed in 96-well plates on monolayer cultures of cells. SulfoRhodamine B was used to measure cell viability after a 48h exposure to the compounds at either a single concentration or 5 point concentration response assay. However, recent work has suggested that cells in 3D culture may respond differently to compounds than in 2D. 3D culture systems produce tumor cell spheroids that exhibit features seen in vivo including greater cell-cell contact, and gradients of nutrients and oxygen between the periphery and the center of the spheroid. We sought to optimize the NCI60 cells for use in a 3D spheroid model that would be suitable for screening compounds. By varying NCI60 cell plating density and incubation times, we optimized the formation of spheroids of a given diameter (500um) in Ultra Low Attachment (ULA) plates. Spheroids were imaged using a high content imaging plate reader and classified into 4 categories based on their apparent morphologies. Comparisons were made in drug sensitivity between 2D and 3D model systems using the NCI60 and cells derived from PDX samples. Data on the optimal cell densities of the NCI60 lines used for spheroid formation as well as concentration response effects of select agents compared in 2D and 3D models are presented. These data will allow others to rapidly utilize these 3D models to determine the differential drug sensitivity of select cell types. Funded by NCI Contract No. HHSN261200800001E.

Citation Format: David M. Evans, Michael Selby, Rene Delosh, Julie Laudeman, Chad Ogle, Russell Reinhart, Thomas Silvers, Ralph E. Parchment, Beverly Teicher. Building better cell models for screening oncology compounds. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 605.

Abstract B67: Sarcoma cell line screen of oncology drugs and investigational agents identifies patterns associated with gene and microRNA expression

The diversity in sarcoma phenotype and genotype make treatment of this family of diseases exceptionally challenging. Sixty-three human adult and pediatric sarcoma lines were screened with 100 FDA approved oncology agents and 345 investigational agents. The investigational agents library enabled comparison of several compounds targeting the same molecular entity allowing comparison of target specificity and heterogeneity of cell line response. Gene expression was derived from exon array data and microRNA expression was derived from direct digital detection assays. The compounds were screened against each cell line at 9 concentrations in triplicate with an exposure time of 96 hrs using Alamar blue as the endpoint. Results are presented for inhibitors of the following targets: aurora kinase, IGF-1R, MEK, BET bromodomain, and PARP1. Chemical structures, IC50 heat maps, concentration response curves, gene expression and miR expression heat maps are presented for selected examples. In addition, two cases of exceptional responders are presented. The drug and compound response, gene expression and microRNA expression data are publicly available at http://sarcoma.cancer.gov. These data provide a unique resource to the cancer research community.

Citation Format: Beverly A. Teicher, Eric Polley, Mark Kunkel, David Evans, Thomas Silvers, Rene Delosh, Julie Laudeman, Chad Ogle, Russell Reinhart, Michael Selby, John Connelly, Erik Harris, Anne Monks, Joel Morris. Sarcoma cell line screen of oncology drugs and investigational agents identifies patterns associated with gene and microRNA expression. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B67.

Sarcoma Cell Line Screen of Oncology Drugs and Investigational Agents Identifies Patterns Associated with Gene and microRNA Expression

The diversity in sarcoma phenotype and genotype make treatment of this family of diseases exceptionally challenging. Sixty-three human adult and pediatric sarcoma lines were screened with 100 FDA-approved oncology agents and 345 investigational agents. The investigational agents' library enabled comparison of several compounds targeting the same molecular entity allowing comparison of target specificity and heterogeneity of cell line response. Gene expression was derived from exon array data and microRNA expression was derived from direct digital detection assays. The compounds were screened against each cell line at nine concentrations in triplicate with an exposure time of 96 hours using Alamar blue as the endpoint. Results are presented for inhibitors of the following targets: aurora kinase, IGF-1R, MEK, BET bromodomain, and PARP1. Chemical structures, IC50 heat maps, concentration response curves, gene expression, and miR expression heat maps are presented for selected examples. In addition, two cases of exceptional responders are presented. The drug and compound response, gene expression, and microRNA expression data are publicly available at http://sarcoma.cancer.gov. These data provide a unique resource to the cancer research community.

Abstract 5450: Screening more than 60 human SCLC lines with approved and investigational agents indicates complex patterns of response: Identification of HSP90 and HDACs as potential targets

Small cell lung cancer (SCLC) is an aggressive cancer with a 5-year survival rate of &lt;5%. While initially responsive to treatments with platinum agents, topoisomerase inhibitors or methotrexate, the tumors frequently recur after chemotherapy. To identify whether approved small molecule drugs or investigational agents may have unexpected effects in SCLC lines, we undertook a systematic large-scale screen with &gt;500 compounds against &gt; 60 well characterized SCLC cell lines in culture. Cells were exposed to 101 Approved Oncology Drugs (AOD) and 433 Investigational Agents. By evaluating compounds at 9 concentrations (10uM to 1.5nM), using cell viability 96h post drug exposure as the endpoint (Cell Titer Glo), we were able to obtain concentration response curves and IC50 values for the compounds and rank activity of these agents. In parallel studies, using Affymetrix exon ST1 arrays and miRNA profiling, we examined these same cell lines for differences in gene expression patterns that may correlate with sensitivity or resistance to select agents in the screen. The Myc oncogene (cMyc, LMyc, or nMyc) is over-expressed in about 40% of SCLC lines. Surprisingly, early analyses of the SCLC screen data have been unable to correlate high Myc expression with response to drugs or investigational agents (there is a trend with bromodomain inhibitors). The large majority of SCLC lines were sensitive to compounds against select target classes (e.g. HSP90 inhibitors and HDAC inhibitors). Examining HSP70 and HSP90 levels by Western blot suggested a slight reduction in HSP90 levels in cells resistant to the HSP90 inhibitor Ganetespib with no change in HSP70 levels. Some inhibitors against these targets showed broader cell activity than others. We are currently determining whether such differential drug sensitivity is correlated with specific changes in gene expression patterns in these cells. Further data analyses from the screen combined with genomic profiling of the cells will be presented.

Funded by NCI Contract No. HHSN261200800001E.

Citation Format: David M. Evans, Rene Delosh, Julie Laudeman, Chad Ogle, Russell Reinhart, Michael Selby, Thomas Silvers, John Connelly, Anne Monks, Eric Polley, Gurmeet Kaur, Joel Morris, Beverly Teicher. Screening more than 60 human SCLC lines with approved and investigational agents indicates complex patterns of response: Identification of HSP90 and HDACs as potential targets. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5450. doi:10.1158/1538-7445.AM2014-5450

Abstract C106: Screening small cell lung cancer lines against approved oncology drugs and investigational agents elucidates patterns of sensitivity

Small cell lung cancer (SCLC) is an aggressive cancer with a 5-year survival rate of &lt;5% that frequently recurs after conventional cytotoxic chemotherapy. We have undertaken a systematic large-scale screening of approved oncology drugs and investigational agents for activity against SCLC in an effort to provide new leads to effective treatment of this disease. Our laboratory compiled a panel of &gt;75 human SCLC lines and is screening approximately 60 (well characterized) lines against 103 agents from the Approved Oncology Drugs (AOD) library) and 420 agents from the Investigational Agents library. Compounds are evaluated at 9 concentrations (10uM to 1.5nM) in comparison with vehicle controls using cell viability 96h post drug exposure as the endpoint - allowing a direct comparison between the IC50, anticipated compound molecular target and the breadth of activity across the cell lines. These cells represent a broad coverage of those available as representatives of SCLC with an array of growth behaviors. Cell lines grow as adherent cultures, in single cell suspension, in suspension as spheres and /or clumps, or mixed cultures. Despite these varied phenotypes, the screen was robust (Z’ score &gt; 0.5) in all of the lines studied to date. Interestingly, SHP77 (an unusual undifferentiated large cell morphological variant with biochemical properties of SCLC) consistently showed lower sensitivity to the drugs than other cell lines tested. Trends emerging from the early data indicate that: 1) Comparing compound activity (IC50 value) by cell line and clustering the compounds based on their reported targets, we could readily observe the target classes that produced the greatest cell growth inhibition across the widest set of the SCLC cell lines; and 2) from these data it appears that discrete HDAC inhibitors and HSP90 inhibitors produce potent growth inhibition across a wide array of SCLC lines (including SHP77). We are expanding the number of SCLC lines under study. Each cell line will be examined for gene expression patterns, miRNA expression patterns and sensitivity to the approved and investigational agents (IC50). These data will allow correlations to be made regarding sensitivity of the cells to agents with discrete cellular targets versus the genomic background in these cells. Data from the drug screens combined with genomic profiling of the cells may allow clinical trials to select therapeutic agents to maximize benefit in patients presenting with SCLC. Further analyses and findings from the data will be presented.

Funded by NCI Contract No. HHSN261200800001E.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C106.

Citation Format: David M. Evans, Rene Delosh, Julie Laudeman, Chad Ogle, Russell Reinhart, Michael Selby, Thomas Silvers, Anne Monks, Gurmeet Kaur, Joel Morris, Beverly A. Teicher. Screening small cell lung cancer lines against approved oncology drugs and investigational agents elucidates patterns of sensitivity. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C106.

Abstract C103: Sarcoma cell line sensitivity towards approved oncology drugs and investigational agents identifies distinct patterns of response which can be interrogated with associated gene expression

Sarcomas represent a heterogeneous group of cancers with significant unmet medical needs. We have examined the response of 64 sarcoma cell lines to treatment with 103 approved oncology drugs (available from The NCI/DTP Open Chemical Repository) and 420 agents in the investigational agents library, using inhibition of proliferation as an endpoint. Cells were exposed to compounds at varying concentrations (10μM to 1.5nM) for 96 h and the effect of compound on cell viability was monitored using Alamar Blue. From curve fitting algorithms we determined the IC50 values of each agent on the cell lines. Adult sarcomas comprise 23% of this sarcoma panel and have a different spectrum of sensitivities to selected agents. They were generally more chemoresistant than the pediatric lines, although they are marginally more sensitive to MEK inhibitors. Synovial tumor cell lines were an exception, being sensitive to several classes including dasatinib and Bcr-abl inhibitors. Ewings tumors tend to be the most sensitive pediatric group responding to Parp-1 and IGF-1R inhibitors. Overall, gene, and to a lesser extent, miRNA profiles from the adult sarcoma's were more similar to the profiles of normal, non-tumor cells, than the pediatric tumors, and this lack of genotypic divergence may underlie the insensitive phenotype observed in the sarcoma panel. From an analysis of sensitivity clustering, IGF-1R inhibitors (8), cluster with some of the AKT (8) and ALK (8) inhibitors. None of the cell lines have the EM4L-ALK translocation, thus we investigated the genes associated with sensitivity to these three mechanisms. Dendrograms identified a close relationship between the IGF-1R and AKT inhibitors, based on the gene expression patterns, while the ALK inhibitors were quite distinct, substantiating known pathways of IGFR-1R signaling through AKT, but unrelated to ALK. Genes associated with ALK sensitivity included several from gluconeogenesis, and potential activation of the MYC response. In contrast, genes associated with AKT and IGF1R sensitivity are focused around FOXO1 transcription factor. Interestingly, the PAX-FOXO1 gene fusion is a hallmark of the aggressive alveolar rhabdomyosarcoma which are more sensitive to these agents than embryonal rhabdomyosarcoma. Thus the combination of drug sensitivity data, together with the gene and miRNA profiles may allow correlations in treatment efficacy that may point to new avenues for clinical development in sarcoma. Funded by NCI Contract No. HHSN261200800001E.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C103.

Citation Format: Anne Monks, David Evans, Thomas Silvers, Rene Delosh, Julie Laudeman, Chad Ogle, Russell Reinhart, Michael Selby, John Connelly, Annamaria Rapisarda, Mark Kunkel, Joel Morris, Kazimierz Wrzeszczynski, Eric Polley, Beverley Teicher. Sarcoma cell line sensitivity towards approved oncology drugs and investigational agents identifies distinct patterns of response which can be interrogated with associated gene expression. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C103.

Abstract 5590: Screening of pediatric and adult sarcoma cell lines reveals novel patterns of sensitivity toward approved oncology drugs and investigational agents

Sarcomas represent a heterogeneous group of neglected cancers with significant unmet medical need. To date, large-scale screening of compounds for activity against sarcomas has not been carried out in any systematic fashion to enable drug discovery. Our laboratory has compiled a panel of &gt; 85 human pediatric and adult sarcoma cell lines, a tumor type not represented in the NCI60, and has carried out a high throughput screen of approximately 60 of these lines against the Approved Oncology Drugs (AOD) and Investigational Agents libraries, using inhibition of proliferation as an endpoint. The AOD library is comprised of 93 FDA-approved anticancer agents, and is available from The NCI/DTP Open Chemical Repository. The Investigational Agents library includes about 350 small molecules of interest. The compounds were screened for inhibition of cell proliferation in 9-point concentration response, starting at 10 uM and diluting by half-logs. The cells were cultured in 384-well plates for 24 hrs, at which time compounds were added with a final DMSO concentration of 0.25%. Viability was determined after 96 hrs of exposure using Alamar Blue. The % viability was determined relative to a vehicle-treated control, and this value was plotted relative to compound concentration to determine the EC50. The Ewing sarcoma lines (19) were unexpectedly more sensitive to pemetrexed, cabazitaxel, and floxuridine, and were, as expected, sensitive to topoisomerase 1 inhibitors relative to other sarcomas and to historical NCI60 data. Synovial sarcoma lines were sensitive to vinorelbine, vandetinib, and gemcitabine relative to other sarcomas. Further analyses and findings from the data will be presented. Funded by NCI Contract no. HHSN261200800001E.

Citation Format: E. Michael August, Rene Delosh, Julie Laudeman, Chad Ogle, Russell Reinhart, Michael Selby, Thomas Silvers, Joel Morris, Beverly A. Teicher. Screening of pediatric and adult sarcoma cell lines reveals novel patterns of sensitivity toward approved oncology drugs and investigational agents. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5590. doi:10.1158/1538-7445.AM2013-5590