High-Throughput Functional Drug Screening and Genomic Analysis to Guide Individualized Therapy for Relapsed/Refractory Multiple Myeloma

Abstract

Background: The response to treatment for patients with relapsed/refractory multiple myeloma (MM) is highly variable. This may in part be related to the broad genomic heterogeneity that has been reported across individual patients. We hypothesize that in vitro functional drug screening and correlated genomic analyses of patient tumor cells is feasible and may improve clinical treatment response. To address this, we developed a custom high-throughput drug sensitivity (HTS) assay enabling simultaneous testing of 170 chemotherapy drugs and targeted inhibitors, as well as correlative gene expression and mutational analysis by next-generation sequencing. We report on the feasibility of this approach in a clinical trial enrolling patients with relapsed/refractory MM (NCT03389347). Patients and Methods: Twenty patients with relapsed/refractory MM or secondary plasma cell leukemia were enrolled in the study and 15 (9 female, 6 male) had a sufficient number of plasma cells for HTS. The average number of prior treatment regimens among the tested patients was 5.8 (range 3-11) and all had previously received a proteasome inhibitor and immunomodulatory drug and 8 had prior autologous stem cell transplants. Nine patients had stage III disease by the Revised International Staging System (R-ISS) and 4 had stage II disease. Eight patients exhibited high-risk cytogenetics, including 4 patients with del(17p), 5 patients with t(4;14), and 2 patients with t(14;16). The sources of plasma cells utilized for the HTS assay included bone marrow aspirate or core biopsies, soft tissue biopsies of plasmacytomas, and blood samples from patients with circulating plasma cells. Additional blood and bone marrow samples were obtained for RNA sequencing, whole-exome sequencing, and targeted sequencing of circulating tumor DNA. The CLIA approved HTS assay was performed at the Quellos HTS Core at the University of Washington using CD138+plasma cells isolated by magnetic bead separation. Tumor cells were tested against a panel of 170 drugs that includes conventional agents and targeted inhibitors, some FDA approved and others investigational. Cell viability was assessed at 72 hours by a luminescent cell viability assay (Cell Titer Glo, Promega) and drug response was determined using the concentration of experimental compound required to achieve 50% in vitro response inhibition (IC50) and area under the dose-response curve (AUC). Results: We report that the HTS assay can be completed in a median of 5 days from sampling (range 4-6 days), establishing feasibility. The mean percentage of bone marrow plasma cells among patients who could be tested was 56% compared to 5% for patients who had insufficient cells. We observed heterogeneity in patient genomic profiles and in vitro drug responses. The drugs with the highest in vitro response include those commonly used in MM such as bortezomib, ixazomib, carfilzomib, and panobinostat, as well as those under investigation including venetoclax and selinexor. Sensitivity was observed for drugs that have not been investigated for the treatment of MM including alvocidib and omacetaxine. Progression on prior therapy was not consistently predictive of in vitro drug responses and could be a consequence of some myeloma cells retaining sensitivity. Correlative genomic analyses were associated with in vitro drug responses for a subset of compounds. Among the 8 patients who received individualized therapy guided by the assay, 6 had an evaluable response and 5 (83%) achieved effective disease control (stable disease or better). Updated clinical treatment outcomes will be reported at the ASH conference. Conclusions: In this study, we successfully demonstrate the feasibility of a CLIA approved HTS assay capable of delivering actionable results in time to inform individualized treatment decisions for patients with MM. Correlative gene expression and mutational analysis are associated with in vitro drug response. Finally, we demonstrate that some of the patients who received treatment guided by the results of the HTS assay achieved a clinical response. These data suggest that using functional drug screening to predict sensitivity or resistance to both approved and experimental agents warrants further testing. Validation of the HTS assay in a larger population of MM patients holds the potential to improve treatment outcomes. Disclosures Cowan: Cellectar: Consultancy; Janssen: Consultancy, Research Funding; Abbvie: Research Funding; Celgene: Consultancy, Research Funding; Juno: Research Funding; Sanofi: Consultancy. Green:Celgene: Consultancy; Cellectar Biosciences: Research Funding; GSK: Consultancy; Juno Therapeutics: Consultancy, Patents & Royalties, Research Funding; Seattle Genetics: Research Funding. Libby:Alnylam: Consultancy; Abbvie: Consultancy; Pharmacyclics and Janssen: Consultancy; Akcea: Consultancy. Silbermann:Janssen, Sanofi: Other: Consultant/Advisor. Becker:The France Foundation: Honoraria; Accordant Health Services/Caremark: Consultancy; AbbVie, Amgen, Bristol-Myers Squibb, Glycomimetics, Invivoscribe, JW Pharmaceuticals, Novartis, Trovagene: Research Funding. OffLabel Disclosure: We will discuss in-vitro sensitivity testing of drugs that have not been approved for the treatment of multiple myeloma.

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“…A fourth dataset obtained through the Seattle Cancer Care Institute (SCCA) consisted of RNASeq, cytogenetics and clinical outcome data for 23 patients at varied disease stages. (31) The RNASeq data for the SCCA cohort was normalized similarly to the IA12 data set. Age and gender distributions for all data sets are shown in Table 1.…”

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“…A tentative approach to link high-throughput drug screening with gene expression profiling and mutational analysis, has been presented at the 2019 ASH meeting. Coffey et al (56) tested simultaneously 170 compounds and their target inhibitors along with NGS profiling to predict sensitivity to drugs. The registered clinical trial NCT03389347 (https://clinicaltrials.gov/ ct2/show/NCT03389347) will analyze the feasibility of using high-throughput drug sensitivity and genomics data to evolve personalized treatments.…”