Measure 170 times, cut once: high-throughput drug screening for multiple myeloma

From Dr. Pamela Becker and Dr. David Coffey, Clinical Research Division

Multiple myeloma (MM) is a highly heterogenous disease, with 63 known recurrent driving mutations. Despite the availability of numerous approved drugs for this malignancy, this cancer exhibits variable drug responses, and the disease remains incurable. In the absence of predictive biomarkers for therapeutic outcomes in MM, personalized treatment decisions are difficult. Led by member of the Fred Hutch Clinical Research Division Dr. David Coffey, Seattle Cancer Care Alliance clinical oncologist Dr. Andrew Cowan, and Cancer Consortium member Dr. Pamela Becker, the investigators developed a high-throughput system for screening MM patient-derived samples against a drug library to predict responses to therapy. Their work, recently published in JCO Precision Oncology, reveals that ex vivo drug testing is a feasible strategy for informing real time therapeutic decisions for MM patients.

The trial recruited MM patients with relapsed or refractory disease, who had each received at least three prior therapies. Fresh plasma cells were collected from biopsies of bone barrow or extramedullary plasmacytomas (localized tumor growths). 16 of the 25 patients who were screened had sufficient plasma cells (at least 600,000) for the high-throughput screen (HTS) assay. The cells were divided amongst the wells of 384-well culture plates and tested against a library of 170 drugs (consisting of both FDA-approved and experimental drugs) at 8 different concentrations. After 3 days’ incubation, the samples were subjected to a cell viability assay, and the median inhibition concentration (IC50; a measure of drug potency) was calculated. IC50s equal to or below 0.2uM, and below the safe and effective dose reported in previous human clinical trials, were recommended for treatment. Actionable results were obtained in less than a week from the time of sample collection for all patients for whom HTS was performed. 

Real time high-throughput drug screening as a precision medicine tool for guiding treatment decisions in multiple myeloma.
Real time high-throughput drug screening as a precision medicine tool for guiding treatment decisions in multiple myeloma. Image provided by Dr. Coffey.

A list of recommended drugs was provided to the patients’ oncologists and treatment choice was left to their discretion. FDA approval status, insurance coverage, prior treatment history, known side effect profiles, and patient preference were all factors considered in decision making. Combination therapies with drugs not included in the screening panel were allowed, and FDA approved drug doses were used regardless of HTS outcomes. Two of the five drugs with the highest cytotoxic responses, panobinostat and bortezomib, were already FDA approved for treatment of MM.13 of the 16 HTS patients received treatments that were recommended by HTS. 92% of those patients achieved at least stable disease, with 31% partial responses and 15% very good partial responses. No complete responses were observed in this heavily pretreated group of patients.

In addition to cells needed for HTS, sufficient samples were gathered for genomic testing, including whole exome sequencing and transcriptional profiling, for a portion of the patients. To find relationships between drug sensitivities and genetic lesions in the cancers, the researchers looked for correlations between recurrent mutations (found in at least two of the patients’ cancers) and HTS results. They found correlations between several genes and drug sensitivity/resistance, but none held statistical significance in such a small cohort. Transcription analysis yielded statistically significant relationships between gene expression and drug toxicity for 79 genes with increased expression and 37 genes with decreased expression.

Importantly, this study identified agents warranting further investigation due to robust efficacy against malignant cells from many patients. The results confirmed cytotoxicity of drugs approved by the FDA for the treatment of relapsed or refractory MM. Further, this work uncovered novel associations between genomic profiling data and drug sensitivity. “This is the first clinical trial to use high-throughput drug sensitivity testing to inform the next line of therapy for patients with relapsed or refractory multiple myeloma,” said Dr. Coffey. He gave a nod to the role of Fred Hutch/UW Cancer Consortium members in this work; “This research could not have been possible without a joint collaboration between investigators at the Fred Hutch, Seattle Cancer Care Alliance, and the University of Washington Quellos High-Throughput Core Facility.”

Moving forward, the group plans to curate a smaller library of drugs for HTS, reducing the total number of cells required for the assay, so that more patients will become eligible for screening. “Having demonstrated the feasibility of ex vivo drug sensitivity testing on isolated plasma cells from patient bone marrow biopsies or extramedullary plasmacytomas, our next step is to evaluate the technology in a larger population of patients with multiple myeloma to validate the assay’s ability to predict clinical response,” said Dr. Coffey. Ongoing studies will also test therapeutic combinations, to reduce the opportunity for acquired drug resistance.

This work was funded by private donations from Ann and Kevin Harrang, the Brotman Baty Institute, the National Cancer Institute, and the Cancer Therapeutics Endowment.

UW/Fred Hutch Cancer Consortium members Andrew Cowan, Damian Green, Edward Libby, Ted Gooley, E Houston Warren, and Pamela Becker contributed to this work.

Coffey DG, Cowan AJ, DeGraaff B, Martins TJ, Curley N, Green DJ, Libby EN, Silbermann R, Chien S, Dai J, Morales A, Gooley TA, Warren EH, Becker PS. High-Throughput Drug Screening and Multi-Omic Analysis to Guide Individualized Treatment for Multiple Myeloma. JCO Precis Oncol. 2021 Apr 6;5:PO.20.00442. doi: 10.1200/PO.20.00442. PMID: 34250400; PMCID: PMC8232547.