Quellos High-Throughput Screening Core

Launched with a charitable gift from the Quellos Group, the Quellos High-Throughput Screening (HTS) Core is the newest ISCRM facility. The brainchild of Dr. Randall Moon, the HTS core was created to serve clients from both the academic and commercial worlds utilizing laboratory automation and robotics. These new tools enable scientists to study complex biological systems and identify potential therapeutic drug candidates in timeframes that were previously improbable. With the capability to perform both functional genomic and chemical screens, the Core’s mission is to provide investigators with laboratory automation, enabling high-throughput approaches for functional genomics and chemical biology studies. The Core’s staff works to bring the power of state of the art high-throughput methodology, as employed by large pharmaceutical corporations, to the innovative projects of our research-oriented clientele. The Quellos HTS Core also offers CLIA-certified “Cancer Drug Sensitivity Test,” an efficient way to rank and compare an individual cancer’s sensitivity to drugs, and guide physicians in rational therapy choices.

Equipment

Besides a typical collection of generalized laboratory equipment (e.g., freezers, refrigerators, CO₂ incubators, etc.), the Quellos HTS Core contains essential instrumentation and equipment that makes high-throughput screening possible:

Liquid Handlers:

Analytik Jena CyBio CyBi-Well Vario Liquid Handler
Analytik Jena CyBio FeliX Liquid Handler
BioTek EL406 Washer/Aspirator/Dispenser w/stacker
FluidX Xrd384 Dispenser w/stacker
Thermo/Matrix Technologies WellMate Dispenser w/stacker

Detection:

PerkinElmer EnVision Multi-label Plate Reader/Detector w/stacker

Formerly the sole domain of large pharmaceutical corporations, HTS has revolutionized the way biomedical research is conducted. Utilizing laboratory automation and robotics, the Quellos HTS Core is converting bench scale assays to automated processes. Applying cell-based and biochemical screening paradigms, the core facility offers this sampling of screening services:

RNA interference or loss of function screening
Chemical Screening against cells or classical biochemical targets
Cancer Drug Sensitivity Test (CDST) —a critical component of precision medicine whereby a patient’s cancer cells are tested in a CLIA Certified setting for sensitivity against a panel of FDA approved drugs

RNAi

The combination of RNA interference (RNAi) and high throughput screening (HTS) has opened a new frontier toward the unbiased discovery of genes essential for specific biological processes or disease states. Utilizing synthetic small RNA duplexes (siRNA) or small RNA hairpins (shRNA), specific genes are inactivated within cells. This “loss of function” assay aids in pinpointing the role specific gene products play in cellular processes. Laboratory automation renders RNAi screening easily applicable to most cell types allowing for the rapid interrogation of gene function of the entire genomes of human, mouse or other model organisms. The potential of RNAi screening is seen in three distinct areas: identification of new targets and canonical pathways for any disease with a cell-based model (e.g., cancer, neurological or cardiac diseases), synthetic lethality (defined as a grouping of deficits in the expression of two or more transcripts leading to cell death, while a deficit in only one of these genes has no effect), and modifier screening to asses transcripts that interact with compounds to produce an enhancement or suppression of compound activity in a biological system.

The Quellos HTS Core offers broad coverage in human and mouse systems and will work with clients to develop cost effective targeted sets for their own research.

Chemical Screening

High-Throughput Screening of chemical (small molecule) libraries and drugs against cells, classical biochemical targets, or patient-derived samples can generate therapeutic leads that may be optimized for “first in man” clinical studies. It can also further insight into the roles that components of intracellular pathways play in biological phenomena, and aid to healthcare providers guiding therapeutic intervention.

The Quellos HTS Core’s chemical library currently contains thousands of separate entities selected for use in a variety of screening endeavors. “Lead Generation” collections, offering diverse coverage of the bioactive chemical space or focused on specific biochemical processes, are designed for pharmacophore delineation, a common goal of medicinal chemistry programs. The more “Experienced” collections are useful due to the wealth of information available on the chemical entities themselves, whether known pharmacological activity or as currently prescribed drugs.

The Quellos HTS Core offers broad coverage of chemical space using the available in-house collections of compounds and drugs, as well as offering services for arraying and screening client-submitted, privately constructed, collections — all under strict confidentiality.

Cancer Drug Sensitivity Test

The Cancer Drug Sensitivity Test (CDST) directly evaluates the sensitivity of a patient’s cancer cells to chemotherapy or other drugs in a laboratory dish set up to mimic in vivo conditions. The individual patient’s cancer cells are isolated within the CLIA-approved ISCRM laboratory. Using laboratory automation, the isolated cancer cells are distributed into thousands of tiny chambers within multi-well plates, delivered drugs or drug combinations, and quantify the ability or particular drugs or combinations of drugs to kill the cancer cells.

Patient cell responses are compared to a database of results acquired from similar tests in clinical trials performed under the auspices of the Fred Hutchinson Cancer Research Center for patients undergoing treatment at University of Washington Medical Center and Seattle Cancer Care Alliance. CDST results, patient history (if provided) and other clinically relevant information contribute to the ultimate choice of appropriate treatment for the patient. Treatment recommendations are based on the final laboratory report, which highlights agents for which there is a therapeutic response. Essentially, the CDST is a critical component of precision medicine that can be combined with molecular information or used as a single modality to pick the best drug regimen for each patient’s cancer.

The Cancer Drug Sensitivity Test or CDST directly assays the sensitivity of a patient’s cancer cells to chemotherapy or other drugs in a laboratory dish set up to mimic the in vivo conditions. The individual patient’s cancer cells are isolated within the CLIA-approved ISCRM laboratory, and robotically distributed into thousands of tiny chambers within multi-well plates. The robotic system then delivers different drugs or drug combinations to each chamber in a dose ranging fashion. Measurement of the percentage of surviving cells in each chamber allows quantification of each drug’s (or drug combination’s) ability to kill the cancer cells. The patient cell responses are compared to a database of results acquired from similar tests performed in clinical trials implemented under the auspices of the Fred Hutchinson Cancer Research Center for patients undergoing treatment at University of Washington Medical Center and Seattle Cancer Care Alliance. CDST results, patient history (if provided) and other clinically relevant information contribute to the ultimate choice of appropriate treatment for the patient. Treatment recommendations are based on the final laboratory report, which highlights agents for which there is a therapeutic response. Essentially, the CDST is a critical component of Precision Medicine that can be combined with molecular information or used as a single modality to pick the best drug regimen for each patient’s cancer.

Are there precedents to this type of testing?

The same concept has been in use for many years by Microbiology laboratories that perform susceptibility testing. In this case, bacteria or other infectious organisms isolated from patients are tested against an array of antibiotics in order to determine the best treatment to eradicate the infection. Our approach to cancer treatment is similar, in that we test a panel of drugs and drug combinations for effectiveness against a patient’s isolated cancer cells.

Our previous clinical research has shown success in application of this approach for patients with Acute Myelogenous Leukemia (AML), Acute Lymphocytic Leukemia (ALL) and Multiple Myeloma (MM). Hence, AML, ALL and MM are the diseases for which we’re currently offering the diagnostic test for aiding the attending physician’s decisions on treatment. Ongoing research at UW Medicine’s ISCRM is testing applicability of the CDST to other cancers, such as chronic myeloid leukemia and solid tumors.

Benefits from the CDST participation?

Timeliness and Turnaround Time

As opposed to next generation sequencing approaches that identify possible gene mutations within specific genes, the CDST is much speedier. Generally, mutation analysis takes at least a few weeks whereas the results from CDST can be expected within the week of sample acquisition from the patient. Moreover, for reasons we do not yet completely understand, only some patients with a given mutation will respond to the drug that targets that mutation. CDST has an advantage in that it can directly test for that sensitivity. Also, it reveals that some patients without the mutation can still respond to the drug. The quick turnaround of CDST also means that informed therapeutic treatment can begin much faster.

Improving Testing for the Future

Due to the state of the art in cancer treatment, knowledge is in a constant state of flux. De-identified patient data (data stripped of private information like patient names) such as CDST results and any follow-up information are used for research purposes for the benefit of others afflicted with cancer. The data would be entered into a database documenting results for ongoing and future analysis in order to improve treatment, drug panels, and the test. Patients may of course choose to opt-out of this research use of their data by signing the “opt-out” box on the requisition form.

How can the test diagnostic be ordered?

Patients should contact their health care providers to determine if CDST would be a good option for them. The Medical Director, Dr. Pamela Becker MD, PhD is available by telephone or email for brief consultation and exchange of information. Forms and detailed instructions will be sent via the web or US Mail and must be completed in full and returned with the patient sample. Please note that currently it is unlikely that insurance will cover this testing, but we anticipate that over time, with increased number of patient samples, insurance companies will step forward.

What type and how much patient sample is required?

Currently, samples for the CDST are only being accepted for AML, ALL and MM. We anticipate that availability of the test and applicability for other cancer types will be forthcoming in the near future as research continues. For most soluble cancers, we can perform CDST on samples derived from blood (25mL), bone marrow aspiration (10mL), or other tissues or fluids after discussion with Medical Director.

How long after sample submission are results available?

Samples must be sent cold (i.e., between 2°C to 8°C) with appropriate biological safety packaging, and they must arrive at the facility within 48 hrs of sample acquisition. Workup will begin immediately upon sample receipt and confirmation of payment. Final report will be communicated via secure FAX / phone call within one week of sample receipt and two weeks via US Mail unless different arrangements are made.

Who to contact?

All communications related to the Cancer Drug Sensitivity Test and prior test results should be directed to the Medical Director, Dr. Pamela Becker MD, PhD.

Email: cdst@uw.edu
Phone: 206-543-9028

Financial Packet Requisition Form

A list of original publications in which the Quellos HTS Core has been mentioned, or to which core staff have been contributing authors. This list serves as a snapshot of the breadth of areas in which the Core has involvement.

Cell-to-Cell Variation in Gene Expression for Cultured Human Cells Is Controlled in Trans by Diverse Genes: Implications for the Pathobiology of Aging

Journals of Gerontology: Biological Sciences, January 2020

High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping

Cell Stem Cell, June 2018

Dissecting the Contributions of Cooperating Gene Mutations to Cancer Phenotypes and Drug Responses with Patient-Derived iPSCs

Stem Cell Reports, May 2018

A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia

Nature Communications, January 2018

A screen for protective drugs against delayed hypoxic injury

PLOS ONE, April 2017

Class I Histone Deacetylase HDAC1 and WRN RECQ Helicase Contribute Additively to Protect Replication Forks upon Hydroxyurea-induced Arrest

Journal of Biological Chemistry, November 2016

Identification of Putative Immunologic Targets for Colon Cancer Prevention Based on Conserved Gene Upregulation from Preinvasive to Malignant Lesions

Cancer Prevention Research, July 2013