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Improve RNAi Screening and Cell Assay Workflows with Acoustic Dispensing

Dr. Jani Saarela

Senior Researcher, High Throughput Biomedicine Unit
Institute for Molecular Medicine Finland (FIMM)
HOME | RESOURCES | Customer Profiles | FIMM - Dr. Jani Saarela

Improve RNAi Screening and Cell Assay Workflows with Acoustic Dispensing

Dr. Jani Saarela a Senior Researcher in the High Throughput Biomedicine Unit, Institute of Molecule Medicine Finland (FIMM) discusses the advantages of acoustic dispensing in automated screening used by the unit, at the Labcyte Genomics Symposium in Edinburgh 2016.

  PRESENTATION VIDEO

Improve RNAi Screening and Cell Assay Workflows with Acoustic Dispensing

with Dr. Jani Saarela

Dr. Jani Saarela a Senior Researcher in the High Throughput Biomedicine Unit, FIMM discussing the advantages of acoustic dispensing in automated screening used by the unit, at the Labcyte Genomics Symposium.

Labcyte and GeneMill

With extensive facilities for high-throughput cell analysis and imaging, the unit provides access to large RNAi and chemical libraries, generating custom library preparations for cell assay screening. The majority of the unit’s activity is focused on drug sensitivity and resistance testing, in particular ex vivo testing of oncology patient cells. Workflows center around the Labcyte Echo 525 liquid handling platform; watch Dr. Saarela discuss the impact of this technology on patient treatment selection and new drug development using selected examples from over 1800 studies on primary leukemia and solid tumor cell lines.

The FIMM High Throughput Biomedicine Unit generates chemical and RNAi libraries for high-throughput screening, including genome-wide siRNAs. Dr. Saarela describes the unit’s extensive array of workstation and standalone laboratory equipment for activities including high-throughput imaging and ultra-miniaturized assays. The chemical library contains over 140, 000 screening chemicals, drugs, and known bioactives and chemical diversity libraries. Dr. Saarela provides more details on whole genome screening of their Ambion Silencer Select genome-wide siRNA library, and drug sensitivity and resistance testing (DSRT) of over 525 oncology drugs on patient cell samples. Acoustic dispensing is used for producing assay ready plates of all libraries, in custom combinations. For siRNA screening, transfection reagents and cells are added to assay plates using the Echo, then incubated in either standard or live-cell imaging equipment. The cells are then fixed and imaged or measured on a plate reader using detection reagents.

In the presentation, Dr. Saarela explains how acoustic dispensing enables miniaturization of commercial and custom assays of the same quality but at a fraction of the volume and cost. Several case studies that apply the library are presented, including siRNA screening for liposome mediated reverse transcription and an siRNA screen based on single nucleotide polymorphism (SNP) data from breast cancer patient cells treated with anthracyclin.

The FIMM oncology collection is currently the most complete collection in the world. Oncology compounds are typically tested at 5 different concentrations with a 10,000-fold concentration range. Using the oncology compound library, drug sensitivity and resistance testing (DSRT) assays are performed on relapsed leukemia patient cell samples. Cells are added to the compounds in assay plates and incubated for three days. Cell viability is measured and combined across concentration ranges to generate dose response curves. Data are compared to control cells and used to guide and enhance patient treatment.


"We were able to miniaturize the assay from the recommended 20 µL to a 1 µL reaction, so the cost reduction was quite good."

Dr. Saarela describes studies linking mutation data to drug response that provide evidence for a new functional classification of acute myeloid leukemia. Future work aims to use imaging and flow cytometry to obtain more in depth information from compound screening assays. Solid tumor samples are challenging to assay, as tissue is often very limited and heterogeneous. Dr. Saarela explains how technology in use at FIMM enables ultra-miniaturization for highly effective screening. Finally, the custom data management system Breeze is introduced, which is a web interface that aids automated control and analysis of DSRT.