The SPARC Drug Discovery (DD) facility is the product of a strategic initiative made by SickKids to provide researchers access to state-of-the-art infrastructure and world-class expertise to develop robust and predictive assays to identify small molecule modulators of biochemical targets and/or cellular phenotypes relevant to human disease. To this end, over the past decade, SPARC-DD has built up the necessary tools and personnel to execute on this mandate, including: acquiring nearly 150,000 small-molecules composed of approved drugs, drug-like scaffolds and targeted libraries; state-of-the-art automation hardware to enable high throughput screening on both biochemical targets and more sophisticated 3D screening of organoids and whole organisms; maintaining archives of molecular biologicals (e.g. cDNA, RNAi) available in plasmid vectors and lentivirus; and, assembling a highly-trained team with extensive drug discovery expertise and experience to best engage with the research community to translate their scientific findings into publications, patents and assets that facilitate commercialization. SPARC DD services are continually evolving in step with changing needs of investigators.

SPARC DD strives to provide leading-edge researchers with the tools and expertise they need to advance their experimental work. Specifically, we increase access to state of the art automation equipment to investigators in order to increase translational drug discovery research projects. We do this by: fostering strong academic collaborations through in-depth consultations, providing lower cost of screening by operating as a non-profit, offering guidance by connecting clients to our partners in drug discovery, and providing access to state-of-the art equipment. These interactions have resulted in the development of several novel assays leading to numerous key discoveries and publications. (Tam et al. Small molecule inhibitors of Clostridium difficile toxin B-induced cellular damage. Chem Biol (2015) vol. 22 (2) pp. 175-85; Hammoud et al. Identification of RSK and TTK as Modulators of Blood Vessel Morphogenesis Using an Embryonic Stem Cell-Based Vascular Differentiation Assay. Stem Cell Reports (2016) 2016 Oct 11;7(4) pp. 787-801.

SPARC-DD involves the design/production/identification of two types of molecules: (i) Small molecules discovered through high-content analysis (HCA)/high-throughput (HTP) chemical biology and screening activities supported by a collection of >150K chemical compounds, and an automated HTP screening platform compatible with in vitro and live-cell-based assays, as well as tissue/organoids/model organism assays. (ii) Molecular biology reagents (e.g. cDNA and RNAi libraries; expression vectors/epitope tags; lentivirus, CRISPR clones) that facilitate the characterization of gene products.

SPARC-DD’s Dual Spinnaker High-Throughput Screening Platform provides a flexible and scalable platform that facilitates automation of most in vitro and cell based screening projects. Drug delivery is performed with the Labcyte Echo, a tipless, non-contact acoustic dispenser is that uses sound energy to dispense precisely-sized droplets of reagent or compounds with a resolution of 2.5 nL with exceptional accuracy and precision, offering enormous flexibility and cost savings to the end user. Three incorporated Multidrop Combi units provide additional efficient bulk reagent delivery. The BioTek Synergy Neo multi-label plate reader is capable of fluorescent (FI, FP), luminescent, TRF, AlphaScreen, and absorbance/transmission detection modes, enabling enormous flexibility in the selection of screening reagents.

Our recently added ImageXpress Micro Confocal System is our key platform that enables automated high throughput image based screening and detailed analysis of 3D structures such as organoids, spheroids, cell clusters, zebrafish embryos, worms (C. elegans), Drosophila eggs and larvae. The IXMC permits reconstruction of 3D structures by rapidly collecting a stack of crisp images in the Z-plan for subsequent 3D analysis. The IXMC can also acquire images from a variety of specialized multi-well formats developed for 3D assays, including round bottom, trans-well and hanging drop plates, which facilitate consistent and controllable formation of 3D organoids, spheroids and cell aggregates. The IXMC can also image through specialized matrices used for the formation and differentiation of organoids. MetaXpress Software provides turnkey application modules to address hundreds of common analysis routines, such as micronucleus detection, neurite outgrowth, angiogenesis tube formation, mitotic index, cell cycle analysis, proliferation, cell health (viability/toxicity, apoptosis, necrosis) and translocation events. The custom module editor provides a flexible toolbox for the 3D analysis and quantification of parameters such as volumes, intensities and distances and dynamic movements such as heart beats and gut motility. Integration of the IXMC with a Spinnaker robotic arm and Cytomat 2C incubator via Momentum software enables fully automated imaging of samples 24/7 for drug screens.

Unique to SPARC DD is the incorporation of our BioSorter large particle flow cytometer. It is the only available flow system that can sort a broad range of diverse fragile multicellular structures ranging in size from 10-1500 microns such as organoids, embryonic stem cell clusters, Drosophila eggs/embryos and larvae, zebrafish embryos and worms for subsequent downstream applications. Sorting is achieved by determining object size by optical density or fluorescence intensity of markers in 3 channels.

Our facility is always looking for new collaborations and we are open to all researchers. For general inquiries, please get in touch with our facilities manager, Chris Fladd at cfladd@sickkids.ca, further information can be found on the SPARC Drug Discover page.

The Genetic and Molecular Epidemiology Laboratory (GMEL) at McMaster University is a premier genomics and proteomics facility offering a broad range of analytical services for academic and industry scientists. Established in 2009 by Guillaume Paré, MD, GMEL offers a broad array of cutting-edge “omics” platforms and technologies for high-throughput analyses of nucleic acids and protein biomarkers. Among the key services that GMEL offers are high-throughput DNA/RNA extraction, quantitation and quality assessment, microarrays (genotyping, gene expression, methylation), next-generation sequencing (exome, RNA, custom target, low-pass whole-genome), and multiplexed protein biomarker assays (>982 biomarkers simultaneously).

GMEL is affiliated with Hamilton Health Sciences’ Population Health Research Institute (PHRI), Thrombosis and Atherosclerosis Research Institute (TAaRI), and McMaster University. GMEL specializes in large-scale population genetic studies, and as such, is capable of handling project sizes ranging from single samples to >10,000 samples. With in-house Principal Investigators, project managers, statisticians, and bioinformaticians, GMEL provides support for experimental design, bioinformatics, statistical analyses, and the interpretation and reporting of results. GMEL is currently involved with multiple epidemiological studies and clinical trials, including CURE, ACTIVE, COMPASS, NAVIGATE ESUS, INTERSTROKE, ORIGIN, and PURE, among others.

While GMEL provides services in all areas of life sciences research, the laboratory has a particular focus on using the most cutting-edge genetic techniques to assess whether the promise of personalized medicine can be realized. The team explores the genetic risk of stroke, diabetes, obesity, and the response to some of the most widely prescribed drugs for those diseases.

Among GMEL’s key achievements was their description that clinical context is important when determining the effectiveness of clopidogrel treatment in patients with acute coronary syndromes or atrial fibrillation. Clopidogrel is used globally to reduce the risk of heart attack and stroke; however, studies by others showed that individuals carrying a CYP2C19 loss-of-function allele have an attenuated benefit from clopidogrel treatment, leading to an FDA black box warning. GMEL’s studies of acute coronary syndrome and atrial fibrillation added context to such findings and showed that the negative effects of loss-of-function alleles do not apply to all patient populations, and that the CYP2C19 gain-of-function allele may be equally or more important than the loss-of-function allele in specific populations. GMEL research also described a pharmacogenetic association between CES1 and the risk of bleed with the novel anticoagulant, dabigatran, and described an association between a COX-2 variant and its effect on aspirin. Research and collaborations from GMEL also identified genetic determinants of lipoprotein concentrations, glucose metabolism, homocysteine concentrations, as well as markers of inflammation, coronary artery disease, stroke, and atrial fibrillation.

Recent studies also resulted in the development of statistical methodologies and bioinformatics tools to identify gene-gene and gene-environment interactions, which have been adopted by multiple other research laboratories. GMEL developed a novel approach to test regional genetic associations, which has recently been expanded to include machine-learning approaches to determine polygenic risk scores. GMEL pioneered the use of Mendelian randomization (MR) to show that diabetes is causally involved in coronary heart disease, and that bile acid sequestrants reduce the risk of heart disease. The team also used MR to show that HER2 is a causal mediator of the protective effect of ACE inhibitors on kidney function.

GMEL has established a broad array of instrumentation for genomic and proteomic analyses. Among such instrumentation is the QIAsymphony instrumentation suite, BioAnalyzer, Fragment Analyzer, Gene Titan Array Scanner, Illumina iScan, Two Ion Torrent Series platforms for exome sequencing, BioNano Genomics Irys System, Thermofisher ViiA7 RT-PCR System, QuantStudio 3D Digital PCR System, Pyromark Q24 instrument, BioMark HD System, Bio-Plex Luminex Multiplex assays, Olink panel assays, and the SomaLogic SOMAscan technology, among others.

GMEL also has the necessary bioinformatics infrastructure (10 dedicated servers) to process large genomics projects at reasonable turnaround times. Among such infrastructure, GMEL uses Cisco Systems platforms, including a Quad Cisco UCSB-B200 bladed system, with combined Intel Xeon based 128 core CPU and 512 GB RAM, running within a VMware ESXi 5.5 environment. GMEL also uses a dedicated Cisco UCS C240 M4 rack application server, with Intel Xeon based 28 core CPU and 384 GB RAM, 3.2 TB Fusion-ion SX300 PCIe SSD and internal 8TB SAS 7.2K SFF HDD, running Linux based distribution.

From start to finish, GMEL provides a full-service analytical platform for researchers’ genomic and proteomic needs. Whether your project includes tens of samples or tens of thousands, GMEL is always willing to establish new collaborations and assist with your research. For more information about GMEL services, please contact Sue McMillan at 905-527-4322 ext. 40377, or smcmill@mcmaster.ca.