PUBLICATIONS

featuring the Echo acoustic technology

105 Total Publications

TITLES and AUTHORS

  • Year
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  • + Abstract
  • Acoustic Dispensing Preserves the Potency of Therapeutic Peptides throughout the Entire Drug Discovery Workflow
  • J Naylor, A Rossi, D Hornigold
  • Institution: Cardiovascular and Metabolic Disease, MedImmune, Cambridge, UK
  • Publication: Journal of Laboratory Automation (JALA)
  • 2015

Routine peptide structure-activity relationship screening requires the serial dilution of peptides to produce full concentration-response curves. Established tip-based protocols involve multiple tip changes and high exposure to plasticware. In the case of peptides, this becomes a challenge, since peptides can adsorb to plastic, resulting in an observed loss of potency. Various methods can be employed to prevent peptide loss during compound handling, such as the inclusion of bovine serum albumin or solvents in assay buffer and the siliconization of plasticware, yet protein binding remains unpredictable. The degree of variation by which peptides will adhere to plasticware can confuse results and cause inaccuracies in potency predictions. We evaluated acoustic noncontact methods for peptide serial dilution and compared it with traditional tip-based methods, on the effect on potency curves for glucagon-like peptide-1 and glucagon peptide analogues. The current study demonstrates the benefits of noncontact dispensing for high-density microplate assay preparation of peptides using nanoliter droplets across our entire drug discovery workflow, from in vitro high-throughput screening to drug exposure determinations from in vivo samples.

  • Low-Cost, High-Throughput Sequencing of DNA Assemblies Using a Highly Multiplexed Nextera Process
  • E Shapland, et. al.
  • Institution: Amyris, Inc. and TOTAL New Energies USA, Inc.
  • Publication: ACS Synth. Biol., Article ASAP DOI: 10.1021/sb500362n
  • 2015
  •  

In recent years, next-generation sequencing (NGS) technology has greatly reduced the cost of sequencing whole genomes, whereas the cost of sequence verification of plasmids via Sanger sequencing has remained high. Consequently, industrial-scale strain engineers either limit the number of designs or take short cuts in quality control. Here, we show that over 4000 plasmids can be completely sequenced in one Illumina MiSeq run for less than $3 each (15× coverage), which is a 20-fold reduction over using Sanger sequencing (2× coverage). We reduced the volume of the Nextera tagmentation reaction by 100-fold and developed an automated workflow to prepare thousands of samples for sequencing. We also developed software to track the samples and associated sequence data and to rapidly identify correctly assembled constructs having the fewest defects. As DNA synthesis and assembly become a centralized commodity, this NGS quality control (QC) process will be essential to groups operating high-throughput pipelines for DNA construction.

  • Publication / Type:ACS Synth. Biol., Article ASAP DOI: 10.1021/sb500362n
  • Related Subject:synthetic biology; next-generation sequencing; NGS; high throughput, DNA Assembly, Sequencing, Echo® Liquid Handler for Screening and OMICS
  • Link:http://pubs.acs.org/doi/full/10.1021/sb500362n
  • Drug screen in patient cells suggests quinacrine to be repositioned for treatment of acute myeloid leukemia
  • A Eriksson, A Osterroos, S Hassan, J Gullbo, L Rickardson, M Jarvius, P Nygren, M Fryknas, R Larsson
  • Institution: Department of Medical Sciences, Uppsala University
  • Publication: Blood Cancer Journal, Nature
  • 2015
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To find drugs suitable for repositioning for use against leukemia, samples from patients with chronic lymphocytic, acute myeloid and lymphocytic leukemias as well as peripheral blood mononuclear cells (PBMC) were tested in response to 1266 compounds from the LOPAC1280 library (Sigma). Twenty-five compounds were defined as hits with activity in all leukemia subgroups (o50% cell survival compared with control) at 10 μM drug concentration. Only one of these compounds, quinacrine, showed low activity in normal PBMCs and was therefore selected for further preclinical evaluation. Mining the NCI-60 and the NextBio databases demonstrated leukemia sensitivity and the ability of quinacrine to reverse myeloid leukemia gene expression. Mechanistic exploration was performed using the NextBio bioinformatic software using gene expression analysis of drug exposed acute myeloid leukemia cultures (HL-60) in the database. Analysis of gene enrichment and drug correlations revealed strong connections to ribosomal biogenesis nucleoli and translation initiation. The highest drug–drug correlation was to ellipticine, a known RNA polymerase I inhibitor. These results were validated by additional gene expression analysis performed in-house. Quinacrine induced early inhibition of protein synthesis supporting these predictions. The results suggest that quinacrine have repositioning potential for treatment of acute myeloid leukemia by targeting of ribosomal biogenesis.

  • Publication / Type:Blood Cancer Journal, Nature
  • Related Subject:screening, cancer, blood cancer, myeloid leukemia
  • Delivering an Automated and Integrated Approach to Combination Screening Using Acoustic-Droplet Technology
  • Cross K, Craggs R, Swift D, Stiaram A, Daya S, Roberts M, Hawley S, Owen P, and Isherwood V
  • Institution: AstraZeneca and Tessela plc.
  • Publication: J Lab Autom. 2015 Apr 2. DOI: 10.1177/2211068215579163
  • 2015
  •  

Drug combination testing in the pharmaceutical industry has typically been driven by late-stage opportunistic strategies rather than by early testing to identify drug combinations for clinical investigation that may deliver improved efficacy. A rationale for combinations exists across a number of diseases in which pathway redundancy or resistance to therapeutics are evident. However, early assays are complicated by the absence of both assay formats representative of disease biology and robust infrastructure to screen drug combinations in a medium-throughput capacity. When applying drug combination testing studies, it may be difficult to translate a study design into the required well contents for assay plates because of the number of compounds and concentrations involved. Dispensing these plates increases in difficulty as the number of compounds and concentration points increase and compounds are subsequently rolled onto additional labware. We describe the development of a software tool, in conjunction with the use of acoustic droplet technology, as part of a compound management platform, which allows the design of an assay incorporating combinations of compounds. These enhancements to infrastructure facilitate the design and ordering of assay-ready compound combination plates and the processing of combinations data from high-content organotypic assays.

  • Publication / Type:J Lab Autom. 2015 Apr 2. DOI: 10.1177/2211068215579163
  • Related Subject:laboratory informatics, combinations, acoustic droplet technology, apothecary, assay-ready plate, high-content screening, sample management
  • Axitinib Effectively Inhibits BCR-ABL1(T315I) with a Distinct Binding Confirmation
  • Pemovska T., Johnson E., Kontro M., Repasky G., Chen J., Wells P, Ciaran N., Cronin C., McTigue M.,
  • Institution: Institute for Molecular Medicine Finland; University of Helsinki; La Jolla Laboratories, Pfizer
  • Publication: Nature 519, 102-105 (March 5, 2015), doi:10.1038/nature14119
  • 2015
  •  

The BCR-ABL1 fusion gene is a driver oncogene in chronic myeloid leukaemia and 30–50% of cases of adult acute lymphoblastic leukaemia1. Introduction of ABL1 kinase inhibitors (for example, imatinib) has markedly improved patient survival2, but acquired drug resistance remains a challenge3, 4, 5. Point mutations in the ABL1 kinase domain weaken inhibitor binding6 and represent the most common clinical resistance mechanism...

  • Delivering an Automated and Integrated Approach to Combination Screening Using Acoustic-Droplet Technology
  • K Cross, R Craggs, D Swift, A Sitaram, S Daya, M Roberts, S Hawley, P Owen, B Isherwood
  • Institution: Discovery Sciences, AstraZeneca R&D, Macclesfield, UK
  • Publication: Journal of Laboratory Automation (JALA)
  • 2015
  •  

Drug combination testing in the pharmaceutical industry has typically been driven by late-stage opportunistic strategies rather than by early testing to identify drug combinations for clinical investigation that may deliver improved efficacy. A rationale for combinations exists across a number of diseases in which pathway redundancy or resistance to therapeutics are evident. However, early assays are complicated by the absence of both assay formats representative of disease biology and robust infrastructure to screen drug combinations in a medium-throughput capacity. When applying drug combination testing studies, it may be difficult to translate a study design into the required well contents for assay plates because of the number of compounds and concentrations involved. Dispensing these plates increases in difficulty as the number of compounds and concentration points increase and compounds are subsequently rolled onto additional labware. We describe the development of a software tool, in conjunction with the use of acoustic droplet technology, as part of a compound management platform, which allows the design of an assay incorporating combinations of compounds. These enhancements to infrastructure facilitate the design and ordering of assay-ready compound combination plates and the processing of combinations data from high-content organotypic assays.

  • Publication / Type:Journal of Laboratory Automation (JALA)
  • Related Subject:laboratory informatics, combinations, acoustic droplet technology, apothecary, assay-ready plate, high-content screening, sample management
  • Link:http://jla.sagepub.com/content/21/1/143.full.pdf+html
  • Identification of b-hematin inhibitors in the MMV Malaria Box
  • Fong K., Sandlin R. and Wright D.
  • Institution: Vanderbilt University
  • Publication: International Journal for Parasitology: Drugs and Drug Resistance, Volume 5, Issue 3, December 2015
  • 2015
  •  

The Malaria Box, assembled by the Medicines for Malaria Venture, is a set of 400 structurally diverse, commercially available compounds with demonstrated activity against blood-stage Plasmodium falciparum. The compounds are a representative subset of the 20,000 in vitro antimalarials identified from the high-throughput screening efforts of St. Jude Children's Research Hospital (TN, USA), Novartis and GlaxoSmithKline. In addition, a small set of active compounds from commercially available libraries was added to this group, but it has not previously been published. Elucidation of the biochemical pathways on which these compounds act is a major challenge; therefore, access to these compounds has been made available free of charge to the investigator community. Here, the Malaria Box compounds were tested for activity against the formation of b-hematin, a synthetic form of the heme detoxification biomineral, hemozoin. Further, the mechanism of action of these compounds within the malaria parasite was explored. Ten of the Malaria Box compounds demonstrated significant inhibition of b-hematin formation. In this assay, doseeresponse data revealed IC50 values ranging from 8.7 to 22.7 mM for these hits, each of which is more potent than chloroquine (a known inhibitor of hemozoin formation). The in vitro antimalarial activity of these ten hits was confirmed in cultures of the chloroquine sensitive D6 strain of the parasite resulting in IC50 values of 135e2165 nM, followed by testing in the multidrug resistant strain, C235. Cultures of P. falciparum (D6) were then examined for their heme distribution following treatment with nine of the commercially available confirmed compounds, seven of which disrupted the hemozoin pathway.

  • A Personalised Medicine Drug Sensitivity and Resistance Testing Platform and Utilisation of Acoustic Droplet Ejection at the Institute for Molecular Medicine Finland
  • Saarela J, Kulesskiy E, Laamanen K, Pemovska T, Pietiainen V, Potdar S, von Schantz-Fant C, Turunen
  • Institution: Institute for Molecular Medicine Finland, University of Helsinki, Finland (FIMM)
  • Publication: Synergy Vol 1, Issue 1, Sep 2014, Pages 78 doi:10.1016/j.synres.2014.07.001
  • 2015
  •  

The High Throughput Biomedicine (HTB) unit at FIMM Technology Centre provides a wide range of biomedical high throughput assays. In collaboration with research groups and the Hospital District of Helsinki and Uusimaa, we have set up drug sensitivity and resistance testing (DSRT) platform with a set of 450 approved and investigational oncology drugs on patient samples. Ex vivo drug testing is currently performed at FIMM with primary cancer cells from patients with leukaemia and multiple myeloma as well as cancer cell lines and the drug sensitivity responses are integrated with molecular profiling such as exome sequencing, transcriptomics and phosphoproteomics. Currently, DSRT is run in 384-well plate format in 5 concentrations for each drug or in 1536-well plate format with 9 concentrations per drug and the assay plates are pre-drugged using acoustic droplet ejection with Labcyte® Echo® 550. The viability and cell death of cells is measured after 72 h and results are analysed using Dotmatics Studies – software and an in-house developed interface, Breeze. Application of the platform to AML patient samples has uncovered taxonomic drug-response subtypes and individualised therapy based on DSRT has resulted in several clinical responses. The DSRT platform enables drug repositioning, provides new combinatorial possibilities and allows for linking drug sensitivities to predictive biomarkers. We are developing the platform with additional readouts and increasing the number of drugs. Our Labcyte Access Workstation, with Echo 550 and Echo® 525 integration, allows development and set-up of miniaturised follow-up assays, such as reverse-phase protein array and qPCR, using non-contact acoustic dispensing. 

  • Quantitative Analysis of Long-Form Aromatase mRNA in the Male and Female Rat Brain
  • Tabatadze N, Sato S and Woolley C
  • Institution: Northwestern University
  • Publication: PLoS ONE
  • 2014
  •  

In vitro studies show that estrogens acutely modulate synaptic function in both sexes. These acute effects may be mediated in vivo by estrogens synthesized within the brain, which could fluctuate more rapidly than circulating estrogens. For this to be the case, brain regions that respond acutely to estrogens should be capable of synthesizing them. To investigate this question, we used quantitative real-time PCR to measure expression of mRNA for the estrogen-synthesizing enzyme, aromatase, in different brain regions of male and female rats. Importantly, because brain aromatase exists in two forms, a long form with aromatase activity and a short form with unknown function, we targeted a sequence found exclusively in long-form aromatase. With this approach, we found highest expression of aromatase mRNA in the amygdala followed closely by the bed nucleus of the stria terminalis (BNST) and preoptic area (POA); we found moderate levels of aromatase mRNA in the dorsal hippocampus and cingulate cortex; and aromatase mRNA was detectable in brainstem and cerebellum, but levels were very low. In the amygdala, gonadal/hormonal status regulated aromatase expression in both sexes; in the BNST and POA, castration of males down-regulated aromatase, whereas there was no effect of estradiol in ovariectomized females. In the dorsal hippocampus and cingulate cortex, there were no differences in aromatase levels between males and females or effects of gonadal/hormonal status. These findings demonstrate that long-form aromatase is expressed in brain regions that respond acutely to estrogens, such as the dorsal hippocampus, and that gonadal/hormonal regulation of aromatase differs among different brain regions.

  • Quantitative Scoring of Differential Drug Sensitivity for Individually Optimized Anticancer Therapies
  • Bhagwan Y., Pemovska T., Szwajda A., Kulesskiy E., Kontro M., Karjalainen R., Majumder M., Malani D.
  • Institution: Institute for Molecular Medicine Finland (FIMM), University of Helsinki; Hematology Research Unit, H
  • Publication: Scientific Reports 4, Article number: 5193; doi: 10.1038/srep05193 Subject terms: predictive medicin
  • 2014
  •  

We developed a systematic algorithmic solution for quantitative drug sensitivity scoring (DSS), based on continuous modeling and integration of multiple dose-response relationships in high-throughput compound testing studies. Mathematical model estimation and continuous interpolation makes the scoring approach robust against sources of technical variability and widely applicable to various experimental settings, both in cancer cell line models and primary patient-derived cells. Here, we demonstrate its improved performance over other response parameters especially in a leukemia patient case study, where differential DSS between patient and control cells enabled identification of both cancer-selective drugs and drug-sensitive patient sub-groups, as well as dynamic monitoring of the response patterns and oncogenic driver signals during cancer progression and relapse in individual patient cells ex vivo. An open-source and easily extendable implementation of the DSS calculation is made freely available to support its tailored application to translating drug sensitivity testing results into clinically actionable treatment options.