Stem cell therapy has the potential to revolutionize the treatment of disease. Pluripotent stem cells are able to differentiate into almost any cell in the body. Their significance in promoting health and longevity is immense. Since the discovery of human stem cells, the development of therapies using progenitor cells presents scientists with a prospective ‘tool kit’ for the repair and replacement of diseased and damaged tissue. Furthermore, as researchers gain further understanding of the signalling pathways involved in development, they are better able to manipulate stem cell differentiation. This improved ability to manipulate cell fate is made more powerful with the advent of induced pluripotent stem (iPS) cell technology, which allows personalized stem cells to be generated from a patient biopsy, heralding an era of ‘silver bullet’ type therapies, avoiding the historical problem of tissue rejection.
The field of stem cell research is growing at breakneck speed and is unique in that it embraces a wide range of disciplines from biochemistry, through to cell biology and genomics, to bioinformatics, drug discovery and tissue engineering. A critical component of any scientific endeavour is the management of the results obtained. Inability to adequately store and retrieve experimental results remains commonplace in research. This can lead to the needless repetition of experiments and, in some cases, incorrect conclusions being made. In this article we explore the pioneering use of IDBS’ ActivityBase Suite to support stem cell research and discuss how this solution can assist experimental workflow, enabling scientists to generate the highest quality of results.
Leading Edge Research at the University of Dundee
The Drug Discovery Unit, College of Life Sciences, University of Dundee, in partnership with Cellartis AB, has been screening human embryonic stem cells since mid-2007 to identify small molecules that influence cell fate. By screening their range of bespoke collections of drug-like small molecules, the team has built a growing portfolio of agents to maintain pluripotency, promote cellular survival or direct cell differentiation to either progenitor cells or mature cell types. Human embryonic stem cells have a tendency to spontaneously differentiate, which necessitates the requirement for selective and non-population based analysis. Therefore, a high content screening (HCS) strategy has been developed to analyze fully pluripotent stem cells in a novel feeder-free culture system.
Stem Cell Screening
Using both 96 and 364 well plate formats, stem cells are screened using single parameter and multiparametric methods. An immunofluorescent assay is performed on selected cells. Specifically, plates are subject to automated imaging and analysis (In Cell 1000 Analyzer, GE), with up to four wavelengths being captured per field and typically multiple fields being captured per well. These associated component and composite images are subject to analysis generating a flat file output (csv).
Need for Results Management and Reporting
The key to success in any screening campaign is the ability to relate all appropriate information together. Raw data, quality assurance plate-based information, images (both composite and component), assay and protocol information must all be related to specific assays and plates. Furthermore, results from the raw data must also be stored, with the ability to review and report on screening campaigns.
Using ActivityBase for Stem Cell Screening
Information generated by image analysis is outputted in a csv format and subsequently imported directly into the ActivityBase Suite. Using import definition files, ActivityBase can be configured to work with a wide variety of HCS instrumentation. Upon import, the result information is associated with the appropriate screening campaign. Users have the option to either interactively or automatically exclude outlying values in the high and low control wells. The quality assurance Z is then generated, upon which a pass or fail decision can be made.
Reporting on single parameter datasets is relatively straightforward, but multiparametric reporting can be more difficult, especially when individual parameters have associated independent variances. This makes the quality assurance of plates challenging. Once statistical criteria have been decided on for hit selection, a cherry picking list is generated and hits are retested. In potency analysis, a problem such as hook effects due to cell toxicity at high compound concentration can be observed and rectified using the software tools within the ActivityBase Suite.
Benefits of ActivityBase
ActivityBase Suite provides one platform for the test management of both high throughput (single parameter) and high content (single or multiparametric) screening. The ability to import txt and csv files directly into the ActivityBase environment significantly reduces transcription errors. Users remain in control of their results and can select the desired level of workflow automation. Quality assurance criteria can be applied to individual plates, or even whole batches, to select whether datasets should be included in analysis, based on control well values. Users have the ability to observe specific erroneous data points and exclude from analysis if necessary.
The secure management of experimental data is paramount to ensure confidence in results and subsequent decision-making. ActivityBase has long been regarded as the gold standard in biological test data management, with a proven ability to adapt to numerous workflows in modern research laboratories. These capabilities are proving equally applicable in the pioneering research performed at the University of Dundee, which is accelerated with the provision of robust data management. Enabling users to analyze the characteristics of stem cells, ActivityBase offers acompliant and accessible solution, allowing scientists to spend more time interpreting results and less time managing data.