The Miami Project to Cure Paralysis finds an on-demand laboratory information management system (LIMS) helps to accelerate discovery in its HCS projects.
Traumatic injury to the central nervous system (CNS) usually results in irreversible loss of function. Consequently, individuals with injured spinal cords can be permanently paralyzed. This function loss occurs because of the death of nerve cells and their support cells as well as the severing of very long processes (called axons) that transmit electrical signals from one nerve cell to others. Transected CNS axons do not re-grow or reestablish connections with their targets.
Injury to the CNS has devastating effects on the structure and function of the brain and spinal cord. Since the early 1980s, immense progress in research has provided hope that injuries to the CNS will one day be repairable. The Miami Project to Cure Paralysis is a spinal cord injury research center housed in the Lois Pope LIFE Center, a Center of Excellence at the University of Miami’s Miller School of Medicine. The goal of Miami Project’s international team of more than 200 scientists, researchers, and clinicians is to take innovative approaches to the challenge of spinal cord injury. The Miami Project to Cure Paralysis has a dedicated laboratory devoted to high-content screening (HCS) of neurons, which is run by Dr. Vance Lemmon and Dr. John Bixby and called the LemBix Laboratory. The Miami Project to Cure Paralysis realized that an on-demand laboratory information management system (LIMS) would be crucial in helping to accelerate discovery in its HCS projects, enabling the entire field to move forward at a faster rate.
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Figure 1: The steps involved in a typical screening pipeline. (All images courtesy Thermo Fisher Scientific) |
The laboratory and its challenges
High-content screening (HCS) offers an ideal way to identify genes, molecular pathways, and, ultimately, drugs that can promote the regeneration of CNS axons. HCS permits the quantification of cell morphology, including the lengths and numbers of axons, of neurons in culture. The approach of HCS itself produces huge amounts of data in the form of images, and also well-based and cell-based phenotypic measures. A single experiment can generate data from 300,000 neurons with 120 parameters per cell. Managing sample workflow and library data, along with the vast amount of experimental results, is challenging.
The goal of the LemBix laboratory is to uncover signal pathways, genes, compounds, or drugs that can be used to promote nerve growth. HCS of various libraries on primary neurons requires a team-based approach, a variety of process steps and complex manipulations of cells and libraries to obtain meaningful results. The laboratory uses an informatics solution to meet the ever-growing data deluge and to turn that data into knowledge. The LemBix laboratory can screen 3000 different genes in primary neurons and measure scores of different parameters in more than six million neurons in the span of a few months.
Screening campaigns using primary neurons are uncommon due to the expense of culturing cells that require complex defined media and also the variability between preparations of nerve cells. The LemBix laboratory tackles the variability between preparations, in part, by including a number of control treatments that are used for normalizing data across experiments. But it is clear that much of the variability between different experiments is due to variability in reagents and cell preparation. In order to rapidly identify sources of variability, it is essential to have a LIMS that tracks supplies, reagents and workflows.
The typical screening pipeline includes many steps (see Figure 1). First, brain regions are harvested and CNS neurons are isolated as single cells before being transfected with expression vectors coding for potential regeneration-associated genes and green fluorescent protein. Then, neurons are plated into 96-well plates and cultured for 48 hours before being fixed and stained to permit visualization of nuclei and neuronal morphology (Figure 2). Sometimes, the neurons are treated with chemicals or drugs instead of or in addition to DNA. The plates are then imaged and analyzed using a Thermo Scientific Cellomics VTI ArrayScan and Cellomics BioApplications.
A solution to data management and workflows
Prior to implementing a Thermo Scientific LIMS the laboratory used paper-based worksheets and manual notebooks. The nature of the work conducted resulted in numerous compound libraries and gene libraries and the laboratory found that it was becoming overwhelmed with all the data it had to oversee. Furthermore, the laboratory was moving from conducting traditional academic research activities, such as hypothesis driven research where it was easier to keep track of information manually in notebooks, to a heavier workload that involved more complicated screening and more people. Keeping track of what each person was doing through the process of preparing the cells and perturbations, staining, and analysis was a challenge. The laboratory determined that a manual, paper-based process was not efficient and that a more automated electronic method was required.
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Figure 2: Visualization of nuclei and neuronal morphology in neurons. |
Within the laboratory’s workload, hundreds of different reagents are used for a particular experiment, and there are dozens of different steps to document the processes, such as recording the number of cells that are inserted into a particular well, how they were treated, when they were put into the incubator, etc. It is crucial that the laboratory keeps track of every detail of these processes. Furthermore, with so many people being involved in the workflow of a particular experiment, an electronic system that can easily be used by all the people who need to enter information is the only efficient way to do this.
Implementing a LIMS enabled the laboratory to track essential information, such as lots of reagents and ensure that standard operating procedures (SOPs) are adhered to. The solution helped laboratory managers enforce business rules and capture details about workflow to identify problems or optimal conditions.
Addressing the project’s needs
The laboratory managers decided to adopt an on-demand solution that better serves the needs to the laboratories goals—to manage its workflows and operations in the most efficient and effective way. Furthermore, the LemBix laboratory had been struggling with in-house maintenance issues associated with the University’s servers. The laboratory was dependant on the University IT staff to maintain the servers; if there was a problem with the server it could take weeks for the issue to be resolved because the laboratory is one of many areas supported by University of Miami IT department, and its needs were not high priority for the IT team. The LemBix Laboratory decided to migrate to an on-demand LIMS in order to remove the IT support bottleneck.
The Miami Project to Cure Paralysis realized that an on-demand LIMS solution would be ideal in helping to reduce overhead for dedicated and specialised IT resources to maintain and support the system. With full featured LIMS functionality available over the Internet, the laboratory can have all the data reliability and security benefits that come from an installed LIMS but without the added hassle of maintaining an implemented application.
Workflow, reagent, and stock tracking are imperative for the lab. The LIMS keeps track of stocks and reagents throughout the different workflows as it is crucial to identify which reagents are worth progressing. For the LemBix Laboratory, the LIMS has improved productivity as well as organized and enhanced the accuracy of its collected data. The on-demand solution has allowed the Lembix Laboratory to realize the benefits of automated workflows and data management, enabling its scientists to spend more time in scientific pursuit and less time overseeing systems for managing the vast amount of data.
Funding benefits
Another challenge in medical research is that often the source of seed money for new research endeavors in academic research institutions are justified to fund buildings and equipment rather than software projects that can appear intangible and have unspecified outcomes or timelines. Thus, obtaining sufficient resources to purchase, install and provide ongoing support of a traditional client-server LIMS for a single or multiple laboratory environment can be a daunting task. The monthly payment structure for LIMS-on-Demand is better suited for this type of funding versus a large upfront capital expenditure and scales nicely for laboratories that need to dial their user base up or down with their workload. Furthermore, since the on-demand model means that the backend IT infrastructure is managed and maintained at the vendor site, laboratories with minimal or no IT staff do not need to take on this added burden.
Conclusion
An on-demand LIMS solution is ideal for scientists undertaking high volumes of screening and for academics in the translational science community confronted with the generation of large quantities of data. High-content screening is uncovering signaling pathways, genes, compounds, or drugs that can be used to promote nerve growth. The screening pipeline includes solid experimental techniques combined with instrumentation and analytical tools. The process produces enormous amounts of data.
The on-demand LIMS solution provided several benefits for the LemBix Laboratory, including all the advantages of a fully installed LIMS, such as built-in workflows, a powerful database, the ability to capture, store and analyze lab data, monitor resources, and integrate with instrumentation and reporting templates. All this can be achieved while minimizing the need for IT resources and eliminating expensive hardware and software. The scientists no longer have to rely on the university’s IT team to maintain the servers and no longer have database licensing issues.
Thermo Scientific LIMS-on-Demand has made it possible for the LemBix laboratory to control its data more easily, freeing up valuable resources in the laboratory to focus on the core mission of finding a cure for spinal cord injury.
About the Author
Vance Lemmon, PhD, is Walter G. Ross Distinguished Chair in Developmental Neuroscience, Professor of Neurological Surgery, The Miami Project to Cure Paralysis, Center for Computational Sciences, John P. Hussman Institute for Human Genomics, Univ. of Miami Miller School of Medicine.
This article was published in Bioscience Technology magazine: Vol. 34, No. 9, September, 2010, pp. 16-18.