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Autranomics – high-throughput cell production

Manual work is out – the rapid production of cells that carry foreign genetic material for use in research and industry can only be achieved with a high degree of automation. A fully automated process is needed to cultivate, analyse and select the cells. One such automated system has been developed by the Fraunhofer Society and the Max Planck Society in a collaborative project called Autranomics.

High-throughput technologies that enable genome sequencing and protein analysis have been making rapid progress. Such technologies enable researchers to study and analyse ever-larger amounts of material in increasingly shorter times. However, while medicine and the bioproduction of drugs and enzymes have already benefited enormously from these developments, such efficiency improvements lead to problems in replenishing the large amounts of material needed. In order to process large amounts of material using high-throughput processes, increasing amounts of raw materials in the form of cell lines need to be made available. And this is where the problem often lies, as manual laboratory production can rarely deliver sufficient standardised quality cells quickly enough. This is what "Autranomics", the joint Fraunhofer/Max Planck project, was seeking to change. In addition to the Fraunhofer Institute for Manufacturing Engineering and Automation (IPA) in Stuttgart, the project also involved the Fraunhofer Institute for Physical Measurement Techniques (IPM) in Freiburg, the Fraunhofer Institute for Applied Information Technology (FIT) in Sankt Augustin and the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden.

Dipl.-Ing. Alexej Domnich has been a scientist and project leader in the Department of Automated Cell- and Tissue Culture at the Fraunhofer IPA in Stuttgart since 2008. His work specifically involves the development of control architectures used in complex mechatronic systems and plants. © Fraunhofer Society

Autranomics, which is short for "Automated Transgenomics", focused on the development of an automated system for the cultivation and handling of cell lines. The "Autranomics" system works as follows: cells of interest are equipped with foreign genetic information that enables them to produce large amounts of specific proteins. Embryonic mouse stem cells (ESC) and HeLa cells (HeLa is a human cell line that has been used by researchers for many decades) were used to develop the automated system. "We start with approximately 300,000 cells per batch and end up with around 150 million cells within ten days or so. Our high-throughput technologies enable us to produce around 500 cell lines per month, around six times more than the manual process does," says Alexej Domnich, project leader at the IPA. He further explains that they are currently only using a pilot system, and that they expect significant efficiency improvements in the future. He comments: "We have not yet reached the maximum production limit."

Autranomics is only the beginning – capacity will be expanded


For Domnich, the project is a success, and not just because of the outstanding results achieved. Autranomics also shows that it is possible for engineers and biologists from different institutions to work together to achieve a common goal. As so often in research, interdisciplinary cooperation between engineers and biologists was both a necessity and a challenge. "Biology dictates its own laws. Many essential biological processes vary with regard to the timing and duration of biological activity in living organisms. Researchers are constantly dealing with flexible processes. The engineers found this quite a challenge, and we had to develop specific concepts that met everybody's needs," said Domnich.

An automated process is used to pick the cells. The two images at the top show the device used to do this, and the bottom two show how it is done. Optical, microscopic monitoring and image processing functions have been integrated into the researchers’ “cell picker model”. © Fraunhofer Society

The cooperation partners worked very well together. The IPM integrated an automated cell microscope into the incubator. "The conditions in the incubator were not exactly ideal for the technical system we wanted to integrate and we had to find ways to ensure that the system functioned stably," said Domnich. The microscope for the optical control of the processes is a key part of the system because imaging and automated analysis make it possible to produce cells autonomously. The microscope shows cell coverage in the culture dishes (24-well microtitre plates) thus providing information about how well the cells are growing. And this is where the competence of the FIT researchers came in. IT experts at the FIT developed special, self-learning evaluation algorithms for the microscope data. The MPI-CBG dealt with everything related to cell biology. The MPI-CBG researchers carried out the transfections, which involved genetic modification of murine ESC and HeLa cells so that they produced specific proteins. All these developments converged at the IPA where a functional system was assembled. "IPA researchers also developed the software for the models and the primary process control; around 80 percent of the hardware was designed at the IPA," said Domnich. Some of the issues the researchers had to deal with related to how and when the microtitre plates needed to be introduced into the device. They also focused on information required by users and how this information could be made available. 

Traceability – an important tool for quality assurance

The Autranomics pilot system requires a surface area of around 12 square metres (approximately 3 x 4 m). © Fraunhofer Society

Tracability was an important issue the researchers had to consider. Domnich explains: "We had to make sure that our system allowed us to trace every single cell colony in the individual wells. This is done by labelling the cells with fluorescent dyes and by putting bar codes on the microtitre plates. This gives us what are called life sciences IDs that provide information about the number of cells that have been expanded and about the cell passage number." It is important to have this information, as the system decides autonomously whether and when the cells are passaged, i.e. transferred from one microtitre plate well to several new wells. The IPA was instrumental in finding ways to record process data and ensure automatic traceability. "We have made an important contribution towards the development of a worldwide standard in this area," says Domnich. This standard, called SiLA, i.e. "Standardisation in Laboratory Automation", is being developed by a consortium of research institutions and companies, including the IPA.

The Autranomics pilot system was originally set up at the MPI-CBG in Dresden, but has since been transferred to Stuttgart where it can be used by research and industry partners for their specific research projects. At the same time, the IPA is working on optimising the system. They plan to integrate an automated cryoconservation module into the system. "This requires us to develop special soft- and hardware protocols that will enable the transfer of the cells into cryowells. We will then be able to remove and ship them to our customers without further treatment," says Domnich highlighting their future plans.

Website address: https://www.gesundheitsindustrie-bw.de/en/article/news/autranomics-high-throughput-cell-production