Cell culture interactomic engineering

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Cell therapy is now coming of age and the number of applications where cells are multiplied and applied to treat patients is blooming. To do so, a new generation of biochemical engineers, able to consistently produce large number of cells of the highest quality, is needed. One of the challenges of these production processes is that each primary cell cultures (PCC), coming directly from a donor, or the patient himself, has very specific biochemical needs that are still not all met. Often, biological additives (BA) of partially undefined nature, such as foetal bovine serum (FBS) are used. However, the potential risks, both in terms of safety and product consistency, of using these BA are high and must be avoided. Still, despite the fact that most of the strong individually-acting factors in these additives have been identified and are now available, we are still missing a good part of BA activity source. Most probably, the remaining effect of these complex mixtures lies in synergistic interactions between minor, unknown components. This proposal therefore aims at identifying these unidentified factors in BA that act on PCC in interaction with each other, BA/PCC interactomes. To do so, we will combine a number of approaches: i) new fractionation methods to separate the molecules comprised in these mixtures in quantities sufficient to test their effects; ii) statistical design of experiment to test in the least number of experiments the largest possible number of synergies; iii) automated fluid handling stations and microscopes to prepare the largest number of test conditions in each single experiment and analyse them in a non-destructive manner through long time period, and iv) cell image morphology analysis algorithms, based on 2D wavelet transform and multivariate statistics to monitor both cell growth AND morphology to ensure cell type integrity is maintained. The combination of these technologies will be performed in an iterative cyclic process, each round generating fractions that are leaner, which will make it possible to analyse them using proteomics to ultimately identify new groups of new compounds acting synergistically on specific cell systems. In a first project the interactome and proteome of FBS will be probed for its effect on human myoblast and keratinocytes. Later, other biological mixtures and cell systems will be studied. The knowledge accumulated during these studies will be structured in a Biological Interactome Database.