One of the last scientific papers from my PhD came out in April this year, as a shared-first author paper in the journal PNAS, and you can find it here. After having worked on biopharmaceutical manufacturing and cell-based therapies, I decided to work on the last remaining major category of current mammalian synthetic biology applications: biocomputing. In biocomputing, cells are treated as small computers which operate according to (Boolean) logic functions. Designing, engineering, and implementing gene circuits into cells then allows these cells to convert the presence or absence of signals (input), such as small molecules or environmental changes, into customized gene expression (output).
For our approach to biocomputing, we made use of the popular CRISPR/Cas9 platform. Mutant versions of the central Cas9 protein (called dead Cas9, or dCas9 for short) are frequently used to regulate gene expression, for instance by fusion with the inhibiting KRAB domain. So by using a cascade of different gRNAs (guide RNAs), we could demonstrate the construction of different logic functions (such as AND or XOR) by simply exchanging gRNAs, which is very easy and cheap by now. Then we went further and added a different Cas9 protein from another species. Basically, the Cas9 proteins were operating as our computation hubs/cores and the gRNAs as our software. Using this set-up, we were able to construct a half-adder circuit, the most complex biocomputing endeavor yet achieved in single mammalian cells. This could be advantageous for the improvement of cell-based therapies or, eventually, for using cells as actual computers.