Genetically Encoded Trensor Circuits Report HeLa Cell Treatment with Polyplexed Plasmid DNA and Small-Molecule Transfection Modulators.

HeLa cell transfection with plasmid DNA (pDNA) is widely used to materialize biologicals and as a preclinical test of nucleic acid-based vaccine efficacy. We sought to genetically encode mammalian transfection sensor (Trensor) circuits and test their utility in HeLa cells for detecting molecules and methods for their propensity to influence transfection. We intended these Trensor circuits to be triggered if their host cell was treated with polyplexed pDNA or certain small-molecule modulators of transfection. We prioritized three promoters, implicated by others in feedback responses as cells import and process foreign material and stably integrated each into the genomes of three different cell lines, each upstream of a green fluorescent protein (GFP) open reading frame within a transgene. All three Trensor circuits showed an increase in their GFP expression when their host HeLa cells were incubated with pDNA and the degraded polyamidoamine dendrimer reagent, SuperFect. We next experimentally demonstrated the modulation of PEI-mediated HeLa cell transient transfection by four different small molecules, with Trichostatin A (TSA) showing the greatest propensity to boost transgene expression. The Trensor circuit based on the TRA2B promoter (Trensor-T) was triggered by incubation with TSA alone and not the other three small molecules. These data suggest that mammalian reporter circuits could enable low-cost, high-throughput screening to identify novel transfection methods and reagents without the need to perform actual transfections requiring costly plasmids or expensive fluorescent labels.

Simultaneous Plate-Reader Characterization of Promoter Activity and Cell Growth in Engineered Mammalian Cells.

Automated high-throughput methods that support tracking of mammalian cell growth are currently needed to advance cell line characterization and identification of desired genetic components required for cell engineering. Here, we describe a high-throughput noninvasive assay based on plate reader measurements. The assay relies on the change in absorbance of the pH indicator phenol red. We show that its basic and acidic absorbance profiles can be converted into a cell growth index consistent with cell count profiles, and that, by adopting a computational pipeline and calibration measurements, it is possible to identify a conversion that enables prediction of cell numbers from plate measurements alone. The assay is suitable for growth characterization of both suspension and adherent cell lines when these are grown under different environmental conditions and treated with chemotherapeutic drugs. The method also supports characterization of stably engineered cell lines and identification of desired promoters based on fluorescence output.

High-Throughput Spectroscopic Analysis of mRNA Capping Level.

Eukaryotic mRNAs are characterized by terminal 5' cap structures and 3' polyadenylation sites, which are essential for posttranscriptional processing, translation initiation, and stability. Here, we describe a novel biosensor method designed to detect the presence of both cap structures and polyadenylation sites on mRNA molecules. This novel biosensor is sensitive to mRNA degradation and can quantitatively determine capping levels of mRNA molecules within a mixture of capped and uncapped mRNA molecules. The biosensor displays a constant dynamic range between 254 nt and 6507 nt with reproducible sensitivity to increases in capping level of at least 20% and a limit of detection of 2.4 pmol of mRNA. Overall, the biosensor can provide key information about mRNA quality before mammalian cell transfection.

Fluorescence diffuse optical monitoring of bioreactors: a hybrid deep learning and model-based approach for tomography.

Biosynthesis in bioreactors plays a vital role in many applications, but tools for accurate in situ monitoring of the cells are still lacking. By engineering the cells such that their conditions are reported through fluorescence, it is possible to fill in the gap using fluorescence diffuse optical tomography (fDOT). However, the spatial accuracy of the reconstruction can still be limited, due to e.g. undersampling and inaccurate estimation of the optical properties. Utilizing controlled phantom studies, we use a two-step hybrid approach, where a preliminary fDOT result is first obtained using the classic model-based optimization, and then enhanced using a neural network. We show in this paper using both simulated and phantom experiments that the proposed method can lead to a 8-fold improvement (Intersection over Union) of fluorescence inclusion reconstruction in noisy conditions, at the same speed of conventional neural network-based methods. This is an important step towards our ultimate goal of fDOT monitoring of bioreactors.

Tetracycline-mediated fluorescence correlates with passage number and ß-galactosidase activity in HeLa and HEK293T cells.

We report data consistent with tetracycline-mediated fluorescence having the potential to be an effective marker of senescence in immortalised cells. HeLa cells that had previously undergone more than 20 passages were transiently transfected with a plasmid encoding a novel tetracycline-inducible transgene featuring an open reading frame for green fluorescent protein. While characterising the performance of this plasmid and transfection procedure, HeLa cell fluorescence was observed to result from incubating cells with media containing 2 µg/ml tetracycline alone, without plasmid or transfection reagent. To investigate this phenomenon further, HeLa and HEK293T cells were purchased from a tissue culture collection and after cultivation over 4-23 passages, incubated with media containing 2 µg/ml tetracycline. For both cell lines, tetracycline-mediated fluorescence increase correlated with passage number increase. This effect in HeLa and HEK293T cells was also borne out by expression of ß-galactosidase activity, an imperfect but widely used marker of cellular senescence. These data suggest tetracycline may have utility as a marker of cellular senescence in immortal cells and can inform future investigation and validation of this previously unreported application for this reagent.