High content analysis of 3-D cell cultures with multidimensional fluorescence imaging

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The response of cells to stimuli depends on cell signalling processes, which are combinations of molecular interactions. Disease is associated with deviations from normal signalling processes and so reading out molecular interactions in cells can help elucidate mechanisms of disease and also provide a means to evaluate potential therapeutic drugs. Many of the signalling molecules in cells are proteins and their interactions are widely studied using microscopy with proteins of interest being labelled with fluorescent molecules ("fluorophores"). For drug discovery, fluorescence imaging of arrays of cells is automated so that the effect of many compounds on cell signalling processes can be "assayed". Fluorophores are "excited" by radiation at a wavelength at which they absorb and the resulting characteristic emission (fluorescence) is recorded using an imaging detector. By labelling different kinds of protein with different fluorophores and comparing the images at their respective emission wavelengths, it is possible to learn about protein interactions by observing when they appear in the same place at the same time. Unfortunately this "co-localisation" is usually limited by diffraction of light to a resolution of a few 100 nm - much larger than the size of typical signalling proteins (~1-10 nm). It is possible, however, to confirm interactions using Förster Resonant Energy transfer (FRET), which entails labelling the proteins with different fluorophores and observing when energy is transferred between them. This energy transfer can only occur if they are within ~10 nm of each other. The most quantitative way to read out interactions using FRET is through the reduction in the fluorescence lifetime of the "donor" fluorophore as it loses energy due to the energy transfer. Fluorescence lifetime measurements can be made in every pixel and this fluorescence lifetime imaging (FLIM) enables protein interactions to be mapped in space and time. Fluorescence lifetime can also be used to distinguish different molecular species or different states of naturally fluorescent molecules that are involved in regulating the consumption of energy in the cell, which can also be altered by disease. For cell biology research and for drug discovery, fluorescence-based studies typically involve imaging thin - and therefore transparent - layers of cells. Unfortunately this is not a physiologically normal environment for cells and they often behave differently compared to when they are in their normal 3-D tissue context. However, it is highly challenging to image cells in native biological tissue and even more so to realise this in a high throughput mode for drug testing. Instead, there is increasing interest in assaying synthetic 3-D cultures comprising many cells that interact with each other, presenting behaviour reminiscent of that in native tissue with greater optically accessibility - although unfortunately they can scatter and absorb light more strongly than thin layers of cells. Such 3-D cell cultures can be arrayed for rapid imaging, however, and we propose to develop an automated platform to provide 3-D images of such cell cultures, utilising FLIM to read out molecular interactions. For this we will optimise the 3-D cell culture and labelling methodologies for fluorescence imaging and will develop and evaluate automated microscopes for FLIM-based assays. For larger samples we will utilise multiphoton excitation, which entails illuminating the fluorophores at twice the wavelength usually required for excitation, such that they need two photons arriving simultaneously. This two photon absorption is intensity-dependent and so can be arranged to occur only in the focal plane of a scanning laser beam such that the emitted photons all originate from a specific depth in the sample. Scanning the focal plane then enables 3-D imaging. The longer wavelength light is less phototoxic and is scattered less by the sample, thus enabling deeper imaging.