Detecting protein interactions in diseases

A tumor does not consist of a homogenous population of cancer cells. Therefore, to understand cancer, the tumor microenvironment and the interplay between the different cell types present in the tumor has to be taken into account, and how this interplay regulates the growth and survival of the cancer cells. A simultaneous analysis of the activity status of multiple signal networks at a single cell level will provide information on what networks are active in cancer cells, the crosstalk between pathways and how this is influenced by mutations. It also allows determination of to what extent signaling varies depending on positioning within the tumor, and in addition reveals how the surrounding non-malignant cells in the tumor microenvironment interact with the cancer cells. This knowledge will enable better diagnostics, improved prediction on response to therapy and possibly also act as an incitement to develop novel drugs that can modify the microenvironment to reduce cancer growth and ability to metastasize.

My on-going research and future plans include both methods development to meet such demands and application of these new methods, mainly in tumor biology. In situ proximity ligation assay (in situ PLA) combines multiple recognitions of affinity reagents with potent signal amplification, utilizing methods for DNA analysis to generate a signal that will be a surrogate marker of the targeted protein, protein-protein interactions or post-translational modifications of proteins. The method is based on pairs of proximity-probes (i.e. antibodies conjugated to strands of DNA) to detect the proteins of interest. Only upon proximal binding of these probes can an amplifiable DNA molecule be generated by ligation, which enhance the selectivity of the method even further. Since the development of in situ PLA (Söderberg et al., Nat Methods, 2006), most of our efforts have been related to the use of in situ PLA and to further improve the method, e.g. for multiplex analysis, simultaneous measurement of proteins and mRNA or to detect protein-DNA interactions. We have also been working on developing novel methods, such as proximity dependent initiation of hybridization chain reaction (proxHCR) (Koos et al., Nat Commun, 2015).