EACR 2016
DNA repair and mutations as targets for personalised therapy
Prof Zoltan Szallasi - Boston Children's Hospital, Boston, USA
We are very much interested in DNA repair pathway aberrations in cancer. So DNA repair is an extremely important process in normal cells, normal cells need to maintain genomic integrity in order to survive and to maintain the normal status of cells and cancer cells very often have major DNA repair pathway aberrations which, it’s a very important point, makes them very often sensitive to certain types of chemotherapeutic agents. So the most famous, or the best known, example of that is homologous recombination deficiency or incompetence and cells in which this error-free repair mechanism doesn’t work, or doesn’t work well, are particularly sensitive to either platinum based therapy or PARP inhibitor based therapy, PARP inhibitors are a recent development in cancer therapy and it seems like one of the most exciting recent success stories in cancer therapy. So my lab is interested in how to quantify, how to detect, different types of DNA repair pathway aberrations in tumour biopsies and I was presenting our results.
Probably it’s easier if I explain it through a particular gene which is the famous Angelina Jolie gene, BRCA1, the BRCA gene. So this gene is very important to maintain homologous recombination. Homologous recombination is a DNA repair pathway that allows error-free DNA repair, especially if the cell encounters a double strand break when the DNA is completely broken, both strands. That’s something the cell really wants to fix because then that part which is away from the centromere will be lost and the cell cannot allow losing huge chunks of a genome so it really wants to fix it. Now, if the BRCA gene is not present or it does not work then those cells will be very sensitive to a particular type of therapeutic approach, PARP inhibitors, that tends to induce, tends to overload the cell with a lot of double strand breaks. So PARP inhibitors and platinum agents tend to induce a lot of double strand breaks and here the point was that the BRCA mutant, the BRCA deficient, cells are not able to fix those double strand breaks at a pace that would be required for the survival of the cells. So that’s why this therapy works and the beauty of it, especially with PARP inhibitors, is that the normal cells, the non-cancerous cells still have BRCA function present. So if you induce double strand breaks in those cells they can fix it. So the normal cells will survive, the tumour cells completely lack this mechanism, that’s why they are very sensitive. This is a very simple point but that’s why. Actually there is a huge therapeutic window, so there is about a thousand-fold difference in the sensitivity between normal cells and cancer cells for these agents.
Now the big question is, and that’s where we enter the game or the picture, is how to tell whether a given tumour lacks this mechanism or not. You can look at BRCA, the BRCA gene and the mutation, and that’s a good first step. All BRCA mutant patients will be like this but there are other BRCA related mechanisms that feed into this pathway and they might also be mutated. So in a BRCA wild-type, in a BRCA proficient cell, there might be other BRCA related mechanisms that are deficient that will cause the very same phenotype and that’s not trivial to find. You can sequence everything, you can do RNA-Seq or you can quantify the gene expression levels but it is much easier to do something else, what we are doing, looking at the DNA aberration profile and based on that we can say that if homologous recombination is not working in this cell then we see this particular type of DNA aberration profile because this is the consequence of the fact that BRCA is not functioning properly. So that’s what we do, again, it’s very, very simplified and for an expert there would be at least a hundred questions and there would be a hundred issues or problems one could raise but this is sort of the gist of it, what we are doing. And we can expand it because we are looking at other DNA repair pathways. We look at what type of DNA aberrations different chemotherapeutic agents induce, is there a difference? Based on this method we understood how one of the resistance mechanisms in PARP inhibitor and platinum based therapy emerges, it seems that actually the therapy itself is very efficiently inducing the resistance mechanism. So when you look at the genome in a detailed fashion you can really learn a lot about how DNA repair pathways work and whether they are functioning or not functioning and what is their relative efficacy. Based on that you can understand a lot about the phenotype of the cell, especially in regards to response to these agents.
Do you also check protein levels?
Not really. We understand and appreciate the fact that it’s a good idea to measure protein levels but we are actually sequencing DNA, we are not looking at RNA expression levels although we do it in other settings. This is the DNA aberration profile. So we could look at the level of the individual proteins that play a role in this but it’s not very easy to do in sufficient detail. Again, if you look at the BRCA genes somehow you can measure the BRCA protein level but even that the BRCA gene is sufficiently expressed there might be another player, another co-player or co-operating factor, that is not present. So measuring every possible player in this pathway is not that trivial and even if they are present at some level maybe there is some sort of a post-translation modification that they do not undergo that will render them inactive. So we might find them being present by immunohistochemistry or Western blot analysis or protein level measurements but they might still not work properly. That’s why what we are saying - we want to see signs, we want to see evidence that this mechanism works properly or does not work properly and since their role is fixing errors in DNA sequence, we just have to sequence and it’s going to be there.
