Other Causes of HRD: Chromosomal LOH, LST, and TAI

Dr. Ian Hagemann: There are signatures associated with the presence of a homologous recombination defect, cells that have HRD deficiency. So, we've agreed that they often have BRCA1 or BRCA2 mutations, and I implied that they might have difficulty repairing double-strand breaks. If you look at the genome of a cancer cell that has the HRD phenotype, that has this so called BRCAness phenotype, you can see certain mutational signatures. You can see numerous small insertions or deletions, 50 or greater nucleotides in length that's called mutational signature three in the catalogue of mutation signatures. You can also see loss of heterozygosity, or LOH that's illustrated on this diagram here. That's a phenotype in which instead of being heterozygous at the majority of low sigh that are able to show variation, the cell has lost one of those copies and repaired it by- repair that locus by duplicating the other locus. So, you'll see a loss of heterozygosity, and that can be picked up by sequencing. There's also a phenomenon or a type of genomic scar that's been designated as large scale state transitions, those are basically large rearrangements greater than 10 megabases in size within the chromosomes. And then finally, telomeric allelic imbalance is a form of genomic scar that looks specifically at the ends of chromosomes. And it's the idea of losing either the mothers or the fathers, haplotype, you've lost either one end of the maternally derived chromosome or the paternally derived chromosome. And I think the reason why these scars happen is that at the ends of the- the ends of the chromosomes are a little bit more susceptible to DNA damage. There's also fewer ways for those chromosomes to repair themselves by homologous recombination, because the ends of the chromosome don't have as many places to overlap with the good copy that the cell still has. Anyway, the take home message would be that these three types of scars LOH, LST and TAI can all be present in cancer cells that have homologous recombination deficit, and they can be picked up by certain assays that are available for characterizing tumors.

Dr. Thomas Herzog: Hey, Ian, let me ask you this, I'm going back to what we were just looking at here. So, a lot of people they get these three platforms, if you will, confused and it gets complicated. And as you know, some companies use three of these, some of them use one of these, some of them use two of these in terms of assessing whether there's going to be a likelihood for homologous recombination deficiency phenotype. And so, of these, which is by far the most important and how do we look at that?

Dr. Ian Hagemann: Well, I'll tell you the LOH is the most highly agreed. I think the LOH is used the most extensively. And so, I'd probably put that one in a little bit bigger print, if I had to. It's computationally a little bit easier to detect by sequencing and used by the most assays. In a survey that our professional organization, the Association for Molecular Pathology has done, it seems that LOH is used more extensively. So, that's - more data on that are forthcoming, but there's a fair amount of intellectual property in this space also. And there's a little bit of a lack of harmonization. There really are not professional guidelines from either our pathology societies or from the gynecologic side, from what we would call clinicians professional guidelines to dictate how HRD testing should be done. So, that's an area for improvement. Depending on how extensive the test is, you might find different rates of mutation and you might get a different determination for a particular patient. The baseline, the lowest level of testing, kind of the simplest test would just be to look for BRCA1/2 mutations. But as I was mentioning, a couple of slides ago, there can be mutations in what we might call the rare HRD gene, something like check two or break one that confer an HRD phenotype. The promoter of BRCA1 can be methylated. So, an assay that doesn't look for BRCA methylation might miss the fact that mutation is present. These genes have hotspots. If you look just at the hotspots, you might miss a non-hotspot mutation. And then another kind of hot topic that I might throw in is that these genomic scars, if they're present, they mean that cancer had HRD at some point. But sometimes under treatment will have reversion mutations where the cells reacquire an HR-proficient phenotype. So that's another complication that we have to think about, especially in patients who have had neoadjuvant therapy.

Dr. Thomas Herzog: So, most of the HRD testing is historical and it tells you where the cell has been not necessarily where it currently is, correct?

Dr. Ian Hagemann: Absolutely. Tells you the state the cell is in now.