Where do we fit into this? We’ve identified some putative drug targets for safer cellular rejuvenation. By applying machine learning ‘driver’ clocks to cellular reprogramming. And we’re ready to validate these targets. We’ve got this list of genes that we want to throw into a cell. And now it’s just a matter of just bringing in slightly more financing, then testing these genes and seeing if the bioinformatics are as exciting as we think they are.
So let’s go back to the beginning. We set out in 2017, with the backing of Jonathan Milner who’s an angel in Cambridge, UK, to tackle mitochondrial DNA mutations. This is a type of damage that accumulates with age. And we had some promising molecules that could combat these mitochondrial DNA mutations.
Something I wanted to look at early on was whether we can show you in an non-arguable way that this is the right approach to therapeutic intervention in aging. And it was actually my investor, Jonathan, that put me in the direction of the epigenetic aging clocks. The moment I found out about these clocks, it presented a fantastic opportunity to audit our hypothesis. So if mitochondrial DNA mutations were really the be-all and end-all of aging, then they should have a dramatic effect on this epigenetic aging clock, which was an agreed upon measure of aging. I know there’s lots of measures of aging, but at the time it (the clock) was relatively new as far as something everybody could agree on. And so we’ve done a mouse experiment with this mouse called the mutator mouse – it has way more mitochondrial DNA mutations, and it gets older faster, you get premature aging. So it’s very provocative, the link between this damage and the aging phenotype. And we had a drug that could slow down some of these aging phenotypes. But there were two questions.
Does this mouse, which shows a premature aging phenotype, show acceleration of the clock? Is there this really strong link between mutations (mitochondrial DNA mutations) and the clock? That’s the first question. Second question was, does our drug impact the clock?
There was no such thing as a mouse clock service that we could send samples off to for measurements. So we recruited our first full time employee, who learned the methods directly from the lab in Cambridge that created the first multi-tissue mouse epigenetic ageing clock, so that we could do what was needed to do. And we measured the clock in our mice, and surprisingly, the mutator mouse, although it showed a premature aging phenotype on the outside, the clock wasn’t accelerated at all. So the clock showed just the chronological age of the mouse, even though the mouse looked dramatically older. So that was a surprise to us. Even more surprising was that we slowed down the epigenetic aging clock in these mice. So there didn’t seem to be a connection between the clock and the mutations, but a drug designed to reduce the mutations did slow down the clock. And we later found out that only in this mouse, we slow down the clock, if we use these drugs in wild type mice, we don’t slow down the clock. So there’s some interesting biology there!
But the main thing about this experiment was that it was trying to find out whether targeting mitochondrial DNA mutations is the best lever for therapeutic intervention in aging. Its certainly an interesting approach for a niche aspect of aging, but for us it (the result) was a pivot point. The clocks told us that perhaps this isn’t the best approach right now.
So where do we go to look for better levers? Around the same time, we took on an intern called Brendan Swain, and we were both really excited about (1) ageing clocks (2) the Tabula Muris Senis, which is a Fantastic aging resource. For those that are not familiar, the Tabula Muris Senis is a database with single cell transcriptomes of the aging mouse at multiple time points, from every single cell, and every organ in the (mouse) body. It is basically a playground for aging scientists, to try and come up with things and look for phenomena. And what me and Brandon were really excited about was the logical extension of aging clocks. Could we create a clock that enabled a CRISPR screen for aging? Could we knock out every gene in the genome, have a clock to get a (ageing) readout, and get a relationship between every gene in the genome and aging, so we could systematically go through everything and let the data do the talking – so the genes will reveal themselves according to their relationship to the clock.
And the technical solution we needed to solve for this CRISPR screen for aging was a single cell aging clock based on a single cell transcriptome. And this was the enabling technology. So we played around with this Tabula Muris Senis, trying to develop methods for accurate single cell ageing clocks. And the short story is we did manage to crack this problem and generate accurate ageing clocks with single cell transcriptomes. And they have advantages. They also have disadvantages. But we did crack this problem. And just before we were going to go ahead and do the CRISPR screen, we realized there were a couple of problems. Firstly, the screen we were planning would just be single CRISPR knockouts. On a 10x Genomics machine, you could do a single CRISPR knockout in each cell and get a simultaneous transcriptome from each cell. But that’s only single gene perturbations. So you limit your question to ‘how can I rejuvenate with a single gene?’ but the more exciting question is ‘how can I rejuvenate, full stop?’ whether that’s a combination of four genes, or five genes, we don’t know. So with the 10x system that we were going to use, we didn’t have access to this combinatorial space. So that was the first problem. And then secondly, we realized that the clock we generated was built out of genes. And these genes were very interesting, some of them were known aging genes. And the more we looked at them, the more we realized we were looking at a lot more than just a single cell aging clock, we were perhaps looking at the aging biology itself. I mean, the original epigenetic aging clock, it’s a big question. Like, what are they? What’s the underlying biology? But with these gene base clocks, those answers were easier to spot. And so now we’re at the The Milner Therapeutics Institute, inside the Jeffrey Cheah Biomedical Centre, and we’re going to try and validate these genes. So, that’s the high level story.