Saturday, 10 September 2016

ARTICLE: Migration, mothers, mitochondria, and medicine

mtDNA diversity in human populations highlights the merit of haplotype matching in gene therapies

EC Røyrvik, JP Burgstaller, IG Johnston
Molecular Human Reproduction 22 (11), 809-817 (2016)
  • The diversity of mtDNA in modern human populations may pose a challenge to gene therapies that aim to prevent the inheritance of deadly mtDNA disease; we use population and census data, and large-scale mtDNA sequence data, to assess this risk and suggest strategies to combat it.
Some mothers carry disease-causing mutations in their mitochondrial DNA (mtDNA), which can be passed on to their children. Amazing cutting-edge therapies are designed to avoid the inheritance of mutant mtDNA, by endowing a child with mtDNA from another woman (let's say Wilma) -- with no dangerous mutations -- instead of the mother's (let's say Miranda's) mtDNA. However, due to technical challenges in the implementation of these therapies, a small amount of the mother's mtDNA may remain in the child. If that initially small amount can become amplified -- say Miranda's mtDNA proliferates more quickly than Wilma's -- it may come to dominate cells in the child. Then the disease which the therapy attempted to avoid may become manifest -- as we've written about before

We have previously found, in mice, that the more different two mtDNA types are, the more likely one is to dominate over another. So if Miranda and Wilma have very different mtDNA, there's a good chance Miranda's might become amplified. But, although these effects are dramatic in natural mouse populations, we don't really know how likely this "winning" and "losing" was between human mtDNAs (as we'd see in the above therapies). Say Matilda and Wilma both come from London. How different will their mtDNA types likely be? And so, what is the risk that Matilda's mtDNA will beat Wilma's, potentially complicating therapies?

Human mtDNA varies by geography -- women from different parts of the world belong to different mtDNA "haplogroups". Some haplogroups are themselves very diverse, and some less so; haplogroups also differ from each other by varying degrees. So we needed to address two questions: (1) what are the likely mtDNA groups of women taken from a given region (say, Birmingham); and (2) how genetically different are two mtDNAs taken from these groups?
(left) Due to the history and evolution of human populations, some mtDNA types -- denoted here by letters -- are historically more common in different world regions. (right) Our analysis of large-scale sequence data tells us how genetically different two mtDNAs from randomly-sampled women from different ancestral backgrounds are likely to be (circle size). The more different, the more likely the therapies involving that pair of women will experience difficulties.

To answer these, we retrieved (from the NCBI database) over 7000 human mtDNA sequences, as well as information about the mtDNA makeup of pre-industrial different regions around the world, and census information about the UK's, London's, and Birmingham's ethnic makeup. We used this information to estimate the mtDNA makeup of modern human populations -- which have become highly mixed through migration in recent times. Using these estimates, we then simulated thousands of Matilda-Wilma pairings in specific regions around the world (including the UK, London, and Birmingham). We recorded the genetic differences between these simulated pairs of mtDNAs to see how different we may expect women from different regions to be. The results have just appeared in Molecular Human Reproduction here; a similar, pre-peer-review version can be viewed for free here.

We found that the size of genetic differences likely to arise when sampling pairs women from modern populations was around 20-80 SNPs (single nucleotide polymorphisms -- specific molecular differences in mtDNA). This level of difference was enough to lead to substantial segregation bias in mouse models, suggesting that unprincipled choice of Wilmas from the general population could be problematic. These large differences are in large part due to modern population mixing, with substantial mixing of African and Asian mtDNA in modern UK cities contributing to the diversity. We showed that "haplotype matching" -- checking that Wilma is genetically similar to Matilda -- decreases these differences and so decreases the likelihood of problems with therapies. We also created a preliminary chart to help this process, showing which human haplotypes are genetically similar to others -- hopefully this will both help scientific understanding and therapeutic implementation in this field. Iain and Ellen

Friday, 2 September 2016

ARTICLE: Controlling the control of our cellular power stations

Modulating mitochondrial quality in disease transmission: towards enabling mitochondrial DNA disease carriers to have healthy children

Alan Diot, Eszter Dombi, Tiffany Lodge, Chunyan Liao, Karl Morten, Janet Carver, Dagan Wells, Tim Child, Iain G Johnston, Suzannah Williams, Joanna Poulton
Biochem Soc Trans (in press) (2016)
  • Dysfunctional mitochondria are recycled by the cell in a process that helps avoid disease; we summarise extending and provide new information about this process, and show -- agreeing with our mathematical theory -- that it can be modulated with drug treatments, providing potentially new therapeutic avenues.
Mitochondria -- a focus of our research -- are "power stations" in our cells that produce the energy we need to live. Like the power stations we build, mitochondria contain machines that work to produce this energy. They also contain the genetic "instructions" on how to build these machines, in the form of mitochondrial DNA (mtDNA). MtDNA can become mutated, spoiling these instructions, giving rise to dysfunctional machines and causing problems in our cells. Thankfully, our cells have systems that helps remove these mutant mtDNAs and recycle the bad machines that they've produced. One example is "mitophagy" (from mito-(chondria) and -phagy (eating)), as we've written about before.

Mitophagy uses "autophagosomes" to remove mtDNA from the cell, but it's hard to observe and measure: our understanding of the process, and how we may influence it to address diseases, is limited. In a recent paper, we summarise current understanding of mitophagy, particularly during early development (of importance for the inheritance of mtDNA diseases). As experiments and models explore the process in more detail, different types of mitophagy (progressing through different pathways) have been identified, as have fascinating "surges" of mitophagy at different developmental stages. In a new paper in Biochemical Society Transactions we discuss how these individual results are helping to build an overall picture of how mtDNA populations are controlled by cells.

Figure: single-cell microscopy determines how many autophagosomes (green), potentially recycling dysfunctional mitochondria, exist in cells during development. Drug treatments (lower row) can influence this number, potentially allowing us to control cellular mtDNA populations.

We also present some interesting preliminary results that may help us better understand, and control, mitophagy. Very soon after fertilisation, as an egg cell starts to divide, it seems that the amount of mtDNA in the growing embryo may decrease, rather more than previously reported. The experimental team, centred on Alan Diot, explored how many autophagosomes existed within cells during this process, and also showed that post-fertilisation treatment with drugs can affect the number of autophagosomes and hence the mtDNA populations in dividing cells (see figure). We've previously shown using mathematical modelling that decreasing mtDNA content may help avoid the inheritance of mtDNA diseases -- these new results highlight the feasibility of these potential new therapeutic strategies to address mtDNA disease inheritance. Iain