Thursday, 25 July 2019

Mitochondrial networks and Ageing in the Variance

Mitochondrial DNA (mtDNA) populations within our cells encode vital energetic machinery. MtDNA is housed within mitochondria, cellular compartments lined by two membranes, that lead a very dynamic life. Individual mitochondria can fuse when they meet, and fused mitochondria can fragment to become individual smaller mitochondria, all the while moving throughout the cell. The reasons for this dynamic activity remain unclear (we’ve compared hypotheses about them before here and here, with blog articles here). But what influence do these physical mitochondrial dynamics have on the genetic composition of mtDNA populations?

MtDNA populations can, naturally or as a result of gene therapies, consist of a mixture of different mtDNA types. Typically, different cells will have different proportions of, say, type A and type B. For example, one cell may be 20% type A, another cell may be 40% type A, and a third may be 70% type A. This variability matters because when a certain threshold (often around 60%) is crossed for some mtDNA types, we get devastating diseases.

We previously showed mathematically (blog) and experimentally (blog) that this cell-to-cell variability in mtDNA proportions (often called “heteroplasmy variance” and sometimes referred to via the “mtDNA bottleneck”) is expected to increase linearly over time. However, this analysis pictured mtDNAs as individual molecules, outside of their mitochondrial compartments. When mitochondria fuse to form larger compartments, their mtDNA is more protected: smaller mitochondria (and their internal mtDNA) are subject to greater degradation. More degradation means more replication, and more opportunities for the fraction of a particular type of mtDNA to change per unit time. In a new paper here in Genetics, we show (using a mathematical tour de force by Juvid) that this protection can dramatically influence cell-to-cell mtDNA variability. Specifically, the rate of heteroplasmy variance increase is scaled by the proportion of mitochondria that exist in a fragmented state. (It turns out that it's the proportion of itochondria that are fragmented that's important -- not whether the rate of fission-fusion is fast or slow).


This has knock-on effects for how the cell can best get rid of low-quality mutant mtDNA. In particular, if mitochondria are allowed to fuse based on their quality (“selective fusion”), we show that intermediate rates of fusion are best for removing mutants. Too much fusion, and all mtDNA is protected; too little, and good mtDNA cannot be sorted from bad mtDNA using the mitochondrial network. This mechanism could help explain why we see different levels of mitochondrial fusion in different conditions. More broadly, this link between mitochondrial physics and genetics (which we’ve also speculated about here (blog) and here) suggests one way that selective pressures and tradeoffs could influence mitochondrial dynamics, giving rise to the wide variety of behaviours that remain unexplained. Juvid, Nick, and Iain

Friday, 19 July 2019

The cell's power station policy


Our cells are filled with populations of mitochondrial DNA (mtDNA) molecules, which encode vital cellular machinery that supports our energy requirements. The cell invests energy in maintaining its mtDNA population, like us using electricity-powered tools to help maintain our power stations. Our cellular power stations can vary in quality (for example, mutations can damage mtDNA), and are subject to random influences. How should the cell best invest energy in controlling and maintaining its power stations? And can we use this answer to design better therapies to address damaged mtDNA?

In a new paper "Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations" free here in PLoS Computational Biology, we attempt to answer this question using mathematical modelling, linking with genetic experiments done by our excellent collaborators at Cambridge (Payam Gammage, Lindsey Van Haute and Michal Minczuk). We first expand a mathematical model for how diverse mtDNA populations within cells change over time – building new power stations and decommissioning old ones, under the “governance” of the cell. We then produce an “energy budget” for the cellular “society” – describing the costs of building, decommissioning, and maintaining different power stations, and the corresponding profits of energy generation.

We find some surprising results. First, it can get harder to maintain a good energy budget in a tissue (a collection of individual cellular “societies”) over time, even if demands stay the same and average mtDNA quality doesn’t change. This is because the cell-to-cell variability in mtDNA quality does increase, carrying with it an added energetic challenge. This increased challenge could be a contributing factor to the collection of problems involved in ageing.

An overview of our approach. A mathematical model for the processes and "budget" involved in controlling mtDNA populations makes a general set of biological predictions and explains gene-therapy observations

Next, we found that cells with only low-quality mtDNA can perform worse than cells with a mix of low- and high-quality mtDNA. This is because low-quality mtDNA may consume less cellular resource, although global efficiency is decreased. Linked to this, removal of low-quality mtDNA (decommissioning bad power stations) alone is not always the best strategy to improve performance. Instead, jointly elevating low- and high-quality mtDNA levels, avoiding this detrimental mixed regime, is the best strategy for some situations. These insights may help explain some of the negative effects recently observed in cells with mixed mtDNA populations.


Our theory suggests that mixed mtDNA populations may do worse than pure ones, even if the pure population is a low-functionality mutant. Image from Hanne's post here 


We identified how best to control cellular mtDNA populations across the full range of possible populations, and used this insight to link with exciting gene therapies where low-quality mtDNA is preferentially removed through an experimental intervention (using so-called “endonucleases” to cut particular mtDNA molecules). We found that strong, single treatments will be outperformed by weaker, longer-term treatments, and identified how the mtDNA variability we know is present can practically effect the outcome of these therapies. We hope that the principles found in this work both add to our basic understanding of ageing and mixed (“heteroplasmic”) mitochondrial populations, and may inform more efficient therapeutic approaches in the future. Iain, Hanne, Nick
(Hanne's also written a post about this paper, you can read it here)

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