Manipulating Existing Methods of Cellular Quality Control to Clear Mutant Mitochondria

The SENS view of mitochondrial damage in aging starts with the fact that deletions accrue to mitochondrial DNA. When those deletions remove one or more of the thirteen genes necessary to the primary processes of energy generation, the mutant becomes either more able to replicate or more able to resist destruction by quality control processes. In some cases, the mutant strain takes over the cell and turns it into a dysfunctional exporter of harmful, reactive molecules. There are even mechanisms by which such broken mitochondria can be exported to surrounding cells, spreading the rot. We accumulate a small but significant population of these malfunctioning cells over the years, and this is one of the root causes of aging and age-related disease. It is a step on the way to the production of oxidized lipids, to pick one example of the downstream consequences, and that contributes to the progression of atherosclerosis.

The SENS approach to remediation involves gene therapy to produce backup copies of the necessary mitochondrial genes, ensuring that the supply of vital protein machinery isn't interrupted by genetic damage in mitochondria. Is it possible, however, to manipulate the existing machinery of mitochondrial quality control to ensure that mutants are reliably destroyed rather than slipping past the net? This is an open question, and good arguments can be made either way: one the one hand, the existing system is pretty comprehensive but still fails catastrophically, allowing mutant mitochondria to very quickly overtake their cells. It isn't clear that simply dialing up quality control activity is going to help at all. On the other hand, cells that are reprogrammed for pluripotency quite clearly rejuvenate their mitochondria. Answering this question is better achieved through action rather than debate: in this open access paper researchers demonstrate clearance of mutant mitochondria with large deletions from fly tissues via manipulation of existing quality control systems as a proof of principle. It isn't at all clear to me from reading the paper that the authors have created a mutant strain that deletes the important genes relevant to aging, however, and therein lies the vital detail. They have, however, created the basis for model organisms that could be used for further exploration of this topic, in a more efficient manner than has been possible in the past.

Mitochondria are membrane-bound organelles present in many copies in most eukaryotic cells. The circular mitochondrial genome (mtDNA) encodes proteins necessary for oxidative phosphorylation, which generates the bulk of ATP in most cells. Individual mitochondria contain multiple copies of mtDNA, each of which is packaged into a structure known as a nucleoid, with primarily a single mtDNA per nucleoid. This multiplicity of genomes per cell, in conjunction with mtDNA's high mutation rate and limited repair capacity, often results in cells carrying mtDNA of different genotypes, a condition known as heteroplasmy. Recent studies suggest that 90% of individuals have some level of heteroplasmy, with 20% harbouring heteroplasmies that are implicated in disease. If the frequency of such a mutation reaches a threshold, pathology results. Heteroplasmy for deleterious mtDNA can also arise in somatic tissues during development and in adulthood. It accumulates throughout life, and is thought to contribute to diseases of aging. These observations emphasize the importance of devising ways to reduce heteroplasmy in vivo.

Mitochondria-targeted site-specific nucleases provide one way to decrease the levels of heteroplasmy. In this approach, a site-specific nuclease is engineered so as to bind and cleave a specific mutant version of the mtDNA genome, promoting its selective degradation. This approach has recently been used to decrease the levels of heteroplasmy in patient-derived cell lines, in oocytes and in single cell embryos. However, these methods are likely to be challenging to implement in the adult, as the nuclease being expressed is a non-self protein; many cells must be targeted without off target cleavage effects; and individuals may be heteroplasmic for multiple deleterious mutations. Here we seek to promote cell biological processes that normally regulate mtDNA quality as an alternative approach to decreasing heteroplasmy in adults.

Mitophagy serves as a form of quality control that promotes the selective removal of damaged mitochondria. In one important pathway, dysfunctional mitochondria are eliminated through a process dependent on PTEN-induced putative kinase 1 (PINK1) and Parkin, loss of which lead to familial forms of Parkinson's disease. Regardless, the fact that mutant mtDNA accumulates in individuals wild type for PINK1 and parkin during aging indicates that if PINK1- and Parkin-dependent mitophagy and/or other pathways promote mtDNA quality control, they are often not active or effective. To identify ways of reducing the mutant mtDNA load in somatic tissues, systems are needed in which a specific deleterious heteroplasmy can be induced in vivo and followed over time, ideally in post-mitotic cells so as to eliminate potential confounding effects associated with stochastic segregation during cell division, and differential cell proliferation and/or cell death. Current in vivo models are cumbersome and limited, but we describe the generation and use of a transgene-based system of heteroplasmy in post-mitotic muscle to identify conditions that result in the selective removal of mutant mtDNA.

We demonstrate that the load of deleterious mtDNA can be decreased through several different interventions. Genetic and chemical screens using such a model should prove useful in identifying molecules that can cleanse tissues of a deleterious genome, via known and unknown mitochondrial quality control pathways. The many tools for regulated spatial and temporal control of gene expression in Drosophila will allow such screens to be carried out in a variety of tissues and environmental contexts, including aging. Our results show that adult muscle has a significant but limited ability to remove mutant mtDNA utilizing genes required for autophagy, and that mutant mtDNA removal can be greatly stimulated in several ways: by limiting the ability of mitochondrial fragments to re-fuse with the network (decreasing Mfn levels), by limiting their ability to undergo repolarization through ATP synthase reversal (ATPIF1 expression), by increasing the tagging of mtDNA-bearing fragments (increasing PINK1 or Parkin levels), and by increasing the frequency with which these tagged fragments are degraded (activation of autophagy). These observations have important implications for new therapies for mitochondrial disease and diseases of aging.


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