Improved Prospects for Measuring Mitochondrial DNA Damage

Higher levels of mitochondrial DNA (mtDNA) damage is one of the characteristic differences between old tissue and young tissue. It is thought to be a major contribution to degenerative aging, via a complex process that causes a small but significant fraction of cells to become overtaken by damaged mitochondria, malfunction, and export large quantities of damaging oxidative waste compounds into the surrounding tissue.

There are still a fair number of scientists who argue against the mitochondrial free radical theory of aging, however. Given the present state of research, my impression has been that the fastest way to prove beyond all doubt that mitochondrial DNA damage is a root cause of aging is to finish up one of the means to repair or replace mitochondria or mitochondrial DNA, and then try it out in mice. Given optimal funding that is only a couple of years distant, as the work is fairly advanced - but that optimal funding doesn't exist yet. Mitochondrial repair isn't a well-funded line of research, more is the pity, and as is the case for most of the best and most promising ways to intervene in the aging process.

Here, however, is a new technology that might have the potential to validate mitochondrial DNA damage as a direct cause of aging, or at least provide much better hard evidence than presently exists:

The accumulation of mtDNA mutations is associated with aging, neuromuscular disorders, and cancer. However, methods to probe the underlying mechanisms behind this mutagenesis have been limited by their inability to accurately quantify and characterize new deletion events, which may occur at a frequency as low as one deletion event per 100 million mitochondrial genomes in normal tissue. To address these limitations, [researchers] developed a ddPCR-based assay known as "Digital Deletion Detection" (3D) that allows for the high-resolution analysis of these rare deletions.

"It is incredibly difficult to study mtDNA mutations, let alone deletions, within the genome. Our 3D assay shows significant improvement in specificity, sensitivity, and accuracy over conventional methods such as those that rely on real-time PCR. The increase in throughput afforded by droplet digital PCR shortened the analysis of deletion events to days compared to months using previous digital PCR methods. Without the technology, we could not have made this discovery."

[The researchers] analyzed eight billion human brain mtDNA genomes and identified more than 100,000 genomes with a deletion. They discovered that, contrary to popular belief, the majority of the increase in mtDNA deletions was not caused by new deletions but rather by the expansion of previous deletions. They hypothesized that the expansion of pre-existing mutations should be considered as the primary factor contributing to age-related accumulation of mtDNA deletions.

Link: http://www.eurekalert.org/pub_releases/2013-09/cg-shi083013.php

Comments

this seems like significant research, but I do not understand what the report means by 'expansion' of existing deletions.

Posted by: JohnD at September 4th, 2013 7:41 PM

@JohnD: They are claiming that mitochondrial DNA that is already damaged is more likely to get damaged again than undamaged mitochondrial DNA is likely to get damaged the first time.

I would imagine that - depending on how exactly they are measuring things - this effect in the data could be caused by clonal expansion of damaged mitochondria, as damaged copies take over the herd of mitochondria in a cell because they are damaged in the right way to evade the quality control mechanisms, which fits with the mitochondrial free radical theory of aging:

https://www.fightaging.org/archives/2006/10/how-age-damaged-mitochondria-cause-your-cells-to-damage-you.php

Alternately, damaged mitochondrial DNA tends to lead to mitochondria that produce more harmful free radicals, which raises the odds of being damaged again.

Posted by: Reason at September 4th, 2013 7:53 PM

@Reason and @JohnD

"They are claiming that mitochondrial DNA that is already damaged is more likely to get damaged again than undamaged mitochondrial DNA is likely to get damaged the first time."

Not quite. The deleted genomes are not accumulating more deletions. Rather, as the mitochondria replicate, the deletion bearing genomes are replicated preferentially. Thus over time 'clones' of the original truncated genomes begin to make up a larger fraction of all the genomes in the organelle. This is what is meant by 'clonal expansion'.

As tissues age, we know that an increasing proportion of mitochondrial genomes contain large deletions of some kind. One of the points of this paper is that this accumulation appears to be driven predominantly by clonal expansion of deletions acquired early in life (as opposed to an increased rate of acquisition of new deletions later in life). They don't address it directly, but these results are not quite consistent with the free radical theory of aging.

Posted by: SeanT at September 10th, 2013 4:50 PM

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