Open Cures: A Protocol Outline for Mitochondrial Protofection

Open Cures is an initiative that aims to accelerate the development of existing longevity-enhancing biotechnologies demonstrated in the laboratory, but which are not being developed for commercial use in humans - largely due to regulatory barriers.

Open Cures is a volunteer initiative, open to everyone willing to help, that aims to speed the advent of biotechnologies that can slow down or repair aspects of the biological damage of aging and thus extend healthy human life. Our primary long-term goal is to bring together (a) promising but undeveloped biotechnologies of longevity and (b) the developers who can bring them to the clinic.

A fellow named Allen is one of the folk whose interest in the Open Cures vision convinced me that I needed to do more than just talk about it: you can see his comments on the old Vegas Group posts here at Fight Aging!, which contain the ideas that led to Open Cures.

The first phase of the Open Cures initiative aims to produce detailed documentation of existing forms of longevity biotechnology from the laboratory, as that documentation is a necessary precursor to bringing these potential foundations for future therapies to a wider audience. One of these nascent-but-demonstrated biotechnologies is mitochondrial protofection: a way to introduce new and undamaged mitochondrial DNA (mtDNA) into mitochondria in an attempt to repair the accumulated defects they bear - defects which contribute meaningfully to aging. You'll want to look back in the Fight Aging! archives for an introduction to that topic.

Mitochondria go bad as a natural consequence of their operation, and if enough go bad in the right way, and manage to escape the natural recycling mechanisms of the cell, then they take over that cell - causing it to malfunction, damage its surroundings, and release harmful reactive molecules that are carried throughout the body. Given enough cells doing this, you will become frail and eventually die as vital systems in your body become too damaged to operate correctly.

Since the launch of Open Cures, Allen has been looking into the published papers on mitochondrial protofection and writing up an outline for a protocol - the detailed step by step instructions that allow a technique in biotechnology to be replicated. The work to date can be found in the Open Cures wiki:

"Protofection" is a word coined by a group of scientists at the University of Virginia. It is the name they have given to a procedure they were developing which could possibly become a way to rejuvenate malfunctioning mitochondria by providing them with a new, undamaged genome.

I have been attempting to write a detailed set of instructions that would allow someone with sufficient knowledge and means to reproduce their work. So far I've come up with a bare-bones skeleton or scaffolding upon which a more experienced and better writer can build - adding detail, correcting errors, and making it more understandable. ... Corrections, additions, improvements, and comments are very welcome.

The next stage in this documentation project, one of many to come, is to find writers - such a grad-level life science students willing to freelance at reasonable rates - to flesh it out into as full a protocol document as can be built from the present state of published scientific work on protofection.

Two of the interesting items we discovered in the course of researching protofection more closely are that (a) a number of research groups attempted to replicate mitochondrial protofection over the past five years but met with no success, and (b) the scientists who initially demonstrated protofection have not yet published a clear explanation of the transcription factor used as a tool when introducing replacement DNA into mitochondria:

TFAM refers to human mitochondrial transcription factor A. This protein plays several roles in the mitochondria. It participates in mtDNA transcription, replication and maintenance. It also non- specifically binds to mtDNA which is the property we want to exploit as we attempt to pull pristine mtDNA into mitochondria which contains damaged DNA

[Missing details: We need to provide the DNA sequence in the format used by DNA synthesis machines. The DNA sequence must be verified as accurate. If we make a mistake here, which would be easy to do, the entire experiment is useless. The amino acid sequence is provided in the 2008 paper and the DNA sequence could be deduced from that, but there are some complications.

A. The published amino acid sequence may not be accurate. For one thing, a ")" symbol appears in the sequence and I have no idea what that means. Also the sequence contains an unusual repeated chain of amino acids which I suspect was not really part of the protofection protein.

B. The DNA will also have to be modified by adding a short sequence to each end of it. These two short sequences must each contain a site that can be cut by EcoI, the restriction endonuclease that will be used to prepare the DNA to be spliced into the bacterial plasmid that will be used later.

C. We also have to carefully check the DNA sequence to be sure that another EcoI restriction site is not found somewhere in the middle of the sequence.]

This second point, the missing definition, doesn't matter as much as you might think for the purposes of producing a good protocol document. When we do eventually find out the correct DNA sequence for the modified TFAM, it will be the work of moments to update the published document, and none of the other materials need to change.

I see this missing information as one good example as to why an initiative like Open Cures is both necessary and helpful: there are gaps that need filling in all these scientific publications and procedures, left there (intentionally and otherwise) because these works are not intended for a wider audience. Yet in order to accelerate progress, that wider audience is absolutely essential.

What are the effects of a large and energetic open development community on an industry? What happens when tens of thousands of people start making their products available for free, sharing data, designs, and improvements openly, and making money for services and expertise rather than through selling protected secrets? Fortunately we don't have speculate on this topic: we know. Look at the software industry, which is presently more vibrant and accomplished than it has ever been, whilst a large proportion of the most important software used around the world is open, freely shared, and constructed by a mix of professional and amateur contributors. Open source software is big business and that community gets things done.

Why is this relevant? It is relevant because what happens in software today will happen in biotechnology tomorrow. The tools and techniques of biotechnology continue to fall in price, and the knowledge of how to use them is already spread widely beyond the ivory towers in which it originated.


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