Milestone achieved in mitochondrial genome editing

Milestone achieved in mitochondrial genome editing
Researchers at Korea’s Institute for Basic Science (IBS) have developed a new gene-editing platform called transcription activator-like effector-linked deaminases, or TALEDs — base editors capable of performing A-to-G base conversion in mitochondria.

The team’s discovery was the culmination of a decades-long journey to cure human genetic diseases, and could be considered to be the final missing piece of the puzzle in gene-editing technology. It has been published in the journal Cell.

From the identification of the first restriction enzyme in 1968, to the invention of polymerase chain reaction (PCR) in 1985 and the demonstration of CRISPR-mediated genome editing in 2013, each new breakthrough discovery in biotechnology further improved our ability to manipulate DNA, the blueprint of life. In particular, the recent development of the CRISPR-Cas system, or ‘genetic scissors’, has allowed for comprehensive genome editing of living cells. This opened new possibilities for treating previously incurable genetic diseases by editing the mutations out of our genome.

However, while gene editing has been largely successful in the nuclear genome of the cells, scientists have been unsuccessful in editing the mitochondria, which also have their own genome. Mitochondria, the so-called ‘powerhouse of the cells’, are tiny organelles in cells that serve as energy-generating factories. As it is an important organelle for energy metabolism, if the gene is mutated, it causes serious genetic diseases related to energy metabolism.

“There are some extremely nasty hereditary diseases arising due to defects in mitochondrial DNA,” said Jin-Soo Kim, Director of the IBS Center for Genome Engineering. “For example, Leber hereditary optic neuropathy (LHON), which causes sudden blindness in both eyes, is caused by a simple single point mutation in mitochondrial DNA.”

Another mitochondrial gene-related disease includes mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS), which slowly destroys the patient’s brain. Some studies even suggest abnormalities in mitochondrial DNA may also be responsible for degenerative diseases such as Alzheimer’s disease and muscular dystrophy.

The mitochondrial genome is inherited from the maternal line. There are 90 known disease-causing point mutations in mitochondrial DNA, which in total affects at least one in 5000 individuals. Many existing genome editing tools cannot be used due to limitations in the method of delivery to mitochondria. For example, the CRISPR-Cas platform is not applicable for editing these mutations in mitochondria, because the guide RNA is unable to enter the organelle itself.

“Another problem is that there is a dearth of animal models of these mitochondrial diseases; This is because it is currently not possible to engineer mitochondrial mutations necessary to create animal models,” Kim said. “Lack of animal models makes it very difficult to develop and test therapeutics for these diseases.”

As such, reliable technology to edit mitochondrial DNA is one of the last frontiers of genome engineering that must be explored in order to conquer all known genetic diseases, and the world’s most scientists have endeavoured for years to make it a reality.

In 2020, researchers led by David R Liu of the Broad Institute of Harvard and MIT created a new base editor named DddA-derived cytosine base editors (DdCBEs) that can perform C-to-T conversion from DNA in mitochondria. This was made possible by creating a new gene-editing technology called base editing, which converts a single nucleotide base into another without breaking the DNA. However, this technique also had its limitations. Not only is it restricted to C-to-T conversion, but it is mostly limited to the TC motif, making it effectively a TC-TT converter. This means that it can correct only nine out of 90 (10%) confirmed pathogenic mitochondrial point mutations. For a long time, A-to-G conversion of mitochondrial DNA was thought to be impossible.

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