GeneBites

Written by: Guest Writer Olivia Conway

Stray bits of DNA can slip into our genomes without warning—not from an invader, but from our own mitochondria. These genetic stowaways, called NUMTs, may cause disease. And new research suggests CRISPR, the tool designed to fix DNA, might actually speed them up.

Scientists have discovered that unfamiliar DNA can sneak into our genomes without detection. Although it may seem like the beginning of a science fiction novel, this DNA is not from a pathogenic invader or alien species. It’s from our own cells. Human cells have two genomes: the genome passed to us from our parents (nuDNA), which encodes thousands of genes to make all of the proteins our bodies need to survive, and mitochondrial DNA (mtDNA), which only encodes genes to make proteins involved in producing energy. Mitochondria are structures within our cells that transform sugars from the food we eat into energy that our cells need to function. The proteins needed for this transformation are encoded by a DNA sequence within the mitochondria that is much smaller than our nuDNA. Usually these two genomes are separated by boundaries within the cell, but sometimes small pieces of mtDNA find their way out of the mitochondria to become nuDNA. These incorporated sequences are called nuclear-mitochondrial DNA segments (NUMTs), and they have the potential to cause disease. DNA editing tools like CRISPR have become incredibly promising for removing dangerous genes, but recent research has found that editing actually accelerates the number of NUMTs in human cells. 

The CRISPR editing system relies on two components to delete genes that can cause diseases. The first component is a genetic sequence that can bind to the gene that will be removed, which provides the specificity needed for accurate editing. The second component is a protein called an endonuclease that cuts DNA. The guide sequence brings the endonuclease to the target gene to ensure that other healthy genes will not be accidentally edited. However, the efficacy of CRISPR editing lies not in cutting the DNA but in the cell’s attempts to repair the break. DNA breaks block DNA replication and expression of critical genes, so cells try to fill in the gap and glue the DNA back together. The cell doesn’t always repair the DNA correctly, and sometimes these new incorrect sequences prevent production of proteins. When researchers use CRISPR to edit DNA, they are relying on this error-prone repair process to block the expression of harmful genes. 

In the race to seal up any breaks in DNA, repair proteins will blindly grab for the closest two DNA sequences and glue them together, even if they don’t match, even if they don’t belong in the nucleus. Pieces of damaged mtDNA are often thrown out of the mitochondria into the rest of the cell, where repair proteins can recruit them for resolving CRISPR-induced damage. This is how mtDNA sneaks into the genome and creates NUMTs. 

Researchers have detected NUMTs in several different kinds of cells from thousands of individuals, but the relationship between NUMT incorporation and editing tools like CRISPR remained unknownTo investigate this question, Dr. Jinchun Wu at Peking University in China used a specialized sequencing method to look for mtDNA at CRISPR editing target sites. With this technique, Dr. Wu determined how frequently mtDNA was incorporated into the genome at different editing sites and in different cell types. She found a significant increase in NUMTs at the CRISPR target sites compared to unedited cells, which suggested that the process of CRISPR editing creates opportunities for mtDNA incorporation. 

The research team also detected NUMTs more frequently after exposing their samples to a drug that induces mitochondrial stress and mtDNA breaks. This means that DNA damage can make it more likely that mtDNA will invade the genome. Interestingly, the researchers found they were able to reduce the number of NUMTs by adding a protein that chews up fragmented mtDNA during the CRISPR editing process. 

NUMTs only occur when two crucial events coincide: 1) fragmented mtDNA is outside the mitochondria, and 2) there are breaks in the nuDNA genome. Since CRISPR editing necessitates creating breaks in the genome, the best way to prevent NUMTs is to reduce the amount of mtDNA fragments floating in the cell. NUMT incorporation is not necessarily harmful, but insertion of new genetic information has the potential to alter our genetic code and could lead to the development of cancer. Dr. Wu has not only identified an important off-target consequence of CRISPR editing, but also presented an innovative way to reduce that effect. 

CRISPR is an undeniably powerful technique with huge therapeutic potential for patients with genetic disorders. Accordingly, it has also inspired a lot of concern among scientists, medical professionals, and policymakers because of its novelty and potential risks. Dr. Wu’s research has highlighted a previously unknown risk that will need to be addressed before CRISPR technology is made widely available to patients or used for genetic changes that could be passed to future generations. CRISPR is a revolutionary method for treating diseases like cystic fibrosis, sickle cell disease, and muscular dystrophy, but researchers will first need to remove the unwanted mtDNA hitching a ride on their miracle cure.

Edited by JP Flores and Jameson Blount