Breaking down brain disease one DNA break at a time

DNA breaks are depicted in this artistic renderingCells throughout the human body are constantly being damaged as a part of natural life, normal cellular processes, UV and chemical exposure and environmental factors — resulting in what are called DNA double-strand breaks. Thankfully, to prevent the accumulation of DNA damage that could eventually lead to cell dysfunction, cancer or death, the healthy human body has developed ways of locating and repairing the damage.

Unfortunately, these DNA repair mechanisms themselves are not impervious to genetic errors. Genetic mutations that disrupt DNA repair can contribute to devastating disease.

Across the early-stage progenitor cells that give rise to the human brain’s 80 billion neuronal cells, genomic alterations impacting DNA repair processes have been linked to neuropsychiatric disorders and the childhood brain cancer medulloblastoma. But until now, it was not known exactly which disruptions in DNA repair were involved.

A Boston Children’s Hospital team led by Frederick Alt, PhD, has finally changed that.

“Over the past decade, we have developed and refined a method called ‘high throughput, genome-wide, translocation sequencing,’ or ‘HTGTS’ for short, to steadfastly zero in on locations in the genome that chronically experience DNA double-strand breaks,” says Alt, who directs the Boston Children’s Program in Cellular and Molecular Medicine.

Their pioneering work, the latest of which was just published in the Proceedings of the National Academy of Sciences, has attracted funding from the Hood Foundation. Bolstered by the Hood Foundation’s grant support, Alt and his team have embarked on a mission to determine the biological factors that impact DNA repair mechanisms and to draw links between specific sites of recurring DNA breaks in human neuron progenitors and neuropsychiatric diseases and cancer.

Homing in on problematic DNA breaks

Essentially, their HTGTS method works by using CRISPR-Cas9 gene editing technology to insert genetic “bait” in  genomes of interest — in this case, those of early-stage progenitor brain cells in mice. The bait, programmed to act like a magnet for DNA breaks, causes broken DNA to switch positions, a process called translocation. Afterwards, sequencing can identify which pieces of DNA have moved, revealing the genomic sites of origin for the DNA breaks.

Using this method, Alt’s team initially identified the locations of more than two dozen clusters of recurrent DNA double strand breaks — many of which were found in genes associated with mental illness and cancer. Most of these clusters were found inside single, long genes made up of an unusually large number of base pairs, which are the molecular A-T-G-C building blocks of DNA.

Boston Children's Hospital researchers have newly pinpointed dozens of genomic locations of recurrent DNA damage in early-stage brain cells. Interestingly, many DNA breaks are found in genes (quantity represented in this infographic) associated with neuropsychiatric and development disorders and cancer.
Interestingly, many of the DNA breaks were found in genes (quantity represented in this infographic) associated with neuropsychiatric and development disorders and cancer.

Now, in their latest paper, they report more than 80 additional sites of DNA double-strand breaks that have never before been identified. In total, they have found more than 100 clusters of recurrent DNA breaks.

“Based on our analysis, we’ve classified these 100 clusters into three distinct types of groups: either occurring within a single, usually very long gene; across multiple genes with at least one long gene; or across multiple small genes,” Alt says.

What’s more, they’ve honed their investigation toward a protein called XRCC4 and its role in DNA repair. In mouse cells where XRCC4 was eliminated, double-strand breaks were more prevalent and pervasive, Alt’s team has observed.

“We are very grateful to the Hood Foundation for recognizing the potential relationships between our recent discoveries and possible mechanisms that contribute to certain pediatric neuropsychiatric diseases and brain cancers,” Alt says. “Their support will help us take the work to the next level to further explore these relationships and hopefully provide insights relevant to treatments.”

More research from the Program in Cellular and Molecular Medicine…