New study reveals how DNA repair genes play a major role in Huntington’s disease

A new UCLA Health study has discovered in mouse models that genes associated with repairing mismatched DNA are critical in eliciting damages to neurons that are most vulnerable in Huntington’s disease and triggering downstream pathologies and motor impairment, shedding light on disease mechanisms and potential new ways to develop therapies. The study is published in the journal Cell.

Huntington’s disease is one of the most common inherited neurodegenerative disorders that typically begins in adulthood and worsens over time. Patients begin to lose neurons in specific regions of the brain responsible for movement control, motor skill learning, language and cognitive function. Patients typically live 15 to 20 years after diagnosis with symptoms worsening over time. There is no known cure or therapy that alters the course of the disease.

The cause of Huntington’s disease was discovered over three decades ago—a “genetic stutter” mutation involves repeats of three letters of the DNA, cytosine-adenine-guanine (CAG), in a gene called huntingtin. Healthy individuals usually have 35 or fewer CAG repeats, but people with an inherited mutation of 40 or more repeats will develop the disease. The more CAG repeats a person inherits, the earlier the disease onset occurs. However, how the mutation causes the disease remains poorly understood.

A longstanding enigma in Huntington’s disease is how the mutated protein derived from the huntingtin gene is present in every cell of the body, but the disease appears to selectively affect certain types of neurons in a few brain regions.

This mystery is shared between Huntington’s disease and many other neurodegenerative brain disorders, including Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis (ALS), albeit different types of neurons are vulnerable to degeneration in each disorder. Solving this mystery could hold insights into disease mechanisms and therapies.

Recently a human genetic study uncovered about a dozen DNA regions in the genome that harbors “modifiers” for Huntington’s disease, which are DNA variants that could hasten or delay the onset of the disease by up to a few years. Intriguingly, these regions contain multiple genes involved in repairing DNA mismatches. However, the mechanistic connections between mismatch DNA repair and selective neuronal vulnerability in Huntington’s disease remained unknown.

The new study from UCLA Health and Jane and Terry Semel Institute for Neuroscience and Human Behavior at UCLA, published in the journal Cell, reveals that a distinct subset of mismatch repair genes are key drivers of Huntington’s disease and how the disease affects specific types of neurons.

“We demonstrate the same DNA mismatch repair genes that are modifiers in the Huntington’s disease patients can drive fast-paced disease processes only in the most vulnerable neurons in a mouse model, leading to a cascade of disease phenotypes,” said lead author Dr. X. William Yang, professor of the UCLA Health Department of Psychiatry and Biobehavioral Sciences and the Terry Semel Chair in Alzheimer’s Disease Research and Treatment at the Semel Institute.

Yang and colleagues used Huntington’s disease model mice with 140 CAG repeats (called Q140 model), as such long repeats are necessary to observe disease features in a mouse model. They asked whether genetically altering nine HD patient-derived modifier genes, including six mismatch repair genes, in this mouse model could alter any disease phenotypes.

Although an HD mouse model lacks overt neuronal cell death, possibly due to the short lifespan of a mouse, they exhibit multiple disease-like phenotypes that are highly selective to the HD vulnerable neurons. They include the dysregulation of the expression of thousands of genes in the striatal neurons and an accumulation of clumps of mutant Huntingtin protein (called aggregates), which are a hallmark of pathology in HD patient brains. The aggregates happen first in the striatal neurons and later in the cortical neurons, and they progressively worsen over time, mimicking the progression of the disease.

Remarkably, HD mice lacking a subset of mismatch repair genes, especially Msh3 and Pms1, correct the vast majority of the gene expression deficits in this mouse model. Moreover, they partially or fully prevent the mutant Huntingtin aggregate pathology throughout the brain.

Besides molecular and pathological benefits, the study also shows targeting Msh3 can ameliorate locomotor and gait deficits, improve neuronal synaptic protein levels, and reduce glial cell over-reactivity.

“We were surprised to see the potent and sustained effects of targeting these mismatch repair genes in HD mice—the benefit lasts up to 20 months of age in a mouse, which would be comparable to about 60 years in humans,” said Yang. “Our study suggests that these genes are not just disease modifiers, as suggested by the previous studies, but are genetic drivers of Huntington’s disease.”

How might mismatch repair genes alter the disease process in HD? Recent studies suggest the mutant Huntingtin CAG repeats are unstable in adult brain cells, especially in the vulnerable neurons such as the striatal medium spiny neurons (MSNs), and such an expansion is associated with gene expression changes and possibly neuronal cell death.

However, the role of modifier genes in the repeat expansion in brain cells remain untested in patients. In mouse models, previous studies show that mismatch repair genes confer high levels of instability in the striatum, the most vulnerable brain region, but only a subset of repeats appear to expand beyond the inherited allele.

“We are puzzled why stopping a subset of CAG repeats from expanding in Msh3- or Pms1-deficient HD mice could lead to a benefit in all striatal neurons,” said Nan Wang, a co-first author in the study.

Wang designed an experiment to purify the nuclei DNA only from the MSNs, the most vulnerable neurons in the striatum, and measure the CAG DNA repeat sizes for mutant Huntingtin. She found that, surprisingly, the repeat sizes for the entire MSN population are increasing at a linear rate of +8.8 repeats per month, with repeats well over 220 repeats by 12 months of age.

If other striatal neuronal types or non-neuronal cells are included in this assay, the majority of repeats remains at 140. Impressively, deleting one copy of Msh3, the CAG expansion rate in MSNs reduced to +2.3 repeats/month, and deleting both copies of Msh3, the rate is essentially stable at 0.35 repeats/month.

Importantly, these findings also reveal that mutant huntingtin aggregation requires a threshold of CAG expansion to 150, and gene expression dysregulation is also highly associated with the expanded CAG length in the MSNs.

“These remarkable results demonstrate that a subset of mismatch repair genes is driving disease in vulnerable neurons because they confer the fastest rate of CAG repeat expansion in these neurons,” said Yang, “and our study provides mechanistic links that help to bridge modifier genes from patients, mismatch repair gene driven repeat expansion, and selective neuronal vulnerability in HD.”

The study provides important therapeutic implications. First, the study tested 6 DNA mismatch repair genes and only four of them appear to strongly (Msh3 and Pms1) or moderately (Msh2 and Mlh1) modify pathogenesis in HD mouse model. Interestingly, these genes together encode a minor mismatch repair complex, which is conserved from yeast to human, but its function in yeast remains unknown. Moreover, although 4 of the 6 mismatch repair genes are associated with cancer in human, Msh3 and Pms1 are not known to be associated with cancer.

This study also showed that aged Msh3 and Pms1 mice are free of notable molecular or pathological changes. Thus, the study reveals that targeting genes encoding this minor mismatch repair complex, either by reducing the expression levels of Msh3, Pms1, or the complex formation, could be therapeutic in HD.

Moreover, this study shows targeting these mismatch repair genes could benefit multiple brain regions, including brain areas with early-onset (striatum) or late-onset (cortex) pathologies. Thus, it implies therapies targeting this disease mechanism could be helpful both at delaying onset or slowing the progression of the disease.

Additionally, this study demonstrates that an HD mouse model, and its constellation of molecular, pathological and behavioral phenotypes could constitute a platform to test novel therapeutics targeting the HD modifier genes involved in CAG repeat expansion or mechanisms improving the resilience or health of HD vulnerable neurons.

Inherited dynamic DNA repeat mutations affect over 30 neurological disorders and several of them also found mismatch repair genes that could affect the repeat instability or disease severity. The mechanistic findings and model platform could help discover therapies for these other disorders as well.

Other study authors are Nan Wang, Shasha Zhang, Peter Langfelder, Lalini Ramanathan, Fuying Gao, Mary Plascencia, Raymond Vaca, Xiaofeng Gu, Linna Deng, Leonardo E. Dionisio from Center for Neurobehavioral Genetics of Semel Institute and Department of Psychiatry and Biobehavioral Sciences at UCLA; Ha Vu, Emily Maciejewski and Jason Ernst from Department of Biological Chemistry at UCLA; Steve Horvath from Department of Human Genetics at David Geffen School of Medicine at UCLA; and Brinda C. Prasad, Thomas F. Vogt, Jeffrey S. Aaronson, and Jim Rosinski from CHDI Management, Inc.

A new UCLA Health study has discovered in mouse models that genes associated with repairing mismatched DNA are critical in eliciting damages to neurons that are most vulnerable in Huntington’s disease and triggering downstream pathologies and motor impairment, shedding light on disease mechanisms and potential new ways to develop therapies. The study is published in the journal Cell.

Huntington’s disease is one of the most common inherited neurodegenerative disorders that typically begins in adulthood and worsens over time. Patients begin to lose neurons in specific regions of the brain responsible for movement control, motor skill learning, language and cognitive function. Patients typically live 15 to 20 years after diagnosis with symptoms worsening over time. There is no known cure or therapy that alters the course of the disease.

The cause of Huntington’s disease was discovered over three decades ago—a “genetic stutter” mutation involves repeats of three letters of the DNA, cytosine-adenine-guanine (CAG), in a gene called huntingtin. Healthy individuals usually have 35 or fewer CAG repeats, but people with an inherited mutation of 40 or more repeats will develop the disease. The more CAG repeats a person inherits, the earlier the disease onset occurs. However, how the mutation causes the disease remains poorly understood.

A longstanding enigma in Huntington’s disease is how the mutated protein derived from the huntingtin gene is present in every cell of the body, but the disease appears to selectively affect certain types of neurons in a few brain regions.

This mystery is shared between Huntington’s disease and many other neurodegenerative brain disorders, including Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis (ALS), albeit different types of neurons are vulnerable to degeneration in each disorder. Solving this mystery could hold insights into disease mechanisms and therapies.

Recently a human genetic study uncovered about a dozen DNA regions in the genome that harbors “modifiers” for Huntington’s disease, which are DNA variants that could hasten or delay the onset of the disease by up to a few years. Intriguingly, these regions contain multiple genes involved in repairing DNA mismatches. However, the mechanistic connections between mismatch DNA repair and selective neuronal vulnerability in Huntington’s disease remained unknown.

The new study from UCLA Health and Jane and Terry Semel Institute for Neuroscience and Human Behavior at UCLA, published in the journal Cell, reveals that a distinct subset of mismatch repair genes are key drivers of Huntington’s disease and how the disease affects specific types of neurons.

“We demonstrate the same DNA mismatch repair genes that are modifiers in the Huntington’s disease patients can drive fast-paced disease processes only in the most vulnerable neurons in a mouse model, leading to a cascade of disease phenotypes,” said lead author Dr. X. William Yang, professor of the UCLA Health Department of Psychiatry and Biobehavioral Sciences and the Terry Semel Chair in Alzheimer’s Disease Research and Treatment at the Semel Institute.

Yang and colleagues used Huntington’s disease model mice with 140 CAG repeats (called Q140 model), as such long repeats are necessary to observe disease features in a mouse model. They asked whether genetically altering nine HD patient-derived modifier genes, including six mismatch repair genes, in this mouse model could alter any disease phenotypes.

Although an HD mouse model lacks overt neuronal cell death, possibly due to the short lifespan of a mouse, they exhibit multiple disease-like phenotypes that are highly selective to the HD vulnerable neurons. They include the dysregulation of the expression of thousands of genes in the striatal neurons and an accumulation of clumps of mutant Huntingtin protein (called aggregates), which are a hallmark of pathology in HD patient brains. The aggregates happen first in the striatal neurons and later in the cortical neurons, and they progressively worsen over time, mimicking the progression of the disease.

Remarkably, HD mice lacking a subset of mismatch repair genes, especially Msh3 and Pms1, correct the vast majority of the gene expression deficits in this mouse model. Moreover, they partially or fully prevent the mutant Huntingtin aggregate pathology throughout the brain.

Besides molecular and pathological benefits, the study also shows targeting Msh3 can ameliorate locomotor and gait deficits, improve neuronal synaptic protein levels, and reduce glial cell over-reactivity.

“We were surprised to see the potent and sustained effects of targeting these mismatch repair genes in HD mice—the benefit lasts up to 20 months of age in a mouse, which would be comparable to about 60 years in humans,” said Yang. “Our study suggests that these genes are not just disease modifiers, as suggested by the previous studies, but are genetic drivers of Huntington’s disease.”

How might mismatch repair genes alter the disease process in HD? Recent studies suggest the mutant Huntingtin CAG repeats are unstable in adult brain cells, especially in the vulnerable neurons such as the striatal medium spiny neurons (MSNs), and such an expansion is associated with gene expression changes and possibly neuronal cell death.

However, the role of modifier genes in the repeat expansion in brain cells remain untested in patients. In mouse models, previous studies show that mismatch repair genes confer high levels of instability in the striatum, the most vulnerable brain region, but only a subset of repeats appear to expand beyond the inherited allele.

“We are puzzled why stopping a subset of CAG repeats from expanding in Msh3- or Pms1-deficient HD mice could lead to a benefit in all striatal neurons,” said Nan Wang, a co-first author in the study.

Wang designed an experiment to purify the nuclei DNA only from the MSNs, the most vulnerable neurons in the striatum, and measure the CAG DNA repeat sizes for mutant Huntingtin. She found that, surprisingly, the repeat sizes for the entire MSN population are increasing at a linear rate of +8.8 repeats per month, with repeats well over 220 repeats by 12 months of age.

If other striatal neuronal types or non-neuronal cells are included in this assay, the majority of repeats remains at 140. Impressively, deleting one copy of Msh3, the CAG expansion rate in MSNs reduced to +2.3 repeats/month, and deleting both copies of Msh3, the rate is essentially stable at 0.35 repeats/month.

Importantly, these findings also reveal that mutant huntingtin aggregation requires a threshold of CAG expansion to 150, and gene expression dysregulation is also highly associated with the expanded CAG length in the MSNs.

“These remarkable results demonstrate that a subset of mismatch repair genes is driving disease in vulnerable neurons because they confer the fastest rate of CAG repeat expansion in these neurons,” said Yang, “and our study provides mechanistic links that help to bridge modifier genes from patients, mismatch repair gene driven repeat expansion, and selective neuronal vulnerability in HD.”

The study provides important therapeutic implications. First, the study tested 6 DNA mismatch repair genes and only four of them appear to strongly (Msh3 and Pms1) or moderately (Msh2 and Mlh1) modify pathogenesis in HD mouse model. Interestingly, these genes together encode a minor mismatch repair complex, which is conserved from yeast to human, but its function in yeast remains unknown. Moreover, although 4 of the 6 mismatch repair genes are associated with cancer in human, Msh3 and Pms1 are not known to be associated with cancer.

This study also showed that aged Msh3 and Pms1 mice are free of notable molecular or pathological changes. Thus, the study reveals that targeting genes encoding this minor mismatch repair complex, either by reducing the expression levels of Msh3, Pms1, or the complex formation, could be therapeutic in HD.

Moreover, this study shows targeting these mismatch repair genes could benefit multiple brain regions, including brain areas with early-onset (striatum) or late-onset (cortex) pathologies. Thus, it implies therapies targeting this disease mechanism could be helpful both at delaying onset or slowing the progression of the disease.

Additionally, this study demonstrates that an HD mouse model, and its constellation of molecular, pathological and behavioral phenotypes could constitute a platform to test novel therapeutics targeting the HD modifier genes involved in CAG repeat expansion or mechanisms improving the resilience or health of HD vulnerable neurons.

Inherited dynamic DNA repeat mutations affect over 30 neurological disorders and several of them also found mismatch repair genes that could affect the repeat instability or disease severity. The mechanistic findings and model platform could help discover therapies for these other disorders as well.

Other study authors are Nan Wang, Shasha Zhang, Peter Langfelder, Lalini Ramanathan, Fuying Gao, Mary Plascencia, Raymond Vaca, Xiaofeng Gu, Linna Deng, Leonardo E. Dionisio from Center for Neurobehavioral Genetics of Semel Institute and Department of Psychiatry and Biobehavioral Sciences at UCLA; Ha Vu, Emily Maciejewski and Jason Ernst from Department of Biological Chemistry at UCLA; Steve Horvath from Department of Human Genetics at David Geffen School of Medicine at UCLA; and Brinda C. Prasad, Thomas F. Vogt, Jeffrey S. Aaronson, and Jim Rosinski from CHDI Management, Inc.