Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genes

How do neurons live long and healthy? The mechanism of neuronal genome integrity

Genome DNA of neurons in the brain is unstable, and mutations caused by inaccurate repair can lead to neurodevelopmental and neurodegenerative disorders. Damage to the neuronal genome is induced both exogenously and endogenously. Rapid cell proliferation of neural stem cells during embryonic brain development can lead to errors in genome duplication. Electrical excitations and drastic changes in gene expression in functional neurons cause risks of damaging genomic DNA. The precise repair of DNA damages caused by events making genomic DNA unstable maintains neuronal functions. The maintenance of the DNA sequence and structure of the genome is known as genomic integrity. Molecular mechanisms that maintain genomic integrity are critical for healthy neuronal function. In this review, we describe recent progress in understanding the genome integrity in functional neurons referring to their disruptions reported in neurological diseases.

DNA damage and its links to neuronal aging and degeneration

DNA damage is a major risk factor for the decline of neuronal functions with age and in neurodegenerative diseases. While how DNA damage causes neurodegeneration is still being investigated, innovations over the past decade have provided significant insights into this issue. Breakthroughs in next-generation sequencing methods have begun to reveal the characteristics of neuronal DNA damage hotspots and the causes of DNA damage. Chromosome conformation capture-based approaches have shown that, while DNA damage and the ensuing cellular response alter chromatin topology, chromatin organization at damage sites also affects DNA repair outcomes in neurons. Additionally, neuronal activity results in the formation of programmed DNA breaks, which could burden DNA repair mechanisms and promote neuronal dysfunction. Finally, emerging evidence implicates DNA damage-induced inflammation as an important contributor to the age-related decline in neuronal functions. Together, these discoveries have ushered in a new understanding of the significance of genome maintenance for neuronal function.

Somatic Mosaicism in Brain Disorders

Research efforts over the past decade have defined the genetic landscape of somatic variation in the brain. Neurons accumulate somatic mutations from development through aging with potentially profound functional consequences. Recent studies have revealed the contribution of somatic mosaicism to various brain disorders including focal epilepsy, neuropsychiatric disease, and neurodegeneration. One notable finding is that the effect of somatic mosaicism on clinical outcomes can vary depending on contextual factors, such as the developmental origin of a variant or the number and type of cells affected. In this review, we highlight current knowledge regarding the role of somatic mosaicism in brain disorders and how biological context can mediate phenotypes. First, we identify the origins of brain somatic variation throughout the lifespan of an individual. Second, we explore recent discoveries that suggest somatic mosaicism contributes to various brain disorders. Finally, we discuss neuropathological associations of brain mosaicism in different biological contexts and potential clinical utility.

Insights from multi-omic modeling of neurodegeneration in xeroderma pigmentosum using an induced pluripotent stem cell system

Xeroderma pigmentosum (XP) is caused by defective nucleotide excision repair of DNA damage. This results in hypersensitivity to ultraviolet light and increased skin cancer risk, as sunlight-induced photoproducts remain unrepaired. However, many XP patients also display early-onset neurodegeneration, which leads to premature death. The mechanism of neurodegeneration is unknown. Here, we investigate XP neurodegeneration using pluripotent stem cells derived from XP patients and healthy relatives, performing functional multi-omics on samples during neuronal differentiation. We show substantially increased levels of 5',8-cyclopurine and 8-oxopurine in XP neuronal DNA secondary to marked oxidative stress. Furthermore, we find that the endoplasmic reticulum stress response is upregulated and reversal of the mutant genotype is associated with phenotypic rescue. Critically, XP neurons exhibit inappropriate downregulation of the protein clearance ubiquitin-proteasome system (UPS). Chemical enhancement of UPS activity in XP neuronal models improves phenotypes, albeit inadequately. Although more work is required, this study presents insights with intervention potential.

Senolytics and cell senescence: historical and evolutionary perspectives

Senolytics are a new class of anti-aging drugs developed to selectively kill 'senescent' cells that are considered harmful in normal aging. More than 20 drug trials are ongoing with diverse 'senolytic cocktails'. This commentary on recent reviews of senolytics gives a historical context of mammalian cell senescence that enabled these new drugs. While cell senescence is considered harmful to aging tissues, many studies show its essential role in some regenerative and developmental processes for which senolytic drugs may interfere. Longer-term studies of side effects are needed before senolytics are considered for general clinical practice. The wide occurrence of cell senescence in eukaryotes, yeast to fish to humans, and suggests an ancient eukaryotic process that evolved multiple phenotypes.

Pangenomics: A new era in the field of neurodegenerative diseases

A pangenome is composed of all the genetic variability of a group of individuals, and its application to the study of neurodegenerative diseases may provide valuable insights into the underlying aspects of genetic heterogenetiy for these complex ailments, including gene expression, epigenetics, and translation mechanisms. Furthermore, a reference pangenome allows for the identification of previously undetected structural commonalities and differences among individuals, which may help in the diagnosis of a disease, support the prediction of what will happen over time (prognosis) and aid in developing novel treatments in the perspective of personalized medicine. Therefore, in the present review, the application of the pangenome concept to the study of neurodegenerative diseases will be discussed and analyzed for its potential to enable an improvement in diagnosis and prognosis for these illnesses, leading to the development of tailored treatments for individual patients from the knowledge of the genomic composition of a whole population.