Aging and neurodegeneration are associated with increased mutations in single human neurons

Abstract

Summary It has long been hypothesized that aging and neurodegeneration are associated with somatic mutation in neurons; however, methodological hurdles have prevented testing this hypothesis directly. We used single-cell whole-genome sequencing to perform genome-wide somatic single-nucleotide variant (sSNV) identification on DNA from 161 single neurons from the prefrontal cortex and hippocampus of fifteen normal individuals (aged 4 months to 82 years) as well as nine individuals affected by early-onset neurodegeneration due to genetic disorders of DNA repair (Cockayne syndrome and Xeroderma pigmentosum). sSNVs increased approximately linearly with age in both areas (with a higher rate in hippocampus) and were more abundant in neurodegenerative disease. The accumulation of somatic mutations with age—which we term genosenium—shows age-related, region-related, and disease-related molecular signatures, and may be important in other human age-associated conditions.

Genomic mosaicism in the developing and adult brain

“…It does face intrinsic limitations, including low throughput, high failure rates of SCNT, low rates of mitotic growth of the newly created cells, incompatibility with humans in requiring the use of laboratory mice, and in some cases a need to generate cloned mice, a process that likely excludes interrogation of cells with highly altered genomes (e.g., aneuploid neurons). Nevertheless, these results demonstrated that individual mitral neurons contain hundreds of unique SNVs, and considering the relatively shorter lifespan of mice vs. humans, the numbers of SNVs in mice are generally consistent with the thousands observed in older human neurons in which SNVs appear to increase with age (Bae et al, ; Lodato et al, ), albeit based upon very few neurons assessed with all of these techniques.…”

“…Also proposed to occur during neurogenesis, mosaic LINE1 insertions, as discussed in a previous section, are theoretically capable of generating GM during the cell cycle (Packer et al, ; Muotri et al, ; Shi et al, ; Singer et al, ; Viollet et al, ; Mita et al, ). By contrast, many neural somatic SNVs have been associated with damage due to transcriptional activity (Lodato et al, ), consistent with increased SNV rates in aged brains (Bae et al, ; Lodato et al, ), suggesting this form of GM is generated in postmitotic neurons. It is entirely possible that other mechanisms could contribute to neural GM, including hypothesized gene recombination, which awaits further investigation.…”

“…The smallest form of somatic DNA sequence change is a SNV that can be identified by single‐cell whole genome sequencing of vastly amplified genomes combined with median 30X sequencing coverage, which has revealed SNVs between individual neurons at the level of single nucleotides (Lodato et al, ; Bae et al, ; Lodato et al, ). A crucial initial step in these investigations is massive amplification of single‐cell genomic DNA through use of techniques like “multiple displacement amplification” (MDA) that employs phi29 DNA polymerase, followed by high coverage, whole genome sequencing with paired end Illumina reads, which has revealed SNVs in neurons of the brain.…”

“…In addition to large DNA alterations, the high coverage data generated by extreme amplification using MDA and high depth sequencing allowed identification of unique SNVs (Lodato et al, ; Lodato et al, ). However, this form of scWGS has a high failure rate (possibly excluding neurons with unique genomic attributes), is cost prohibitive for more than a few cells, and regional genome bias under the reported conditions using MDA precludes examination of large structural variants such as CNVs.…”

Identifying genes in Parkinson disease: state of the art

“…It is important to note that the genetic findings thus far are germline variants that were detected in biological materials collected from non‐invasive, non‐pathogenic sites such as lymphocytes from peripheral blood. However, there is increasing awareness that somatic mutations that arise during development or accumulate with age 26 , 27 at the site of disease pathology 28 , 29 may also account for some sporadic cases of PD. These mutations are only detectable in post‐mortem brain tissue and therefore are not useful for diagnostics or risk prediction, but could nevertheless point to potential novel pathways and druggable targets.…”