Method for Identifying Genomic Age via Single-Nucleotide Variants in Single Cell Neurons

Background

Aging in humans brings increased incidence of nearly all diseases, including neurodegeneration. Markers of DNA damage increase in the brain with age, and genetic progeroid diseases such as Cockayne syndrome (CS) and Xeroderma pigmentosum (XP), both caused by defects in DNA damage repair (DDR), are associated with neurodegeneration and premature aging. 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. Accordingly, a need exists for improved compositions and methods for examining whether permanent somatic mutations accumulate during aging in the human brain.

Technology Overview

Boston Children’s Hospital researchers examined whether aging or disorders of defective DNA damage repair (DDR) result in more somatic mutations in single postmitotic human neurons. The methods involve identifying a single-nucleotide variant (sSNV) in a single cell by detecting a variant nucleotide on forward and reverse strands of genomic DNA, wherein the presence of the variant nucleotide on the forward and reverse strands identifies a double-stranded mutation that is a single-nucleotide variant.

Single-cell whole-genome sequencing was used 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 (CS and XP). This study discovered sSNVs accumulate in human neurons in aging with regional specificity and in progeroid diseases (e.g., CS and XP).

Applications

• Determining the genomic age of a subject;
• Measuring the rate of accumulation of genome-wide somatic single-nucleotide variants (sSNVs);
• Measuring somatic mutation burden.

Advantages

• Previous studies using mouse models of aging, CS, and XP have shown inconsistent relationships between these conditions and the accumulation of permanent somatic mutations in brain and non-brain tissue, and it was not known whether permanent somatic mutations accumulate with age in mature neurons of the human brain. While the present disclosure tested and confirmed the accumulation of somatic mutations with age shows age-related, region-related, and disease-related molecular signatures in the human brain.
• The invention provides kits for determining the genomic age of a subject, measuring the rate of accumulation of genome-wide somatic single-nucleotide variants (SNVs), and/or measuring somatic mutation burden.

Publications

• Craig L Bohrson, et al.  Linked-read analysis identifies mutations in single-cell DNA-sequencing data. Nat Genet. 2019 Apr;51(4):749-754. doi: 10.1038/s41588-019-0366-2. Epub 2019 Mar 18.
• Gilad D Evrony, et al. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell. 2012 Oct 26;151(3):483-96. doi: 10.1016/j.cell.2012.09.035.
• Michael A Lodato, et al. Aging and neurodegeneration are associated with increased mutations in single human neurons. Science. 2018 Feb 2;359(6375):555-559. doi: 10.1126/science.aao4426. Epub 2017 Dec 7.