Somatic mutations in Alzheimer’s disease neurons
Original author: Michael B. Miller et al. Nature, 604, 714 (2022) (DOI: 10.1038/s41586-022-04640-1)
Sr. scientist – Omics
September 14, 2022
Alzheimer’s disease (AD) is a common age-associated neurodegenerative disorder. It is associated with the deposition of amyloid-beta oligomers and tau proteins. However, the underneath cellular dysfunction is still not well understood. In the current paper, researchers explore genomic mutations in AD-associated neurons at the single-cell level. Through single cell whole genome sequencing (scWGS) the researchers have compared somatic mutations in AD patients and neurotypical control individuals.
scWGS was performed on pyramidal neurons collected from two regions of the brain, the prefrontal cortex (PFC) and the CA1 subfield of the hippocampus region. Cells were collected during post-mortem from 8 AD patients and 18 neurotypical control individuals of different age groups. For scWGS, whole genome amplification was done using the multiple displacement amplification (MDA) method. Mutational signatures, defined in earlier studies, were analyzed to identify underneath specific processes causing somatic mutations in neurons collected from AD patients.
Results & discussion
It is observed that for both regions of the brain, sSNVs accumulated with age. However, the amount of accumulation was more in the case of AD patients.
AD neurons showed an increase in 'signature C' compared to controls but ‘signature A’ increased in all the samples. Moreover, the ‘signature C’ burden showed higher variation between neurons compared to that of ‘signature A’. It means ‘signature A’ represents age-related mutations and ‘signature C’ is from irregular ‘calamitous’ events. DNA oxidation also may be responsible for excess sSNVs because higher oxidized nucleotides were observed in AD neurons. Interestingly, no somatic mutation was observed in classic AD risk genes (APP, PSEN1, PSEN2, and APOE).
The ‘signature A’ mutations were correlated with gene expression values but not ‘signature C’ mutations, as ‘signature A’ mutations occurred during transcription. The 'signature C' inversely correlated with expression values.
There are multiple consequences of somatic mutations, including neuronal dysfunction, direct impairment of transcription, protein stability alterations, and neoantigen creation. As somatic mutations accumulate in the genome, the likelihood of two deleterious exonic alterations in the same gene, producing a knockout cell, increases exponentially. The mathematical model suggests that dysfunctional neurons would be markedly more abundant in AD resulting in compromised neuronal functions.
To rule out any artifact of the genome amplification method, apart from MDA, researchers followed primary template-directed amplification (PTA) for a subset of samples. PTA-based scWGS also confirmed enhanced sSNVs in AD neurons and mutational signatures were also similar to the MDA method. It also suggested that PTA-detected sSNVs represented double-stranded somatic mutations.
In the end, the researchers tried to correlate the role of sSNVs in the pathogenesis of AD. Amyloid beta peptide (Aβ) initiates a cascade of events. It induces the conversion of tau proteins to neurofibrillary tangles and the accumulation of reactive oxidative species (ROS) molecules. Somatic mutations develop due to the damage caused by ROS and/or other mutagens. NER pathway conducts the repair mechanism. However, the accelerated accumulation of oxidized nucleotides overwhelms the repair pathway.
Impact of the research
This article reports accumulation pattern of sSNVs in AD neurons differs from normal aging neurons. No somatic mutation was observed in known AD-associated genes including APP, the precursor of Aβ. Amyloid beta aggregation causes lipid peroxidation and oxidative stress. Aβ oligomers outside neurons spur tau neurofibrillary tangles and reactive oxygen species inside the neuron. This continuous process damages DNA and overcomes the repair mechanisms. As a result, single-nucleotide variations occur and persist as somatic mutations, leading to neuron death.
This research concludes that AD patients accumulate more sSNVs compared to their normal counterparts. Previously known AD risk genes do not show any mutation and copy number changes. Aβ aggregation plays an important role in disease pathogenesis. Aβ induces the conversion of tau proteins to neurofibrillary tangles and the accumulation of (ROS) molecules. Somatic mutations develop due to the damage caused by ROS and/or other mutagens which further lead to neuron death.