Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer’s disease neurons

Abstract

BackgroundAlzheimer’s disease (AD) is a neurodegenerative disease of the brain and the most common form of dementia in the elderly. Aneuploidy, a state in which cells have an abnormal number of chromosomes, has been proposed to play a role in neurodegeneration in AD patients. Several studies using fluorescence in situ hybridization have shown that the brains of AD patients contain an increased number of aneuploid cells. However, because the reported rate of aneuploidy in neurons ranges widely, a more sensitive method is needed to establish a possible role of aneuploidy in AD pathology.ResultsIn the current study, we used a novel single-cell whole genome sequencing (scWGS) approach to assess aneuploidy in isolated neurons from the frontal cortex of normal control individuals (n = 6) and patients with AD (n = 10). The sensitivity and specificity of our method was shown by the presence of three copies of chromosome 21 in all analyzed neuronal nuclei of a Down’s syndrome sample (n = 36). Very low levels of aneuploidy were found in the brains from control individuals (n = 589) and AD patients (n = 893). In contrast to other studies, we observe no selective gain of chromosomes 17 or 21 in neurons of AD patients.ConclusionscWGS showed no evidence for common aneuploidy in normal and AD neurons. Therefore, our results do not support an important role for aneuploidy in neuronal cells in the pathogenesis of AD. This will need to be confirmed by future studies in larger cohorts.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0976-2) contains supplementary material, which is available to authorized users.

CIN and Aneuploidy: Different Concepts, Different Consequences

“…These studies suggest that the level of aneuploidy in brain and liver is much lower than previously reported, with aneuploidy only affecting $2-5% of the cells, similar to the low rates of aneuploidy which were reported for epidermis. [62][63][64] Together these data suggest that many human tissues, including brain, skin and liver, contain a low level of aneuploidy. However, the exact contribution of aneuploid cells to in vivo tissues still needs to be more accurately quantified.…”

Does Aneuploidy in the Brain Play a Role in Neurodegenerative Disease?

“…On the other hand, in a recent study, a twofold increase in X chromosome aneuploidy was found in AD neurons when compared to age matched controls [65]. To summarize, although again the rates of aneuploidy and which chromosomes are afected difer between studies, the overall trends suggest that aneuploidy might be increased in AD [66].…”

“…All of these single cell sequencing studies use cells of which the chromosome copy numbers are known as validation of the method: human male trisomy 21 ibroblasts [82], human male trisomy 18 neurons [81], mouse trisomy 16 brain cells [87] and human female trisomy 21 neurons [66]. In each case, the known aneuploidy as well as the correct number of X chromosomes, male or female, was detected with 100% accuracy, conirming the sensitivity of single cell sequencing.…”

“…After sequencing, the individual reads are split into libraries for each individual cell based on the cellular barcode (demultiplexing), and the copy numbers of individual chromosomes can be determined by comparing the read density on each chromosome. An extra copy of a chromosome is expected to result in 50% increase in read density, while loss of a chromosome leads to a 50% reduction of the read density on that chromosome [66,85,86]. Depending on the sequencing depth, single cell sequencing can, in addition to whole chromosome aneuploidies, also reveal smaller copy number changes.…”

“…aneuploidy both in controls and AD [66]. All of these single cell sequencing studies use cells of which the chromosome copy numbers are known as validation of the method: human male trisomy 21 ibroblasts [82], human male trisomy 18 neurons [81], mouse trisomy 16 brain cells [87] and human female trisomy 21 neurons [66].…”