Somatic gene recombination of amyloid precursor protein (APP) in human neurons has been identified, encompassing thousands of genomic variants occurring mosaically in normal and sporadic Alzheimer’s disease (AD) brains. Multiple sequencing strategies and junction-specific genomic in situ hybridization revealed APP recombination, lacking introns and having precise exonic junctions, termed genomic cDNAs (gencDNAs), often with multiple recombined junctions contained within a single nucleus. Most variants showed structural changes, particularly deletion of central exons with partial exons fused together, forming intra-exonic junctions, containing single nucleotide variations. APP is a causal gene mutated in forms of AD, and our studies identified variants enriched in sporadic AD neurons, including 10 mutations identical to those in published familial AD, yet arising somatically. Additional studies linked APP neuronal RNA transcription to the appearance of gencDNAs that could be preferentially transcribed to generate myriad gene variants contributing to diversity and function in the normal and diseased brain.

Previous reports have shown that individual neurons of the brain can display somatic genomic mosaicism of unknown function. In this study, we report altered genomic mosaicism in single, sporadic Alzheimer's disease (AD) neurons characterized by increases in DNA content and amyloid precursor protein (APP) gene copy number. AD cortical nuclei displayed large variability with average DNA content increases of ∼8% over non-diseased controls that were unrelated to trisomy 21. Two independent single-cell copy number analyses identified amplifications at the APP locus. The use of single-cell qPCR identified up to 12 copies of APP in sampled neurons. Peptide nucleic acid (PNA) probes targeting APP, combined with super-resolution microscopy detected primarily single fluorescent signals of variable intensity that paralleled single-cell qPCR analyses. These data identify somatic genomic changes in single neurons, affecting known and unknown loci, which are increased in sporadic AD, and further indicate functionality for genomic mosaicism in the CNS.DOI: http://dx.doi.org/10.7554/eLife.05116.001

Since the discovery of DNA, the normal developing and functioning brain has been assumed to be composed of cells with identical genomes, which remains the dominant view even today. However, this pervasive assumption is incorrect, as proven by increasing numbers of reports within the last 20 years that have identified multiple forms of somatically produced genomic mosaicism (GM), wherein brain cells – especially neurons – from a single individual show diverse alterations in DNA, distinct from the germline. Critically, these changes alter the actual DNA nucleotide sequences – in contrast to epigenetic mechanisms – and almost certainly contribute to the remarkably diverse phenotypes of single brain cells, including single-cell transcriptomic profiles. Here we review the history of GM within the normal brain, including its major forms, initiating mechanisms, and possible functions. GM forms include aneuploidies and aneusomies, smaller copy number variations (CNVs), long interspersed nuclear element type 1 (LINE1) repeat elements, and single nucleotide variations (SNVs), as well as DNA content variation (DCV) that reflects all forms of GM with greatest coverage of large, brain cell populations. In addition, technical considerations are examined, along with relationships amongst GM forms and multiple brain diseases. GM affecting genes and loci within the brain contrast with current neural discovery approaches that rely on sequencing non-brain DNA (e.g., genome-wide association studies (GWAS)). Increasing knowledge of neural GM has implications for mechanisms of development, diversity, and function, as well as understanding diseases, particularly the overwhelming prevalence of sporadic brain GM unlinked to germline mutations.