Mapping the Complex Genetic Landscape of Human Neurons

Abstract

When somatic cells acquire complex karyotypes, they are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, ″CNV neurons″), but previous analyses of CNV neurons have been limited by relatively small sample sizes. Here, we developed an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We applied this approach to 2,125 frontal cortical neurons from a neurotypical human brain. This approach identified 226 CNV neurons, as well as a class of CNV neurons with complex karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we found that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contained fewer, but longer, genes.

Cell type-specific enrichment of somatic aneuploidy in the mammalian brain

“…Our data show that aneuploidy is rare in the adult mouse brain, affecting <1% of cells, in line with previous scWGS studies based on smaller numbers of cells 1,11,31 . However, we found an intriguing and non-random pattern of aneuploidy with recurrent trisomy of chromosome 16 and enrichment of aneuploidies in specific cell types, including Pons neurons and oligodendrocyte precursor cells.…”

“…Studies based on in situ hybridization, spectral karyotyping techniques 7,28,29 , and more recently multiplexed FISH 30 , reported high rates of aneuploidy in human and mouse neurons ranging from ∼10 to ∼60% of cells. By contrast, single-cell whole genome sequencing (scWGS) yields far lower rates of aneuploidy in human neurons, from 0.5 to ∼5% of cells 1,11,25,26,31 . Although single-cell sequencing is considered a gold standard for measuring somatic mutations 32 , previous studies using scWGS have sampled only up to several hundred cells from a single brain region.…”

High-resolution detection of copy number alterations in single cells with HiScanner

“…This was done separately for bin sizes of 5 Mb and 100 kb. Regardless of bin size, we noticed a tendency for high ploidy predictions and overfitting, similar to what was reported previously 22 . To address this, we fine-tuned several parameters in the chisel_calling module to optimize the method performance.…”

“…We assessed the quality of these calls by inspection of the BAF distribution in the putative CNAs and found that a considerable proportion of Ginkgo's calls disagreed with local BAF signals (Fig 4f-j): 73% (330/451) of CNAs called in oligodendrocytes and 61% (1110/1847) of CNAs called in neurons were discordant. This suggests that Ginkgo's calls in PTA scWGS data should be filtered based on CNA size or be subjected to BAF-based post-call filtering strategies 22 to ensure the reliability of small CNA calls. In contrast, HiScanner's integration of BAF and RDR signals was effective in preventing these types of errors.…”

“…CHISEL is not tuned for the discovery of small CNAs (e.g., <5 Mb) potentially obscuring certain biological processes. SCOVAL 22 also utilizes BAF information, but it is primarily a validation approach and not a CNA caller. HiScanner offers robust detection of rare CNA events across a broad spectrum of sizes, including sub-megabase events, thereby extending the accessible landscape of CNAs in single-cell genomes.…”