Somatic copy number variant load in neurons of healthy controls and Alzheimer’s disease patients. undefined

The possible role of somatic copy number variations (CNVs) in Alzheimer's disease (AD) aetiology has been controversial. Although cytogenetic studies suggested increased CNV loads in AD brains, a recent single-cell whole-genome sequencing (scWGS) experiment, studying frontal cortex brain samples, found no such evidence. Here we readdressed this issue using low-coverage scWGS on pyramidal neurons dissected using laser capture microdissection (LCM) across five brain regions: entorhinal cortex, temporal cortex, hippocampal CA 1, hippocampal CA 3, and the cerebellum. Studying data from 1301 cells obtained from 20 brains, we found a low CNV load across all tested brain regions. Among reliably detected CNVs, deletions were more frequent compared to duplications. We did not find any difference between brains from AD (13 individuals, n=688 cells) and control samples (7 individuals, n=613 cells) in terms of CNV frequency. Interestingly, LCM-isolated cells show higher within-cell read depth variation compared to cells isolated with fluorescence activated cell sorting (FACS), which we argue may have both biological and technical causes. Indeed, we found that LCM-isolated neurons in AD patients harbour slightly more read depth variability than neurons of healthy controls, which might be related to the reported hyperploid profiles of some AD-affected neurons. We also propose a principal component analysis-based denoising approach that significantly reduces within-cell read depth variation in scWGS data.

体细胞拷贝数变异（somatic copy number variations, CNVs）在阿尔茨海默病（Alzheimer's disease, AD）病因学中的潜在作用长期颇具争议。尽管细胞遗传学研究提示AD患者脑组织中CNV负荷升高，但近期一项针对额叶皮层脑样本的单细胞全基因组测序（single-cell whole-genome sequencing, scWGS）研究并未发现此类证据。
本研究借助激光捕获显微切割（laser capture microdissection, LCM）分离锥体神经元，对5个脑区——内嗅皮层、颞叶皮层、海马CA1区、海马CA3区及小脑——开展低覆盖度scWGS，重新探讨了这一争议问题。
本研究分析了20例脑组织的1301个细胞的测序数据，发现所有受试脑区的CNV负荷均处于较低水平。在可靠检测到的CNV中，缺失型变异的发生频率高于重复型变异。在CNV发生频率方面，AD患者脑组织（13例个体，共688个细胞）与对照样本（7例个体，共613个细胞）之间未观察到显著差异。
值得注意的是，与通过荧光激活细胞分选（fluorescence activated cell sorting, FACS）分离的细胞相比，LCM分离的细胞表现出更高的胞内读深度变异。我们认为该现象可能兼具生物学与技术层面的成因。进一步分析显示，AD患者中LCM分离的神经元的读深度变异略高于健康对照的神经元，这或与此前报道的部分受累AD神经元的超倍体特征相关。
此外，本研究还提出了一种基于主成分分析的降噪方法，该方法可显著降低scWGS数据中的胞内读深度变异。