Autism spectrum disorder (ASD) is a set of highly heterogeneous neurodevelopmental diseases whose genetic etiology is not completely understood. Several investigations have relied on transcriptome analysis from peripheral tissues to dissect ASD into homogenous molecular phenotypes. Recently, analysis of changes in gene expression from postmortem brain tissues has identified sets of genes that are involved in pathways previously associated with ASD etiology. In addition to protein-coding transcripts, the human transcriptome is composed by a large set of non-coding RNAs and transposable elements (TEs). Advancements in sequencing technologies have proven that TEs can be transcribed in a regulated fashion, and their dysregulation might have a role in brain diseases. We exploited published datasets comprising RNA-seq data from (1) postmortem brain of ASD subjects, (2) in vitro cell cultures where ten different ASD-relevant genes were knocked out and (3) blood of discordant siblings. We measured the expression levels of evolutionarily young full-length transposable L1 elements and characterized the genomic location of deregulated L1s assessing their potential impact on the transcription of ASD-relevant genes. We analyzed every sample independently, avoiding to pool together the disease subjects to unmask the heterogeneity of the molecular phenotypes. We detected a strong upregulation of intronic full-length L1s in a subset of postmortem brain samples and in in vitro differentiated neurons from iPSC knocked out for ATRX. L1 upregulation correlated with an high number of deregulated genes and retained introns. In the anterior cingulate cortex of one subject, a small number of significantly upregulated L1s overlapped with ASD-relevant genes that were significantly downregulated, suggesting the possible existence of a negative effect of L1 transcription on host transcripts. Our analyses must be considered exploratory and will need to be validated in bigger cohorts. The main limitation is given by the small sample size and by the lack of replicates for postmortem brain samples. Measuring the transcription of locus-specific TEs is complicated by the repetitive nature of their sequence, which reduces the accuracy in mapping sequencing reads to the correct genomic locus. L1 upregulation in ASD appears to be limited to a subset of subjects that are also characterized by a general deregulation of the expression of canonical genes and an increase in intron retention. In some samples from the anterior cingulate cortex, L1s upregulation seems to directly impair the expression of some ASD-relevant genes by a still unknown mechanism. L1s upregulation may therefore identify a group of ASD subjects with common molecular features and helps stratifying individuals for novel strategies of therapeutic intervention.

中文翻译：

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自闭症中 L1 逆转录转座子表达的探索性分析

自闭症谱系障碍（ASD）是一组高度异质性的神经发育疾病，其遗传病因尚不完全清楚。一些研究依赖于外周组织的转录组分析，将自闭症谱系障碍剖析成同质的分子表型。最近，对死后脑组织基因表达变化的分析发现了一组参与先前与 ASD 病因相关的通路的基因。除了蛋白质编码转录本外，人类转录组还由大量非编码 RNA 和转座元件 (TE) 组成。测序技术的进步已经证明，TE 可以以受调控的方式转录，并且它们的失调可能在脑部疾病中发挥作用。我们利用了已发表的数据集，其中包含来自以下各项的 RNA 序列数据：(1) ASD 受试者死后大脑，(2) 体外细胞培养物，其中 10 个不同的 ASD 相关基因被敲除，以及 (3) 不一致兄弟姐妹的血液。我们测量了进化上年轻的全长转座 L1 元件的表达水平，并表征了失调的 L1 的基因组位置，评估了它们对 ASD 相关基因转录的潜在影响。我们独立分析每个样本，避免将疾病受试者集中在一起以揭示分子表型的异质性。我们在死后大脑样本的子集中以及来自 ATRX 敲除的 iPSC 的体外分化神经元中检测到内含子全长 L1 的强烈上调。L1 上调与大量失调基因和保留内含子相关。在一名受试者的前扣带皮层中，少数显着上调的 L1 与显着下调的 ASD 相关基因重叠，表明 L1 转录可能对宿主转录物存在负面影响。我们的分析必须被认为是探索性的，并且需要在更大的群体中进行验证。主要限制是样本量小以及死后大脑样本缺乏重复。位点特异性 TE 的转录因其序列的重复性质而变得复杂，这降低了将测序读数映射到正确基因组位点的准确性。自闭症谱系障碍 (ASD) 中 L1 的上调似乎仅限于一部分受试者，这些受试者的特征还包括规范基因表达的普遍失调和内含子保留的增加。在前扣带皮层的一些样本中，L1s 上调似乎通过仍未知的机制直接损害了一些 ASD 相关基因的表达。因此，L1s 上调可能会识别一组具有共同分子特征的 ASD 受试者，并有助于对个体进行分层，以制定新的治疗干预策略。