Multi-scale consequences of variants in the schizophrenia risk gene SETD1A in a population isolate.

项目摘要。 具有大效应的罕见变异为描述复杂性的因果机制提供了极好的机会。 紊乱最近，精神分裂症的大规模外显子组测序发现，罕见的蛋白质截短和 包含SET结构域1A（SETD 1A）的错义变体与大约4至20倍的 增加精神分裂症的风险，使其成为大约10个基因中的最高风险基因（P = 2.0e-12），这些基因具有强的 支持. SETD 1A编码一种染色质修饰酶，负责在染色体上赖氨酸4的三甲基化。 组蛋白3尾（H3 K4 me 3），在活性启动子处的重要组蛋白修饰。描述影响的特征 SETD 1A变体已成为了解因果机制最令人兴奋的前景之一 精神分裂症的潜在风险然而，质疑这些影响受到两个关键因素的阻碍， 障碍：首先，由于SETD 1A变体非常罕见，因此很难确定足够数量的 携带者以充分表征SETD 1A的临床表型。其次，部分出于同样的原因， 没有研究自然发生在人类神经细胞中的SETD 1A变体。在这里，我们提出实验， 克服这两个障碍，利用我们发现的七个有害的，非同义的SETD 1A 变种丰富的本地访问的创始人人口，旧秩序阿米什人。我们将总共招募128名 SETD 1A变体的阿米什携带者及其血亲，确定深层认知和精神症状 表型，以及关于等位基因异质性、等位基因频率依赖性、剂量 依赖性，以及与常见变异的多基因风险的相互作用。接下来，我们将获得诱导多能 从这些个体的子集中提取干细胞以鉴定细胞和神经发育表型， 在细胞水平上表征等位基因异质性，并检验细胞表型可以被 通过恢复H3 K4 me 3的水平来拯救。最后，我们将测试SETD 1A变异改变了基因表达的假设。 利用尖端的单细胞多组学技术和网络， 建模技术我们令人兴奋的初步结果表明，Amish富集的SETD 1A变体是 与精神病、认知缺陷、细胞增殖减少、 易受DNA损伤，神经突起形成效率低下，神经突起生长不足， 在神经干细胞中，未成熟的细胞周期退出和未成熟的转录特征。

Project Summary. Rare variants with large effects provide excellent opportunities to characterize causal mechanisms for complex disorders. Recently, large-scale exome sequencing of schizophrenia found that rare protein-truncating and missense variants in SET Domain Containing 1A (SETD1A) are associated with approximately 4- to 20-fold increased risk for schizophrenia, making this the top risk gene (P = 2.0e-12) among about ten genes with strong support. SETD1A encodes a chromatin modifying enzyme responsible for tri-methylation of lysine 4 on the histone 3 tail (H3K4me3), an important histone modification at active promoters. Characterizing the effects of SETD1A variants has emerged as one of the most exciting prospects to understand causal mechanisms underlying risk for schizophrenia. However, interrogating these effects has been hindered by two critical obstacles: First, since SETD1A variants are very rare, it has been difficult to ascertain sufficient numbers of carriers to fully characterize SETD1A’s clinical phenotype. Second, in part for the same reason, there have been no studies of naturally occurring SETD1A variants in human neural cells. Here, we propose experiments to overcome both of these obstacles, leveraging our discovery of seven deleterious, nonsynonymous SETD1A variants enriched in a locally accessible founder population, the Old Order Amish. We will recruit a total of 128 Amish carriers of SETD1A variants and their blood relatives, ascertain deep cognitive and psychiatric symptom phenotypes, and test hypotheses regarding allelic heterogeneity, allele frequency dependence, dose dependence, and interactions with polygenic risk from common variants. Next, we will obtain induced pluripotent stem cells from a subset of these individuals to identify cellular and neurodevelopmental phenotypes, characterize allelic heterogeneity at a cellular level, and test the hypothesis that cellular phenotypes can be rescued by restoring levels of H3K4me3. Finally, we will test the hypothesis that SETD1A variants alter the chromatin potential of developing neurons, using cutting-edge single-cell multi-omic technologies and network modeling techniques. Our exciting preliminary results demonstrate that Amish-enriched SETD1A variants are associated with increased risk for psychosis, cognitive deficits, reduced cellular proliferation, increased vulnerability to DNA damage, inefficient formation of neural rosettes, deficits in neurite outgrowth, and transcriptional signatures of premature cell cycle exit and premature maturation in neural stem cells.