Elucidating the effects of extra chromosome elimination in mosaic aneuploidy syndromes: Pallister-Killian syndrome as a model

阐明额外染色体消除对嵌合非整倍体综合征的影响：以 Pallister-Killian 综合征为模型

• 批准号: 10431449
• 负责人: Kosuke Izumi
• 金额: $ 28.08万
• 依托单位: CHILDREN'S HOSP OF PHILADELPHIA
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-08 至 2023-04-01
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10431449
• 关键词: 12p; Address; Aneuploidy; Cell Culture Techniques; Cell Line; Cell physiology; Cells; ChIP-seq; Characteristics; Child; Chromosome Markers; Chromosome abnormality; Chromosomes; Clinical; Complementary DNA; Congenital Abnormality; Congenital chromosomal disease; Data; Developmental Disabilities; Disease; Epigenetic Process; Fibroblasts; Gene Dosage; Gene Expression; Gene Expression Alteration; Gene set enrichment analysis; Genes; Genetic; Genetic Transcription; Genomics; Goals; Image; Individual; Isochromosomes; Meiosis; Memory; Mitosis; Modeling; Modification; Molecular; Mosaicism; Nature; Outcome; Pallister-Killian Syndrome; Pathogenesis; Patients; Phenotype; Play; Population; Process; Public Health; Research; Role; Severities; Skin; Symptoms; Syndrome; Testing; Therapeutic Effect; Tissues; Transcript; Trisomy; Work; X Inactivation; arm; base; clinical phenotype; congenital anomaly; differential expression; epigenome; epigenomics; genome-wide; histone modification; improved; induced pluripotent stem cell; insight; novel; novel therapeutics; prototype; restoration; single-cell RNA sequencing; therapeutic target; transcriptome; transcriptome sequencing; transcriptomics; zygote

Project Summary/Abstract The presence of an extra chromosome (trisomy or marker chromosome) is a common cause of congenital anomalies and developmental disabilities. Approximately 1% of chromosomal abnormalities are mosaic, and these patients have two cellular populations with and without chromosomal abnormalities. Pallister-Killian syndrome (PKS) is a common mosaic chromosomal disorder, and this syndrome is caused by the presence of an extra supernumerary marker chromosome, isochromosome 12p (i(12p), composed of two 12p arms that are mirror-images). We previously demonstrated that the i(12p) in PKS is formed during meiosis. All PKS zygotes contain i(12p), but during mitosis, some cells lose the i(12p) through a process known as aneuploid rescue. Consequently, all patients with PKS demonstrate mosaicism. In mosaic chromosomal disorders, altered gene dosage is believed to be the primary driver of the clinical phenotype, and the rescued cells without the chromosome abnormality are thought to be “normal.” Based on this premise, it has been proposed that there exists a correlation between the mosaic ratio (proportion of the cells possessing chromosomal abnormality in any given tissue) and the severity of patient’s clinical symptoms, but we previously demonstrated the lack of such a correlation in PKS. One possible explanation for the lack of correlation is that cells that have lost the extra chromosome continue to demonstrate functional alterations. By taking advantage of the mosaic nature of chromosomal abnormality seen in PKS, we assessed if aneuploid-rescued PKS cells retain gene expression and epigenetic abnormalities without i(12p), and we discovered similar transcriptome and histone modification profiles between PKS cells with and without the extra 12p. Hence, our data points to an ongoing “memory” effect of the i(12p) on both the transcriptome and epigenome that are not restored after the elimination of i(12p) by aneuploid rescue. The long-term goal of this project is to identify treatments to improve the clinical features associated with PKS and other numerical chromosomal disorders in children. Our preliminary data suggest that, for the full restoration of cellular functions in PKS, not only elimination of the extra chromosome but also epigenetic resetting is needed. The overall objective of this study is to investigate the role of i(12p) in the transcriptional and epigenetic alterations observed in PKS. To achieve our overall objective, we will perform further genomic analyses through two Specific Aims. In Aim 1, we will investigate gene expression alterations at the single-cell level using single-cell RNA-sequencing and mosaic PKS skin fibroblast cell lines. In Aim 2, we will investigate whether induced pluripotent stem cell reprogramming can alleviate transcriptome and epigenome alterations seen in PKS cells without i(12p). This project has a potential to drive a paradigm shift in our understanding of the basic pathobiology of mosaic chromosomal disorders. This work will have significant relevance for ongoing efforts to develop novel therapies for a wide range of chromosomal disorders.

项目概要/摘要 额外染色体（三体性或标记染色体）的存在是先天性遗传病的常见原因 异常和发育障碍。大约 1% 的染色体异常是嵌合体，并且 这些患者有两种细胞群，有或没有染色体异常。帕利斯特-基利安 综合征（PKS）是一种常见的镶嵌染色体疾病，该综合征是由于存在 额外的额外标记染色体，同染色体 12p (i(12p))，由两个 12p 臂组成， 镜像）。我们之前证明 PKS 中的 i(12p) 是在减数分裂过程中形成的。所有 PKS 受精卵 含有 i(12p)，但在有丝分裂期间，一些细胞通过称为非整倍体拯救的过程失去 i(12p)。 因此，所有 PKS 患者都表现出嵌合现象。在镶嵌染色体疾病中，基因改变 剂量被认为是临床表型的主要驱动因素，并且拯救的细胞没有 染色体异常被认为是“正常的”。基于这个前提，有人提出 镶嵌率（在细胞中具有染色体异常的细胞的比例）之间存在相关性 任何给定的组织）和患者临床症状的严重程度，但我们之前证明缺乏 PKS 中存在这样的相关性。缺乏相关性的一种可能的解释是，失去了相关性的细胞 额外的染色体继续表现出功能改变。通过利用马赛克性质 PKS 中出现染色体异常，我们评估非整倍体拯救的 PKS 细胞是否保留基因表达 和没有 i(12p) 的表观遗传异常，我们发现了类似的转录组和组蛋白修饰 有和没有额外 12p 的 PKS 细胞之间的概况。因此，我们的数据指向持续的“记忆” i(12p) 对转录组和表观基因组的影响在消除 i(12p) 后不会恢复 通过非整倍体救援。该项目的长期目标是确定改善临床特征的治疗方法 与儿童 PKS 和其他数值染色体疾病有关。我们的初步数据表明 认为，为了在PKS中完全恢复细胞功能，不仅要消除多余的染色体，还要消除多余的染色体。 需要进行表观遗传重置。本研究的总体目标是研究 i(12p) 在 PKS 中观察到的转录和表观遗传改变。为了实现我们的总体目标，我们将执行 通过两个具体目标进行进一步的基因组分析。在目标 1 中，我们将研究基因表达改变 在单细胞水平上使用单细胞 RNA 测序和镶嵌 PKS 皮肤成纤维细胞系。在目标 2 中，我们 将研究诱导多能干细胞重编程是否可以减轻转录组和 在没有 i(12p) 的 PKS 细胞中观察到表观基因组改变。该项目有潜力推动范式转变 我们对嵌合染色体疾病基本病理学的理解。这项工作将具有重大意义 与持续努力开发针对广泛染色体疾病的新疗法的相关性。