Single-cell Multi-omic Profiling of Drug Responses Using Pooled iPSC-CM Differentiation

使用汇集 iPSC-CM 分化进行药物反应的单细胞多组学分析

• 批准号: 10671175
• 负责人: MARK MERCOLA
• 金额: $ 61.82万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-05-01 至 2027-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10671175
• 关键词: 3-Dimensional; Adverse effects; Affect; Aging; Alleles; Biological Process; CRISPR/Cas technology; Calcium; Cardiac Myocytes; Cardiotoxicity; Cardiovascular Diseases; Cardiovascular system; Cell Line; Cell Survival; Cells; Chromosome Mapping; Circulation; Coculture Techniques; Coupled; DNA Damage; Dose; Doxorubicin; Drug Screening; Etiology; Exposure to; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genotype; Grant; Heart; Hour; Human; Individual; Individual Differences; Journals; Knowledge; Maps; Methodology; Modeling; Nature; Patients; Pharmaceutical Preparations; Population Heterogeneity; Predisposition; Production; Publishing; Quantitative Trait Loci; RARG gene; Research Personnel; Risk; Role; Series; Stains; Technology; Time; Toxic effect; Transcription Initiation Site; XCL1 gene; cancer complication; cancer therapy; cardiac tissue engineering; cytotoxic; differentiation protocol; dosage; epigenome; experimental study; gene function; genetic variant; genome editing; genome sequencing; genome-wide; induced pluripotent stem cell; induced pluripotent stem cell derived cardiomyocytes; inter-individual variation; multiple omics; novel; precision drugs; response; single cell analysis; single cell sequencing; single-cell RNA sequencing; stem cells; transcriptome; whole genome

PROJECT SUMMARY Cardiovascular complications of cancer therapy significantly contribute to the global burden of cardiovascular diseases. Although remarkable progress has been made in understanding the genetic basis of doxorubicin- induced cardiotoxicity (DIC), we cannot predict which patients will be affected by DIC or protect patients at risk for suffering from DIC adequately. Here, we will use a novel multiplexing methodology of creating a "cell village" by pooling multiple patients' induced pluripotent stem cell (iPSC) lines in a dish to map the genetic basis of inter- individual differences in response to doxorubicin. In Aim 1, we will co-culture 100 iPSC lines in 10 distinct "cell villages," where each "cell village" contains ten independent patient-specific iPSC lines. Next, we will differentiate each "cell village" into iPSC-derived cardiomyocytes (iPSC-CMs). Finally, we will perform a single-cell multi- omics sequencing analysis of the "cell villages" to understand the impact of genetic variability on cardiomyocyte gene regulation and functions at baseline. In Aim 2, we will employ a single-cell multi-omic approach to uncover and validate the role of response eQTL in DIC prediction. We will treat iPSC-CMs in each "cell village" with doxorubicin at various doses. Next, we will perform single-cell multi-omics profiling to model the contribution of genetics to variability in responses to doxorubicin treatment. In Aim 3, we will employ 3D engineered heart tissues (EHTs) and CRISPR/cas9 genome-editing to comprehensively study the functional role of two candidate doxorubicin response genes. All in all, the proposed experiments will serve as a proof-of- principle in using the "cell village" model as a high throughput personalized drug screening platform.

项目摘要 癌症治疗的心血管并发症显著增加了全球心血管疾病负担。 疾病尽管在了解阿霉素的遗传基础方面取得了显著进展， 我们无法预测哪些患者会受到DIC的影响，也无法保护处于风险中的患者 患上弥散性血管内凝血在这里，我们将使用一种新颖的多路复用方法来创建一个“细胞村”。 通过在培养皿中汇集多个患者的诱导多能干细胞（iPSC）系， 对阿霉素反应的个体差异。在目标1中，我们将在10个不同的“细胞”中共培养100个iPSC系。 其中每个“细胞村”包含十个独立的患者特异性iPSC系。接下来，我们将区分 将每个“细胞村”转化为iPSC衍生的心肌细胞（iPSC-CM）。最后，我们将执行一个单细胞多- “细胞村”的组学测序分析，以了解遗传变异对心肌细胞的影响 基因调控和功能基线。在目标2中，我们将采用单细胞多组学方法来揭示 验证了反应eQTL在DIC预测中的作用。我们将在每个“细胞村”治疗iPSC-CM， 不同剂量的阿霉素。接下来，我们将进行单细胞多组学分析，以模拟 遗传学对多柔比星治疗反应的变异性。在目标3中，我们将使用3D工程心脏组织 （EHTs）和CRISPR/cas9基因组编辑，以全面研究两种候选基因的功能作用。 阿霉素反应基因。总而言之，所提出的实验将作为使用 “细胞村”模式作为高通量个性化药物筛选平台。

项目成果

Generation of two induced pluripotent stem cell lines from patients with cardiac amyloidosis carrying heterozygous transthyretin (TTR) mutation.

• DOI: 10.1016/j.scr.2023.103215
• 发表时间: 2023-10
• 期刊: STEM CELL RESEARCH
• 影响因子: 1.2
• 作者: Bonilauri, Bernardo;Shin, Hye Sook;Htet, Min;Yan, Christopher D.;Wittles, Ronald M.;Sallam, Karim;Wu, Joseph C.
• 通讯作者: Wu, Joseph C.

Utilization of induced pluripotent stem cells to model the molecular network regulating congenital heart disease.

利用诱导多能干细胞来模拟调节先天性心脏病的分子网络。

• DOI: 10.1093/cvr/cvab373
• 发表时间: 2022
• 期刊: Cardiovascular research
• 影响因子: 10.8
• 作者: Mullen,McKayMS;Wu,JosephC
• 通讯作者: Wu,JosephC

Generation of two induced pluripotent stem cell lines from Duchenne muscular dystrophy patients.

从杜氏肌营养不良症患者中产生两种诱导多能干细胞系。

• DOI: 10.1016/j.scr.2023.103207
• 发表时间: 2023
• 期刊: Stem cell research
• 影响因子: 1.2
• 作者: Liu,Wenqiang;Zeng,Wenshu;Kong,Xiaohui;Htet,Min;Yu,Rebecca;Wheeler,Matthew;Day,JohnW;Wu,JosephC
• 通讯作者: Wu,JosephC