A novel human T-cell platform to define biological effects of genome editing

一种新型人类 T 细胞平台，用于定义基因组编辑的生物学效应

基本信息

批准号：
10434027
负责人：
Shengdar Tsai
金额：
$ 61万
依托单位：
ST. JUDE CHILDREN'S RESEARCH HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-09-12 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10434027
关键词：
Address Advanced Development Adverse effects Affect Artificial Intelligence Bar Codes Benign Biochemical Bioinformatics Biological Biological Assay Cell model Cell physiology Cells Chromatin Clonal Expansion Complex Coupled DNA Methylation Detection Engineering Epitopes Frequencies Gene Expression Genes Genetic Genetic Diseases Genetic Transcription Genetic Variation Genome Genomic medicine Genomics Goals HIV Human Human Genetics Human Genome Immunologic Deficiency Syndromes In Vitro Inherited Malignant Neoplasms Maps Mature T-Lymphocyte Measures Methods Modeling Mutation Oncogenic Organizational Change Outcome Peptide Library Peripheral Blood Mononuclear Cell Phenotype Population Proto-Oncogenes Regulatory Element Retroviral Vector Ribonucleoproteins Safety Site Site-Directed Mutagenesis Standardization Streptococcus pyogenes T cell receptor repertoire sequencing T cell response T-Cell Proliferation T-Lymphocyte T-cell receptor repertoire Technology Testing Therapeutic Training Variant adaptive immune response adverse outcome base base editor comparative genomics cytokine deep learning model detection limit effective therapy epigenomics functional genomics gene therapy genome editing genome-wide genotoxicity histone modification human disease immunogenic immunogenicity improved in vivo machine learning method next generation novel novel therapeutics off-target mutation off-target site response safety assessment safety testing side effect therapeutic development therapeutic gene therapeutic genome editing transcriptome sequencing

项目摘要

PROJECT SUMMARY Genome editing technologies have extraordinary potential as new genomic medicines that address underlying genetic causes of human disease; however, it remains challenging to predict their long-term safety, because we do not know the consequences of potential side effects of genome editing such as off-target mutations or immunogenicity. Our long-term goal is to understand and predict such unintended biological effects to advance the development of safe and effective therapies. T-cells are an ideal cellular model because: 1) they are highly relevant as the most widely used cells for development of therapeutic genome editing strategies (such as cell-based treatments for HIV and cancer) and 2) mature T-cells encode a diverse T-cell receptor repertoire that can be exploited as built-in cellular barcodes for quantifying clonal expansion or depletion in response to specific treatments. We, therefore, propose the following specific aims: 1) to predict which unintended editing sites have biological effects on human T-cells by integrating large-scale genome-wide activity and epigenomic profiles with state-of-the-art deep learning models and 2) to develop a human primary T-cell platform to detect functional effects of genome editing by measuring clonal representation, off-target mutation frequencies, immunogenicity, or gene expression. If successful, our experimental and predictive framework will profoundly increase confidence in the safety of the next generation of promising genome editing therapies.

项目摘要基因组编辑技术具有针对潜在的新基因组药物的非凡潜力人类疾病的遗传原因；但是，预测他们的长期安全仍然是一项挑战，因为我们不知道基因组编辑的潜在副作用的后果，例如脱靶突变或免疫原性。我们的长期目标是了解和预测这种意外的生物学效应以促进安全有效疗法的发展。 T细胞是理想的蜂窝模型，因为：1）它们是高度的与最广泛使用的细胞相关，用于开发治疗性基因组编辑策略（例如基于细胞的HIV和癌症治疗）和2）成熟的T细胞编码可以多样化的T细胞受体库，可以被用作内置的蜂窝条形码，以量化克隆膨胀或耗竭。治疗。因此，我们提出以下具体目的：1）预测哪些意想不到的编辑站点具有通过将大规模基因组活性和表观基因组谱与与人类T细胞的生物学作用最先进的深度学习模型和2）开发人类的主要T细胞平台来检测功能通过测量克隆表示，脱靶突变频率，免疫原性，通过测量基因组编辑的影响或基因表达。如果成功，我们的实验和预测框架将深刻提高信心在下一代有前途的基因组编辑疗法的安全中。

项目成果

期刊论文数量（9）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

In vivo engineered B cells secrete high titers of broadly neutralizing anti-HIV antibodies in mice.

DOI：
10.1038/s41587-022-01328-9
发表时间：
2022-08
期刊：
Nature biotechnology
影响因子：
46.9
作者：
Nahmad AD;Lazzarotto CR;Zelikson N;Kustin T;Tenuta M;Huang D;Reuveni I;Nataf D;Raviv Y;Horovitz-Fried M;Dotan I;Carmi Y;Rosin-Arbesfeld R;Nemazee D;Voss JE;Stern A;Tsai SQ;Barzel A
通讯作者：
Barzel A

Defining genome-wide CRISPR-Cas genome-editing nuclease activity with GUIDE-seq.

DOI：
10.1038/s41596-021-00626-x
发表时间：
2021-12
期刊：
NATURE PROTOCOLS
影响因子：
14.8
作者：
Malinin, Nikolay L.;Lee, GaHyun;Lazzarotto, Cicera R.;Li, Yichao;Zheng, Zongli;Nguyen, Nhu T.;Liebers, Matthew;Topkar, Ved V.;Iafrate, A. John;Le, Long P.;Aryee, Martin J.;Joung, J. Keith;Tsai, Shengdar Q.
通讯作者：
Tsai, Shengdar Q.

Trichostatin A for Efficient CRISPR-Cas9 Gene Editing of Human Pluripotent Stem Cells.