Automated Forward Genetic Analysis of Adaptive Immunity

适应性免疫的自动正向遗传分析

• 批准号: 10623164
• 负责人: BRUCE A BEUTLER
• 金额: $ 196.23万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-20 至 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10623164
• 关键词: Affect; Alleles; Amino Acids; Antibody Response; B-Lymphocytes; Binding; Biological Assay; CRISPR/Cas technology; Candidate Disease Gene; Categories; Cell physiology; Cells; Code; Computer software; Data; Databases; Defect; Development; Elements; Ethylnitrosourea; Etiology; Fingerprint; Flow Cytometry; Funding; Genes; Genetic Screening; Genetic Transcription; Genetic study; Genome; Germ-Line Mutation; Immune; Immune System Diseases; Immune system; Immunity; Immunization; Immunoglobulin M; Immunologics; Immunology; Individual; Induced Mutation; Knock-out; Knowledge; Laboratories; Link; Lymphocyte; Lymphoid; Maps; Measurement; Measures; Meiosis; Messenger RNA; Metabolism; Molecular; Mus; Mutagenesis; Mutant Strains Mice; Mutate; Mutation; Names; Nonsense-Mediated Decay; Paper; Pathway interactions; Patients; Phenotype; Probability; Productivity; Proteins; Publications; Publishing; RNA Processing; RNA Splicing; Recurrence; Regulation; Research Personnel; Role; Signal Transduction; Signaling Protein; Source; Supporting Cell; Surveys; Testing; Time; Transducers; Transfer RNA; Translations; Update; Validation; Vesicle; Work; Writing; adaptive immune response; adaptive immunity; causal variant; computerized tools; cytokine; gene discovery; gene product; genetic analysis; genetic pedigree; immune function; improved; insight; interest; loss of function mutation; mutation screening; novel; phenotypic data; protein complex; protein folding; receptor; response; screening; tool; trafficking; vesicle transport

PROJECT SUMMARY During the past four years, we have made outstanding progress in mutagenizing the mouse germline genome while keeping immunity under close surveillance. Now four years into the five-year project, we have thoroughly examined viable hypomorphic mutations in more than half of all protein-encoding genes. We have declared with high confidence that 1,298 mutations in 638 genes are causative of phenotypes in FACS and/or antibody response screens. Many of these genes were novel in that their necessity for immune function had been unknown, and were re-targeted by CRISPR/Cas9 to verify causation. 154 of the 638 candidate genes (24%; almost all of them novel) were either knocked out or modified with the ENU allele using CRISPR/Cas9 editing, expanded into pedigrees, and retested for causation of phenotypes detected in screening and automated mapping. 148 of the 154 genes (96%) were verified as the source of phenotype(s) declared. An additional 156 CRISPR/Cas9 projects are active at this time, some close to completion. Some of our discoveries have been published; many more are works in progress. However, all results of FACS assays on all mutations, whether declared causative of phenotype or not, have been de-restricted for public viewing on Mutagenetix, together with tools that enable search, examination of the original phenotypes and meiotic mapping data, filtering by P-value, and direction and magnitude of individual phenotypic effects. This will enable other laboratories to pursue mechanisms of immunological phenotypes alongside us. Knowledge of genes with non-redundant function in the development and activation of adaptive immune responses is fundamental to immunology and we plan to pursue screening further. We also plan deeper studies of the mechanism(s) behind phenotypes of particular interest. Of the phenotypes named for study in our earlier proposal, we have come to understand those caused by mutations in Trp53bp1, Ampd3, Rnps1, Prkd2, and Snrnp40, and have published papers describing mechanism. Additional phenotypes (not named in the original proposal) caused by mutations in Rabl3, Gpr89, Pdia6, Ncstn, Lmbr1l, Stk4, Pacs1, Wdr37, and Mfsd1 have also been elucidated and published or submitted for publication. We now propose to examine newly verified phenotypes, all the while creating novel phenotypes for study by ourselves and others. Our work is now guided by a tool (Similarity Heatmap) that measures relatedness of phenotypes. In flow cytometry screening, a minimum of 34 measurements are made from each mouse. The results constitute a phenotypic “fingerprint” amenable to tests of statistical similarity. Mutations in some genes yield results very similar to mutations in other genes, and we can sometimes infer that multiple genes operate within a single complex of proteins or enzymatic pathway. We have also written software (Candidate Explorer) to evaluate phenotypes in advance of declaring causation, telling us the likelihood of validation should we attempt to re-target any gene in question. We restrict our efforts to the most likely novel candidates, confident that all true causative relationships will ultimately manifest as saturation advances.

项目摘要 在过去的四年中，我们在诱变小鼠Germaline基因组方面取得了出色的进步 在密切监视的同时，将免疫力彻底进行四个 我们宣称的所有蛋白质基因的一半以上。 高度信心对638个基因的1,298个突变是FACS和/或抗体中表型的原因 响应筛选。 未知，并被CRISPR/CAS9重新定位，以验证因果关系。 几乎所有这些都是新颖的）要么使用Cas9 Edis9编辑用ENU等位基因敲定或修饰， 扩展为血统书，并返回以筛选和自动化中检测到的表型的因果关系 154个基因中的148个（96％）被验证为表型的来源 CRISPR/CAS9项目目前很活跃，有些接近压缩。 出版； 是否宣布表型的原因是在与诱变的公众观看的情况下被取消限制。 可以搜索，检查原始表型和减数分裂映射数据的工具，通过p值进行过滤， 以及个人表型效应的方向和大幅度。 与我们旁边的免疫表型的机制。 适应性免疫反应的发展和激活是免疫学的基础，我们计划 进一步进行筛选。 兴趣。 通过TRP53BP1，AMPD3，RNPS1，PRKD2和SNRNP40中的突变，并发表了论文描述 机构。 PDIA6，NCSTN，LMBR1L，STK4，PACS1，WDR37和MFSD1也已被elucidididididididididididididididididididididididDID 出版 为了我们自己和他人学习。 流式细胞仪筛选中的表型的相关性，每个测量 鼠标。 在其他基因的突变中产生类似于mutatar的sield 基因在蛋白质或酶促途径的单个复合物中运行。 （候选探险家）在减少因果关系之前评估表型，告诉我们的可能性。 我们应该尝试重新定位任何基因。 候选人充满信心，所有真正的病因关系最终都将随着饱和度的发展而表现出来。

项目成果

The class I myosin MYO1D binds to lipid and protects against colitis.

I 类肌球蛋白 MYO1D 与脂质结合并预防结肠炎。

• DOI: 10.1242/dmm.035923
• 发表时间: 2018
• 期刊: Disease models & mechanisms
• 影响因子: 4.3
• 作者: McAlpine,William;Wang,Kuan-Wen;Choi,JinHuk;SanMiguel,Miguel;McAlpine,SarahGrace;Russell,Jamie;Ludwig,Sara;Li,Xiaohong;Tang,Miao;Zhan,Xiaoming;Choi,Mihwa;Wang,Tao;Bu,ChunHui;Murray,AnneR;Moresco,EvaMarieY;Turer,EmreE

Essential role of MFSD1-GLMP-GIMAP5 in lymphocyte survival and liver homeostasis.

MFSD1-GLMP-GIMAP5 在淋巴细胞存活和肝脏稳态中的重要作用。

• DOI: 10.1073/pnas.2314429120
• 发表时间: 2023
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Zhong,Xue;Moresco,JamesJ;Diedrich,JoleneK;Pinto,AntonioM;SoRelle,JeffreyA;Wang,Jianhui;Keller,Katie;Ludwig,Sara;Moresco,EvaMarieY;Beutler,Bruce;Choi,JinHuk
• 通讯作者: Choi,JinHuk

OVOL2 sustains postnatal thymic epithelial cell identity.

• DOI: 10.1038/s41467-023-43456-z
• 发表时间: 2023-11-27
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Zhong, Xue;Peddada, Nagesh;Wang, Jianhui;Moresco, James J;Zhan, Xiaowei;Shelton, John M;SoRelle, Jeffrey A;Keller, Katie;Lazaro, Danielle Renee;Moresco, Eva Marie Y;Choi, Jin Huk;Beutler, Bruce
• 通讯作者: Beutler, Bruce