Base editing and prime editing for sickle cell disease

镰状细胞病的碱基编辑和引物编辑

基本信息

批准号：
10579903
负责人：
DAVID R LIU
金额：
$ 77.71万
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：
2021
资助国家：
美国
起止时间：
2021-01-01 至 2024-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10579903
关键词：
Acute Pain Adenosine Adult Affect Affinity Alanine Alleles Allogenic American Amino Acids Antisickling Agents Architecture Autologous Base Pairing Benign Biochemical Biological Assay Blood CD34 gene Caring Cell Death Cell Line Cell Therapy Cell physiology Cells Cessation of life Chromosomal Rearrangement Clinical Research Codon Nucleotides Complex DNA DNA Double Strand Break Deterioration Development Disease Elements Engineering Engraftment Enzymes Erythrocytes Erythroid Cells Erythroid Progenitor Cells Escherichia coli Evolution Fetal Hemoglobin Frequencies Functional disorder Future Gene Expression Gene Silencing Genes Genetic Genetic Diseases Genetic Engineering Genetic Template Genome Genomic DNA Genomics Globin Guide RNA HLA Antigens Hematological Disease Hematopoietic Hematopoietic Stem Cell Transplantation Hematopoietic stem cells Hemoglobin Hemoglobin F Disease Hemolytic Anemia Human Hypoxia In Vitro Individual Inherited Maintenance Malignant - descriptor Mediating Medical Messenger RNA Methods Missense Mutation Modification Morbidity - disease rate Multiple Organ Failure Mus Mutation Nucleotides Organ Outcome Pain Patients Polymers Proteins Quality of life RNA Reagent Recombinants Regulation Research Safety Sickle Cell Sickle Cell Anemia Sickle Cell Trait Sickle Hemoglobin Site Technology Testing Therapeutic Toxic effect Transcriptional Silencer Elements Transplantation Treatment Efficacy Valine Variant Xenograft procedure base editing base editor beta Globin chronic pain curative treatments experience gene therapy genetic approach genetic information genetic manipulation genome editing improved in vivo insight manufacture mortality mouse model mutant new technology novel novel strategies off-target mutation polymerization precision genetics premature prevent prime editing prime editor promoter repaired safety testing sickle erythroid sickling targeted treatment therapeutic target tool

项目摘要

PROJECT SUMMARY Despite advances in the medical care of sickle cell disease (SCD), most patients continue to experience severe pain, poor quality of life, progressive organ deterioration and premature death. Allogeneic hematopoietic stem cell transplantation (HSCT) can cure SCD but is associated with numerous toxicities and only 20% of patients have Human Leukocyte Antigen (HLA)-matched donors. Therefore, improved and more widely accessible curative therapies are needed. Genetic modification of autologous HSCs is a promising experimental approach for treating SCD that circumvents some of the problems associated with allogeneic HSCT, although the optimal technical strategies are not yet established. This proposal explores the use of adenosine base editors (ABEs) and prime editors (PEs) for genetic correction of SCD. In contrast to conventional genome editing, these novel approaches create precise nucleotide alterations independent of double-stranded DNA breaks (DSBs), which can cause structural DNA abnormalities, cell death or malignant transformation. Adenosine base editors convert targeted A·T base pairs to G·C pairs. Prime editors copy edited sequence information from a guide RNA template into a targeted DNA locus. We will test these potentially transformative tools in 3 different strategies for SCD therapy. Aim 1 employs ABEs to create HSC alterations that recapitulate hereditary persistence of fetal hemoglobin (HPFH), a benign genetic condition that alleviates the pathophysiology of co-inherited SCD by inducing the expression of red blood cell (RBC) fetal hemoglobin (HbF), a potent anti-sickling agent. We have used protein evolution strategies to create new high-efficiency ABEs that generate HPFH mutations at frequencies of up to 60% in CD34+ hematopoietic stem and progenitor cells (HSPCs), with HbF being induced to levels that inhibit hypoxic sickling of erythroid progeny. Aim 2 uses ABEs to convert the mutant SCD codon from valine to alanine, thereby generating “Hemoglobin Makassar (HbG)”, a naturally occurring benign non- sickling variant. We have developed an altered PAM-specific ABE that converts HbS alleles to HbG in SCD donor HSPCs at frequencies of up to 80%, with inhibition of RBC sickling. Aim 3 employs prime editing to revert the mutant SCD codon to normal (Val→Glu), which we have shown to occur efficiently in the HEK293T cell line and now aim to optimize in HSPCs from affected individuals. Overall, our preliminary studies have shown proof of principle for three novel, independent editing approaches to treating SCD without the need to enrich for edited cells or to create DSBs. Through the proposed research, we seek to optimize the efficiency of these approaches in primary HSPCs and to further determine their safety and efficacy by using mouse models, in vitro culture methods and biochemical assays. Developing three approaches simultaneously will enable us to compare their outcomes directly and to determine the best therapeutic strategy to pursue in future clinical studies. More generally, our planned studies have the potential to generate new paradigms for using base editors and PEs to treat numerous genetic blood disorders via precise genetic manipulation of HSCs.

项目概要尽管镰状细胞病 (SCD) 的医疗护理取得了进步，但大多数患者仍然面临严重的症状疼痛、生活质量差、进行性器官恶化和同种异体造血干细胞过早死亡。细胞移植 (HSCT) 可以治愈 SCD，但与多种毒性相关，只有 20% 的患者能够治愈拥有人类白细胞抗原 (HLA) 匹配的供体，因此得到改进且更容易获得。自体造血干细胞的基因改造是一种有前途的实验方法。用于治疗 SCD，可避免与同种异体 HSCT 相关的一些问题，尽管最佳方案该提案探讨了腺苷碱基编辑器（ABE）的使用。和用于 SCD 基因校正的主要编辑器 (PE) 与传统的基因组编辑相比，这些小说。方法创建独立于双链 DNA 断裂 (DSB) 的精确核苷酸改变，这可导致 DNA 结构异常、细胞死亡或恶性转化。目标 A·T 碱基对到 G·C Prime 编辑器从引导 RNA 模板复制编辑后的序列信息。我们将在 3 种不同的 SCD 策略中测试这些潜在的变革工具。目标 1 利用 ABE 来产生 HSC 改变，以重现胎儿的遗传持续性。血红蛋白 (HPFH) 是一种良性遗传病，可通过以下方式缓解共同遗传性 SCD 的病理生理学诱导红细胞 (RBC) 胎儿血红蛋白 (HbF) 的表达，这是一种有效的抗镰状化剂。使用蛋白质进化策略创建新的高效 ABE，在 CD34+ 造血干细胞和祖细胞 (HSPC) 中的频率高达 60%，并诱导 HbF 达到抑制红系后代缺氧镰状化的水平 Aim 2 使用 ABE 转换突变 SCD 密码子。从缬氨酸到丙氨酸，从而产生“望加锡血红蛋白（HbG）”，一种天然存在的良性非我们开发了一种改变的 PAM 特异性 ABE，可将 SCD 中的 HbS 等位基因转化为 HbG。供体 HSPC 的频率高达 80%，并抑制 RBC 镰状化，Aim 3 采用 Prime 编辑来恢复。将突变的 SCD 密码子转换为正常密码子 (Val→Glu)，我们已证明这种情况在 HEK293T 细胞系中有效发生现在的目标是优化受影响个体的 HSPC 总体而言，我们的初步研究已经证明了这一点。三部小说的独立编辑方法来治疗 SCD，无需丰富编辑内容通过拟议的研究，我们寻求优化这些方法的效率。并通过使用小鼠模型、体外培养进一步确定其安全性和有效性同时开发三种方法将使我们能够比较它们。直接结果并确定未来临床研究中追求的最佳治疗策略。一般来说，我们计划的研究有可能产生使用碱基编辑器和 PE 的新范例通过对 HSC 进行精确的基因操作来治疗多种遗传性血液疾病。