Machine learning-enabled Comparative Transcriptomic Profiling to Validate NanoScript-induced Inner Ear Hair Cells

支持机器学习的比较转录组分析来验证 NanoScript 诱导的内耳毛细胞

• 批准号: 10412274
• 负责人: KELVIN YUI-HANG KWAN
• 金额: $ 31.11万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-05-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10412274
• 关键词: Address; Adult; Affect; American; Aminoglycosides; Artificial Intelligence; Award; Binding; Biological; Biological Process; Biomedical Research; Biomimetics; Cartilage; Cell Differentiation process; Cell physiology; Cells; Characteristics; Chromatin Structure; Cochlea; Complex; DNA Sequence; Data; Data Files; Data Set; Development; Eating; Elements; Endogenous Factors; Ensure; Environment; Epigenetic Process; Exposure to; GFI1 gene; Gene Expression; Generations; Genes; Genotype; Goals; Grant; Hair Cells; Human; In Vitro; Individual; Inner Hair Cells; Labyrinth; Learning; Loudness; Machine Learning; Measurement; Modeling; Mus; Muscle; Nerve Degeneration; Neurons; Outer Hair Cells; Parents; Pathway interactions; Patients; Pattern; Peptides; Performance; Phenotype; Proteins; Publications; Regenerative Medicine; Research Personnel; Sample Size; Sampling; Sensorineural Hearing Loss; Sensory Hair; Social Functioning; Social isolation; Source; Supporting Cell; Technology; Tertiary Protein Structure; Testing; United States National Institutes of Health; Viral; afferent nerve; base; bone; bony labyrinth; cell replacement therapy; cell type; clinical translation; comparative; deafness; design; differential expression; early childhood; experimental study; hearing impairment; hearing restoration; in silico; innovation; mRNA Differential Displays; machine learning method; membranous labyrinth; nanoparticle; nerve damage; overexpression; postnatal; single-cell RNA sequencing; small molecule; social skills; sound; stem cell differentiation; supplemental instruction; tool; transcription factor; transcriptome; transcriptome sequencing; transcriptomics; transdifferentiation; web site

PROJECT SUMMARY Hearing loss during early childhood significantly affects learning and acquisition of social skills, while hearing loss in adults can often result in social isolation and the inability to perform many routine social functions. A leading cause of sensorineural hearing loss is the loss of sensory hair cells of the inner ear. A lifetime exposure to aminoglycoside and loud sounds will result in an estimated 15% of adult Americans (~36 million) having some form of hearing loss. A promising approach to mitigate hearing loss and deafness is a cell replacement therapy by transdifferentiating supporting cells into hair cells. Unfortunately, current approaches for transdifferentiation rely on viral delivery may be unsafe and impractical for clinical translation. Therefore, there is a critical need to develop alternative platforms for regulating gene expression and inducing transdifferentiation in an efficient, non- viral manner that is suitable for restoration of hearing. To this end, our long-term goal is to develop NanoScript, an innovative, tunable nanoparticle-based artificial transcription factor platform capable of effectively regulating gene expression in a non-viral manner. Using NanoScript, we will transdifferentiate supporting cells into functional hair cells. NanoScript consists of a nanoparticle functionalized with specific small molecules and peptides that are designed to mimic the individual domains of natural transcription factor (TF) proteins. TFs are endogenous, multi-domain proteins that orchestrate many cellular functions, including differentiation. Since NanoScript is a functional replica of TF proteins, it can replace virally-delivered TFs for regenerative medicine-based applications. The overall objective of this proposal is to design three NanoScripts that mimic three TFs essential for hair cell differentiation (Gfi1, Pou4f3, and Atoh1; GPA). We will test whether GPA-NanoScript binds to the same DNA sequence and activate gene expression in vitro. Next, we will determine if the addition of epigenetic modulators to GPA-NanoScript will bind to the same targets as the TF proteins, locally alter the chromatin structure and enhance gene expression. Finally, we will use cochlear explants to determine whether GPA-NanoScript promotes transdifferentiation of supporting cells into hair cells by single-cell transcriptome analysis. Generation of nascent hair cells using an ex vivo model will serve as a springboard to test NanoScript technology for regenerative medicine. It will also establish NanoScript as an effective and non-viral tool for researchers to generate functional cells via direct reprogramming.

项目摘要 儿童早期的听力损失会显著影响学习和社交技能的获得， 成年人的丧失往往会导致社会孤立和无法履行许多日常社会职能。一 感音神经性听力损失的主要原因是内耳感觉毛细胞的损失。持久接触 氨基糖苷类药物和响亮的声音将导致估计15%的成年美国人（约3600万）有一些 听力损失的类型细胞替代疗法是一种很有前途的减轻听力损失和耳聋的方法 通过将支持细胞转分化为毛细胞不幸的是，目前的转分化方法 依赖病毒递送对于临床转化可能是不安全和不切实际的。因此，迫切需要 开发用于调节基因表达和诱导转分化的替代平台， 适合听力恢复的病毒性方式。 为此，我们的长期目标是开发NanoScript，一种创新的、可调的基于纳米颗粒的人工 本发明涉及能够以非病毒方式有效调节基因表达的转录因子平台。使用 NanoScript，我们将支持细胞转分化为功能性毛细胞。NanoScript由一个 用特定的小分子和肽功能化的纳米颗粒， 天然转录因子（TF）蛋白的结构域。TF是内源性的多结构域蛋白， 许多细胞功能，包括分化。由于NanoScript是TF蛋白的功能复制品，因此它可以 替代病毒递送的TF用于基于再生医学的应用。本提案的总体目标是 是设计三种Nanoparticles，其模拟毛细胞分化所必需的三种TF（Gfi 1、Pou 4f 3和Atoh 1; GPA）。我们将测试GPA-NanoScript是否与相同的DNA序列结合并激活基因表达。 体外接下来，我们将确定在GPA-NanoScript中添加表观遗传调节剂是否会与相同的 作为TF蛋白的靶点，局部改变染色质结构并增强基因表达。最后我们将 使用耳蜗外植体来确定GPA-NanoScript是否促进支持细胞的转分化 通过单细胞转录组分析转化为毛细胞。使用离体模型产生新生毛细胞将 作为跳板来测试再生医学的NanoScript技术。它还将建立NanoScript 作为研究人员通过直接重编程产生功能细胞的有效和非病毒工具。

项目成果

Structurally Defined Water-Soluble Metallofullerene Derivatives towards Biomedical Applications.

用于生物医学应用的结构明确的水溶性金属富勒烯衍生物。

• DOI: 10.1002/anie.202211704
• 发表时间: 2023-01-16
• 期刊: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
• 影响因子: 16.6
• 作者: Li, Yanbang;Biswas, Rohin;Kopcha, William P.;Dubroca, Thierry;Abella, Laura;Sun, Yue;Crichton, Ryan A.;Rathnam, Christopher;Yang, Letao;Yeh, Yao-Wen;Kundu, Krishnendu;Rodriguez-Fortea, Antonio;Poblet, Josep M.;Lee, Ki-Bum;Hill, Stephen;Zhang, Jianyuan
• 通讯作者: Zhang, Jianyuan