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 童年时期的听力损失会显着影响学习和获得社交技能，同时听力 成人的损失通常会导致社会隔离和无法执行许多常规社会功能。一个 感官听力丧失的主要原因是内耳感官毛细胞的丧失。终身暴露 氨基糖苷和响亮的声音将导致估计有15％的成年美国人（约3600万） 听力损失的形式。减轻听力丧失和耳聋的一种有希望的方法是一种细胞替代疗法 通过将支撑细胞转变为毛细胞。不幸的是，当前的转变方法 依靠病毒输送可能不安全，并且对于临床翻译而言是不切实际的。因此，迫切需要 开发替代平台来调节基因表达并在有效的，非 - 适合恢复听力的病毒方式。 为此，我们的长期目标是开发纳米本，一种创新的，可调的纳米颗粒的人造 转录因子平台，能够以非病毒方式有效调节基因表达。使用 纳米文字，我们将转化的支撑细胞转变为功能性毛细胞。纳米字样由 纳米颗粒用特定的小分子和肽官能化，这些分子和肽旨在模仿个体 自然转录因子（TF）蛋白的结构域。 TF是内源性的多域蛋白，编排 许多细胞功能，包括分化。由于纳米本是TF蛋白的功能复制品，因此可以 替换病毒传递的TFS用于基于再生医学的应用。该提议的总体目标 是设计三个模拟三个TF的纳米录，对于毛细胞分化至关重要（GFI1，POU4F3和ATOH1； 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绑定到相同 靶标作为TF蛋白，在局部改变染色质结构并增强基因表达。最后，我们会的 使用耳蜗外植体确定GPA-Nanoscript是否促进了支持细胞的转变 通过单细胞转录组分析进入毛细胞。使用离体模型生成新生的毛细胞将 用作测试纳米文本技术的跳板。它还将建立纳米录 作为研究人员通过直接重编程生成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