Mapping the non-coding RNA landscape in skeletal muscle health and disease

绘制骨骼肌健康和疾病中非编码 RNA 的图谱

基本信息

批准号：
10666261
负责人：
Benjamin David Cosgrove
金额：
$ 75.95万
依托单位：
CORNELL UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-04-17 至 2029-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10666261
关键词：
Adult Algorithms Antisense Oligonucleotide Therapy Antisense Oligonucleotides Atlases Bioinformatics Biological Markers Biology Biopsy Blood Cell Communication Cell Differentiation process Cell Fate Control Cell Nucleus Cells Code Communication Custom D4Z4 Data Development Diagnostic Disease Epigenetic Process Etiology Facioscapulohumeral Muscular Dystrophy Gene Expression Genes Genetic Transcription Genomics Health Heterogeneity Histopathology Homeobox Homeostasis Human Image Immune In Situ Individual Inherited Injury Ligands Maps Measures Mental Depression Messenger RNA Methods MicroRNAs Molecular Mus Muscle Muscle Cells Muscle Fibers Muscle Weakness Muscle satellite cell Muscular Dystrophies Myopathy Outcome Paracrine Communication Pathogenesis Pathogenicity Pathologic Pathology Pattern Pilot Projects Plasma Plasma Cells Poly A Polyadenylation Process Proteins RNA Recovery Regulation Resolution Role Sampling Severities Skeletal Muscle Small Nucleolar RNA Specific qualifier value Spottings Tail Technology Time Tissues Transcript Untranslated RNA Variant adenylate biological adaptation to stress cell type cellular pathology cohort derepression diagnostic biomarker effective therapy immune activation injury and repair insight meter molecular pathology mouse model muscle regeneration muscular dystrophy mouse model myogenesis new technology next generation receptor reconstitution repaired response to injury skeletal spatial integration therapy outcome tool transcriptome transcriptome sequencing transcriptomics treatment response virulence gene

项目摘要

Project Summary Skeletal muscle tissues are developed and maintained through the coordinated action of myogenic and non- myogenic cells. Dysregulation of myogenic cell identities and functions are commonly observed in skeletal muscle disease. Facioscapulohumeral muscular dystrophy (FSHD) is the second most common inherited muscular dystrophy and results in progressive muscle weakness without any effective therapies. Numerous cellular etiologies are observed in FSHD, such as loss of myogenic cells, including muscle stem cells and myofibers, and increased fibrogenic, adipogenic, and immune cells. The most common form of FSHD arises from aberrant expression of the DUX4 gene caused by epigenetic de-repression of the D4Z4 locus. DUX4 expression in FSHD individuals is regionally varied and highly sporadic within skeletal muscle tissue. Notably, DUX4 expression is both induced by and has pathogenic mechanisms related to noncoding RNAs (ncRNAs). Noncoding RNAs (including miRNAs, lncRNAs, snoRNAs, and eRNAs) are critical regulators of skeletal muscle cell identities and functions in health and diseases and act through modulation of transcriptional networks. Comprehensive understanding of ncRNA networks and mechanisms is lacking due to a paucity of ncRNA profiling technologies. Conventional single-cell and spatial RNA-sequencing technologies preferentially detect polyadenylated, protein-coding mRNAs, and do not efficiently capture most ncRNAs due to their lack of polyadenylation. In this proposal, we will apply a new RNA mapping technology called STRS-HD that is uniquely capable of efficiently and comprehensively detecting the total transcriptome, including both polyadenylated and non-adenylated transcripts, with single-cell spatial resolution to reveal global ncRNA expression heterogeneity in diverse cell types within skeletal muscles. We will leverage this new spatial total RNA-sequencing method to broadly interrogate noncoding RNAs in healthy skeletal myogenesis and in FSHD pathogenesis. In Aim 1, we will implement this total transcriptomic method to investigate how noncoding RNAs impact cell fate regulation adult skeletal muscle regeneration in mice. We will explore cell type-specific ncRNA expression variation and use spatial transcriptomics to map ncRNA features onto spatially resolved cell-cell communication interactions to provide insights into ncRNA regulation of myogenic cell fates. In Aim 2, we apply these methods to resolve how ncRNAs vary in FSHD pathologies using two mouse models subject to DUX4 anti-sense oligonucleotide therapy. We will integrate spatial total transcriptome maps with histopathology to reveal ncRNA determinants of altered myogenic cell specification and myofiber damage in FSHD. In Aim 3, we will extend the STRS-HD approach to human FSHD biopsies and compare ncRNA features to unaffected familial controls and contrast spatial ncRNA maps to cell-free RNA-sequencing in donor plasma to identify new total RNA biomarkers of FSHD. These new total transcriptomic technologies will be broadly applicable to the study of ncRNAs in developmental and disease biology of skeletal muscle and other tissues.

项目概要骨骼肌组织是通过肌源性和非肌源性的协调作用而发育和维持的。肌原细胞。肌源性细胞特性和功能的失调在骨骼肌中常见肌肉疾病。面肩肱型肌营养不良症 (FSHD) 是第二常见的遗传性肌营养不良症肌营养不良症并导致进行性肌肉无力，而没有任何有效的治疗方法。很多的在 FSHD 中观察到细胞病因，例如肌原细胞的丢失，包括肌肉干细胞和肌纤维，并增加纤维形成、脂肪形成和免疫细胞。最常见的 FSHD 形式是 D4Z4 基因座的表观遗传去抑制导致 DUX4 基因的异常表达。多克斯4 FSHD 个体的表达存在区域差异，并且在骨骼肌组织内高度分散。尤其， DUX4 表达既由非编码 RNA (ncRNA) 诱导，也具有与非编码 RNA (ncRNA) 相关的致病机制。非编码 RNA（包括 miRNA、lncRNA、snoRNA 和 eRNA）是骨骼肌的关键调节因子健康和疾病中的细胞身份和功能，并通过转录网络的调节发挥作用。由于 ncRNA 的缺乏，缺乏对 ncRNA 网络和机制的全面了解分析技术。传统的单细胞和空间RNA测序技术优先检测多聚腺苷酸化、蛋白质编码 mRNA，并且由于缺乏聚腺苷酸化。在本提案中，我们将应用一种名为 STRS-HD 的新 RNA 作图技术，该技术具有独特的能够高效、全面地检测总转录组，包括聚腺苷酸化和非腺苷酸化转录本，具有单细胞空间分辨率以揭示全局 ncRNA 表达异质性骨骼肌内的不同细胞类型。我们将利用这种新的空间总 RNA 测序方法广泛探究健康骨骼肌发生和 FSHD 发病机制中的非编码 RNA。在目标 1 中，我们将实施这种全转录组学方法来研究非编码RNA如何影响细胞命运调控小鼠成年骨骼肌再生。我们将探索细胞类型特异性 ncRNA 表达变异使用空间转录组学将 ncRNA 特征映射到空间解析的细胞间通讯相互作用上提供对肌原细胞命运的 ncRNA 调控的见解。在目标 2 中，我们应用这些方法来解决使用受 DUX4 反义寡核苷酸影响的两种小鼠模型观察 ncRNA 在 FSHD 病理学中的变化治疗。我们将整合空间总转录组图与组织病理学，以揭示 ncRNA 决定因素 FSHD 中肌源性细胞规格的改变和肌纤维损伤的改变。在目标 3 中，我们将扩展 STRS-HD 人类 FSHD 活检的方法，并将 ncRNA 特征与未受影响的家族对照和对比进行比较空间 ncRNA 映射到供体血浆中的无细胞 RNA 测序，以识别 FSHD 的新总 RNA 生物标志物。这些新的全转录组技术将广泛应用于发育过程中 ncRNA 的研究以及骨骼肌和其他组织的疾病生物学。