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.

项目摘要骨骼肌组织是通过肌原性和非 - 肌原细胞。在骨骼中通常观察到肌原细胞身份和功能的失调肌肉疾病。 Facioscapulohumeral肌肉营养不良（FSHD）是第二常见的遗传肌肉营养不良并导致进行性肌肉无力，而无需进行任何有效的疗法。很多的在FSHD中观察到细胞病因，例如肌源性细胞的丧失，包括肌肉干细胞和肌纤维，增加纤维纤维，成脂和免疫细胞。 FSHD最常见的形式出现来自D4Z4基因座的表观遗传学抑制引起的DUX4基因的异常表达。 dux4 FSHD个体中的表达在骨骼肌组织中遍布区域变化，高度零星。尤其， DUX4表达既由与非编码RNA（NCRNA）相关的致病机制。非编码RNA（包括miRNA，LNCRNA，SNORNA和ERNAS）是骨骼肌的关键调节剂细胞身份和健康和疾病的功能，并通过转录网络的调节来起作用。由于NCRNA的匮乏，缺乏对NCRNA网络和机制的全面了解分析技术。常规的单细胞和空间RNA - 序列技术优先检测聚腺苷酸化的蛋白质编码mRNA，并且由于缺乏缺乏的大多数NCRNA 聚腺苷酸化。在此提案中，我们将应用一种称为STRS-HD的新的RNA映射技术，它是独特的能够有效，全面地检测总转录组，包括聚腺苷酸化和具有单细胞空间分辨率的非辅助转录本，以揭示全局NCRNA表达异质性在骨骼肌内的各种细胞类型中。我们将利用这种新的空间总RNA测序方法在健康骨骼肌发生和FSHD发病机理中广泛询问非编码RNA。在AIM 1中，我们将实施这种总转录组方法来研究非编码RNA如何影响细胞命运调节小鼠成人骨骼肌再生。我们将探索细胞类型特异性的NCRNA表达变化和使用空间转录组学将NCRNA特征映射到空间分辨的细胞 - 细胞通信相互作用为了洞悉肌源性细胞命运的NCRNA调节。在AIM 2中，我们将这些方法应用于解决 NCRNA在FSHD病理中如何使用两种鼠标构成DUX4抗固定寡核苷酸治疗。我们将将空间总转录组图与组织病理学相结合，以揭示NCRNA的决定因素 FSHD中的肌源细胞规格和肌纤维损伤改变了。在AIM 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控制和对比进行比较空间ncRNA图到供体等离子体中无细胞的RNA测序，以鉴定FSHD的新总RNA生物标志物。这些新的总转录组技术将广泛适用于发展中NCRNA的发展以及骨骼肌和其他组织的疾病生物学。