title: Systematic Reconstruction of Molecular Cascades Regulating GP Development Using Single-Cell RNA-Seq.
abstract: The growth plate (GP) comprising sequentially differentiated cell layers is a critical structure for bone elongation and regeneration. Although several key regulators in GP development have been identified using genetic perturbation, systematic understanding is still limited. Here, we used single-cell RNA-sequencing (RNA-seq) to determine the gene expression profiles of 217 single cells from GPs and developed a bioinformatics pipeline named Sinova to de novo reconstruct physiological GP development in both temporal and spatial high resolution. Our unsupervised model not only confirmed prior knowledge, but also enabled the systematic discovery of genes, potential signal pathways, and surface markers CD9/CD200 to precisely depict development. Sinova further identified the effective combination of transcriptional factors (TFs) that regulates GP maturation, and the result was validated using an in vitro EGFP-Col10a screening system. Our case systematically reconstructed molecular cascades in GP development through single-cell profiling, and the bioinformatics pipeline is applicable to other developmental processes. VIDEO ABSTRACT.
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Junxiang
authors.initials: J
authors.lastname: Li
authors.affiliation: School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Haofei
authors.initials: H
authors.lastname: Luo
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.affiliation: School of Medicine, Tsinghua University, Beijing 10084, China.
authors.forename: Jidong
authors.initials: J
authors.lastname: Lang
authors.affiliation: School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Siyu
authors.initials: S
authors.lastname: Zhu
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Zhenming
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: School of Medicine, Tsinghua University, Beijing 10084, China.
authors.forename: Jianhuo
authors.initials: J
authors.lastname: Fang
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Keke
authors.initials: K
authors.lastname: Qu
authors.affiliation: School of Medicine, Tsinghua University, Beijing 10084, China.
authors.forename: Yuting
authors.initials: Y
authors.lastname: Lin
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic & System Biology, Tsinghua University, Beijing 10084, China.
authors.forename: Haizhou
authors.initials: H
authors.lastname: Long
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic & System Biology, Tsinghua University, Beijing 10084, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Yao
authors.affiliation: School of Medicine, Tsinghua University, Beijing 10084, China.
authors.forename: Geng
authors.initials: G
authors.lastname: Tian
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, Tsinghua University, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic & System Biology, Tsinghua University, Beijing 10084, China. Electronic address: wuqiong@tsinghua.edu.cn.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wu
mesh_terms: D000818:Animals; D000831:Animals, Newborn; D015415:Biomarkers / Q000378:metabolism; D019521:Body Patterning / Q000235:genetics; D005434:Flow Cytometry; D053263:Gene Regulatory Networks; D006132:Growth Plate / Q000196:embryology* / Q000378:metabolism*; D008810:Mice, Inbred C57BL; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*; D015398:Signal Transduction / Q000235:genetics*; D059010:Single-Cell Analysis / Q000379:methods*; D013997:Time Factors; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D015415:Biomarkers; D014157:Transcription Factors