Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart
Tài liệu tham khảo
Anders, 2015, HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, 31, 166, 10.1093/bioinformatics/btu638
Bamforth, 2001, Cardiac malformations, adrenal agenesis, neural crest defects and exencephaly in mice lacking Cited2, a new Tfap2 co-activator, Nat. Genet., 29, 469, 10.1038/ng768
Barger, 2000, PPAR signaling in the control of cardiac energy metabolism, Trends Cardiovasc. Med., 10, 238, 10.1016/S1050-1738(00)00077-3
Bassat, 2017, The extracellular matrix protein agrin promotes heart regeneration in mice, Nature, 547, 179, 10.1038/nature22978
Belke, 2002, Insulin signaling coordinately regulates cardiac size, metabolism, and contractile protein isoform expression, J. Clin. Invest., 109, 629, 10.1172/JCI0213946
Bowen, 2015, Cadherin-11 coordinates cellular migration and extracellular matrix remodeling during aortic valve maturation, Dev. Biol., 407, 145, 10.1016/j.ydbio.2015.07.012
Bruneau, 2013, Signaling and transcriptional networks in heart development and regeneration, Cold Spring Harb. Perspect. Biol., 5, a008292, 10.1101/cshperspect.a008292
Buckingham, 2005, Building the mammalian heart from two sources of myocardial cells, Nat. Rev. Genet., 6, 826, 10.1038/nrg1710
Cai, 2008, A myocardial lineage derives from Tbx18 epicardial cells, Nature, 454, 104, 10.1038/nature06969
Chen, 2004, BMP10 is essential for maintaining cardiac growth during murine cardiogenesis, Development, 131, 2219, 10.1242/dev.01094
Chen, 2009, ToppGene Suite for gene list enrichment analysis and candidate gene prioritization, Nucleic Acids Res., 37, W305, 10.1093/nar/gkp427
Csardi, G., and Nepusz, T. (2006). The igraph software package for complex network research. https://pdfs.semanticscholar.org/1d27/44b83519657f5f2610698a8ddd177ced4f5c.pdf.
de la Pompa, 1998, Role of the NF-ATc transcription factor in morphogenesis of cardiac valves and septum, Nature, 392, 182, 10.1038/32419
DeLaughter, 2016, Single-Cell Resolution of Temporal Gene Expression during Heart Development, Dev. Cell, 39, 480, 10.1016/j.devcel.2016.10.001
Doppler, 2017, Cardiac fibroblasts: more than mechanical support, J. Thorac. Dis., 9, S36, 10.21037/jtd.2017.03.122
Dutko, 2011, SnapShot: BMP signaling in development, Cell, 145, 636, 10.1016/j.cell.2011.05.001
Garside, 2015, SOX9 modulates the expression of key transcription factors required for heart valve development, Development, 142, 4340, 10.1242/dev.125252
Grego-Bessa, 2007, Notch signaling is essential for ventricular chamber development, Dev. Cell, 12, 415, 10.1016/j.devcel.2006.12.011
Harris, 2010, Development of the endocardium, Pediatr. Cardiol., 31, 391, 10.1007/s00246-010-9642-8
High, 2008, The multifaceted role of Notch in cardiac development and disease, Nat. Rev. Genet., 9, 49, 10.1038/nrg2279
Hinton, 2006, Extracellular matrix remodeling and organization in developing and diseased aortic valves, Circ. Res., 98, 1431, 10.1161/01.RES.0000224114.65109.4e
Islam, 2011, Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq, Genome Res., 21, 1160, 10.1101/gr.110882.110
Jain, 2015, HEART DEVELOPMENT. Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts, Science, 348, aaa6071, 10.1126/science.aaa6071
Kim, 2016, The role of CD36 in the regulation of myocardial lipid metabolism, Biochim. Biophys. Acta, 1861, 1450, 10.1016/j.bbalip.2016.03.018
Koshiba-Takeuchi, 2006, Cooperative and antagonistic interactions between Sall4 and Tbx5 pattern the mouse limb and heart, Nat. Genet., 38, 175, 10.1038/ng1707
Krishnan, 2014, A detailed comparison of mouse and human cardiac development, Pediatr. Res., 76, 500, 10.1038/pr.2014.128
Kuruc, 1988, Transient coexpression of desmin and cytokeratins 8 and 18 in developing myocardial cells of some vertebrate species, Differentiation, 38, 177, 10.1111/j.1432-0436.1988.tb00212.x
La Manno, 2016, Molecular diversity of midbrain development in mouse, human, and stem cells, Cell, 167, 566, 10.1016/j.cell.2016.09.027
Lachmann, 2016, ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information, Bioinformatics, 32, 2233, 10.1093/bioinformatics/btw216
Lake, 2016, Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain, Science, 352, 1586, 10.1126/science.aaf1204
Lefebvre, 2010, A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers, Mol. Syst. Biol., 6, 377, 10.1038/msb.2010.31
Li, 2015, Identification of cardiovascular lineage descendants at single-cell resolution, Development, 142, 846, 10.1242/dev.116897
Li, 2016, Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells, Dev. Cell, 39, 491, 10.1016/j.devcel.2016.10.014
Li, 2017, Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions, Cell Stem Cell, 20, 891, 10.1016/j.stem.2017.05.009
Lockhart, 2011, Extracellular matrix and heart development, Birth Defects Res. A Clin. Mol. Teratol., 91, 535, 10.1002/bdra.20810
Luxán, 2013, Mutations in the NOTCH pathway regulator MIB1 cause left ventricular noncompaction cardiomyopathy, Nat. Med., 19, 193, 10.1038/nm.3046
Mächler, M., Rousseeuw, P., Struyf, A., Hubert, M., and Hornik, K. (2012). Cluster: cluster analysis basics and extensions. https://www.researchgate.net/publication/272176869_Cluster_Cluster_Analysis_Basics_and_Extensions.
Magadum, 2017, Live cell screening platform identifies PPARδ as a regulator of cardiomyocyte proliferation and cardiac repair, Cell Res., 27, 1002, 10.1038/cr.2017.84
Margolin, 2006, ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context, BMC Bioinformatics, 7, S7, 10.1186/1471-2105-7-S1-S7
McFadden, 2005, The Hand1 and Hand2 transcription factors regulate expansion of the embryonic cardiac ventricles in a gene dosage-dependent manner, Development, 132, 189, 10.1242/dev.01562
Misra, 2013, Compacting the heart with Notch, Nat. Med., 19, 133, 10.1038/nm.3071
Morikawa, 2017, Dystrophin-glycoprotein complex sequesters Yap to inhibit cardiomyocyte proliferation, Nature, 547, 227, 10.1038/nature22979
2016, Database resources of the national center for biotechnology information, Nucleic Acids Res., 44, D7, 10.1093/nar/gkv1290
Olson, 2006, Gene regulatory networks in the evolution and development of the heart, Science, 313, 1922, 10.1126/science.1132292
Olson, 1996, Molecular pathways controlling heart development, Science, 272, 671, 10.1126/science.272.5262.671
Owens, 2004, Molecular regulation of vascular smooth muscle cell differentiation in development and disease, Physiol. Rev., 84, 767, 10.1152/physrev.00041.2003
Pérez-Pomares, 2002, Experimental studies on the spatiotemporal expression of WT1 and RALDH2 in the embryonic avian heart: a model for the regulation of myocardial and valvuloseptal development by epicardially derived cells (EPDCs), Dev. Biol., 247, 307, 10.1006/dbio.2002.0706
Picelli, 2014, Full-length RNA-seq from single cells using Smart-seq2, Nat. Protoc., 9, 171, 10.1038/nprot.2014.006
Risebro, 2015, Characterisation of the human embryonic and foetal epicardium during heart development, Development, 142, 3630, 10.1242/dev.127621
Ruiz-Villalba, 2012, The expanding role of the epicardium and epicardial-derived cells in cardiac development and disease, Curr. Opin. Pediatr., 24, 569, 10.1097/MOP.0b013e328357a532
Satija, 2015, Spatial reconstruction of single-cell gene expression data, Nat. Biotechnol., 33, 495, 10.1038/nbt.3192
Scuderi, 2017, Naturally Engineered Maturation of Cardiomyocytes, Front. Cell Dev. Biol., 5, 50, 10.3389/fcell.2017.00050
Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. USA, 102, 15545, 10.1073/pnas.0506580102
Sylva, 2014, Development of the human heart, Am. J. Med. Genet. A., 164A, 1347, 10.1002/ajmg.a.35896
Tallquist, 2017, Redefining the identity of cardiac fibroblasts, Nat. Rev. Cardiol., 14, 484, 10.1038/nrcardio.2017.57
Tian, 2014, Vessel formation. De novo formation of a distinct coronary vascular population in neonatal heart, Science, 345, 90, 10.1126/science.1251487
Tirosh, 2016, Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq, Science, 352, 189, 10.1126/science.aad0501
Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120
Trapnell, 2014, The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells, Nat. Biotechnol., 32, 381, 10.1038/nbt.2859
Wagner, 2005, Coronary vessel development requires activation of the TrkB neurotrophin receptor by the Wilms’ tumor transcription factor Wt1, Genes Dev., 19, 2631, 10.1101/gad.346405
Wagner, 2010, BMPs: from bone to body morphogenetic proteins, Sci. Signal., 3, mr1
Wessels, 2004, The epicardium and epicardially derived cells (EPDCs) as cardiac stem cells, Anat. Rec. A Discov. Mol. Cell. Evol. Biol., 276, 43, 10.1002/ar.a.10129
Wessels, 2003, Developmental anatomy of the heart: a tale of mice and man, Physiol. Genomics, 15, 165, 10.1152/physiolgenomics.00033.2003
Wu, 2013, Nfatc1 directs the endocardial progenitor cells to make heart valve primordium, Trends Cardiovasc. Med., 23, 294, 10.1016/j.tcm.2013.04.003
Xiao, 2018, Hippo Signaling Plays an Essential Role in Cell State Transitions during Cardiac Fibroblast Development, Dev. Cell, 45, 153, 10.1016/j.devcel.2018.03.019
Yang, 2007, Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study, BMC Med. Genet., 8, S12, 10.1186/1471-2350-8-S1-S12
Yee, 2015
Zeisberg, 2007, Endothelial-to-mesenchymal transition contributes to cardiac fibrosis, Nat. Med., 13, 952, 10.1038/nm1613
Zhang, 2015, AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors, Nucleic Acids Res., 43, D76, 10.1093/nar/gku887
Zhou, 2008, Epicardial progenitors contribute to the cardiomyocyte lineage in the developing heart, Nature, 454, 109, 10.1038/nature07060
Zhou, 2010, Genetic fate mapping demonstrates contribution of epicardium-derived cells to the annulus fibrosis of the mammalian heart, Dev. Biol., 338, 251, 10.1016/j.ydbio.2009.12.007