• Chung, A. S., Lee, J. & Ferrara, N. Targeting the tumour vasculature: insights from physiological angiogenesis. Nat. Rev. Cancer 10, 505–514 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Potente, M. & Mäkinen, T. Vascular heterogeneity and specialization in development and disease. Nat. Rev. Mol. Cell Biol. 18, 477–494 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jain, R. K. et al. Angiogenesis in brain tumours. Nat. Rev. Neurosci. 8, 610–622 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bergers, G. & Benjamin, L. E. Tumorigenesis and the angiogenic switch. Nat. Rev. Cancer 3, 401–410 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stapor, P. C., Sweat, R. S., Dashti, D. C., Betancourt, A. M. & Murfee, W. L. Pericyte dynamics during angiogenesis: new insights from new identities. J. Vasc. Res. 51, 163–174 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Lee, H.-W., Shin, J. H. & Simons, M. Flow goes forward and cells step backward: endothelial migration. Exp. Mol. Med. 54, 711–719 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kalucka, J. et al. Single-cell transcriptome atlas of murine endothelial cells. Cell 180, 764–779 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Niu, G. & Chen, X. Vascular endothelial growth factor as an anti-angiogenic target for cancer therapy. Curr. Drug Targets 11, 1000–1017 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Khan, K. A. & Kerbel, R. S. Improving immunotherapy outcomes with anti-angiogenic treatments and vice versa. Nat. Rev. Clin. Oncol. 15, 310–324 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huinen, Z. R., Huijbers, E. J. M., van Beijnum, J. R., Nowak-Sliwinska, P. & Griffioen, A. W. Anti-angiogenic agents—overcoming tumour endothelial cell anergy and improving immunotherapy outcomes. Nat. Rev. Clin. Oncol. 18, 527–540 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Zhu, R. et al. Chemokine expression profiles of ovarian endometriotic stromal cells in three-dimensional culture. J. Reprod. Immunol. 138, 103100 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hernández-García, R., Iruela-Arispe, M. L., Reyes-Cruz, G. & Vázquez-Prado, J. Endothelial RhoGEFs: a systematic analysis of their expression profiles in VEGF-stimulated and tumor endothelial cells. Vasc. Pharmacol. 74, 60–72 (2015).

    Article 

    Google Scholar
     

  • Zou, Z. et al. A single-cell transcriptomic atlas of human skin aging. Dev. Cell 56, 383–397 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Haghverdi, L., Buettner, F. & Theis, F. J. Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics 31, 2989–2998 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gulati, G. S. et al. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 367, 405–411 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nunes, S. S. et al. Implanted microvessels progress through distinct neovascularization phenotypes. Microvasc. Res. 79, 10–20 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • De Smet, F., Segura, I., De Bock, K., Hohensinner, P. J. & Carmeliet, P. Mechanisms of vessel branching: filopodia on endothelial tip cells lead the way. Arterioscler. Thromb. Vasc. Biol. 29, 639–649 (2009).

    Article 
    PubMed 

    Google Scholar
     

  • Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Siemerink, M. J., Klaassen, I., Van Noorden, C. J. F. & Schlingemann, R. O. Endothelial tip cells in ocular angiogenesis: potential target for anti-angiogenesis therapy. J. Histochem. Cytochem. 61, 101–115 (2012).

    Article 
    PubMed 

    Google Scholar
     

  • Whittall, C. et al. A chemokine self-presentation mechanism involving formation of endothelial surface microstructures. J. Immunol. 190, 1725–1736 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Savant, S. et al. The orphan receptor Tie1 controls angiogenesis and vascular remodeling by differentially regulating Tie2 in Tip and stalk cells. Cell Rep. 12, 1761–1773 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Augustin, H. G., Young Koh, G., Thurston, G. & Alitalo, K. Control of vascular morphogenesis and homeostasis through the angiopoietin–Tie system. Nat. Rev. Mol. Cell Biol. 10, 165–177 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Park, J. S. et al. Normalization of tumor vessels by Tie2 activation and Ang2 inhibition enhances drug delivery and produces a favorable tumor microenvironment. Cancer Cell 30, 953–967 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Scharpfenecker, M., Fiedler, U., Reiss, Y. & Augustin, H. G. The Tie-2 ligand angiopoietin-2 destabilizes quiescent endothelium through an internal autocrine loop mechanism. J. Cell Sci. 118, 771–780 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ambade, A. S., Hassoun, P. M. & Damico, R. L. Basement membrane extracellular matrix proteins in pulmonary vascular and right ventricular remodeling in pulmonary hypertension. Am. J. Respir. Cell Mol. Biol. 65, 245–258 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kuo, C. J. et al. Oligomerization-dependent regulation of motility and morphogenesis by the collagen XVIII NC1/endostatin domain. J. Cell Biol. 152, 1233–1246 (2001).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Moulton, K. S. et al. Loss of collagen XVIII enhances neovascularization and vascular permeability in atherosclerosis. Circulation 110, 1330–1336 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xu, C. et al. Arteries are formed by vein-derived endothelial tip cells. Nat. Commun. 5, 5758 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hasan, S. S. et al. Endothelial Notch signalling limits angiogenesis via control of artery formation. Nat. Cell Biol. 19, 928–940 (2017).

    Article 
    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tammela, T. et al. VEGFR-3 controls tip to stalk conversion at vessel fusion sites by reinforcing Notch signalling. Nat. Cell Biol. 13, 1202–1213 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, W. et al. Arterialization requires the timely suppression of cell growth. Nature 589, 437–441 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ferrara, N., Hillan, K. J., Gerber, H.-P. & Novotny, W. Discovery and development of bevacizumab, an anti-VEGF antibody for treating cancer. Nat. Rev. Drug Discov. 3, 391–400 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Flister, M. J. et al. Inflammation induces lymphangiogenesis through up-regulation of VEGFR-3 mediated by NF-κB and Prox1. Blood 115, 418–429 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ayroldi, E. et al. Modulation of T-cell activation by the glucocorticoid-induced leucine zipper factor via inhibition of nuclear factor κB. Blood 98, 743–753 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Teuwen, L.-A. et al. Tumor vessel co-option probed by single-cell analysis. Cell Rep. 35, 109253 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nwadozi, E., Rudnicki, M. & Haas, T. L. Metabolic coordination of pericyte phenotypes: therapeutic implications. Front. Cell Dev. Biol. 8, 77 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • De Bock, K. et al. Role of PFKFB3-driven glycolysis in vessel sprouting. Cell 154, 651–663 (2013).

    Article 
    PubMed 

    Google Scholar
     

  • Cantelmo, A. R. et al. Inhibition of the glycolytic activator PFKFB3 in endothelium induces tumor vessel normalization, impairs metastasis, and improves chemotherapy. Cancer Cell 30, 968–985 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Månberg, A. et al. Altered perivascular fibroblast activity precedes ALS disease onset. Nat. Med. 27, 640–646 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Binet, F. & Sapieha, P. ER stress and angiogenesis. Cell Metab. 22, 560–575 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Edagawa, M. et al. Role of activating transcription factor 3 (ATF3) in endoplasmic reticulum (ER) stress-induced sensitization of p53-deficient human colon cancer cells to tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL)-mediated apoptosis through up-regulation of death receptor 5 (DR5) by zerumbone and celecoxib. J. Biol. Chem. 289, 21544–21561 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ma, Y. & Zhou, X. Spatially informed cell-type deconvolution for spatial transcriptomics. Nat. Biotechnol. 40, 1349–1359 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Goswami, D. et al. Endothelial CD99 supports arrest of mouse neutrophils in venules and binds to neutrophil PILRs. Blood 129, 1811–1822 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Geldhof, V. et al. Single cell atlas identifies lipid-processing and immunomodulatory endothelial cells in healthy and malignant breast. Nat. Commun. 13, 5511 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zheng, S. et al. Mesenchymal stromal cells rapidly suppress TCR signaling-mediated cytokine transcription in activated T cells through the ICAM-1/CD43 interaction. Front. Immunol. 12, 609544 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ausprunk, D. H. & Folkman, J. Migration and proliferation of endothelial cells in preformed and newly formed blood vessels during tumor angiogenesis. Microvasc. Res. 14, 53–65 (1977).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lee, H. W. et al. Role of venous endothelial cells in developmental and pathologic angiogenesis. Circulation 144, 1308–1322 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rohlenova, K. et al. Single-cell RNA sequencing maps endothelial metabolic plasticity in pathological angiogenesis. Cell Metab. 31, 862–877 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pitulescu, M. E. et al. Dll4 and Notch signalling couples sprouting angiogenesis and artery formation. Nat. Cell Biol. 19, 915–927 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kanda, A., Hirose, I., Noda, K., Murata, M. & Ishida, S. Glucocorticoid-transactivated TSC22D3 attenuates hypoxia- and diabetes-induced Müller glial galectin-1 expression via HIF-1α destabilization. J. Cell. Mol. Med. 24, 4589–4599 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bergers, G. & Song, S. The role of pericytes in blood-vessel formation and maintenance. Neuro Oncol. 7, 452–464 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mayer, J. U. et al. Homeostatic IL-13 in healthy skin directs dendritic cell differentiation to promote TH2 and inhibit TH17 cell polarization. Nat. Immunol. 22, 1538–1550 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Dura, B. et al. scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3′ mRNA profiling. Nucleic Acids Res. 47, e16 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Klein, AllonM. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187–1201 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wen, L. et al. The blood flow-klf6a-tagln2 axis drives vessel pruning in zebrafish by regulating endothelial cell rearrangement and actin cytoskeleton dynamics. PLoS Genet. 17, e1009690 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wolock, S. L., Lopez, R. & Klein, A. M. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zheng, L. et al. Pan-cancer single-cell landscape of tumor-infiltrating T cells. Science 374, abe6474 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • van den Brink, S. C. et al. Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations. Nat. Methods 14, 935–936 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Xue, R. et al. Liver tumour immune microenvironment subtypes and neutrophil heterogeneity. Nature 612, 141–147 (2022).

  • He, Z., Brazovskaja, A., Ebert, S., Camp, J. G. & Treutlein, B. CSS: cluster similarity spectrum integration of single-cell genomics data. Genome Biol. 21, 224 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, Q. et al. Charting human development using a multi-endodermal organ atlas and organoid models. Cell 184, 3281–3298 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • He, Z. et al. Lineage recording in human cerebral organoids. Nat. Methods 19, 90–99 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Muhl, L. et al. Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination. Nat. Commun. 11, 3953 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, L. et al. Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature 564, 268–272 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhao, Q. et al. Single-cell transcriptome analyses reveal endothelial cell heterogeneity in tumors and changes following antiangiogenic treatment. Cancer Res. 78, 2370–2382 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, Z. et al. Single-cell transcriptome analyses reveal novel targets modulating cardiac neovascularization by resident endothelial cells following myocardial infarction. Eur. Heart J. 40, 2507–2520 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goveia, J. et al. An integrated gene expression landscape profiling approach to identify lung tumor endothelial cell heterogeneity and angiogenic candidates. Cancer Cell 37, 21–36 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stassen, S. V., Yip, G. G. K., Wong, K. K. Y., Ho, J. W. K. & Tsia, K. K. Generalized and scalable trajectory inference in single-cell omics data with VIA. Nat. Commun. 12, 5528 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Angerer, P. et al. destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics 32, 1241–1243 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Qiu, X. et al. Mapping transcriptomic vector fields of single cells. Cell 185, 690–711 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lange, M. et al. CellRank for directed single-cell fate mapping. Nat. Methods 19, 159–170 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marxsen, J. H. et al. Hypoxia-inducible factor-1 (HIF-1) promotes its degradation by induction of HIF-α-prolyl-4-hydroxylases. Biochem. J. 381, 761–767 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Belaiba, R. S. et al. Hypoxia up-regulates hypoxia-inducible factor-1α transcription by involving phosphatidylinositol 3-kinase and nuclear factor κB in pulmonary artery smooth muscle cells. Mol. Biol. Cell 18, 4691–4697 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Han, H. et al. TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic Acids Res. 46, D380–D386 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Semenza, G. L. Hypoxia-inducible factor 1: oxygen homeostasis and disease pathophysiology. Trends Mol. Med. 7, 345–350 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Holland, C. H. et al. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Genome Biol. 21, 36 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Badia, I. M. P. et al. decoupleR: ensemble of computational methods to infer biological activities from omics data. Bioinform. Adv. 2, vbac016 (2022).

    Article 

    Google Scholar
     

  • Camp, J. G. et al. Multilineage communication regulates human liver bud development from pluripotency. Nature 546, 533–538 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Van den Berge, K. et al. Trajectory-based differential expression analysis for single-cell sequencing data. Nat. Commun. 11, 1201 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shen, W.-K. et al. AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations. Nucleic Acids Res. 51, D39–D45 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Browaeys, R., Saelens, W. & Saeys, Y. NicheNet: modeling intercellular communication by linking ligands to target genes. Nat. Methods 17, 159–162 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bilous, M. et al. Metacells untangle large and complex single-cell transcriptome networks. BMC Bioinform. 23, 336 (2022).

    Article 
    CAS 

    Google Scholar
     

  • Efremova, M., Vento-Tormo, M., Teichmann, S. A. & Vento-Tormo, R. CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat. Protoc. 15, 1484–1506 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chu, T., Wang, Z., Pe’er, D. & Danko, C. G. Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. Nat. Cancer 3, 505–517 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pan, X. et al. Codes for ‘Tumour vasculature at the single-cell resolution’. Zenodo https://doi.org/10.5281/zenodo.11188740 (2024).



  • Source link

    Leave a Reply

    Your email address will not be published. Required fields are marked *