Effect of a retinoic acid analogue on BMP-driven pluripotent stem cell chondrogenesis – Scientific Reports

  • James, S. L. et al. Global, regional, and national incidence, prevalence, and years lived with disability for 354 Diseases and Injuries for 195 countries and territories, 1990–2017: A systematic analysis for the Global Burden of Disease Study 2017. Lancet 392(10159), 1789–1858 (2018).

    Article 

    Google Scholar
     

  • Zhang, W., Ouyang, H., Dass, C. R. & Xu, J. Current research on pharmacologic and regenerative therapies for osteoarthritis. Bone Res. 4(October 2015), 15040 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yamanaka, S. Pluripotent stem cell-based cell therapy—Promise and challenges. Cell Stem Cell 27(4), 523–531 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jevotovsky, D. S., Alfonso, A. R., Einhorn, T. A. & Chiu, E. S. Osteoarthritis and stem cell therapy in humans: A systematic review. Osteoarthr. Cartil. 26(6), 711–729 (2018).

    Article 
    CAS 

    Google Scholar
     

  • Craft, A. M. et al. Generation of articular chondrocytes from human pluripotent stem cells. Nat. Biotechnol. 33(6), 638–645 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Smith, C. A. et al. Directed differentiation of hPSCs through a simplified lateral plate mesoderm protocol for generation of articular cartilage progenitors. PLoS One 18(1), e0280024 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Loh, K. M. M. et al. Mapping the pairwise choices leading from pluripotency to human bone, heart, and other mesoderm cell types. Cell 166(2), 451–467 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chijimatsu, R. & Saito, T. Mechanisms of synovial joint and articular cartilage development. Cell. Mol. Life Sci. 76(20), 3939–3952 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Humphreys, P. A. et al. Developmental principles informing human pluripotent stem cell differentiation to cartilage and bone. Semin. Cell Dev. Biol. 127(July 2021), 17–36 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sumi, T., Tsuneyoshi, N., Nakatsuji, N. & Suemori, H. Defining early lineage specification of human embryonic stem cells by the orchestrated balance canonical Wnt/β-catenin, activin/Nodal and BMP signaling. Development 135(17), 2969–2979 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Row, R. H. et al. BMP and FGF signaling interact to pattern mesoderm by controlling basic helix-loop-helix transcription factor activity. Elife 7, 1–27 (2018).

    Article 

    Google Scholar
     

  • Pignatti, E., Zeller, R. & Zuniga, A. To BMP or not to BMP during vertebrate limb bud development. Semin. Cell Dev. Biol. 32, 119–127 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ray, A., Singh, P. N. P., Sohaskey, M. L., Harland, R. M. & Bandyopadhyay, A. Precise spatial restriction of BMP signaling is essential for articular cartilage differentiation. Development 142(6), 1169–1179 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kobayashi, T., Lyons, K. M., McMahon, A. P. & Kronenberg, H. M. BMP signaling stimulates cellular differentiation at multiple steps during cartilage development. Proc. Natl. Acad. Sci. U. S. A. 102(50), 18023–18027 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yoon, B. S. & Lyons, K. M. Multiple functions of BMPs in chondrogenesis. J. Cell. Biochem. 93(1), 93–103 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Oldershaw, R. A. et al. Directed differentiation of human embryonic stem cells toward chondrocytes. Nat. Biotechnol. 28(11), 1187–1194 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, T. et al. Enhanced chondrogenesis from human embryonic stem cells. Stem Cell Res. 39(May), 101497 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Diederichs, S., Klampfleuthner, F. A. M., Moradi, B. & Richter, W. Chondral differentiation of induced pluripotent stem cells without progression into the endochondral pathway. Front. Cell Dev. Biol. 7(November), 1–10 (2019).


    Google Scholar
     

  • Kawata, M. et al. Simple and robust differentiation of human pluripotent stem cells toward chondrocytes by two small-molecule compounds. Stem Cell Rep. 13(3), 530–544 (2019).

    Article 
    CAS 

    Google Scholar
     

  • Weston, A. D., Chandraratna, R. A. S., Torchia, J. & Underhill, T. M. Requirement for RAR-mediated gene repression in skeletal progenitor differentiation. J. Cell Biol. 158(1), 39–51 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pacifici, M., Cossu, G., Molinaro, M. & Tato, F. Vitamin A inhibits chondrogenesis but not myogenesis. Exp. Cell Res. 129(2), 469–474 (1980).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hoffman, L. M. et al. BMP action in skeletogenesis involves attenuation of retinoid signaling. J. Cell Biol. 174(1), 101–113 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Langston, A. W. & Gudas, L. J. Retinoic acid and homeobox gene regulation. Curr. Opin. Genet. Dev. 4(4), 550–555 (1994).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Boncinelli, E., Simeone, A., Acampora, D. & Mavilio, F. HOX gene activation by retinoic acid. Trends Genet. 7(10), 329–334 (1991).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bel-Vialar, S., Itasaki, N. & Krumlauf, R. Initiating Hox gene expression: In the early chick neural tube differential sensitivity to FGF and RA signaling subdivides the HoxB genes in two distinct groups. Development 129(22), 5103–5115 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shen, P. et al. Rapid induction and long-term self-renewal of neural crest-derived ectodermal chondrogenic cells from hPSCs. npj Regen. Med. 7(1), 1–15 (2022).

    Article 
    CAS 

    Google Scholar
     

  • Xu, S. C., Harris, M. A., Rubenstein, J. L. R., Mundy, G. R. & Harris, S. E. Bone morphogenetic protein-2 (BMP-2) signaling to the Col2α1 gene in chondroblasts requires the homeobox gene Dlx-2. DNA Cell Biol. 20(6), 359–365 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lafont, J. E., Poujade, F. A., Pasdeloup, M., Neyret, P. & Mallein-Gerin, F. Hypoxia potentiates the BMP-2 driven COL2A1 stimulation in human articular chondrocytes via p38 MAPK. Osteoarthr. Cartil. 24(5), 856–867 (2016).

    Article 
    CAS 

    Google Scholar
     

  • Fernández-Lloris, R. et al. Induction of the Sry-related factor SOX6 contributes to bone morphogenetic protein-2- induced chondroblastic differentiation of C3H10T1/2 cells. Mol. Endocrinol. 17(7), 1332–1343 (2003).

    Article 
    PubMed 

    Google Scholar
     

  • Kim, H. S., Neugebauer, J., Mcknite, A., Tilak, A. & Christian, J. L. BMP7 functions predominantly as a heterodimer with BMP2 or BMP4 during mammalian embryogenesis. 1–22 (2019).

  • James, R. G. & Schultheiss, T. M. Bmp signaling promotes intermediate mesoderm gene expression in a dose-dependent, cell-autonomous and translation-dependent manner. Dev. Biol. 288(1), 113–125 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huang, D., Li, J., Hu, F., Xia, C., Weng, Q., Wang, T. et al. Lateral plate mesoderm cell-based organoid system for NK cell regeneration from human pluripotent stem cells. Cell Discov. 8(1) (2022).

  • Xi, H. et al. In vivo human somitogenesis guides somite development from hPSCs. Cell Rep. 18(6), 1573–1585 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, C. L. et al. Single cell transcriptomic analysis of human pluripotent stem cell chondrogenesis. Nat. Commun. 12(1), 362 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Umeda, K. et al. Human chondrogenic paraxial mesoderm, directed specification and prospective isolation from pluripotent stem cells. Sci. Rep. 2(455), 1–11 (2012).


    Google Scholar
     

  • Araoka, T., Mae, S. I., Kurose, Y., Uesugi, M., Ohta, A., Yamanaka, S. et al. Efficient and rapid induction of human iPSCs/ESCs into nephrogenic intermediate mesoderm using small molecule-based differentiation methods. PLoS One, 9(1), epub (1–14) (2014).

  • Zhang, P. et al. Short-term BMP-4 treatment initiates mesoderm induction in human embryonic stem cells. Blood 111(4), 1933–1941 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Winnier, G., Blessing, M., Labosky, P. A. & Hogan, B. L. M. Bone morphogenetic protein-4 is required for mesoderm formation and patterning in the mouse. Genes Dev. 9(17), 2105–2116 (1995).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chalamalasetty, R. B. et al. Mesogenin 1 is a master regulator of paraxial presomitic mesoderm differentiation. Development 141(22), 4285–4297 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chapman, D. L., Agulnik, I., Hancock, S., Silver, L. M. & Papaioannou, V. E. Tbx6, a mouse T-box gene implicated in paraxial mesoderm formation at gastrulation. Dev. Biol. 180(2), 534–542 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kashyap, V. & Gudas, L. J. Epigenetic regulatory mechanisms distinguish retinoic acid-mediated transcriptional responses in stem cells and fibroblasts. J. Biol. Chem. 285(19), 14534–14548 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cheng, A. et al. Cartilage repair using human embryonic stem cell-derived chondroprogenitors. Stem Cells Transl. Med. 3(11), 1287–1294 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, L. et al. Activin/Smad2-induced histone H3 Lys-27 trimethylation (H3K27me3) reduction is crucial to initiate mesendoderm differentiation of human embryonic stem cells. J. Biol. Chem. 292(4), 1339–1350 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fowler, D. A. & Larsson, H. C. E. The tissues and regulatory pattern of limb chondrogenesis. Dev. Biol. 463(2), 124–134 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Waxman, J. S., Keegan, B. R., Roberts, R. W., Poss, K. D. & Yelon, D. Hoxb5b acts downstream of retinoic acid signaling in the forelimb field to restrict heart field potential in zebrafish. Dev. Cell 15(6), 923–934 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Feneck, E. & Logan, M. The role of retinoic acid in establishing the early limb bud. Biomolecules 10(2) (2020).

  • Cunningham, T. J. & Duester, G. Mechanisms of retinoic acid signalling and its roles in organ and limb development. Nat. Rev. Mol. Cell Biol. 16(2), 110–123 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nishimoto, S., Wilde, S. M., Wood, S. & Logan, M. P. O. RA acts in a coherent feed-forward mechanism with Tbx5 to control limb bud induction and initiation. Cell Rep. 12(5), 879–891 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jepsen, K. et al. Combinatorial roles of the nuclear receptor corepressor in transcription and development. Cell 102(6), 753–763 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Simeone, A., Acampora, D., Arcioni, L., Andrews, P. W., Boncinelli, E. & Mavilio, F. Sequential activation of HOX2 homeobox genes by retinoic acid in human embryonal carcinoma cells. Nat. 1990 3466286, 346(6286), 763–766 (1990).

  • Kmita, M. & Duboule, D. Organizing axes in time and space; 25 years of colinear tinkering. Science (80-.) 301(5631), 331–333 (2003).

    Article 
    CAS 

    Google Scholar
     

  • Papalopulu, N., Lovel-badage, R. & Krumlauf, R. The expression of murine Hox-2 genes is dependent on the differentiation pathway and displays a collinear sensitivity to retinoic acid in F9 cells and Xenopus embryos. Nucleic Acids Res. 19(20), 5497 (1991).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • De, K. B. et al. Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Res. 25(8), 1229–1243 (2015).

    Article 

    Google Scholar
     

  • Mori, S. et al. Self-organized formation of developing appendages from murine pluripotent stem cells. Nat. Commun. 10(1), 1–13 (2019).

    Article 

    Google Scholar
     

  • Sheth, R. et al. Decoupling the function of Hox and Shh in developing limb reveals multiple inputs of Hox genes on limb growth. Development 140(10), 2130–2138 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yamada, D. et al. Induction and expansion of human PRRX1+ limb-bud-like mesenchymal cells from pluripotent stem cells. Nat. Biomed. Eng. 5(8), 926–940 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rosselot, C. et al. Non-cell-autonomous retinoid signaling is crucial for renal development. Development 137(2), 283–292 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jacobs, S. et al. Retinoic acid is required early during adult neurogenesis in the dentate gyrus. Proc. Natl. Acad. Sci. U. S. A. 103(10), 3902–3907 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wiesinger, A., Boink, G. J. J., Christoffels, V. M. & Devalla, H. D. Retinoic acid signaling in heart development: Application in the differentiation of cardiovascular lineages from human pluripotent stem cells. Stem Cell Rep. 16(11), 2589–2606 (2021).

    Article 
    CAS 

    Google Scholar
     

  • Lorberbaum, D. S., Kishore, S., Rosselot, C., Sarbaugh, D., Brooks, E. P., Aragon, E. et al. Retinoic acid signaling within pancreatic endocrine progenitors regulates mouse and human β cell specification. Development 147(12) (2020).

  • Fernandes-Silva, H., Araújo-Silva, H., Correia-Pinto, J. & Moura, R. S. Retinoic acid: A key regulator of lung development. Biomolecules 10(1), 1–18 (2020).

    Article 

    Google Scholar
     

  • Das, M. & Pethe, P. Differential expression of retinoic acid alpha and beta receptors in neuronal progenitors generated from human embryonic stem cells in response to TTNPB (a retinoic acid mimetic). Differentiation 121, 13–24 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Duong, T. B., Holowiecki, A. & Waxman, J. S. Retinoic acid signaling restricts the size of the first heart field within the anterior lateral plate mesoderm. Dev. Biol. 473, 119–129 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sumitani, Y. et al. Inhibitory effect of retinoic acid receptor agonists on in vitro chondrogenic differentiation. Anat. Sci. Int. 95(2), 202–208 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cho, S. H., Oh, C. D., Kim, S. J., Kim, I. C. & Chun, J. S. Retinoic acid inhibits chondrogenesis of mesenchymal cells by sustaining expression of N-cadherin and its associated proteins. J. Cell. Biochem. 89(4), 837–847 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • He, N., Brysk, H., Tyring, S. K., Ohkubo, I. & Brysk, M. M. Transcriptional suppression of Sox9 expression in chondrocytes by retinoic acid. J. Cell. Biochem. 81(SUPPL. 36), 71–78 (2001).


    Google Scholar
     

  • Pacifici, M. Retinoid roles and action in skeletal development and growth provide the rationale for an ongoing heterotopic ossification prevention trial. Bone 109, 267–275 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Niederreither, K., Subbarayan, V., Dollé, P. & Chambon, P. Embryonic retinoic acid synthesis is essential for early mouse post-implantation development. Nat. Genet. 21(4), 444–448 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Niederreither, K., Vermot, J., Schuhbaur, B., Chambon, P. & Dollé, P. Embryonic retinoic acid synthesis is required for forelimb growth and anteroposterior patterning in the mouse. Development 129(15), 3563–3574 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Riedl, M., Witzmann, C., Koch, M., Lang, S., Kerschbaum, M., Baumann, F. et al. Attenuation of hypertrophy in human mscs via treatment with a retinoic acid receptor inverse agonist. Int. J. Mol. Sci. 21(4) (2020).

  • Cohen, A. J., Lassová, L., Golden, E. B., Niu, Z. & Adams, S. L. Retinoids directly activate the collagen X promoter in prehypertrophic chondrocytes through a distal retinoic acid response element. J. Cell. Biochem. 99(1), 269–278 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, W., Chen, J., Zhang, S. & Ouyang, H. W. Inhibitory function of parathyroid hormone-related protein on chondrocyte hypertrophy: The implication for articular cartilage repair. Arthritis Res. Ther. 14(4), 1–10 (2012).

    Article 

    Google Scholar
     

  • Oh, C. D. et al. SOX9 regulates multiple genes in chondrocytes, including genes encoding ECM proteins, ECM modification enzymes, receptors, and transporters. PLoS One 9(9), 107577 (2014).

    Article 

    Google Scholar
     

  • Timur, U. T., Caron, M., Akker van den, G., Windt van der, A., Visser, J., Rhijn van, L. et al. Increased TGF-β and BMP levels and improved chondrocyte-specific marker expression in vitro under cartilage-specific physiological osmolarity. Int. J. Mol. Sci. 20(4) (2019).

  • Shu, B. et al. BMP2, but not BMP4, is crucial for chondrocyte proliferation and maturation during endochondral bone development. J. Cell Sci. 124(20), 3428–3440 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kramer, J. et al. Embryonic stem cell-derived chondrogenic differentiation in vitro: Activation by BMP-2 and BMP-4. Mech. Dev. 92(2), 193–205 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Murphy, M. K., Huey, D. J., Hu, J. C. & Athanasiou, K. A. TGF-β1, GDF-5, and BMP-2 stimulation induces chondrogenesis in expanded human articular chondrocytes and marrow-derived stromal cells. Stem Cells 33(3), 762–773 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Davidson, E. N. B. et al. Elevated extracellular matrix production and degradation upon bone morphogenetic protein-2 (BMP-2) stimulation point toward a role for BMP-2 in cartilage repair and remodeling. Arthritis Res. Ther. 9(5), 1–11 (2007).

    Article 

    Google Scholar
     

  • Gründer, T. et al. Bone morphogenetic protein (BMP)-2 enhances the expression of type II collagen and aggrecan in chondrocytes embedded in alginate beads. Osteoarthr. Cartil. 12(7), 559–567 (2004).

    Article 

    Google Scholar
     

  • Liao, J., Hu, N., Zhou, N., Zhao, C., Liang, X., Chen, H., et al. Sox9 potentiates BMP2-induced chondrogenic differentiation and inhibits BMP2-induced osteogenic differentiation. Regen. Med. Plast. Surg. 263–280 (2019).

  • Phimphilai, M., Zhao, Z., Boules, H., Roca, H. & Franceschi, R. T. BMP signaling is required for RUNX2-dependent induction of the osteoblast phenotype. J. Bone Miner. Res. 21(4), 637–646 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhou, G. et al. Dominance of SOX9 function over RUNX2 during skeletogenesis. Proc. Natl. Acad. Sci. U. S. A. 103(50), 19004–19009 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Haseeb, A. et al. SOX9 keeps growth plates and articular cartilage healthy by inhibiting chondrocyte dedifferentiation/ osteoblastic redifferentiation. Proc. Natl. Acad. Sci. U. S. A. 118(8), 1–11 (2021).

    Article 

    Google Scholar
     

  • Kirimoto, A., Takagi, Y., Ohya, K. & Shimokawa, H. Effects of retinoic acid on the differentiation of chondrogenic progenitor cells, ATDC5. J. Med. Dent. Sci. 52(3), 153–162 (2005).

    PubMed 

    Google Scholar
     

  • Pacifici, M., Golden, E. B., Iwamoto, M. & Adams, S. L. Retinoic acid treatment induces type X collagen gene expression in cultured chick chondrocytes. Exp. Cell Res. 195(1), 38–46 (1991).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Richard, D. et al. Lineage-specific differences and regulatory networks governing human chondrocyte development. Elife 12, 79925 (2023).

    Article 

    Google Scholar
     

  • Ye, J. et al. High quality clinical grade human embryonic stem cell lines derived from fresh discarded embryos. Stem Cell Res. Ther. 8(1), 1–13 (2017).

    Article 

    Google Scholar
     

  • Woods, S. et al. Generation of human-induced pluripotent stem cells from anterior cruciate ligament. J. Orthop. Res. 38(1), 92–104 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Streeter I., Harrison P. W., Faulconbridge A., Consortium T. H. S., Flicek P., Parkinson H., et al. The human-induced pluripotent stem cell initiative—Data resources for cellular genetics. Nucleic Acids Res. 45 (D1), D691–D697 (2017).

  • Ye, J. et al. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinform. 13, 134 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Xie, Z. et al. Gene set knowledge discovery with enrichr. Curr. Protoc. 1(3), e90 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kuleshov, M. V. et al. Enrichr: A comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44(May), 90–97 (2016).

    Article 

    Google Scholar
     

  • Chen, E. et al. Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform. 14(128), 1–14 (2013).

    Article 

    Google Scholar
     

  • Goedhart J. & Luijsterburg M.S. VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots. Sci. Rep. 2020 101, 10(1), 1–5 (2020).

  • Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A. 95(25), 14863–14868 (1998).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Humphreys, P. A. et al. Optogenetic control of the BMP signaling pathway. ACS Synth. Biol. 9(11), 3067–3078 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar