Eming, S. A., Martin, P. & Tomic-Canic, M. Wound repair and regeneration: Mechanisms, signaling, and translation. Sci. Transl. Med. 6, 265sr6–265sr6 (2014).
Wilkinson, H. N. & Hardman, M. J. Wound healing: Cellular mechanisms and pathological outcomes. Open Biol. 10, 20023 (2020).
Dvorak, H. F. Tumors: Wounds that do not heal. Similarities between tumor stroma generation and wound healing. N. Engl. J. Med. 315, 1650–1659 (1986).
Google Scholar
Dvorak, H. F. Tumors: Wounds that do not heal–Redux. Cancer Immunol. Res. 3, 1–11 (2015).
Google Scholar
Schäfer, M. & Werner, S. Cancer as an overhealing wound: An old hypothesis revisited. Nat. Rev. Mol. Cell Biol. 9, 628–638 (2008).
Google Scholar
MacCarthy-Morrogh, L. & Martin, P. The hallmarks of cancer are also the hallmarks of wound healing. Sci. Signal. 13, eaay8690 (2020).
Trigos, A. S., Pearson, R. B., Papenfuss, A. T. & Goode, D. L. How the evolution of multicellularity set the stage for cancer. Br. J. Cancer 118, 145–152 (2018).
Google Scholar
Bely, A. E. & Nyberg, K. G. Evolution of animal regeneration: Re-emergence of a field. Trends Ecol. Evol. 25, 161–170 (2010).
Google Scholar
Bosch, T. C. G. Why polyps regenerate and we don’t: Towards a cellular and molecular framework for Hydra regeneration. Dev. Biol. 303, 421–433 (2007).
Google Scholar
Gurtner, G. C., Werner, S., Barrandon, Y. & Longaker, M. T. Wound repair and regeneration. Nature 453, 314–321 (2008).
Google Scholar
Slack, J. M. Animal regeneration: Ancestral character or evolutionary novelty?. EMBO Rep. 18, 1497–1508 (2017).
Google Scholar
Wenger, Y., Buzgariu, W., Reiter, S. & Galliot, B. Injury-induced immune responses in Hydra. Semin. Immunol. 26, 277–294 (2014).
Google Scholar
Poss, K. D., Wilson, L. G. & Keating, M. T. Heart regeneration in zebrafish. Science (80-. ). 298, 2188–2190 (2002).
Kao, D., Felix, D. & Aboobaker, A. The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. BMC Genomics 14, 1–17 (2013).
Gehrke, A. R. et al. Acoel genome reveals the regulatory landscape of whole-body regeneration. Science (80-. ). 363 (2019).
DuBuc, T. Q., Traylor-Knowles, N. & Martindale, M. Q. Initiating a regenerative response; cellular and molecular features of wound healing in the cnidarian Nematostella vectensis. BMC Biol. 12, 24 (2014).
Google Scholar
Cary, G. A., Wolff, A., Zueva, O., Pattinato, J. & Hinman, V. F. Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa. BMC Biol. 17, 16 (2019).
Google Scholar
Owlarn, S. et al. Generic wound signals initiate regeneration in missing-tissue contexts. Nat. Commun. 8, 1–13 (2017).
Google Scholar
Ramon-Mateu, J., Ellison, S. T., Angelini, T. E. & Martindale, M. Q. Regeneration in the ctenophore Mnemiopsis leidyi occurs in the absence of a blastema, requires cell division, and is temporally separable from wound healing. BMC Biol. 17, 80 (2019).
Google Scholar
Pawlik, J. R. & Deignan, L. K. Cowries graze Verongid sponges on Caribbean reefs. Coral Reefs 34, 663 (2015).
Google Scholar
Rice, M. M., Ezzat, L. & Burkepile, D. E. Corallivory in the anthropocene: Interactive effects of anthropogenic stressors and corallivory on coral reefs. Front. Mar. Sci. 5, 1–14 (2019).
Pawlik, J. R., Loh, T.-L., McMurray, S. E. & Finelli, C. M. Sponge communities on Caribbean coral reefs are structured by factors that are top-down, not bottom-up. PLoS One 8, e62573 (2013).
Mortimer, C., Dunn, M., Haris, A., Jompa, J. & Bell, J. Estimates of sponge consumption rates on an Indo-Pacific reef. Mar. Ecol. Prog. Ser. 672, 123–140 (2021).
Google Scholar
de Goeij, J. M. et al. Surviving in a marine desert: the sponge loop retains resources within coral reefs. Science (80-. ). 342, 108–10 (2013).
Rix, L. et al. Differential recycling of coral and algal dissolved organic matter via the sponge loop. Funct. Ecol. 31, 778–789 (2016).
Maldonado, M. et al. Sponge grounds as key marine habitats: A synthetic review of types, structure, functional roles and conservation concerns. Mar. Animal Forests https://doi.org/10.1007/978-3-319-17001-5 (2015).
Google Scholar
Soubigou, A., Ross, E. G., Touhami, Y., Chrismas, N. & Modepalli, V. Regeneration in sponge Sycon ciliatum partly mimics postlarval development. Development https://doi.org/10.1242/dev.193714 (2020).
Google Scholar
Telford, M. J., Moroz, L. L. & Halanych, K. M. A sisterly dispute. Nature 529, 286–287 (2016).
Google Scholar
Feuda, R. et al. Improved modeling of compositional heterogeneity supports sponges as sister to all other animals. Curr. Biol. https://doi.org/10.1016/j.cub.2017.11.008 (2017).
Google Scholar
Dunn, C. W., Leys, S. P. & Haddock, S. H. D. The hidden biology of sponges and ctenophores. Trends Ecol. Evol. 30, 282–291 (2015).
Google Scholar
Borisenko, I. E., Adamska, M., Tokina, D. B. & Ereskovsky, A. V. Transdifferentiation is a driving force of regeneration in Halisarca dujardini (Demospongiae, Porifera). PeerJ 3, e1211 (2015).
Lavrov, A. I., Bolshakov, F. V., Tokina, D. B. & Ereskovsky, A. V. Sewing up the wounds: The epithelial morphogenesis as a central mechanism of calcaronean sponge regeneration. J. Exp. Zool. Part B Mol. Dev. Evol. 330, 351–371 (2018).
Ereskovsky, A. V. et al. Transdifferentiation and mesenchymal‐to‐epithelial transition during regeneration in Demospongiae (Porifera). J. Exp. Zool. Part B Mol. Dev. Evol. 334, 37–58 (2020).
Alexander, B. E. et al. Cell kinetics during regeneration in the sponge Halisarca caerulea: how local is the response to tissue damage? PeerJ 3, e820 (2015).
Pozzolini, M. et al. Insights into the evolution of metazoan regenerative mechanisms: TGF superfamily member roles in tissue regeneration of the marine sponge Chondrosia reniformis Nardo, 1847. J. Exp. Biol. 222, jeb207894 (2019).
Kenny, N. J. et al. Towards the identification of ancestrally shared regenerative mechanisms across the Metazoa: A transcriptomic case study in the demosponge Halisarca caerulea. Mar. Genomics 37, 135–147 (2018).
Google Scholar
Pawlik, J. R. Handbook of marine natural products. in Handbook of Marine Natural Products (eds. Fattorusso, E., Gerwick, W. H. & Taglialatela-Scafati, O.) 677–705 (Springer, New York, 2012). https://doi.org/10.1007/978-90-481-3834-0
Walters, K. D. & Pawlik, J. R. Is there a trade-off between wound-healing and chemical defenses among Caribbean reef sponges?. Integr. Comp. Biol. 45, 352–358 (2005).
Google Scholar
Becerro, M. A., Turon, X., Uriz, M. J. & Templado, J. Can a sponge feeder be a herbivore? Tylodina perversa (Gastropoda) feeding on Aplysina aerophoba (Demospongiae). Biol. J. Linn. Soc. 78, 429–438 (2003).
Wu, Y.-C. et al. Opisthobranch grazing results in mobilisation of spherulous cells and re-allocation of secondary metabolites in the sponge Aplysina aerophoba. Sci. Rep. 10, 21934 (2020).
Google Scholar
Pita, L., Hoeppner, M. P., Ribes, M. & Hentschel, U. Differential expression of immune receptors in two marine sponges upon exposure to microbial-associated molecular patterns. Sci. Rep. 8, 16081 (2018).
Google Scholar
Stewart, F. J., Ottesen, E. A. & Delong, E. F. Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J. 4, 896–907 (2010).
Google Scholar
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible read trimming tool for Illumina NGS data. Bioinformatics btu170 (2014).
Menzel, P. & Krogh, A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7, 11257 (2015).
Google Scholar
Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nat. Protoc. 8, 1494 (2013).
Google Scholar
Smith-Unna, R., Boursnell, C., Patro, R., Hibberd, J. M. & Kelly, S. TransRate: Reference free quality assessment of de-novo transcriptome assemblies. Genome Res. 26, 1134–1144 (2016).
Google Scholar
Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. Genome analysis BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
Google Scholar
Bryant, D. M. et al. A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors. Cell Rep. 18, 762–776 (2017).
Google Scholar
Kanehisa, M. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
Google Scholar
Conesa, A. et al. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676 (2005).
Google Scholar
Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 6, e21800 (2011).
Wickham, H. ggplot2: Elegant graphics for data analysis. (Springer, Berlin, 2016).
Team, R. C. R: A language and environment for statistical computing. (2019).
Team, Rs. RStudio: Integrated Development for R. (2015).
Szklarczyk, D. et al. STRING v11: Protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607–D613 (2019).
Google Scholar
Pritchard, L., Jones, S. & Cock, P. IBioIC Introd. Bioinform. Train. Course https://doi.org/10.5281/zenodo.1184095 (2018).
Forbes, S. A. et al. The catalogue of somatic mutations in cancer (COSMIC). Curr. Protoc. Hum. Genet. 57 (2008).
Trigos, A. S., Pearson, R. B., Papenfuss, A. T. & Goode, D. L. Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer. Elife 8, 1–28 (2019).
Cerenius, L. & Söderhäll, K. Coagulation in invertebrates. J. Innate Immun. 3, 3–8 (2011).
Google Scholar
Davie, E. W., Fujikawa, K. & Kisiel, W. The coagulation cascade: Initiation, maintenance, and regulation. Biochemistry 30, 10363–10370 (1991).
Google Scholar
Richardson, V. R., Cordell, P., Standeven, K. F. & Carter, A. M. Substrates of factor XIII-A: Roles in thrombosis and wound healing. Clin. Sci. 124, 123–137 (2013).
Google Scholar
Domazet-Lošo, T. & Tautz, D. Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. BMC Biol. 8, 1–10 (2010).
Trigos, A. S., Pearson, R. B., Papenfuss, A. T. & Goode, D. L. Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors. Proc. Natl. Acad. Sci. USA 114, 6406–6411 (2017).
Google Scholar
Rohani, M. G. & Parks, W. C. Matrix remodeling by MMPs during wound repair. Matrix Biol. 44–46, 113–121 (2015).
Google Scholar
Grose, R. et al. A crucial role of beta 1 integrins for keratinocyte migration in vitro and during cutaneous wound repair. Development 129, 2303–2315 (2002).
Google Scholar
Sebé-Pedrós, A. et al. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat. Ecol. Evol. 2, 1176–1188 (2018).
Google Scholar
Paps, J. & Holland, P. W. H. Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty. Nat. Commun. 9, 1730 (2018).
Google Scholar
Sharrocks, A. D. The ETS-domain transcription factor family. Nat. Rev. Mol. Cell Biol. 2, 827–837 (2001).
Google Scholar
Larroux, C. et al. Developmental expression of transcription factor genes in a demosponge: Insights into the origin of metazoan multicellularity. Evol. Dev. 8, 150–173 (2006).
Google Scholar
Petersen, H. O. et al. A comprehensive transcriptomic and proteomic analysis of Hydra head regeneration. Mol. Biol. Evol. 32, 1928–1947 (2015).
Google Scholar
Cardozo, M. J., Mysiak, K. S., Becker, T. & Becker, C. G. Reduce, reuse, recycle—Developmental signals in spinal cord regeneration. Dev. Biol. 432, 53–62 (2017).
Google Scholar
Adamska, M. et al. Wnt and TGF-β expression in the sponge Amphimedon queenslandica and the origin of metazoan embryonic patterning. PLoS One 2, e1031 (2007).
Stewart, Z. K. et al. Transcriptomic investigation of wound healing and regeneration in the cnidarian Calliactis polypus. Sci. Rep. 7, 41458 (2017).
Google Scholar
Chablais, F. & Jazwinska, A. The regenerative capacity of the zebrafish heart is dependent on TGF signaling. Development 139, 1921–1930 (2012).
Google Scholar
Chen, H., Lin, F., Xing, K. & He, X. The reverse evolution from multicellularity to unicellularity during carcinogenesis. Nat. Commun. 6, 1–10 (2015).
Google Scholar
Srivastava, M. et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466, 720–726 (2010).
Google Scholar
Ćetković, H., Halasz, M. & Herak Bosnar, M. Sponges: A reservoir of genes implicated in human cancer. Mar. Drugs 16, 20 (2018).
Google Scholar
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