Transcriptomic responses to wounding: meta-analysis of gene expression microarray data - Publikacja - MOST Wiedzy


Transcriptomic responses to wounding: meta-analysis of gene expression microarray data


Background A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first study to compare gene expression profiles in response to wounding in as different tissues as heart, liver, skin, bones, and spinal cord, and species, including rat, mouse and human. Results We collected available microarray transcriptomic profiles obtained from different tissue injury experiments and selected the genes showing a minimum twofold change in expression in response to wounding in prevailing number of experiments for each of five wound healing stages we distinguished: haemostasis & early inflammation, inflammation, early repair, late repair and remodelling. During the initial phases after wounding, haemostasis & early inflammation and inflammation, the transcriptomic responses showed little consistency between different tissues and experiments. For the later phases, wound repair and remodelling, we identified a number of genes displaying similar transcriptional responses in all examined tissues. As revealed by ontological analyses, activation of certain pathways was rather specific for selected phases of wound healing, such as e.g. responses to vitamin D pronounced during inflammation. Conversely, we observed induction of genes encoding inflammatory agents and extracellular matrix proteins in all wound healing phases. Further, we selected several genes differentially upregulated throughout different stages of wound response, including established factors of wound healing in addition to those previously unreported in this context such as PTPRC and AQP4. Conclusions We found that transcriptomic responses to wounding showed similar traits in a diverse selection of tissues including skin, muscles, internal organs and nervous system. Notably, we distinguished transcriptional induction of inflammatory genes not only in the initial response to wounding, but also later, during wound repair and tissue remodelling.


  • 5


  • 4

    Web of Science

  • 4


Informacje szczegółowe

Publikacja w czasopiśmie
artykuł w czasopiśmie wyróżnionym w JCR
Opublikowano w:
BMC GENOMICS nr 18, strony 850 - 861,
ISSN: 1471-2164
Rok wydania:
Opis bibliograficzny:
Sass P., Dąbrowski M., Charzyńska A., Sachadyn P.: Transcriptomic responses to wounding: meta-analysis of gene expression microarray data// BMC GENOMICS. -Vol. 18, (2017), s.850-861
Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1186/s12864-017-4202-8
Bibliografia: test
  1. Stroncek JD, Reichert WM. Overview of wound healing in different tissue types. In: Reichert WM, editor. Indwelling neural implants: strategies for contending with the in vivo environment. Boca Raton (FL): CRC Press; 2008. otwiera się w nowej karcie
  2. Weyrich AS, Schwertz H, Kraiss LW, Zimmerman GA. Protein synthesis by platelets: historical and new perspectives. J Thromb Haemost. 2009;7(2):241-6. otwiera się w nowej karcie
  3. Kumar A, Brockes JP. Nerve dependence in tissue, organ, and appendage regeneration. Trends Neurosci. 2012;35(11):691-9. otwiera się w nowej karcie
  4. Palatinus JA, Rhett JM, Gourdie RG. Translational lessons from scarless healing of cutaneous wounds and regenerative repair of the myocardium. J Mol Cell Cardiol. 2010;48(3):550-7. otwiera się w nowej karcie
  5. Taub R. Liver regeneration: from myth to mechanism. Nat Rev Mol Cell Biol. 2004;5(10):836-47. otwiera się w nowej karcie
  6. Lorenz HP, Longaker MT, Perkocha LA, Jennings RW, Harrison MR, Adzick NS. Scarless wound repair: a human fetal skin model. Development. 1992; 114(1):253-9.
  7. Ferguson MW, O'Kane S. Scar-free healing: from embryonic mechanisms to adult therapeutic intervention. Philos Trans R Soc Lond B Biol Sci. 2004; 359(1445):839-50. otwiera się w nowej karcie
  8. Podolak-Popinigis J, Ronowicz A, Dmochowska M, Jakubiak A, Sachadyn P. The methylome and transcriptome of fetal skin: implications for scarless healing. Epigenomics. 2016;8(10):1331-45. otwiera się w nowej karcie
  9. Fraser JF, Cuttle L, Kempf M, Phillips GE, O'Rourke PK, Choo K, Hayes MT, Kimble RM. Deep dermal burn injury results in scarless wound healing in the ovine fetus. Wound Repair Regen. 2005;13(2):189-97. otwiera się w nowej karcie
  10. Rolfe KJ, Grobbelaar AO. A review of fetal scarless healing. ISRN Dermatol. 2012;2012:698034. otwiera się w nowej karcie
  11. Porrello ER, Mahmoud AI, Simpson E, Hill JA, Richardson JA, Olson EN, Sadek HA. Transient regenerative potential of the neonatal mouse heart. Science. 2011;331(6020):1078-80. otwiera się w nowej karcie
  12. Gornikiewicz B, Ronowicz A, Krzeminski M, Sachadyn P. Changes in gene methylation patterns in neonatal murine hearts: implications for the regenerative potential. BMC Genomics. 2016;17:231. otwiera się w nowej karcie
  13. Seifert AW, Kiama SG, Seifert MG, Goheen JR, Palmer TM, Maden M. Skin shedding and tissue regeneration in African spiny mice (Acomys). Nature. 2012;489(7417):561-5. otwiera się w nowej karcie
  14. Gawronska-Kozak B, Bogacki M, Rim JS, Monroe WT, Manuel JA. Scarless skin repair in immunodeficient mice. Wound Repair Regen. 2006;14(3):265-76. otwiera się w nowej karcie
  15. Da Wei Huang BTS, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2008;4(1):44-57.
  16. Hoffmann DC, Textoris C, Oehme F, Klaassen T, Goppelt A, Romer A, Fugmann B, Davidson JM, Werner S, Krieg T, et al. Pivotal role for alpha1- antichymotrypsin in skin repair. J Biol Chem. 2011;286(33):28889-901. otwiera się w nowej karcie
  17. Low QE, Drugea IA, Duffner LA, Quinn DG, Cook DN, Rollins BJ, Kovacs EJ, DiPietro LA. Wound healing in MIP-1alpha(−/−) and MCP-1(−/−) mice. Am J Pathol. 2001;159(2):457-63. otwiera się w nowej karcie
  18. Walker JT, Elliott CG, Forbes TL, Hamilton DW. Genetic deletion of Galectin-3 does not impair full-thickness Excisional skin healing. J Investig Dermatol. 2016;136(5):1042-50. otwiera się w nowej karcie
  19. Ansorge HL, Beredjiklian PK, Soslowsky LJ. CD44 deficiency improves healing tendon mechanics and increases matrix and cytokine expression in a mouse patellar tendon injury model. J Orthop Res. 2009;27(10):1386-91. otwiera się w nowej karcie
  20. Madala SK, Pesce JT, Ramalingam TR, Wilson MS, Minnicozzi S, Cheever AW, Thompson RW, Mentink-Kane MM, Wynn TA. Matrix metalloproteinase 12- deficiency augments extracellular matrix degrading metalloproteinases and attenuates IL-13-dependent fibrosis. J Immunol. 2010;184(7):3955-63. otwiera się w nowej karcie
  21. Owings RA, Boerma M, Wang J, Berbee M, Laderoute KR, Soderberg LS, Vural E, Jensen MH. Selective deficiency of HIF-1α in myeloid cells influences secondary intention wound healing in mouse skin. In Vivo. 2009;23(6):879-84.
  22. Mack JA, Abramson SR, Ben Y, Coffin JC, Rothrock JK, Maytin EV, Hascall VC, Largman C, Stelnicki EJ. Hoxb13 knockout adult skin exhibits high levels of hyaluronan and enhanced wound healing. FASEB J. 2003;17(10):1352-4. otwiera się w nowej karcie
  23. Ishida Y, Kondo T, Takayasu T, Iwakura Y, Mukaida N. The essential involvement of cross-talk between IFN-γ and TGF-β in the skin wound- healing process. J Immunol. 2004;172(3):1848-55. otwiera się w nowej karcie
  24. Eming SA, Werner S, Bugnon P, Wickenhauser C, Siewe L, Utermöhlen O, Davidson JM, Krieg T, Roers A. Accelerated wound closure in mice deficient for interleukin-10. Am J Pathol. 2007;170(1):188-202. otwiera się w nowej karcie
  25. Bradshaw AD, Reed MJ, Sage EH. SPARC-null mice exhibit accelerated cutaneous wound closure. J Histochem Cytochem. 2002;50(1):1-10. otwiera się w nowej karcie
  26. Martinez-Ferrer M, Afshar-Sherif A-R, Uwamariya C, de Crombrugghe B, Davidson JM, Bhowmick NA. Dermal transforming growth factor-β responsiveness mediates wound contraction and epithelial closure. Am J Pathol. 2010;176(1):98-107. otwiera się w nowej karcie
  27. Thomay AA, Daley JM, Sabo E, Worth PJ, Shelton LJ, Harty MW, Reichner JS, Albina JE. Disruption of interleukin-1 signaling improves the quality of wound healing. Am J Pathol. 2009;174(6):2129-36. otwiera się w nowej karcie
  28. Mori R, Kondo T, Ohshima T, Ishida Y, Mukaida N. Accelerated wound healing in tumor necrosis factor receptor p55-deficient mice with reduced leukocyte infiltration. FASEB J. 2002;16(9):963-74. otwiera się w nowej karcie
  29. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M. Global quantification of mammalian gene expression control. Nature. 2011;473(7347):337-3z42. otwiera się w nowej karcie
Politechnika Gdańska

wyświetlono 16 razy

Publikacje, które mogą cię zainteresować

Meta Tagi