Identification and Functional Analysis of Healing Regulators in
Two major challenges in our understanding of epithelial repair and regeneration is the identification of the signals triggered after injury and the characterization of mechanisms initiated during tissue repair. From a clinical perspective, a key question that remains unanswered is “Why do some wounds fail to heal?” Considering the low genetic redundancy of Drosophila and its high degree of conservation of fundamental functions, the analysis of wound closure in imaginal discs, whose features are comparable to other post-injury events, seems to be a good model. To proceed to genomic studies, we developed a healing-permissive in vitro culture system for discs. Employing this method and microarray analysis, we aimed to identify relevant genes that are involved in healing. We compared cells that were actively involved in healing to those not involved, and identified a set of upregulated or downregulated genes. They were annotated, clustered by expression profiles, chromosomal locations, and presumptive functions. Most importantly, we functionally tested them in a healing assay. This led to the selection of a group of genes whose changes in expression level and functionality are significant for proper tissue repair. Data obtained from these analyses must facilitate the targeting of these genes in gene therapy or pharmacological studies in mammals.
Vyšlo v časopise:
Identification and Functional Analysis of Healing Regulators in. PLoS Genet 11(2): e32767. doi:10.1371/journal.pgen.1004965
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1004965
Souhrn
Two major challenges in our understanding of epithelial repair and regeneration is the identification of the signals triggered after injury and the characterization of mechanisms initiated during tissue repair. From a clinical perspective, a key question that remains unanswered is “Why do some wounds fail to heal?” Considering the low genetic redundancy of Drosophila and its high degree of conservation of fundamental functions, the analysis of wound closure in imaginal discs, whose features are comparable to other post-injury events, seems to be a good model. To proceed to genomic studies, we developed a healing-permissive in vitro culture system for discs. Employing this method and microarray analysis, we aimed to identify relevant genes that are involved in healing. We compared cells that were actively involved in healing to those not involved, and identified a set of upregulated or downregulated genes. They were annotated, clustered by expression profiles, chromosomal locations, and presumptive functions. Most importantly, we functionally tested them in a healing assay. This led to the selection of a group of genes whose changes in expression level and functionality are significant for proper tissue repair. Data obtained from these analyses must facilitate the targeting of these genes in gene therapy or pharmacological studies in mammals.
Zdroje
1. Martin P, Parkhurst SM (2004) Parallels between tissue repair and embryo morphogenesis. Development 131: 3021–3034. doi: 10.1242/dev.01253 15197160
2. Harden N (2002) Signaling pathways directing the movement and fusion of epithelial sheets: lessons from dorsal closure in Drosophila. Differentiation 70: 181–203. doi: 10.1046/j.1432-0436.2002.700408.x 12147138
3. Wood W, Jacinto A, Grose R, Woolner S, Gale J, et al. (2002) Wound healing recapitulates morphogenesis in Drosophila embryos. Nature Cell Biology 4: 907–912. doi: 10.1038/ncb875 12402048
4. Martin P (1997) Wound healing--aiming for perfect skin regeneration. Science 276: 75–81. doi: 10.1126/science.276.5309.75 9082989
5. McCluskey J, Martin P (1995) Analysis of the tissue movements of embryonic wound healing--DiI studies in the limb bud stage mouse embryo. Developmental Biology 170: 102–114. doi: 10.1006/dbio.1995.1199 7601301
6. Martin P, Lewis J (1992) Actin cables and epidermal movement in embryonic wound healing. Nature 360: 179–183. doi: 10.1038/360179a0 1436096
7. Martin-Blanco E, Pastor-Pareja JC, Garcia-Bellido A (2000) JNK and decapentaplegic signaling control adhesiveness and cytoskeleton dynamics during thorax closure in Drosophila. Proc Natl Acad Sci U S A 97: 7888–7893. doi: 10.1073/pnas.97.14.7888 10884420
8. Li G, Gustafson-Brown C, Hanks SK, Nason K, Arbeit JM, et al. (2003) c-Jun is essential for organization of the epidermal leading edge. Developmental Cell 4: 865–877. doi: 10.1016/S1534-5807(03)00159-X 12791271
9. Zenz R, Scheuch H, Martin P, Frank C, Eferl R, et al. (2003) c-Jun regulates eyelid closure and skin tumor development through EGFR signaling. Developmental Cell 4: 879–889. doi: 10.1016/S1534-5807(03)00161-8 12791272
10. Mace KA, Pearson JC, McGinnis W (2005) An epidermal barrier wound repair pathway in Drosophila is mediated by grainy head. Science 308: 381–385. doi: 10.1126/science.1107573 15831751
11. Galko MJ, Krasnow MA (2004) Cellular and genetic analysis of wound healing in Drosophila larvae. PLoS biology 2: E239. doi: 10.1371/journal.pbio.0020239 15269788
12. Ramet M, Lanot R, Zachary D, Manfruelli P (2002) JNK signaling pathway is required for efficient wound healing in Drosophila. Developmental Biology 241: 145–156. doi: 10.1006/dbio.2001.0502 11784101
13. Bosch M, Serras F, Martin-Blanco E, Baguna J (2005) JNK signaling pathway required for wound healing in regenerating Drosophila wing imaginal discs. Developmental Biology 280: 73–86. doi: 10.1016/j.ydbio.2005.01.002 15766749
14. Bergantinos C, Corominas M, Serras F (2010) Cell death-induced regeneration in wing imaginal discs requires JNK signalling. Development 137: 1169–1179. doi: 10.1242/dev.045559 20215351
15. Nishimura M, Kumsta C, Kaushik G, Diop SB, Ding Y, et al. (2014) A dual role for integrin-linked kinase and beta1-integrin in modulating cardiac aging. Aging Cell 13: 431–440. doi: 10.1111/acel.12193 24400780
16. Patel U, Myat MM (2013) Receptor guanylyl cyclase Gyc76C is required for invagination, collective migration and lumen shape in the Drosophila embryonic salivary gland. Biol Open 2: 711–717. doi: 10.1242/bio.20134887 23862019
17. Agnes F, Suzanne M, Noselli S (1999) The Drosophila JNK pathway controls the morphogenesis of imaginal discs during metamorphosis. Development 126: 5453–5462. 10556069
18. Pastor-Pareja JC, Grawe F, Martin-Blanco E, Garcia-Bellido A (2004) Invasive cell behavior during Drosophila imaginal disc eversion is mediated by the JNK signaling cascade. Developmental Cell 7: 387–399. doi: 10.1016/j.devcel.2004.07.022 15363413
19. Calleja M, Moreno E, Pelaz S, Morata G (1996) Visualization of gene expression in living adult Drosophila. Science 274: 252–255. doi: 10.1126/science.274.5285.252 8824191
20. Bryant PJ, Fraser SE (1988) Wound healing, cell communication, and DNA synthesis during imaginal disc regeneration in Drosophila. Developmental Biology 127: 197–208. doi: 10.1016/0012-1606(88)90201-1 2452103
21. Schubiger G (1971) Regeneration, duplication and transdetermination in fragments of the leg disc of Drosophila melanogaster. Developmental Biology 26: 277–295. doi: 10.1016/0012-1606(71)90127-8 5003476
22. Frydman J, Nimmesgern E, Ohtsuka K, Hartl FU (1994) Folding of nascent polypeptide chains in a high molecular mass assembly with molecular chaperones. Nature 370: 111–117. doi: 10.1038/370111a0 8022479
23. Brackley KI, Grantham J (2009) Activities of the chaperonin containing TCP-1 (CCT): implications for cell cycle progression and cytoskeletal organisation. Cell Stress Chaperones 14: 23–31. doi: 10.1007/s12192-008-0057-x 18595008
24. Reinhardt CA, Hodgkin NM, Bryant PJ (1977) Wound healing in the imaginal discs of Drosophila. I. Scanning electron microscopy of normal and healing wing discs. Developmental Biology 60: 238–257.
25. Pavlidis P, Noble WS (2001) Analysis of strain and regional variation in gene expression in mouse brain. Genome biology 2: RESEARCH0042. doi: 10.1186/gb-2001-2-10-research0042 11597334
26. Stevens LJ, Page-McCaw A (2012) A secreted MMP is required for reepithelialization during wound healing. Molecular Biology of the Cell 23: 1068–1079. doi: 10.1091/mbc.E11-09-0745 22262460
27. Abreu-Blanco MT, Verboon JM, Parkhurst SM (2011) Cell wound repair in Drosophila occurs through three distinct phases of membrane and cytoskeletal remodeling. Journal of Cell Biology 193: 455–464. doi: 10.1083/jcb.201011018 21518790
28. Brown NH, Gregory SL, Rickoll WL, Fessler LI, Prout M, et al. (2002) Talin is essential for integrin function in Drosophila. Dev Cell 3: 569–579. doi: 10.1016/S1534-5807(02)00290-3 12408808
29. Yagi R, Ishimaru S, Yano H, Gaul U, Hanafusa H, et al. (2001) A novel muscle LIM-only protein is generated from the paxillin gene locus in Drosophila. EMBO Rep 2: 814–820. doi: 10.1093/embo-reports/kve178 11520860
30. Sokol NS, Cooley L (1999) Drosophila filamin encoded by the cheerio locus is a component of ovarian ring canals. Curr Biol 9: 1221–1230. doi: 10.1016/S0960-9822(99)80502-8 10556087
31. Konsolaki M, Schupbach T (1998) windbeutel, a gene required for dorsoventral patterning in Drosophila, encodes a protein that has homologies to vertebrate proteins of the endoplasmic reticulum. Genes Dev 12: 120–131. doi: 10.1101/gad.12.1.120 9420336
32. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25: 25–29. doi: 10.1038/75556
33. Aza-Blanc P, Ramirez-Weber FA, Laget MP, Schwartz C, Kornberg TB (1997) Proteolysis that is inhibited by hedgehog targets Cubitus interruptus protein to the nucleus and converts it to a repressor. Cell 89: 1043–1053. doi: 10.1016/S0092-8674(00)80292-5 9215627
34. Grantham J, Brackley KI, Willison KR (2006) Substantial CCT activity is required for cell cycle progression and cytoskeletal organization in mammalian cells. Exp Cell Res 312: 2309–2324. doi: 10.1016/j.yexcr.2006.03.028 16765944
35. Coue M, Brenner SL, Spector I, Korn ED (1987) Inhibition of actin polymerization by latrunculin A. FEBS Lett 213: 316–318. doi: 10.1016/0014-5793(87)81513-2 3556584
36. Stramer B, Winfield M, Shaw T, Millard TH, Woolner S, et al. (2008) Gene induction following wounding of wild-type versus macrophage-deficient Drosophila embryos. EMBO Reports 9: 465–471. doi: 10.1038/embor.2008.34 18344972
37. Blanco E, Ruiz-Romero M, Beltran S, Bosch M, Punset A, et al. (2010) Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs. BMC Dev Biol 10: 94.
38. Bosch M, Baguna J, Serras F (2008) Origin and proliferation of blastema cells during regeneration of Drosophila wing imaginal discs. Int J Dev Biol 52: 1043–1050. doi: 10.1387/ijdb.082608mb 18956337
39. Lee N, Maurange C, Ringrose L, Paro R (2005) Suppression of Polycomb group proteins by JNK signalling induces transdetermination in Drosophila imaginal discs. Nature 438: 234–237. doi: 10.1038/nature04120 16281037
40. Mattila J, Omelyanchuk L, Kyttala S, Turunen H, Nokkala S (2005) Role of Jun N-terminal Kinase (JNK) signaling in the wound healing and regeneration of a Drosophila melanogaster wing imaginal disc. Int J Dev Biol 49: 391–399. doi: 10.1387/ijdb.052006jm 15968584
41. Bergantinos C, Vilana X, Corominas M, Serras F (2010) Imaginal discs: Renaissance of a model for regenerative biology. Bioessays 32: 207–217. doi: 10.1002/bies.200900105 20127699
42. McCawley LJ, Matrisian LM (2001) Matrix metalloproteinases: they’re not just for matrix anymore! Curr Opin Cell Biol 13: 534–540. doi: 10.1016/S0955-0674(00)00248-9 11544020
43. Werner S, Grose R (2003) Regulation of wound healing by growth factors and cytokines. Physiol Rev 83: 835–870. 12843410
44. Singer A, Clark R (1999) Cutaneous Wound Healing. New England Journal of Medicine 341: 738–746. doi: 10.1056/NEJM199909023411006 10471461
45. Braddock M (2001) The transcription factor Egr-1: a potential drug in wound healing and tissue repair. Annals of Medicine 33: 313–318. doi: 10.3109/07853890109002083 11491188
46. Brock J, Midwinter K, Lewis J, Martin P (1996) Healing of incisional wounds in the embryonic chick wing bud: characterization of the actin purse-string and demonstration of a requirement for Rho activation. Journal of Cell Biology 135: 1097–1107. doi: 10.1083/jcb.135.4.1097 8922389
47. Su YC, Treisman JE, Skolnik EY (1998) The Drosophila Ste20-related kinase misshapen is required for embryonic dorsal closure and acts through a JNK MAPK module on an evolutionarily conserved signaling pathway. Genes & Development 12: 2371–2380. doi: 10.1101/gad.12.15.2371
48. Stronach B, Perrimon N (2002) Activation of the JNK pathway during dorsal closure in Drosophila requires the mixed lineage kinase, slipper. Genes & Development 16: 377–387. doi: 10.1101/gad.953002
49. Yin J, Lu J, Yu FS (2008) Role of small GTPase Rho in regulating corneal epithelial wound healing. Invest Ophthalmol Vis Sci 49: 900–909. doi: 10.1167/iovs.07-1122 18326710
50. Baek SH, Kwon YC, Lee H, Choe KM (2010) Rho-family small GTPases are required for cell polarization and directional sensing in Drosophila wound healing. Biochem Biophys Res Commun 394: 488–492. doi: 10.1016/j.bbrc.2010.02.124 20184864
51. Zeidler MP, Bach EA, Perrimon N (2000) The roles of the Drosophila JAK/STAT pathway. Oncogene 19: 2598–2606. doi: 10.1038/sj.onc.1203482 10851058
52. Pastor-Pareja JC, Wu M, Xu T (2008) An innate immune response of blood cells to tumors and tissue damage in Drosophila. Dis Model Mech 1: 144–154. doi: 10.1242/dmm.000950 19048077
53. Wu M, Pastor-Pareja JC, Xu T (2010) Interaction between Ras(V12) and scribbled clones induces tumour growth and invasion. Nature 463: 545–548. doi: 10.1038/nature08702 20072127
54. Adachi-Yamada T, Fujimura-Kamada K, Nishida Y, Matsumoto K (1999) Distortion of proximodistal information causes JNK-dependent apoptosis in Drosophila wing. Nature 400: 166–169. doi: 10.1038/22112 10408443
55. Ryoo HD, Gorenc T, Steller H (2004) Apoptotic cells can induce compensatory cell proliferation through the JNK and the Wingless signaling pathways. Developmental Cell 7: 491–501. doi: 10.1016/j.devcel.2004.08.019 15469838
56. Campos I, Geiger J.A., Santos A.C., Carlos V., and Jacinto A. (2010) Genetic Screen in Drosophila melanogaster Uncovers a Novel Set of Genes Required for Embryonic Epithelial Repair. Genetics 184: 129–140. doi: 10.1534/genetics.109.110288 19884309
57. Lesch C, Jo J., Wu Y., Fish G.S., and Galko M.J. (2010) A Targeted UAS-RNAi Screen in Drosophila Larvae Identifies Wound Closure Genes Regulating Distinct Cellular Processes. Genetics 186: 943–957. doi: 10.1534/genetics.110.121822 20813879
58. Juarez MT, Patterson RA, Sandoval-Guillen E, McGinnis W (2011) Duox, Flotillin-2, and Src42A are required to activate or delimit the spread of the transcriptional response to epidermal wounds in Drosophila. PLoS Genetics 7: e1002424. doi: 10.1371/journal.pgen.1002424 22242003
59. Belacortu Y, and Paricio N. (2011) Drosophila as a Model of Wound Healing and Tissue Regeneration in Vertebrates. Developmental Dynamics 240: 2379–2404. doi: 10.1002/dvdy.22753 21953647
60. Schäfer M, and Werner S. (2007) Transcriptional Control of Wound Repair. Annu Rev Cell Dev Biol 23: 69–92. doi: 10.1146/annurev.cellbio.23.090506.123609 17474876
61. Dean M, Rzhetsky A, Allikmets R (2001) The human ATP-binding cassette (ABC) transporter superfamily. Genome Research 11: 1156–1166. doi: 10.1101/gr.GR-1649R 11435397
62. Andersen CB, Becker T, Blau M, Anand M, Halic M, et al. (2006) Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Nature 443: 663–668. doi: 10.1038/nature05126 16929303
63. Gomez-Skarmeta JL, Diez del Corral R, de la Calle-Mustienes E, Ferre-Marco D, Modolell J (1996) Araucan and caupolican, two members of the novel iroquois complex, encode homeoproteins that control proneural and vein-forming genes. Cell 85: 95–105. doi: 10.1016/S0092-8674(00)81085-5 8620542
64. Kankel MW, Hurlbut GD, Upadhyay G, Yajnik V, Yedvobnick B, et al. (2007) Investigating the genetic circuitry of mastermind in Drosophila, a notch signal effector. Genetics 177: 2493–2505. doi: 10.1534/genetics.107.080994 18073442
65. Rosin D, Schejter E, Volk T, Shilo BZ (2004) Apical accumulation of the Drosophila PDGF/VEGF receptor ligands provides a mechanism for triggering localized actin polymerization. Development 131: 1939–1948. doi: 10.1242/dev.01101 15056618
66. Cho NK, Keyes L, Johnson E, Heller J, Ryner L, et al. (2002) Developmental control of blood cell migration by the Drosophila VEGF pathway. Cell 108: 865–876. doi: 10.1016/S0092-8674(02)00676-1 11955438
67. Ishimaru S, Ueda R, Hinohara Y, Ohtani M, Hanafusa H (2004) PVR plays a critical role via JNK activation in thorax closure during Drosophila metamorphosis. EMBO Journal 23: 3984–3994. doi: 10.1038/sj.emboj.7600417 15457211
68. McDonald JA, Pinheiro EM, Montell DJ (2003) PVF1, a PDGF/VEGF homolog, is sufficient to guide border cells and interacts genetically with Taiman. Development 130: 3469–3478. doi: 10.1242/dev.00574 12810594
69. Wu Y, Brock AR, Wang Y, Fujitani K, Ueda R, et al. (2009) A blood-borne PDGF/VEGF-like ligand initiates wound-induced epidermal cell migration in Drosophila larvae. Current Biology 19: 1473–1477. doi: 10.1016/j.cub.2009.07.019 19646875
70. Vaduva G, Martin NC, Hopper AK (1997) Actin-binding verprolin is a polarity development protein required for the morphogenesis and function of the yeast actin cytoskeleton. J Cell Biol 139: 1821–1833. doi: 10.1083/jcb.139.7.1821 9412475
71. Jiang WG, Ye L, Patel G, Harding KG (2010) Expression of WAVEs, the WASP (Wiskott-Aldrich syndrome protein) family of verprolin homologous proteins in human wound tissues and the biological influence on human keratinocytes. Wound Repair Regen 18: 594–604. doi: 10.1111/j.1524-475X.2010.00630.x 20946142
72. Schafer DA, Cooper JA (1995) Control of actin assembly at filament ends. Annu Rev Cell Dev Biol 11: 497–518. doi: 10.1146/annurev.cb.11.110195.002433 8689567
73. Machesky LM, Cooper JA (1999) Cell motility. Bare bones of the cytoskeleton. Nature 401: 542–543.
74. Janody F, Treisman JE (2006) Actin capping protein alpha maintains vestigial-expressing cells within the Drosophila wing disc epithelium. Development 133: 3349–3357. doi: 10.1242/dev.02511 16887822
75. Ogienko AA, Karagodin DA, Lashina VV, Baiborodin SI, Omelina ES, et al. (2013) Capping protein beta is required for actin cytoskeleton organisation and cell migration during Drosophila oogenesis. Cell Biol Int 37: 149–159. doi: 10.1002/cbin.10025 23339103
76. Bretscher A (1981) Fimbrin is a cytoskeletal protein that crosslinks F-actin in vitro. Proc Natl Acad Sci U S A 78: 6849–6853. doi: 10.1073/pnas.78.11.6849 6947259
77. Wu JQ, Bahler J, Pringle JR (2001) Roles of a fimbrin and an alpha-actinin-like protein in fission yeast cell polarization and cytokinesis. Mol Biol Cell 12: 1061–1077. doi: 10.1091/mbc.12.4.1061 11294907
78. Dobie KW, Kennedy CD, Velasco VM, McGrath TL, Weko J, et al. (2001) Identification of chromosome inheritance modifiers in Drosophila melanogaster. Genetics 157: 1623–1637. 11290718
79. Sternlicht H, Farr GW, Sternlicht ML, Driscoll JK, Willison K, et al. (1993) The t-complex polypeptide 1 complex is a chaperonin for tubulin and actin in vivo. Proc Natl Acad Sci U S A 90: 9422–9426. doi: 10.1073/pnas.90.20.9422 8105476
80. Kubota H, Hynes G, Willison K (1995) The chaperonin containing t-complex polypeptide 1 (TCP-1). Multisubunit machinery assisting in protein folding and assembly in the eukaryotic cytosol. Eur J Biochem 230: 3–16.
81. Coghlin C, Carpenter B, Dundas SR, Lawrie LC, Telfer C, et al. (2006) Characterization and over-expression of chaperonin t-complex proteins in colorectal cancer. J Pathol 210: 351–357. doi: 10.1002/path.2056 16981251
82. Kitamura A, Kubota H, Pack CG, Matsumoto G, Hirayama S, et al. (2006) Cytosolic chaperonin prevents polyglutamine toxicity with altering the aggregation state. Nat Cell Biol 8: 1163–1170. doi: 10.1038/ncb1478 16980958
83. Spiess C, Miller EJ, McClellan AJ, Frydman J (2006) Identification of the TRiC/CCT substrate binding sites uncovers the function of subunit diversity in eukaryotic chaperonins. Mol Cell 24: 25–37. doi: 10.1016/j.molcel.2006.09.003 17018290
84. Satish L, Johnson S, Wang JH, Post JC, Ehrlich GD, et al. (2010) Chaperonin containing T-complex polypeptide subunit eta (CCT-eta) is a specific regulator of fibroblast motility and contractility. PLoS One 5: e10063. doi: 10.1371/journal.pone.0010063 20442790
85. Cole J, Tsou R., Wallace K., Gibran N., and Isik F. (2001) Early gene expression profile of human skin to injury using high-density cDNA microarrays. Wound Repair & Regeneration 9: 360–370. doi: 10.1046/j.1524-475x.2001.00360.x
86. Cooper L, Johnson C., Burslem F., and Martin P. (2005) Wound healing and inflammation genes revealed by array analysis of “macrophageless” PU.1 null mice. Genome Biol 6: R5. doi: 10.1186/gb-2004-6-1-r5 15642097
87. Lin G, Zhang X, Ren J, Pang Z, Wang C, et al. (2013) Integrin signaling is required for maintenance and proliferation of intestinal stem cells in Drosophila. Dev Biol 377: 177–187. doi: 10.1016/j.ydbio.2013.01.032 23410794
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Genetika Reprodukčná medicínaČlánok vyšiel v časopise
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