Large-scale identification of human genes implicated in epidermal barrier function

Genome Biology

Volumn 8, Issue 6, 2007, Pages

  Toulza, Eve ^a   Mattiuzzo, Nicolas R ^a   Galliano, Marie Florence ^a   Jonca, Nathalie ^a   Dossat, Carole ^b   Jacob, Daniel ^c   de Daruvar, Antoine ^c   Wincker, Patrick ^b   Serre, Guy ^a   Guerrin, Marina ^a  

^a CNRS   (France)

^b Genoscope   (France)

^c UNIVERSITÉ DE BORDEAUX   (France)

Author keywords

[No Author keywords available]

Indexed keywords

FILAGGRIN; LIPID; PROTEINASE; PROTEINASE INHIBITOR; TRANSCRIPTOME; TRIACYLGLYCEROL LIPASE;

ARTICLE; CHROMOSOME 10Q; CONTROLLED STUDY; EPIDERMIS; EXPRESSED SEQUENCE TAG; FRAMESHIFT MUTATION; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN GENOME; HUMAN TISSUE; KERATINOCYTE; LIPID METABOLISM; LIPID TRANSPORT; NUCLEOTIDE SEQUENCE; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SKIN FUNCTION; UNINDEXED SEQUENCE; AMINO ACID SEQUENCE; CELL CULTURE; CYTOLOGY; GENE EXPRESSION PROFILING; GENETICS; MOLECULAR GENETICS; PHYSIOLOGY; SKIN DISEASE;

AMINO ACID SEQUENCE; CELLS, CULTURED; EPIDERMIS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; KERATINOCYTES; MOLECULAR SEQUENCE DATA; SKIN DISEASES;

EID: 39549101237     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-6-r107     Document Type: Article

References (73)

1. Watt FM Celso CL Silva-Vargas V Epidermal stem cells: An update. Curr Opin Genet Dev 2006 16 518-524 10.1016/j.gde.2006.08.006 16919447
2. Park GT Lim SE Jang SI Morasso MI Suprabasin, a novel epidermal differentiation marker and potential cornified envelope precursor. J Biol Chem 2002 277 45195-45202 1283087 12228223 10.1074/jbc.M205380200
3. Oomizu S Sahuc F Asahina K Inamatsu M Matsuzaki T Sasaki M Obara M Yoshizato K Kdap, a novel gene associated with the stratification of the epithelium. Gene 2000 256 19-27 10.1016/S0378-1119(00)00357-7 11054531
4. Makino T Takaishi M Morohashi M Huh NH Hornerin, a novel profilaggrin-like protein and differentiation-specific marker isolated from mouse skin. J Biol Chem 2001 276 47445-47452 10.1074/jbc.M107512200 11572870
5. Lee WH Jang S Lee JS Lee Y Seo EY You KH Lee SC Nam KI Kim JM Kee SH Molecular cloning and expression of human keratinocyte proline-rich protein (hKPRP), an epidermal marker isolated from calcium-induced differentiating keratinocytes. J Invest Dermatol 2005 125 995-1000 10.1111/j.0022-202X.2005.23829.x 16297201
6. Kalinin AE Kajava AV Steinert PM Epithelial barrier function: Assembly and structural features of the cornified cell envelope. Bioessays 2002 24 789-800 10.1002/bies.10144 12210515
7. Elias PM Cullander C Mauro T Rassner U Komuves L Brown BE Menon GK The secretory granular cell: The outermost granular cell as a specialized secretory cell. J Investig Dermatol Symp Proc 1998 3 87-100 9734820
8. Guerrin M Simon M Montezin M Haftek M Vincent C Serre G Expression cloning of human corneodesmosin proves its identity with the product of the S gene and allows improved characterization of its processing during keratinocyte differentiation. J Biol Chem 1998 273 22640-22647 10.1074/ jbc.273.35.22640 9712893
9. Dias Neto E Correa RG Verjovski-Almeida S Briones MR Nagai MA da Silva W Jr Zago MA Bordin S Costa FF Goldman GH Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc Natl Acad Sci USA 2000 97 3491-3496 16267 10737800 10.1073/pnas.97.7.3491
10. Vandesompele J De Preter K Pattyn F Poppe B Van Roy N De Paepe A Speleman F Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002 3 RESEARCH0034 126239 12184808 10.1186/gb-2002-3-7-research0034
11. Bonnet-Duquennoy M Abaibou H Tailhardat M Lazou K Bosset S Le Varlet B Cleuziat P Kurfurst R Study of housekeeping gene expression in human keratinocytes using OLISAtrade mark, a long-oligonucleotide microarray and qRT-PCR. Eur J Dermatol 2006 16 136-140 16581563
12. Magnaldo T Fowlis D Darmon M Galectin-7, a marker of all types of stratified epithelia. Differentiation 1998 63 159-168 10.1046/ j.1432-0436.1998.6330159.x 9697310
13. Fisher C Angus B Rees J In-situ hybridization using digoxigenin-labelled probes in human skin. Br J Dermatol 1991 125 516-520 10.1111/ j.1365-2133.1991.tb14787.x 1760355
14. Sondell B Jonsson M Dyberg P Egelrud T In situ evidence that the population of Langerhans cells in normal human epidermis may be heterogeneous. Br J Dermatol 1997 136 687-693 10.1046/ j.1365-2133.1997.6571642.x 9205500
15. Matsui T Hayashi-Kisumi F Kinoshita Y Katahira S Morita K Miyachi Y Ono Y Imai T Tanigawa Y Komiya T Identification of novel keratinocyte-secreted peptides dermokine-alpha/-beta and a new stratified epithelium-secreted protein gene complex on human chromosome 19q13.1. Genomics 2004 84 384-397 10.1016/j.ygeno.2004.03.010 15234001
16. Moffatt P Salois P St-Amant N Gaumond MH Lanctot C Identification of a conserved cluster of skin-specific genes encoding secreted proteins. Gene 2004 334 123-131 10.1016/j.gene.2004.03.010 15256262
17. Toulza E Galliano MF Jonca N Gallinaro H Mechin MC Ishida-Yamamoto A Serre G Guerrin M The human dermokine gene: Description of novel isoforms with different tissue-specific expression and subcellular location. J Invest Dermatol 2006 126 503-506 10.1038/sj.jid.5700033 16374476
18. Kent WJ BLAT - the BLAST-like alignment tool. Genome Res 2002 12 656 664 187518 11932250 10.1101/gr.229202. Article published online before March 2002
19. UCSC Custom Track: ORESTES from Granular Keratinocytes of Human Epidermis http://genome.ucsc.edu/cgi-bin/hgTracks?org= human&hgt.customText=http://udear.cnrs.free.fr/orestes.txt
20. Brandner JM Kief S Wladykowski E Houdek P Moll I Tight junction proteins in the skin. Skin Pharmacol Physiol 2006 19 71-77 10.1159/000091973 16685145
21. Furuse M Hata M Furuse K Yoshida Y Haratake A Sugitani Y Noda T Kubo A Tsukita S Claudin-based tight junctions are crucial for the mammalian epidermal barrier: A lesson from claudin-1-deficient mice. J Cell Biol 2002 156 1099-1111 10.1083/jcb.200110122 11889141
22. Vinckenbosch N Dupanloup I Kaessmann H Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci USA 2006 103 3220-3225 1413932 16492757 10.1073/pnas.0511307103
23. Rogers MS Kobayashi T Pittelkow MR Strehler EE Human calmodulin-like protein is an epithelial-specific protein regulated during keratinocyte differentiation. Exp Cell Res 2001 267 216-224 10.1006/excr.2001.5254 11426940
24. The snoRNABase http://www-snorna.biotoul.fr/
25. Weber MJ Mammalian small nucleolar RNAs are mobile genetic elements. PLoS Genet 2006 2 e205 1687206 17154719 10.1371/journal.pgen.0020205
26. Smith CM Steitz JA Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5′-terminal oligopyrimidine gene family reveals common features of snoRNA host genes. Mol Cell Biol 1998 18 6897-6909 109273 9819378
27. Ji P Diederichs S Wang W Boing S Metzger R Schneider PM Tidow N Brandt B Buerger H Bulk E MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 2003 22 8031-8041 10.1038/sj.onc.1206928 12970751
28. Geirsson A Paliwal I Lynch RJ Bothwell AL Hammond GL Class II transactivator promoter activity is suppressed through regulation by a trophoblast noncoding RNA. Transplantation 2003 76 387-394 10.1097/ 01.TP.0000073612.04525.46 12883198
29. Zhang Y Tycko B Monoallelic expression of the human H19 gene. Nat Genet 1992 1 40-44 10.1038/ng0492-40 1363808
30. Thorvaldsen JL Duran KL Bartolomei MS Deletion of the H19 differentially methylated domain results in loss of imprinted expression of H19 and Igf2. Genes Dev 1998 12 3693-3702 317260 9851976
31. Blakytny R Jude EB Martin Gibson J Boulton AJ Ferguson MW Lack of insulin-like growth factor 1 (IGF1) in the basal keratinocyte layer of diabetic skin and diabetic foot ulcers. J Pathol 2000 190 589-594 10.1002/(SICI)1096-9896(200004)190:5<589::AID-PATH553>3.0.CO;2-T 10727985
32. Bennett WR Crew TE Slack JM Ward A Structural-proliferative units and organ growth: Effects of insulin-like growth factor 2 on the growth of colon and skin. Development 2003 130 1079-1088 10.1242/dev.00333 12571100
33. Katayama S Tomaru Y Kasukawa T Waki K Nakanishi M Nakamura M Nishida H Yap CC Suzuki M Kawai J Antisense transcription in the mammalian transcriptome. Science 2005 309 1564-1566 10.1126/science.1112009 16141073
34. Strausberg RL Feingold EA Grouse LH Derge JG Klausner RD Collins FS Wagner L Shenmen CM Schuler GD Altschul SF Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci USA 2002 99 16899-16903 139241 12477932 10.1073/ pnas.242603899
35. Kraut J Serine proteases: Structure and mechanism of catalysis. Annu Rev Biochem 1977 46 331-358 10.1146/annurev.bi.46.070177.001555 332063
36. Brzozowski AM Derewenda U Derewenda ZS Dodson GG Lawson DM Turkenburg JP Bjorkling F Huge-Jensen B Patkar SA Thim L A model for interfacial activation in lipases from the structure of a fungal lipase-inhibitor complex. Nature 1991 351 491-494 10.1038/351491a0 2046751
37. Smith TP Grosse WM Freking BA Roberts AJ Stone RT Casas E Wray JE White J Cho J Fahrenkrug SC Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res 2001 11 626-630 311058 11282978 10.1101/gr.170101
38. Hida K Wada J Eguchi J Zhang H Baba M Seida A Hashimoto I Okada T Yasuhara A Nakatsuka A Visceral adipose tissue-derived serine protease inhibitor: A unique insulin-sensitizing adipocytokine in obesity. Proc Natl Acad Sci USA 2005 102 10610-10615 1180799 16030142 10.1073/ pnas.0504703102
39. Singh G Lykke-Andersen J New insights into the formation of active nonsense-mediated decay complexes. Trends Biochem Sci 2003 28 464-466 10.1016/S0968-0004(03)00176-2 13678954
40. Matsufuji S Matsufuji T Miyazaki Y Murakami Y Atkins JF Gesteland RF Hayashi S Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme. Cell 1995 80 51-60 10.1016/0092-8674(95)90450-6 7813017
41. Hahn Y Lee B Identification of nine human-specific frameshift mutations by comparative analysis of the human and the chimpanzee genome sequences. Bioinformatics 2005 21 Suppl 1 i186-194 10.1093/ bioinformatics/bti1000 15961456
42. Wang X Grus WE Zhang J Gene losses during human origins. PLoS Biol 2006 4 e52 1361800 16464126 10.1371/journal.pbio.0040052
43. Winter H Langbein L Krawczak M Cooper DN Jave-Suarez LF Rogers MA Praetzel S Heidt PJ Schweizer J Human type I hair keratin pseudogene phihHaA has functional orthologs in the chimpanzee and gorilla: Evidence for recent inactivation of the human gene after the Pan-Homo divergence. Hum Genet 2001 108 37-42 10.1007/s004390000439 11214905
44. Hahn Y Lee B Human-specific nonsense mutations identified by genome sequence comparisons. Hum Genet 2006 119 169-178 10.1007/ s00439-005-0125-6 16395595
45. Marques AC Dupanloup I Vinckenbosch N Reymond A Kaessmann H Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 2005 3 e357 1251493 16201836 10.1371/journal.pbio.0030357
46. Zeeuwen PL Epidermal differentiation: The role of proteases and their inhibitors. Eur J Cell Biol 2004 83 761-773 10.1078/0171-9335-00388 15679120
47. Zeeuwen PL van Vlijmen-Willems IM Hendriks W Merkx GF Schalkwijk J A null mutation in the cystatin M/E gene of ichq mice causes juvenile lethality and defects in epidermal cornification. Hum Mol Genet 2002 11 2867-2875 10.1093/hmg/11.23.2867 12393798
48. Miyata T Inagi R Nangaku M Imasawa T Sato M Izuhara Y Suzuki D Yoshino A Onogi H Kimura M Overexpression of the serpin megsin induces progressive mesangial cell proliferation and expansion. J Clin Invest 2002 109 585-593 150894 11877466 10.1172/JCI200214336
49. Askew YS Pak SC Luke CJ Askew DJ Cataltepe S Mills DR Kato H Lehoczky J Dewar K Birren B SERPINB12 is a novel member of the human ov-serpin family that is widely expressed and inhibits trypsin-like serine proteinases. J Biol Chem 2001 276 49320-49330 10.1074/jbc.M108879200 11604408
50. Caubet C Jonca N Lopez F Esteve JP Simon M Serre G Homo-oligomerization of human corneodesmosin is mediated by its N-terminal glycine loop domain. J Invest Dermatol 2004 122 747-754 10.1111/ j.0022-202X.2004.22331.x 15086562
51. Grundmann U Romisch J Siebold B Bohn H Amann E Cloning and expression of a cDNA encoding human placental protein 11, a putative serine protease with diagnostic significance as a tumor marker. DNA Cell Biol 1990 9 243-250 2350438
52. Hagiwara K Kikuchi T Endo Y Huqun Usui K Takahashi M Shibata N Kusakabe T Xin H Hoshi S Mouse SWAM1 and SWAM2 are antibacterial proteins composed of a single whey acidic protein motif. J Immunol 2003 170 1973-1979 12574366
53. Cousin X Hotelier T Giles K Lievin P Toutant JP Chatonnet A The alpha/ beta fold family of proteins database and the cholinesterase gene server ESTHER. Nucleic Acids Res 1997 25 143-146 146416 9016525 10.1093/nar/ 25.1.143
54. Du H Witte DP Grabowski GA Tissue and cellular specific expression of murine lysosomal acid lipase mRNA and protein. J Lipid Res 1996 37 937-949 8725147
55. Anderson RA Sando GN Cloning and expression of cDNA encoding human lysosomal acid lipase/cholesteryl ester hydrolase. Similarities to gastric and lingual lipases. J Biol Chem 1991 266 22479-22484 1718995
56. Bodmer MW Angal S Yarranton GT Harris TJ Lyons A King DJ Pieroni G Riviere C Verger R Lowe PA Molecular cloning of a human gastric lipase and expression of the enzyme in yeast. Biochim Biophys Acta 1987 909 237-244 3304425
57. Ohman H Vahlquist A In vivo studies concerning a pH gradient in human stratum corneum and upper epidermis. Acta Derm Venereol 1994 74 375-379 7817676
58. Hanson KM Behne MJ Barry NP Mauro TM Gratton E Clegg RM Two-photon fluorescence lifetime imaging of the skin stratum corneum pH gradient. Biophys J 2002 83 1682-1690 1302264 12202391
59. Fluhr JW Mao-Qiang M Brown BE Wertz PW Crumrine D Sundberg JP Feingold KR Elias PM Glycerol regulates stratum corneum hydration in sebaceous gland deficient (asebia) mice. J Invest Dermatol 2003 120 728-737 10.1046/j.1523-1747.2003.12134.x 12713573
60. Norlen L Nicander I Lundh Rozell B Ollmar S Forslind B Inter- and intra-individual differences in human stratum corneum lipid content related to physical parameters of skin barrier function in vivo. J Invest Dermatol 1999 112 72-77 10.1046/j.1523-1747.1999.00481.x 9886267
61. Menon GK Grayson S Elias PM Cytochemical and biochemical localization of lipase and sphingomyelinase activity in mammalian epidermis. J Invest Dermatol 1986 86 591-597 10.1111/1523-1747.ep12355263 3018090
62. Lefevre C Jobard F Caux F Bouadjar B Karaduman A Heilig R Lakhdar H Wollenberg A Verret JL Weissenbach J Mutations in CGI-58, the gene encoding a new protein of the esterase/lipase/thioesterase subfamily, in Chanarin-Dorfman syndrome. Am J Hum Genet 2001 69 1002-1012 1274347 11590543 10.1086/324121
63. Kazantseva A Goltsov A Zinchenko R Grigorenko AP Abrukova AV Moliaka YK Kirillov AG Guo Z Lyle S Ginter EK Human hair growth deficiency is linked to a genetic defect in the phospholipase gene LIPH. Science 2006 314 982-985 10.1126/science.1133276 17095700
64. Liu Z Yang X Tan F Cullion K Thiele CJ Molecular cloning and characterization of human Castor, a novel human gene upregulated during cell differentiation. Biochem Biophys Res Commun 2006 344 834-844 10.1016/j.bbrc.2006.03.207 16631614
65. Olson MV When less is more: Gene loss as an engine of evolutionary change. Am J Hum Genet 1999 64 18-23 1377697 9915938 10.1086/302219
66. Leerkes MR Caballero OL Mackay A Torloni H O'Hare MJ Simpson AJ de Souza SJ In silico comparison of the transcriptomederived from purified normal breast cells and breast tumor cell lines reveals candidate upregulated genes in breast tumor cells. Genomics 2002 79 257-265 10.1006/ geno.2002.6691 11829496
67. RepeatMasker Open-3.0 http://www.repeatmasker.org
68. PHRAP Software http://www.phrap.org/
69. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997 25 3389-3402 146917 9254694 10.1093/nar/ 25.17.3389
70. Rozen S Skaletsky H Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000 132 365-386 10547847
71. Corpet F Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 1988 16 10881-10890 338945 2849754 10.1093/nar/ 16.22.10881
72. TreeTop: Phylogenetic Tree Prediction http://www.genebee.msu.su/services/ phtree_reduced.html
73. Blanchette M Kent WJ Riemer C Elnitski L Smit AF Roskin KM Baertsch R Rosenbloom K Clawson H Green ED Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004 14 708-715 383317 15060014 10.1101/gr.1933104