title: Large-scale proteomics differentiates cholesteatoma from surrounding tissues and identifies novel proteins related to the pathogenesis.
abstract: Cholesteatoma is the growth of keratinizing squamous epithelium in the middle ear. It is associated with severe complications and has a poorly understood etiopathogenesis. Here, we present the results from extensive bioinformatics analyses of the first large-scale proteomic investigation of cholesteatoma. The purpose of this study was to take an unbiased approach to identifying alterations in protein expression and in biological processes, in order to explain the characteristic phenotype of this skin-derived tumor. Five different human tissue types (cholesteatoma, neck of cholesteatoma, tympanic membrane, external auditory canal skin, and middle ear mucosa) were analyzed. More than 2,400 unique proteins were identified using nanoLC-MS/MS based proteomics (data deposited to the ProteomeXchange), and 295 proteins were found to be differentially regulated in cholesteatoma. Validation analyses were performed by SRM mass spectrometry. Proteins found to be up- or down-regulated in cholesteatoma were analyzed using Ingenuity Pathway Analysis and clustered into functional groups, for which activation state and associations to disease processes were predicted. Cholesteatoma contained high levels of pro-inflammatory S100 proteins, such as S100A7A and S100A7. Several proteases, such as ELANE, were up-regulated, whereas extracellular matrix proteins, such as COL18A1 and NID2, were under-represented. This may lead to alterations in integrity and differentiation of the tissue (as suggested by the up-regulation of KRT4 in the cholesteatoma). The presented data on the differential protein composition in cholesteatoma corroborate previous studies, highlight novel protein functionalities involved in the pathogenesis, and identify new areas for targeted research that hold therapeutic potential for the disease.
authors.affiliation: Department of Otorhinolaryngology, Head and Neck Surgery, Aarhus University Hospital, Aarhus, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Britze
authors.affiliation: Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
authors.forename: Rune Isak Dupont
authors.initials: RI
authors.lastname: Birkler
authors.affiliation: Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
authors.forename: Niels
authors.initials: N
authors.lastname: Gregersen
authors.affiliation: Department of Otorhinolaryngology, Head and Neck Surgery, Aarhus University Hospital, Aarhus, Denmark.
authors.forename: Therese
authors.initials: T
authors.lastname: Ovesen
authors.affiliation: Research Unit for Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
authors.forename: Johan
authors.initials: J
authors.lastname: Palmfeldt
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D002648:Child; D002781:Cholesteatoma / Q000209:etiology* / Q000378:metabolism*; D019295:Computational Biology; D003238:Connective Tissue / Q000378:metabolism; D015536:Down-Regulation; D005260:Female; D006801:Humans; D007633:Keratins / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D015854:Up-Regulation; D055815:Young Adult
chemical_list: D020543:Proteome; D007633:Keratins
references.citation: Dan Med Bull. 2010 Oct;57(10):A4186
references.pmid: 21040679
references.citation: Laryngoscope. 2003 May;113(5):808-14
references.pmid: 12792315
references.citation: J Proteome Res. 2011 Apr 1;10(4):1794-805
references.pmid: 21254760
references.citation: Acta Otorhinolaryngol Ital. 2009 Aug;29(4):197-202
references.pmid: 20161877
references.citation: Oncol Rep. 2011 Oct;26(4):813-23
references.pmid: 21725608
references.citation: Eur Arch Otorhinolaryngol. 2006 Jul;263(7):603-7
references.pmid: 16538507
references.citation: Acta Otolaryngol. 2009 Oct;129(10):1067-71
references.pmid: 19707901
references.citation: J Biol Chem. 2006 Mar 10;281(10):6124-9
references.pmid: 16377621
references.citation: BMC Cancer. 2012 Jun 22;12:266
references.pmid: 22727333
references.citation: Acta Otolaryngol. 1993 May;113(3):364-8
references.pmid: 7685977
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9
references.pmid: 23203882
references.citation: FASEB J. 2011 May;25(5):1567-76
references.pmid: 21282207
references.citation: Laryngoscope. 2012 Dec;122(12):2818-23
references.pmid: 23239141
references.citation: Eur Arch Otorhinolaryngol. 2013 Mar;270(4):1203-8
references.pmid: 22711004
references.citation: Acta Otolaryngol. 1999;119(5):568-72
references.pmid: 10478597
references.citation: Am J Physiol Renal Physiol. 2010 Mar;298(3):F662-71
references.pmid: 20007347
references.citation: J Lipid Res. 2003 Jul;44(7):1268-78
references.pmid: 12730293
references.citation: Otol Neurotol. 2011 Apr;32(3):504-7
references.pmid: 21307812
references.citation: Otolaryngol Head Neck Surg. 2011 Oct;145(4):628-34
references.pmid: 21593461
references.citation: Laryngoscope. 1995 Nov;105(11):1232-7
references.pmid: 7475882
references.citation: Acta Otolaryngol. 2006 Jul;126(7):691-7
references.pmid: 16803706
references.citation: Acta Otolaryngol. 1994 Mar;114(2):188-92
references.pmid: 7515549
references.citation: J Immunol. 2011 May 1;186(9):5435-42
references.pmid: 21441456
references.citation: J Otolaryngol. 1990 Apr;19(2):83-5
references.pmid: 2348510
references.citation: Acta Otolaryngol. 2014 Jan;134(1):41-50
references.pmid: 24256045
references.citation: Mol Cell Biol. 2002 Oct;22(19):6820-30
references.pmid: 12215539
references.citation: Eur Arch Otorhinolaryngol. 2004 Jan;261(1):6-24
references.pmid: 12835944
references.citation: J Biol Chem. 2005 Feb 11;280(6):4696-703
references.pmid: 15507446
references.citation: Mol Cancer. 2012 Sep 28;11:74
references.pmid: 23021083
references.citation: Ann Otol Rhinol Laryngol. 1992 Nov;101(11):931-8
references.pmid: 1280020
references.citation: J Invest Dermatol. 2004 Jul;123(1):23-33
references.pmid: 15191538
references.citation: Acta Otolaryngol. 1978 Jul-Aug;86(1-2):71-88
references.pmid: 358734
references.citation: Cancer Lett. 2009 May 8;277(1):101-7
references.pmid: 19136201
references.citation: Acta Otolaryngol. 2004 Sep;124(7):783-8
references.pmid: 15370560
references.citation: Nat Biotechnol. 2008 Dec;26(12):1367-72
references.pmid: 19029910
references.citation: Histochem Cell Biol. 2012 Aug;138(2):251-69
references.pmid: 22481617
references.citation: Histol Histopathol. 2007 Jan;22(1):37-42
references.pmid: 17128409
references.citation: Arch Otolaryngol Head Neck Surg. 1993 Mar;119(3):272-5
references.pmid: 8435164
references.citation: Mol Cancer. 2007 Feb 28;6:17
references.pmid: 17328794
references.citation: Eur Arch Otorhinolaryngol. 1996;253(1-2):21-4
references.pmid: 8932424
references.citation: Otol Neurotol. 2012 Feb;33(2):177-83
references.pmid: 22246384
references.citation: Mol Cell Proteomics. 2010 Jul;9(7):1499-513
references.pmid: 20332082
references.citation: Laryngoscope. 2006 Jul;116(7):1180-4
references.pmid: 16826057
references.citation: Brief Funct Genomic Proteomic. 2006 Dec;5(4):261-72
references.pmid: 16772273
references.citation: Ann Otol Rhinol Laryngol. 1996 Oct;105(10):804-10
references.pmid: 8865776
references.citation: Acta Otolaryngol. 1995 Nov;115(6):804-10
references.pmid: 8749203
references.citation: Med Sci Monit. 2006 Aug;12(8):CR337-40
references.pmid: 16865065
references.citation: J Am Coll Cardiol. 2012 Aug 21;60(8):775-85
references.pmid: 22818064
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5
references.pmid: 22102590
references.citation: Arch Otolaryngol Head Neck Surg. 1994 Oct;120(10):1102-11
references.pmid: 7522469
references.citation: Laryngorhinootologie. 1995 Jan;74(1):33-5
references.pmid: 7888019
references.citation: J Laryngol Otol. 2010 Jun;124(6):587-93
references.pmid: 20156369
references.citation: Am J Otol. 2000 Nov;21(6):786-92
references.pmid: 11078064
references.citation: Exp Mol Pathol. 2010 Apr;88(2):316-23
references.pmid: 20045407
references.citation: PLoS One. 2011;6(10):e26634
references.pmid: 22046318
references.citation: Eur Arch Otorhinolaryngol. 2006 May;263(5):409-13
references.pmid: 16378223
references.citation: J Invest Dermatol. 2010 May;130(5):1355-64
references.pmid: 20107483
references.citation: Endocr Rev. 2005 Apr;26(2):171-202
references.pmid: 15561802
references.citation: Proc Natl Acad Sci U S A. 2005 Apr 26;102(17):6021-6
references.pmid: 15855271
references.citation: Histopathology. 2003 Apr;42(4):387-94
references.pmid: 12653951
references.citation: PLoS One. 2012;7(12):e52718
references.pmid: 23285167
references.citation: Otol Neurotol. 2007 Jun;28(4):504-9
references.pmid: 17287660
references.citation: Free Radic Biol Med. 2009 Feb 15;46(4):443-53
references.pmid: 19028565
references.citation: Pharmacol Rev. 2010 Dec;62(4):726-59
references.pmid: 21079042
references.citation: Arch Otolaryngol Head Neck Surg. 2002 Oct;128(10):1129-33
references.pmid: 12365883
references.citation: Histochem Cell Biol. 2008 Jun;129(6):705-33
references.pmid: 18461349
references.citation: Laryngoscope. 2013 Oct;123 Suppl S5:S1-21
references.pmid: 23670528
references.citation: ORL J Otorhinolaryngol Relat Spec. 2010;72(6):325-31
references.pmid: 20847582
references.citation: Biochem Soc Trans. 2007 Aug;35(Pt 4):669-71
references.pmid: 17635117
references.citation: Exp Dermatol. 2006 Apr;15(4):300-7
references.pmid: 16512877
references.citation: J Membr Biol. 2013 Jul;246(7):519-24
references.pmid: 23756625
references.citation: Cancer Cell. 2012 Nov 13;22(5):615-30
references.pmid: 23153535
references.citation: Am J Respir Crit Care Med. 2008 Sep 15;178(6):592-604
references.pmid: 18556627
references.citation: J Invest Dermatol. 2012 May;132(5):1416-24
references.pmid: 22402441
references.citation: Arch Otolaryngol Head Neck Surg. 1996 Aug;122(8):825-32
references.pmid: 8703383
references.citation: Am J Otol. 2000 Nov;21(6):793-8
references.pmid: 11078065
references.citation: Eur Arch Otorhinolaryngol. 2007 Oct;264(10):1137-43
references.pmid: 17534638
references.citation: Eur Arch Otorhinolaryngol. 2005 Sep;262(9):731-6
references.pmid: 15754169
references.citation: ORL J Otorhinolaryngol Relat Spec. 1996 Jan-Feb;58(1):23-6
references.pmid: 8718533
references.citation: Int J Mol Sci. 2013 Jul 11;14(7):14439-59
references.pmid: 23852020
references.citation: Neoplasma. 2012;59(4):409-15
references.pmid: 22489696
references.citation: Acta Otolaryngol. 2003 Apr;123(3):377-82
references.pmid: 12737294