Proteomics analysis of tissue samples from patients with squamous cell carcinoma of the penis and positive to human papillomavirus

Koifman, Leandro; Ornellas, Paulo; Ornellas, Antonio Augusto; Pereira, Denise de Abreu; Zingali, Benedeta Russolina; Cavalcanti, Silvia Maria Baeta; Afonso, Larissa Alves; Sandim, Vanessa; Alves, Gilda

doi:10.1590/S1677-5538.IBJU.2014.0051

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Original Article • Int. braz j urol. 41 (4) • Jul-Aug 2015 • https://doi.org/10.1590/S1677-5538.IBJU.2014.0051 copy

Proteomics analysis of tissue samples from patients with squamous cell carcinoma of the penis and positive to human papillomavirus

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT

Purpose:

The aim of this study was to identify possible protein biomarkers and/or candidates for therapeutic targets in tissues of patients with SCCP, infected by HPV, applying one dimensional electrophoresis (1DE), followed by direct mass spectrometry (MS) analysis.

Materials and Methods:

Tissues from 10 HPV positive patients with SCCP and from 10 patients with HPV negative non-tumorous penile foreskins were analyzed applying 1D electrophoresis, followed by analysis with direct mass spectrometry (MS).

Results:

Sixty-three different proteins were identified in the first group and 50 in the second group. Recognition was possible for 28 proteins exclusively detected in Group 1 and 21 proteins presented only in Group 2.

Conclusion:

Some proteins in the first group are directly involved in the development of other types of cancer, and therefore, suitable for analysis. Complement C3 protein is a strong candidate for evaluating SCCP patients.

Key words:
Carcinoma; Squamous Cell; Penis; Human papillomavirus

Pts	Histology	Grade	Stage TNM	HPV type	Surgery
1	Squamous cell carcinoma	G2	T4N2Mx	MY-/16+	Total Amputation + Bilateral RIL
2	Squamous cell carcinoma	G1	T2N3Mx	MY-/18+	Partial Amputation + Bilateral RIL
3	Squamous cell carcinoma	G2	T2N0Mx	16+;45+	Partial Amputation + Bilateral RIL
4	Squamous cell carcinoma	G2	T2N0Mx	MY-/18+	Partial Amputation + Bilateral RIL
5	Squamous cell carcinoma	G1	T1N1Mx	MY-/45+	Partial Amputation + Bilateral RIL
6	Squamous cell carcinoma	G2	T1N0Mx	45+	Partial Amputation + Bilateral RIL
7	Squamous cell carcinoma	G1	T2N0Mx	MY-/16+ 45+	Partial Amputation + Bilateral RIL
8	Squamous cell carcinoma	G2	T2N1Mx	MY+/45+	Partial Amputation + Bilateral RIL
9	Squamous cell carcinoma	G2	T2N1Mx	MY+/16+	Partial Amputation + Bilateral RIL
10	Squamous cell carcinoma	G2	T2N0Mx	MY-/45+	Partial Amputation + Bilateral RIL

Gel Slice	NCBI ID	Proteins	Score	Representative Peptides	KEGG	Function	Cell Compartment
T1	gi\|179212	Na+ K+ ATPase alpha subunit	41	R.SPDFTNENPLETR.N	hsa:476	ATP biosynthesis	Cell membrane
T2;3	gi\|189036	Nonmuscle myosin heavy chain (Myosin 9)	78	K.ALELDSNLYR.I K.HSQAVEELAEQLEQTKR.V	hsa:4627	Cell communication	Cytosol
T2	gi\|1296662	Plectin	74	R.SQVEEELFSVR.V K.VLALPEPSPAAPTLR.S	hsa:5339	Apoptosis	Cytosol, cytoskeletal
T2	gi\|93141049	Collagen alpha-1 (XII) chain short isoform precursor	60	K.ALALGALQNIR.Y R.WYSPVDGTRPSESIVVPGNTR.M	hsa:1303	Cell adhesion	Extracellular matrix
T5	gi\|4507677	Endoplasmin	44	K.SILFVPTSAPR.G	hsa:7184	Proteins processing	Cytosol
T6	gi\|223170	Fibrinogen gamma	58	K.EGFGHLSPTGTTEFWLGNEK.I K.MLEEIMKYEASILTHDSSIR.Y K.AIQLTYNPDESSKPNMIDAATLK.S	hsa:2266	Blood coagulation	Secreted
T9	gi\|5729877	Heat Shock cognate 71-kDa protein isoform 1	41	K.DAGTIAGLNVLR.I(U)	hsa:3312	Stress response, transcription regulation	Cytosol, nucleus, cell surface
T11	gi\|2982019	Chain B, Fab Fragment of engineered Human Monoclonal Antibody A5b7	47	K.GPSVFPLAPCSR.S/ R.STSESTAALGCLVK.D/ E.VQLLESGGGLVQPGGSLR.L	Unknown	Cell defense	Secreted
T11;12	gi\|178375	Aldehyde dehydrogenase	44	K.LPEWAADEPVEK.T/ R.SLEEAIQFINQR.E	hsa:218	Glycolysis, metabolism of amino acids and xenobiotics	Cytosol
T13	gi\|4503571	Alpha-enolase isoform 1		R.GNPTVEVDLFTSK.G/ R.YISPDQLADLYK.S/ K.WIGMDVAASEFFR.S + Oxidation (M) / K.VNQIGSVTESLQACK.L / K.YNQLLRIEEELGSK.A/	hsa:2023	Glicolysis; gliconeogenese	Cytosol
			90	K.LAMQEFMILPVGAANFR.E + 2 Oxidation (M) /R.EIFDSRGNPTVEVDLFTSK.G/ K.DATNVGDEGGFAPNILENKEGLELLK.T
T13	gi\|1710248	Protein disulfide isomerase-related protein 5	55	R.TGEAIVDAALSALR.Q/ K.LAAVDATVNQVLASR.Y	hsa:10130	Proteins processing	Endoplasmatic reticulum
T13	gi\|31170	Chain A, Crystal Structure Of Human Beta Enolase Enob	44	K.VNQIGSVTESIQACK.L	hsa:2027	Glicolysis	Cytosol, fosfopiruvat hydratase complex
T13	gi\|40068518	6-phosphogluconate dehydrogenase, decarboxylating	42	K.IISYAQGFMLLR.Q + Oxidation (M) / K.GILFVGSGVSGGEEGAR.Y	hsa:5226	Pentose pathways	Cytosol
T14	gi\|4505763	Phosphoglycerate kinase 1	39	K.ITLPVDFVTADKFDENAK.T	hsa:5230	Glicolysis	Cytosol
T14	gi\|306882	Haptoglobin precursor	36	K.VTSIQDWVQK.T/ K.SPVGVQPILNEHTFCAGMSK.Y + Oxidation (M)	hsa:3240	Defense	Secreted
T15	gi\|35222	70-kDa heat shock protein	43	R.TTPSYVAFTDTER.L (U)	hsa:3312	Regulation of cell cycle; cellular membrane organization	Cytosol; plasma membrane
T16	gi\|63252913	Macrophage-capping protein	44	R.QAALQVAEGFISR.M	hsa:822	Actin filament organization	Cytosol
T17	gi\|5174391	Alcohol dehydrogenase [NADP+]	44	K.GLVQALGLSNFNSR.Q/ R.GLEVTAYSPLGSSDR.A	hsa:10327	Glicolysis, glicerolipids metabolism	Cytosol
T17	gi\|31397	Fibronectin precursor	40	R.VPGTSTSATLTGLTR.G	hsa:2335	Angiogenesis, cell adhesion, platelet activation and degranulation	Secreted, extracellular matrix
T18	gi\|31645	Glyceraldehyde- 3-phosphate dehydrogenase	46	R.GALQNIIPASTGAAK.A/ R.VPTANVSVVDLTCR.L/ K.LISWYDNEFGYSNR.V/ K.LTGMAFRVPTANVSVVDLTCR.L + Oxidation (M) / K.IKWGDAGAEYVVESTGVFTTMEK.A + Oxidation (M) / K.VIHDNFGIVEGLMTTVHAITATQK.T + Oxidation (M)	hsa:2597	Glycolysis	Cytosol, plasma membrane
T19;20	gi\|809185	Chain A, The Effect Of Metal Binding On The Structure Of Annexin V And Implications For Membrane Binding	52	RSEIDLFNIRK/ KGLGTDEESILTLLTSRS/ KWGTDEEKFITIFGTRS/ RGTVTDFPGFDERADAETLRK	hsa:308	Blood coagulation	Cytosol
T19	gi\|2906146	Malate dehydrogenase precursor	46	K.IFGVTTLDIVR.A/ K.VDFPQDQLTALTGR.I	hsa:4191	Citric acid cycle	Mitochondria
T19	gi\|4826643	Annexin A3	37	K.MLISILTER.S +Oxidation (M)/ K.GAGTNEDALIEILTTR.T	hsa:306	Defense response	Phagocytic vesicle
T19	gi\|4929769	Glyoxalase domain-containing protein 4 (CGI-150 protein)	36	K.ILTPLVSLDTPGK.A(U)	hsa:51031	Unknown	Mitochondria
T20	gi\|4502599	Carbonyl reductase [NADPH] 1	46	R.LFSGDVVLTAR.D/ R.VVNVSSIMSVR.A/ R.GQAAVQQLQAEGLSPR.F/ K.VADPTPFHIQAEVTMK.T + Oxidation	hsa:873	Lipid metabolism -arachidonic acid	Cytosol
T23	gi\|9844110	cAMP-specific phosphodiesterase 4D	42	K.LSPVISPR.N	hsa:5144	Smooth muscle contraction; regulation of receptor activity	Cytosol
T24	gi\|2204207	Glutathione S-transferase	75	M.PPYTVVYFPVR.G -.MPPYTVVYFPVR.G + Oxidation (M) M.PPYTVVYFPVRGR.C K.EEVVTVETWQEGSLK.A K.FQDGDLTLYQSNTILR.H K.ALPGQLKPFETLLSQNQGGK.T K.YISLIYTNYEAGKDDYVK.A	hsa:2940	Amino acids metabolism	Cytosol
T26	gi\|181250	Cyclophilin	20	K.TVDNFVALATGEK.G	hsa:5480	Signal transduction	Cytosol

Gel Slice	NCBI ID	Proteins	Score	Representative Peptides	KEGG	Function	Cell Compartment
C1	gi\|78101267	Chain A, Human Complement Component C3	57	K.TIYTPGSTVLYR.I R.IPIEDGSGEVVLSR.K R.LVAYYTLIGASGQR.E	hsa:718	Inflammatory response; innate immunity; lipid metabolism	Secreted
C2	gi\|28243	Filamin A	49	R.IANLQTDLSDGLR.L R.SAGQGEVLVYVEDPAGHQEEAK.V K.LDVQFSGLTK.G K.SPFSVAVSPSLDLSK.I R.EGPYSISVLYGDEEVPR.S R.FGGEHVPNSPFQVTALAGDQPSVQPPLR.S	hsa:2316	Actin coupler	Cytosol
C3	gi\|2104553	Myosin heavy chain (MHY11)(5′partial)	59	K.HAQAVEELTEQLEQFKR.A R.ALEEALEAKEELER.T K.IAQLEEQVEQEAREK.Q	hsa:4629	Vascular muscle contraction; cell communication	Extracellular matrix
C7	gi\|34228	Prelamin-A/C isoform 1 precursor; lamin A protein; progerin	56	R.VAVEEVDEEGKFVR.L	hsa:4000	Intermediate filament	Nucleus
C7	gi\|386758	GRP78 (Glucose-regulated protein 78) precursor	45	R.ITPSYVAFTPEGER.L R.IINEPTAAAIAYGLDKR.E	hsa:3309	Anti-apoptosis	Endoplasmic reticulum
C7	gi\|23200154	Chain A, NMR Structures Of The C-Terminal Globular Domain Of Human Lamin AC	43	R.VAVEEVDEEGKFVR.L	hsa:4000	Structural molecule activity	Nucleus
C8	gi\|762885	Plakoglobin	72	K.SAIVHLINYQDDAELATR.A R.ALMGSPQLVAAVVR.T Oxidation (M) R.LVQNCLWTLR.N R.NEGTATYAAAVLFR.I	hsa:3728	Cell adhesion, cell migration	Cytosol; plasmatic membrane
C8	gi\|642534	Lumican	42	K.SLEYLDLSFNQIAR.L	hsa:4060	Collagen fibrils organization	Extracellular matrix
C8	gi\|110590597	Chain A, Apo-Human Serum Transferrin (Non-Glycosylated)	36	K.FYLGYEYVTAIR.N	hsa:7018	Mineral absorption	Secreted
C10	gi\|35505	Pyruvate kinase	39	R.TATESFASDPILYRPVAVALDTKGPEIR.T R.EAEAAIYHLQLFEELRR.L	hsa:5315	Glycolysis	Cytosol; plasmatic membrane
C11;13; 15; 16	gi\|3411130	Mutant Desmin	48	R.FLEQQNAALAAEVNR.L	hsa:1674	Cytoskeleton structural protein activity	Intermediate filament C
C13	gi\|340219	Vimentin	60	K.ILLAELEQLK.G K.ILLAELEQLKGQGK.S K.LQEEMLQREEAENTLQSFR.Q Oxidation (M) R.KVESLQEEIAFLK.K R.QVQSLTCEVDALKGTNESLER.Q R.EYQDLLNVK.M K.MALDIEIATYR.K Oxidation (M) R.ISLPLPNFSSLNLR.E	hsa:7431	Apoptosis; cell mobility	Cytosol
C13	gi\|704416	Elongation factor Tu	45	K.LLDAVDTYIPVPAR.D	hsa:7284	Oxidative phosphorylation	Mitochondria
C15	gi\|34234	Laminin-binding protein	75	R.AIVAIENPADVSVISSR.N R.FTPGTFTNQIQAAFREPR.L	hsa:3921	Ribosome	Cytosol
C16	gi\|47519616	Tropomyosin beta chain isoform 2	73	R.IQLVEEELDR.A R.IQLVEEELDRAQER.L R.LATALQKLEEAEK.A	hsa:7169	Muscle contraction	Cytosol
C17	gi\|31645	Glyceraldehyde-3-phosphate dehydrogenase	72	K.VIHDNFGIVEGLMTTVHAITATQK.T Oxidation (M) R.DGRGALQNIIPASTGAAK.A R.GALQNIIPASTGAAK.A R.VPTANVSVVDLTCR.L K.LISWYDNEFGYSNR.V	hsa:2597	Glycolysis	Cytosol; plasmatic membrane
C19	gi\|4505773	Prohibitin	91	R.IFTSIGEDYDER.V R.FDAGELITQR.E	hsa:5245	DNA synthesis	Mitochondrial membrane
C19	gi\|66473265	Beta globin chain	50	K.VNVDEVGGEALGR.L R.LLVVYPWTKR.F	hsa:5245	Oxygen transport	Hemoglobin
C21	gi\|494066	Chain A, Three- Dimensional Structure Of Class Pi Glutathione S-Transferase From Human Placenta In Complex With S-Hexylglutathione At2.8 Angstroms Resolution	36	.PPYTVVYFPVRGR.C K.FQDGDLTLYQSNTILR.H	hsa:2940	Amino acids metabolism	Cytosol

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[1] Correspondence address: Antonio Augusto Ornellas, MD, PhD Instituto Nacional de Câncer - Department of Urology Praça da Cruz Vermelha 23 Centro Rio de Janeiro, RJ, 20230-130, Brazil E-mail: ornellasa@hotmail.com