OR Oncology Reports 1021-335X 1791-2431 D.A. Spandidos 10.3892/or.2013.2612 or-30-04-1609 Articles Analysis of protein expression regulated by lumican in PANC-1 cells using shotgun proteomics YAMAMOTOTETSUSHI KUDOMITSUHIRO PENGWEI-XIA NAITOZENYA Departments of Pathology and Integrative Oncological Pathology, Nippon Medical School, Bunkyo-ku, Tokyo 113-8602, Japan Correspondence to: Professor Zenya Naito, Departments of Pathology and Integrative Oncological Pathology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan, E-mail: naito@nms.ac.jp 10 2013 11 07 2013 30 4 1609 1621 19 03 2013 30 05 2013 Copyright © 2013, Spandidos Publications 2013 This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.

Lumican, a member of the class II small leucine-rich proteoglycan family, regulates the assembly and diameter of collagen fibers in the extracellular matrix of various tissues. We previously reported that lumican expression in the stromal tissues of pancreatic ductal adenocarcinoma (PDAC) correlates with tumor invasion, and tends to correlate with poor prognosis. Lumican stimulates growth and inhibits the invasion of a PDAC cell line. In the present study, we performed a global shotgun proteomic analysis using lumican-overexpressing PANC-1 cells and lumican downregulated PANC-1 cells to identify candidate proteins that are regulated by lumican and related to cell growth and invasion in PDAC cells. A total of 448 proteins were identified from lumican-overexpressing PANC-1 and control cells. Additionally, 451 proteins were identified from lumican-downregulated PANC-1 cells and control cells. As a result of semi-quantification based on spectral counting, 174 differentially expressed proteins were identified by lumican upregulation, and 143 differentially expressed proteins were identified by lumican downregulation. The expression levels of 24 proteins, including apoptosis- and invasion-related proteins correlated with lumican expression levels. It is likely that the expression of these proteins is regulated by lumican, and that they are involved in apoptosis and invasion in PDAC. These findings suggest that lumican may be involved in cell growth and invasion through the regulation of these 24 proteins expressed in PDAC.

 lumican proteoglycan proteomic analysis pancreatic cancer Introduction

Lumican is a member of the class II small leucine-rich proteoglycan (SLRP) family. Members of this family have relatively small molecular sizes, with core proteins of approximately 40 kDa, and possess 6–10 leucine-rich repeat units in the core protein (1,2). Amino acid sequencing indicates that lumican has 4 potential sites for N-linked keratan sulfate (KS) or oligosaccharides (3,4). Therefore, lumican includes a core protein, glycoprotein and proteoglycan forms due to glycosylation (5). Lumican is a secreted collagen-binding extracellular matrix protein of the cornea, dermis and tendon stroma, arterial wall, and intestinal submucosa (6–9). Corneal opacity, as well as skin and tendon fragility due to disorganized and loosely packed collagen fibers in lumican-null mice suggest that lumican plays an important role in collagen fibrillogenesis (10,11).

Lumican was first reported as one of the major KS proteoglycans in the chicken cornea (12). In addition to the cornea, lumican expression has been reported in various human tissues, including malignant tumor tissues (5,13–27). Among the clinicopathological characteristics of pancreatic ductal adenocarcinoma (PDAC), the localization of lumican in the stromal tissue adjacent to cancer cells correlates with advanced cancer stage, retroperitoneal and duodenal invasion, and residual tumor, and tends to correlate with shorter survival (21). These reports suggest that lumican localized in the stromal tissue is secreted from cancer cells and affects cancer cells through an autocrine and paracrine mechanism. We previously reported that PANC-1 cells, one of the PDAC cell lines, secrete only 70-kDa glycosylated lumican into the extracellular space. We also demonstrated that the secreted lumican stimulated cell growth through ERK activation and inhibited cell invasion and matrix metalloproteinase (MMP)-9 activation using lumican-overexpressing PANC-1 cells and lumican-downregulated PANC-1 cells (28). However, the mechanism of how lumican affects cell growth and invasion remains unclear.

In the present study, we performed shotgun liquid chromatography (LC)/mass spectrometry (MS)-based global proteomic analysis using protein from lumican-overexpressing PANC-1 cells and lumican-downregulated PANC-1 cells to examine how lumican regulates cell growth and invasion in PDAC cells. We identified 24 candidate proteins that may play an important role in cell growth and invasion and could be regulated by lumican.

 Materials and methods Materials

The following materials were purchased from Wako Pure Chemical Industries (Osaka, Japan): urea, 3-(3-cholamidopropyl) dimethylammonio-1-propanesulphonate (CHAPS), dithiothreitol (DTT), Tris (2-carboxyethyl) phosphine hydrochloride (TCEP) and iodoacetamide (IAA); Amicon Ultra 0.5-ml 3K was from Millipore (Tokyo, Japan), and thiourea from Nacalai Tesque, Inc. (Kyoto, Japan). All other chemicals and reagents were purchased from Sigma Chemical Corp. (St. Louis, MO, USA).

 PDAC cell line

PANC-1 cells were obtained from the Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University (Sendai, Japan).

 Protein extraction of lumican-regulated PANC-1 cells

The lumican-overexpressing PANC-1 cells, lumican-downregulated PANC-1 cells, and control cell lines (Mock and NC, respectively) were prepared as previously described (28). The lumican-regulated PANC-1 cells were cultured at a density of 5×105 cells in a 100-mm dish in RPMI-1640 medium with 10% fetal bovine serum (FBS) for 72 h. Then, cells were solubilized in urea lysis buffer (7 M urea, 2 M thiourea, 5% CHAPS, 1% Triton X-100). Protein concentration was measured using the Bradford method.

 In-solution trypsin digestion

A gel-free digestion approach was performed in accordance with the protocol described by Bluemlein and Ralser (29). In brief, 10 μg of protein extract from each sample was reduced by addition of 45 mM DTT and 20 mM TCEP and was then alkylated using 100 mM IAA. Following alkylation, samples were digested with Proteomics Grade Trypsin (Agilent Technologies, Inc., Santa Clara, CA, USA) at 37°C for 24 h. Next, digests were evaporated in a vacuum concentrator centrifuge and the residue was resuspended in 0.1% trifluoroacetic acid/5% acetonitrile. The digests were filtered through Amicon Ultra 0.5-ml 3K to remove undigested proteins and the flow-through was used in the following analyses.

 LC-MS/MS analysis of protein identification

Approximately 2-μg peptide samples were injected into a peptide L-trap column (Chemicals Evaluation and Research Institute, Tokyo, Japan) using an HTC PAL autosampler (CTC Analytics, Zwingen, Switzerland) and further separated through an Advance-nano UHPLC using a Reverse-Phase C18-column (Zaplous column α, 3-μm diameter gel particles and 100 Å pore size, 0.1×150 mm; both from AMR, Inc., Tokyo, Japan). The mobile phase consisted of solution A (0.1% formic acid in water) and solution B (acetonitrile). The column was developed at a flow rate of 500 nl/min with a concentration gradient of acetonitrile from 5 to 45% B over 120 min. Gradient-eluted peptides were analyzed using an amaZon ETD ion-trap mass spectrometer (Bruker Daltonics, Billerica, MA, USA). The results were acquired in a data-dependent manner in which MS/MS fragmentation was performed on the 10 most intense peaks of every full MS scan.

All MS/MS spectra data were searched against the SwissProt Homo sapiens database using Mascot (v2.3.01; Matrix Science, London, UK). The search criteria was set as follows: enzyme, trypsin; allowance of up to two missed cleavage peptides; mass tolerance ± 0.5 Da and MS/MS tolerance ± 0.5 Da; and modifications of cysteine carbamidomethylation and methionine oxidation.

 Semi-quantitative analysis of identified proteins

The fold-changes in expressed proteins on the base 2 logarithmic scale were calculated using Rsc based upon spectral counting (30). Relative amounts of identified proteins were also calculated using the normalized spectral abundance factor (NSAF) (31). Differentially expressed proteins were chosen so that their Rsc satisfy >1 or <−1, which correspond to fold-changes of >2 or <0.5.

 Bioinformatics

Functional annotations for the identified proteins whose expression level was regulated by lumican were processed using the Database for Annotation, Visualization and Integrated Discovery (DAVID), v6.7 (http://david.abcc.ncifcrf.gov/home.jsp) (32–34).

 Results Protein identification and profile in lumican-regulated PANC-1 cells

To examine the effect of lumican on cell growth and invasion of PDAC cells, we created two types of PANC-1 cells whose lumican expression level was regulated: lumican-overexpressing PANC-1 cells and lumican-downregulated PANC-1 cells (28). We then investigated the molecular profile of proteins whose expression level was regulated by lumican using shotgun proteomics. Fig. 1 shows the Venn map for the identified proteins in lumican-regulated PANC-1 cells. In lumican-overexpressing PANC-1 cells (Lum), 321 proteins were identified, and 347 were identified in control cells (Mock) under the search parameter settings used (Fig. 1A). On the other hand, 388 proteins were identified in lumican-downregulated PANC-1 cells (siLum) and 287 in control cells (NC) (Fig. 1B). Among the 448 proteins identified from lumican upregulated cells, 220 (49.1%) proteins were identified in both cell lines, while 101 (22.6%) and 127 (28.3%) proteins were unique to Lum and Mock, respectively (Fig. 1A). Of the 451 total proteins identified from lumican downregulated cells, 224 (49.7%) proteins were identified in both cell lines, whereas 164 (36.3%) and 63 (14.0%) proteins were unique to siLum and NC, respectively (Fig. 1B).

 Semi-quantitative comparison of identified proteins in lumican-regulated PANC-1 cells

Next, we performed a label-free semi-quantitative method based on spectral counting, as described in the Materials and methods section, to find proteins whose expression levels were regulated by lumican. The Rsc value was plotted against the corresponding protein (X-axis) from left to right for proteins identified in the Lum and Mock groups (Fig. 2A). The positive and negative Rsc values indicate increased and decreased expression, respectively, in the Lum group. The NSAF value (bar) plotted against the corresponding protein (X-axis), NSAF of Lum (black bar) and Mock (gray bar) proteins are indicated above and below the X-axis, respectively (Fig. 2A). Proteins with either a high positive or negative Rsc value were considered candidate proteins whose expression level was regulated by lumican. Fig. 2B shows the Rsc and NSAF values of the siLum and NC groups as described above. In the lumican upregulated cells, the Rsc of metallothionein (MT)-1X was positive, and the Rsc of galectin-1 was negative (Fig. 2A). In the lumican downregulated cells, the Rsc of Annexin A5 was positive and the Rsc of vinculin was negative (Fig. 2B). Housekeeping proteins such as β-actin, histone H4 and GAPDH were located near the center of the X-axis (Fig. 2).

As a result of semi-quantification, 174 differentially expressed proteins were identified in lumican upregulated PANC-1 cells (Table I), and a total of 143 differentially expressed proteins were identified in lumican downregulated PANC-1 cells (Table II). However, the expression level of housekeeping proteins such as β-actin, GAPDH and histone H4 was not changed in lumican upregulated cells or lumican downregulated cells. In order to identify proteins whose expression levels were regulated by lumican, we selected proteins whose Rsc value was inversely associated between lumican upregulated cells and lumican downregulated cells. Twenty four proteins were identified as candidates (Table III).

 Functional annotation of proteins whose expression level is regulated by lumican

Gene ontology (GO) analyses were performed using the identified candidate proteins for each molecular function (Fig. 3), biological process (Fig. 4) and cellular component (Fig. 5) using DAVID. We also analyzed pathway terms, but no significant category was found. Functional annotations were counted by normalizing to the total number of proteins identified. Since a multifunctional protein yields more than one annotation and some proteins are not defined by GO terms yet, the total number of classified proteins resulted in more or less than 100% (Fig. 3). Major GO molecular function categories of the identified proteins were 34.8% structural molecule activity, 17.4% structural constituents of ribosomes, and 21.7% RNA binding proteins (Fig. 3).

 Discussion

In the present study, we used a gel-free LC-MS-based proteomics approach to examine the effect of lumican on cell growth and invasion. Using semi-quantitative methods based on spectral counting, we successfully identified several proteins whose expression levels were altered more than 2-fold in both lumican upregulated PANC-1 cells and lumican downregulated PANC-1 cells. A limitation of spectral counting is in its accurate quantitative capacity (35). Therefore, we selected candidate proteins whose expression level was regulated by lumican using the analysis results of two types of cells; lumican upregulated cells and lumican downregulated cells. Thus, we identified 24 proteins whose Rsc values were inversely correlated among differentially expressed proteins in lumican upregulated and downregulated cells as candidate proteins (Fig. 3).

To examine the role of these candidate proteins in the effect of lumican on cell growth and invasion, we performed a functional classification of the candidate proteins by GO analysis. Although the GO terms for molecular function, biological processes, and cellular components were examined, we focused on molecular function. The molecular functions of candidate proteins were mainly classified in the ‘structural molecule activity’ category. Since structural molecule activity proteins contribute to the formation of complexes within or outside of the cell, such candidate proteins may be related to cell invasion regulated by lumican.

Annexin A5 expression may be regulated by lumican since Annexin A5 expression was negatively correlated with the lumican expression level. Annexin A5, also known as Annexin V, is widely known as a marker of early stage apoptosis (36,37). We previously demonstrated that the PDAC cell line secretes 70-kDa glycosylated lumican and that this secreted lumican stimulates cell growth (28). Thus, the induction of cell growth by lumican may be related to an inhibition of apoptosis through Annexin A5 expression. However, previous reports suggest that lumican plays an important role in apoptosis induction (22,38–40). This discrepancy may be derived from the differences between glycosylated lumican secreted from the PDAC cell line and other cells.

Furthermore, MT-1X expression levels positively correlated with the lumican expression level. MT family proteins are encoded by 10 functional isoforms (MT-1A, MT-1B, MT-1E, MT-1F, MT-1G, MT-1H, MT-1X, MT-2A, MT-3 and MT-4), and seven non-functional isoforms (MT-1C, MT-1D, MT-1I, MT-1J, MT-1K, MT-L and MT-2B). MT family proteins are involved in essential metal homeostasis, cellular free radical scavenging, cell proliferation, apoptosis, and metal detoxification. MT-1X and MT-2A transcripts were significantly upregulated under hypoxia in human prostate cancer cell lines, and siRNA-MT-2A treatment inhibited cell growth and induction of apoptosis, but an effect of MT-1X on cell growth and apoptosis was not demonstrated (41). Zinc is an abundant metal in the human prostate, and zinc inhibits cell growth and induces apoptosis in human prostate cancer cell lines (42,43). These findings suggest that MT-2A may play an important role in cell growth and apoptosis in prostate cancer through intracellular zinc homeostasis. MT-1X function in cancer cells, particularly PDAC, is not well understood. MT-1X is a known zinc-binding protein, and MT-1X mRNA expression was induced, as well as MT-2A, under hypoxic conditions (41). Thus, MT-1X may inhibit apoptosis as well as MT-2A. Furthermore, Ryu et al(44) suggested that MT-1E could enhance the migration and invasion of human glioma cells by inducing MMP-9 activation. MT-1X may have functions resembling MT-1E, since MMP-9 is a zinc-requiring enzyme, and MT-1X is classified into isoforms such as MT-1E. As mentioned above, it may be postulated that MT-1X plays an important role in cell growth and invasion by lumican. Further study is required to validate the expression levels of these candidate proteins, and to clarify the effect of candidate proteins, including MT-1X, on cell growth and invasion that are affected by lumican.

In conclusion, we identified more than 400 proteins from both lumican upregulated and lumican downregulated cells using global shotgun proteomics. A label-free semi-quantitative method based on spectral counting led to 24 candidate proteins whose expression was regulated by lumican. These candidate proteins included apoptosis-related and invasion-related proteins. Therefore, lumican may be involved in cell growth and invasion by altering the expression of these proteins.

 Acknowledgements

The authors thank K. Teduka and T. Fujii for their technical assistance (Department of Pathology, Integrative Oncological Pathology). The present study was supported by a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science to T.Y. (C, no. 24591019) and Z.N. (C, no. 23590477).

 References NikitovicDKatonisPTsatsakisAKaramanosNKTzanakakisGNLumican, a small leucine-rich proteoglycanIUBMB Life608188232008 IozzoRVMatrix proteoglycans: from molecular design to cellular functionAnnu Rev Biochem676096521998 GroverJChenXNKorenbergJRRoughleyPJThe human lumican gene. Organization, chromosomal location, and expression in articular cartilageJ Biol Chem27021942219491995 ChakravartiSStallingsRLSundarRajNCornuetPKHassellJRPrimary structure of human lumican (keratan sulfate proteoglycan) and localization of the gene (LUM) to chromosome 12q21.3–q22Genomics274814881995 NaitoZRole of the small leucine-rich proteoglycan (SLRP) family in pathological lesions and cancer cell growthJ Nippon Med Sch721371452005 RadaJACornuetPKHassellJRRegulation of corneal collagen fibrillogenesis in vitro by corneal proteoglycan (lumican and decorin) core proteinsExp Eye Res566356481993 SvenssonLNärlidIOldbergAFibromodulin and lumican bind to the same region on collagen type I fibrilsFEBS Lett4701781822000 ChakravartiSFunctions of lumican and fibromodulin: lessons from knockout miceGlycoconj J192872932002 VogelKGPaulssonMHeinegårdDSpecific inhibition of type I and type II collagen fibrillogenesis by the small proteoglycan of tendonBiochem J2235875971984 ChakravartiSMagnusonTLassJHJepsenKJLaMantiaCCarrollHLumican regulates collagen fibril assembly: skin fragility and corneal opacity in the absence of lumicanJ Cell Biol141127712861998 JepsenKJWuFPeragalloJHA syndrome of joint laxity and impaired tendon integrity in lumican- and fibromodulin-deficient miceJ Biol Chem27735532355402002 BlochbergerTCCornuetPKHassellJRIsolation and partial characterization of lumican and decorin from adult chicken corneas. A keratan sulfate-containing isoform of decorin is developmentally regulatedJ Biol Chem26720613206191992 DolhnikoffMMorinJRoughleyPJLudwigMSExpression of lumican in human lungsAm J Respir Cell Mol Biol195825871998 QinHIshiwataTAsanoGEffects of the extracellular matrix on lumican expression in rat aortic smooth muscle cells in vitroJ Pathol1956046082001 BabaHIshiwataTTakashiEXuGAsanoGExpression and localization of lumican in the ischemic and reperfused rat heartJpn Circ J654454502001 OndaMIshiwataTKawaharaKWangRNaitoZSugisakiYExpression of lumican in thickened intima and smooth muscle cells in human coronary atherosclerosisExp Mol Pathol721421492002 Ping LuYIshiwataTAsanoGLumican expression in alpha cells of islets in pancreas and pancreatic cancer cellsJ Pathol1963243302002 LuYPIshiwataTKawaharaKExpression of lumican in human colorectal cancer cellsPathol Int525195262002 KelemenLECouchFJAhmedSGenetic variation in stromal proteins decorin and lumican with breast cancer: investigations in two case-control studiesBreast Cancer Res10R982008 TroupSNjueCKliewerEVReduced expression of the small leucine-rich proteoglycans, lumican, and decorin is associated with poor outcome in node-negative invasive breast cancerClin Cancer Res92072142003 IshiwataTChoKKawaharaKRole of lumican in cancer cells and adjacent stromal tissues in human pancreatic cancerOncol Rep185375432007 VuillermozBKhoruzhenkoAD’OnofrioMFThe small leucine-rich proteoglycan lumican inhibits melanoma progressionExp Cell Res2962943062004 ShinjiSTajiriTIshiwataTSeyaTTanakaNNaitoZDifferent expression levels of lumican in human carcinoid tumor and neuroendocrine cell carcinomaInt J Oncol268738802005 SeyaTTanakaNShinjiSLumican expression in advanced colorectal cancer with nodal metastasis correlates with poor prognosisOncol Rep16122512302006 MatsudaYYamamotoTKudoMExpression and roles of lumican in lung adenocarcinoma and squamous cell carcinomaInt J Oncol33117711852008 LeygueESnellLDotzlawHExpression of lumican in human breast carcinomaCancer Res58134813521998 NaitoZIshiwataTKurbanGExpression and accumulation of lumican protein in uterine cervical cancer cells at the periphery of cancer nestsInt J Oncol209439482002 YamamotoTMatsudaYKawaharaKIshiwataTNaitoZSecreted 70kDa lumican stimulates growth and inhibits invasion of human pancreatic cancerCancer Lett32031392012 BluemleinKRalserMMonitoring protein expression in whole-cell extracts by targeted label- and standard-free LC-MS/MSNat Protoc68598692011 OldWMMeyer-ArendtKAveline-WolfLComparison of label-free methods for quantifying human proteins by shotgun proteomicsMol Cell Proteomics4148715022005 ZybailovBColemanMKFlorensLWashburnMPCorrelation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labelingAnalytical chemistry77621862242005 DennisGJrShermanBTHosackDADAVID: Database for Annotation, Visualization, and Integrated DiscoveryGenome Biol4P32003 Huang daWShermanBTLempickiRASystematic and integrative analysis of large gene lists using DAVID bioinformatics resourcesNat Protoc444572009 Huang daWShermanBTLempickiRABioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene listsNucleic Acids Res371132009 LundgrenDHHwangSIWuLHanDKRole of spectral counting in quantitative proteomicsExpert Rev Proteomics739532010 VermesIHaanenCSteffens-NakkenHReutelingspergerCA novel assay for apoptosis. Flow cytometric detection of phosphatidylserine expression on early apoptotic cells using fluorescein labelled Annexin VJ Immunol Methods18439511995 AubryJPBlaeckeALecoanet-HenchozSAnnexin V used for measuring apoptosis in the early events of cellular cytotoxicityCytometry371972041999 VijNRobertsLJoyceSChakravartiSLumican suppresses cell proliferation and aids Fas-Fas ligand mediated apoptosis: implications in the corneaExp Eye Res789579712004 BrezillonSVenteoLRamontLExpression of lumican, a small leucine-rich proteoglycan with antitumour activity, in human malignant melanomaClin Exp Dermatol324054162007 WilliamsKEFulfordLAAlbigARLumican reduces tumor growth via induction of fas-mediated endothelial cell apoptosisCancer Microenviron41151262010 YamasakiMNomuraTSatoFMimataHMetallothionein is up-regulated under hypoxia and promotes the survival of human prostate cancer cellsOncol Rep18114511532007 LiangJYLiuYYZouJFranklinRBCostelloLCFengPInhibitory effect of zinc on human prostatic carcinoma cell growthProstate402002071999 FengPLiTLGuanZXFranklinRBCostelloLCDirect effect of zinc on mitochondrial apoptogenesis in prostate cellsProstate523113182002 RyuHHJungSJungTYRole of metallothionein 1E in the migration and invasion of human glioma cell linesInt J Oncol41130513132012

The Venn map of proteins identified from lumican-regulated PANC-1 cells. (A) In lumican-overexpressing PANC-1 cells (Lum), 321 proteins were identified and 347 were identified in control cells (Mock). (B) In lumican-downregulated PANC-1 cells (siLum), 388 proteins were identified and 287 were identifed in control cells (NC).

Semi-quantitative comparisons of the proteins identified in lumican-regulated PANC-1 cells. Rsc and normalized spectral abundance factor (NSAF) values were calculated for the proteins identified (X-axis). Protein expression was compared between (A) Lum vs. Mock and (B) siLum vs. control cells (NC). Proteins highly expressed in either Lum or Mock cells were to the right or left sides of the X-axis. Housekeeping proteins were located near the center along the X-axis.

Analysis of identified proteins by gene ontology (GO) molecular function. Proteins assigned to a GO molecular function category; only significant categories (P<0.05) are shown.

Analysis of identified proteins in the gene ontology biological process category. Only significant categories (P<0.05) are shown.

Analysis of identified proteins in the gene ontology cellular component. Only significant categories (P<0.05) are shown.

Differentially expressed proteins in lumican upregulated PANC-1 cells.

Spectral counting
No. ID Accession no. and description No. of amino acids Mock Lum Fold-change (Rsc)
1 ACTH_HUMAN (P63267) Actin, γ-enteric smooth muscle 376 35 0 −4.69652
2 ACTC_HUMAN (P68032) Actin, α cardiac muscle 1 377 18 0 −3.7706617
3 TBB2A_HUMAN (Q13885) Tubulin β-2A chain 445 10 0 −2.9897736
4 H2B1H_HUMAN (Q93079) Histone H2B type 1-H 126 9 0 −2.8547299
5 HS904_HUMAN (Q58FG1) Putative heat shock protein HSP 90-α A4 418 8 0 −2.7058891
6 TBA4A_HUMAN (P68366) Tubulin α-4A chain 448 8 0 −2.7058891
7 H2AJ_HUMAN (Q9BTM1) Histone H2A.J 129 7 0 −2.540088
8 H2B3B_HUMAN (Q8N257) Histone H2B type 3-B 126 7 0 −2.540088
9 RLA0_HUMAN (P05388) 60S acidic ribosomal protein P0 317 7 0 −2.540088
10 H2B1O_HUMAN (P23527) Histone H2B type 1-O 126 4 0 −1.885788
11 K2C71_HUMAN (Q3SY84) Keratin, type II cytoskeletal 71 523 4 0 −1.885788
12 NDKB_HUMAN (P22392) Nucleoside diphosphate kinase B 152 4 0 −1.885788
13 RA1L2_HUMAN (Q32P51) Heterogeneous nuclear ribonucleoprotein A1-like 2 320 4 0 −1.885788
14 CH10_HUMAN (P61604) 10 kDa heat shock protein, mitochondrial 102 4 0 −1.885788
15 H2A1H_HUMAN (Q96KK5) Histone H2A type 1-H 128 3 0 −1.5801931
16 HNRPK_HUMAN (P61978) Heterogeneous nuclear ribonucleoprotein K 463 3 0 −1.5801931
17 K1C25_HUMAN (Q7Z3Z0) Keratin, type I cytoskeletal 25 450 3 0 −1.5801931
18 K22O_HUMAN (Q01546) Keratin, type II cytoskeletal 2 oral 638 3 0 −1.5801931
19 MYL6_HUMAN (P60660) Myosin light polypeptide 6 151 3 0 −1.5801931
20 NFH_HUMAN (P12036) Neurofilament heavy polypeptide 1026 3 0 −1.5801931
21 TAGL3_HUMAN (Q9UI15) Transgelin-3 199 3 0 −1.5801931
22 YI016_HUMAN (A6NKZ8) Putative tubulin β chain-like protein 372 3 0 −1.5801931
23 ANXA5_HUMAN (P08758) Annexin A5 320 3 0 −1.5801931
24 MT1G_HUMAN (P13640) Metallothionein-1G 62 3 0 −1.5801931
25 K1C14_HUMAN (P02533) Keratin, type I cytoskeletal 14 472 6 1 −1.5040946
26 K2C80_HUMAN (Q6KB66) Keratin, type II cytoskeletal 80 452 5 1 −1.2892288
27 ACTBL_HUMAN (Q562R1) β-actin-like protein 2 376 13 4 −1.259281
28 1433B_HUMAN (P31946) 14-3-3 protein β/α 246 2 0 −1.1924301
29 AINX_HUMAN (Q16352) α-internexin 499 2 0 −1.1924301
30 H2AZ_HUMAN (H2AZ_HUMAN) Histone H2A.Z 128 2 0 −1.1924301
31 H2B1D_HUMAN (P58876) Histone H2B type 1-D 126 2 0 −1.1924301
32 H2B1J_HUMAN (P06899) Histone H2B type 1-J 126 2 0 −1.1924301
33 K1C13_HUMAN (P13646) Keratin, type I cytoskeletal 13 458 2 0 −1.1924301
34 K2C6C_HUMAN (P48668) Keratin, type II cytoskeletal 6C 564 2 0 −1.1924301
35 KRT85_HUMAN (P78386) Keratin, type II cuticular Hb5 507 2 0 −1.1924301
36 MLL3_HUMAN (Q8NEZ4) Histone-lysine N-methyltransferase MLL3 4911 2 0 −1.1924301
37 NDK8_HUMAN (O60361) Putative nucleoside diphosphate kinase 137 2 0 −1.1924301
38 NFM_HUMAN (P07197) Neurofilament medium polypeptide 916 2 0 −1.1924301
39 SERPH_HUMAN (P50454) Serpin H1 418 2 0 −1.1924301
40 U17L5_HUMAN (A8MUK1) Ubiquitin carboxyl-terminal hydrolase 17-like protein 5 530 2 0 −1.1924301
41 URFB1_HUMAN (Q6BDS2) UHRF1-binding protein 1 1440 2 0 −1.1924301
42 MDHM_HUMAN (P40926) Malate dehydrogenase, mitochondrial 338 2 0 −1.1924301
43 IF5A1_HUMAN (P63241) Eukaryotic translation initiation factor 5A-1 154 2 0 −1.1924301
44 SFPQ_HUMAN (P23246) Splicing factor, proline- and glutamine-rich 707 2 0 −1.1924301
45 NACA_HUMAN (Q13765) Nascent polypeptide-associated complex subunit α 215 2 0 −1.1924301
46 EF1B_HUMAN (P24534) Elongation factor 1-β 225 2 0 −1.1924301
47 RS4X_HUMAN (P62701) 40S ribosomal protein S4, X isoform 263 2 0 −1.1924301
48 IF4A2_HUMAN (Q14240) Eukaryotic initiation factor 4A-II 407 9 3 −1.0866682
49 EF2_HUMAN (P13639) Elongation factor 2 858 16 6 −1.0697973
50 HSP72_HUMAN (P54652) Heat shock-related 70 kDa protein 2 639 11 4 −1.0396137
51 DESM_HUMAN (P17661) Desmin 470 13 5 −1.0068984
52 LEG1_HUMAN (P09382) Galectin-1 135 13 5 −1.0068984
53 CC113_HUMAN (Q9H0I3) Coiled-coil domain-containing protein 113 377 0 1 1.03639903
54 H11_HUMAN (Q02539) Histone H1.1 215 0 1 1.03639903
55 UBA1_HUMAN (P22314) Ubiquitin-like modifier-activating enzyme 1 1058 0 1 1.03639903
56 TCPH_HUMAN (Q99832) T-complex protein 1 subunit eta 543 0 1 1.03639903
57 RL31_HUMAN (P62899) 60S ribosomal protein L31 125 0 1 1.03639903
58 ADT4_HUMAN (Q9H0C2) ADP/ATP translocase 4 315 0 1 1.03639903
59 BRE1B_HUMAN (O75150) E3 ubiquitin-protein ligase BRE1B 1001 0 1 1.03639903
60 CALX_HUMAN (P27824) Calnexin 592 0 1 1.03639903
61 CAP1_HUMAN (Q01518) Adenylyl cyclase-associated protein 1 475 0 1 1.03639903
62 CAZA1_HUMAN (P52907) F-actin-capping protein subunit α-1 286 0 1 1.03639903
63 CCNT1_HUMAN (O60563) Cyclin-T1 726 0 1 1.03639903
64 CGNL1_HUMAN (Q0VF96) Cingulin-like protein 1 1302 0 1 1.03639903
65 CISY_HUMAN (O75390) Citrate synthase, mitochondrial 466 0 1 1.03639903
66 CLIP1_HUMAN (P30622) CAP-Gly domain-containing linker protein 1 1438 0 1 1.03639903
67 CN37_HUMAN (P09543) 2′,3′-cyclic-nucleotide 3′-phosphodiesterase 421 0 1 1.03639903
68 CTSR1_HUMAN (Q8NEC5) Cation channel sperm-associated protein 1 780 0 1 1.03639903
69 CX057_HUMAN (Q6NSI4) Uncharacterized protein CXorf57 855 0 1 1.03639903
70 DDX21_HUMAN (Q9NR30) Nucleolar RNA helicase 2 783 0 1 1.03639903
71 DYXC1_HUMAN (Q8WXU2) Dyslexia susceptibility 1 candidate gene 1 protein 420 0 1 1.03639903
72 EFTU_HUMAN (P49411) Elongation factor Tu, mitochondrial 452 0 1 1.03639903
73 EHD1_HUMAN (Q9H4M9) EH domain-containing protein 1 534 0 1 1.03639903
74 EIF3H_HUMAN (O15372) Eukaryotic translation initiation factor 3 subunit H 352 0 1 1.03639903
75 EHD1_HUMAN (Q9H4M9) EH domain-containing protein 1 534 0 1 1.03639903
76 FETUA_HUMAN (P02765) α-2-HS-glycoprotein 367 0 1 1.03639903
77 HIP1R_HUMAN (O75146) Huntingtin-interacting protein 1-related protein 1068 0 1 1.03639903
78 HMGN1_HUMAN (P05114) Non-histone chromosomal protein HMG-14 100 0 1 1.03639903
79 HMGN4_HUMAN (O00479) High mobility group nucleosome-binding domain- containing protein 4 90 0 1 1.03639903
80 HNRH3_HUMAN (P31942) Heterogeneous nuclear ribonucleoprotein H3 346 0 1 1.03639903
81 IDE_HUMAN (P14735) Insulin-degrading enzyme 1019 0 1 1.03639903
82 IMA2_HUMAN (P52292) Importin subunit α-2 529 0 1 1.03639903
83 IMDH2_HUMAN (P12268) Inosine-5′-monophosphate dehydrogenase 2 514 0 1 1.03639903
84 K1C26_HUMAN (Q7Z3Y9) Keratin, type I cytoskeletal 26 468 0 1 1.03639903
85 K6PL_HUMAN (P17858) 6-phosphofructokinase, liver type 780 0 1 1.03639903
86 MYH11_HUMAN (P35749) Myosin-11 1972 0 1 1.03639903
87 MYH14_HUMAN (Q7Z406) Myosin-14 1995 0 1 1.03639903
88 PAR10_HUMAN (Q53GL7) Poly [ADP-ribose] polymerase 10 1025 0 1 1.03639903
89 PI3R4_HUMAN (Q99570) Phosphoinositide 3-kinase regulatory subunit 4 1358 0 1 1.03639903
90 PRDX4_HUMAN (Q13162) Peroxiredoxin-4 271 0 1 1.03639903
91 PRS6A_HUMAN (P17980) 26S protease regulatory subunit 6A 439 0 1 1.03639903
92 PSB3_HUMAN (P49720) Proteasome subunit β type-3 205 0 1 1.03639903
93 PTN22_HUMAN (Q9Y2R2) Tyrosine-protein phosphatase non-receptor type 22 807 0 1 1.03639903
94 RAB10_HUMAN (P61026) Ras-related protein Rab-10 200 0 1 1.03639903
95 RBBP7_HUMAN (Q16576) Histone-binding protein RBBP7 425 0 1 1.03639903
96 RL18A_HUMAN (Q02543) 60S ribosomal protein L18a 176 0 1 1.03639903
97 RL27A_HUMAN (P46776) 60S ribosomal protein L27a 148 0 1 1.03639903
98 RL34_HUMAN (P49207) 60S ribosomal protein L34 117 0 1 1.03639903
99 RL3L_HUMAN (Q92901) 60S ribosomal protein L3-like 407 0 1 1.03639903
100 RL40_HUMAN (P62987) Ubiquitin-60S ribosomal protein L40 128 0 1 1.03639903
101 ROAA_HUMAN (Q99729) Heterogeneous nuclear ribonucleoprotein A/B 332 0 1 1.03639903
102 SET_HUMAN (Q01105) Protein SET 290 0 1 1.03639903
103 SODC_HUMAN (P00441) Superoxide dismutase [Cu-Zn] 154 0 1 1.03639903
104 SPSY_HUMAN (P52788) Spermine synthase 366 0 1 1.03639903
105 SYRC_HUMAN (P54136) Arginyl-tRNA synthetase, cytoplasmic 660 0 1 1.03639903
106 TADBP_HUMAN (Q13148) TAR DNA-binding protein 43 414 0 1 1.03639903
107 TALDO_HUMAN (P37837) Transaldolase 337 0 1 1.03639903
108 TECT2_HUMAN (Q96GX1) Tectonic-2 697 0 1 1.03639903
109 TEBP_HUMAN (Q15185) Prostaglandin E synthase 3 160 0 1 1.03639903
110 TPD54_HUMAN (O43399) Tumor protein D54 206 0 1 1.03639903
111 UGPA_HUMAN (Q16851) UTP - glucose-1-phosphate uridylyltransferase 508 0 1 1.03639903
112 WDR53_HUMAN (Q7Z5U6) WD repeat-containing protein 53 358 0 1 1.03639903
113 ZC12A_HUMAN (Q5D1E8) Ribonuclease ZC3H12A 599 0 1 1.03639903
114 RL22_HUMAN (P35268) 60S ribosomal protein L22 128 0 1 1.03639903
115 RL13_HUMAN (P26373) 60S ribosomal protein L13 211 0 1 1.03639903
116 RL23_HUMAN (P62829) 60S ribosomal protein L23 140 0 1 1.03639903
117 RS11_HUMAN (P62280) 40S ribosomal protein S11 158 0 1 1.03639903
118 SUMO2_HUMAN (P61956) Small ubiquitin-related modifier 2 95 0 1 1.03639903
119 TFR1_HUMAN (P02786) Transferrin receptor protein 1 760 0 1 1.03639903
120 RL11_HUMAN (P62913) 60S ribosomal protein L11 178 0 1 1.03639903
121 EF1A2_HUMAN (Q05639) Elongation factor 1-α 2 463 10 19 1.04422777
122 CBX1_HUMAN (P83916) Chromobox protein homolog 1 185 1 3 1.10688593
123 RL12_HUMAN (P30050) 60S ribosomal protein L12 165 1 3 1.10688593
124 RAN_HUMAN (P62826) GTP-binding nuclear protein Ran 216 1 3 1.10688593
125 PDIA6_HUMAN (Q15084) Protein disulfide-isomerase A6 440 1 3 1.10688593
126 RL10L_HUMAN (Q96L21) 60S ribosomal protein L10-like 214 1 3 1.10688593
127 SRC8_HUMAN (Q14247) Src substrate cortactin 550 1 3 1.10688593
128 RL8_HUMAN (P62917) 60S ribosomal protein L8 257 1 3 1.10688593
129 RS23_HUMAN (P62266) 40S ribosomal protein S23 143 1 3 1.10688593
130 RS13_HUMAN (P62277) 40S ribosomal protein S13 151 1 3 1.10688593
131 RL24_HUMAN (P83731) 60S ribosomal protein L24 157 1 3 1.10688593
132 RL37A_HUMAN (P61513) 60S ribosomal protein L37a 92 2 5 1.13371212
133 PAL4A_HUMAN (Q9Y536) Peptidylprolyl cis-trans isomerase A-like 4A/B/C 164 2 5 1.13371212
134 RL18_HUMAN (Q07020) 60S ribosomal protein L18 188 2 5 1.13371212
135 K1C9_HUMAN (P35527) Keratin, type I cytoskeletal 9 623 8 17 1.17638585
136 TBB1_HUMAN (Q9H4B7) Tubulin β-1 chain 451 3 8 1.31408061
137 PAIRB_HUMAN (Q8NC51) Plasminogen activator inhibitor 1 RNA-binding protein 408 2 6 1.34868122
138 CATD_HUMAN (P07339) Cathepsin D 412 0 2 1.56775608
139 FLNB_HUMAN (O75369) Filamin-B 2602 0 2 1.56775608
140 MYL6B_HUMAN (P14649) Myosin light chain 6B 208 0 2 1.56775608
141 PSB2_HUMAN (P49721) Proteasome subunit β type-2 201 0 2 1.56775608
142 RS7_HUMAN (P62081) 40S ribosomal protein S7 194 0 2 1.56775608
143 IQGA1_HUMAN (P46940) Ras GTPase-activating-like protein IQGAP1 1657 0 2 1.56775608
144 DX39B_HUMAN (Q13838) Spliceosome RNA helicase DDX39B 428 0 2 1.56775608
145 GANAB_HUMAN (Q9BS14)Neutral α-glucosidase AB 944 0 2 1.56775608
146 H13_HUMAN (P16402) Histone H1.3 221 0 2 1.56775608
147 H14_HUMAN (P10412) Histone H1.4 219 0 2 1.56775608
148 HNRH2_HUMAN (P55795) Heterogeneous nuclear ribonucleoprotein H2 449 0 2 1.56775608
149 ATPA_HUMAN (P25705) ATP synthase subunit α, mitochondrial 553 0 2 1.56775608
150 H31T_HUMAN (Q16695) Histone H3.1t 136 0 2 1.56775608
151 RL10A_HUMAN (P62906) 60S ribosomal protein L10a 217 0 2 1.56775608
152 H12_HUMAN (P16403) Histone H1.2 213 0 2 1.56775608
153 TBB8_HUMAN (Q3ZCM7) Tubulin β-8 chain 444 5 15 1.57505162
154 EF1D_HUMAN (P29692) Elongation factor 1-δ 281 1 5 1.6649664
155 RLA0L_HUMAN (Q8NHW5) 60S acidic ribosomal protein P0-like 317 1 6 1.8799355
156 RS8_HUMAN (P62241) 40S ribosomal protein S8 208 0 3 1.95562202
157 CCD50_HUMAN (Q8IVM0) Coiled-coil domain-containing protein 50 306 0 3 1.95562202
158 K2C6A_HUMAN (P02538) Keratin, type II cytoskeletal 6A 564 0 3 1.95562202
159 MT1X_HUMAN (P80297) Metallothionein-1X 61 0 3 1.95562202
160 RL17_HUMAN (P18621) 60S ribosomal protein L17 184 0 3 1.95562202
161 RS26_HUMAN (P62854) 40S ribosomal protein S26 115 0 3 1.95562202
162 H15_HUMAN (P16401) Histone H1.5 226 0 3 1.95562202
163 ATPB_HUMAN (P06576) ATP synthase subunit β, mitochondrial 529 1 7 2.06719342
164 ADT1_HUMAN (P12235) ADP/ATP translocase 1 298 0 4 2.26131991
165 H2A1_HUMAN (P0C0S8) Histone H2A type 1 130 0 4 2.26131991
166 RS6_HUMAN (P62753) 40S ribosomal protein S6 249 0 4 2.26131991
167 H2B1B_HUMAN (P33778) Histone H2B type 1-B 126 0 4 2.26131991
168 FLNA_HUMAN (P21333) Filamin-A 2647 1 9 2.38204237
169 H2B1M_HUMAN (Q99879) Histone H2B type 1-M 126 0 6 2.72867159
170 H2AX_HUMAN (P16104) Histone H2A.x 143 0 7 2.9159295
171 H2A1B_HUMAN (P04908) Histone H2A type 1-B/E 130 0 9 3.23077846
172 H2A1A_HUMAN (Q96QV6) Histone H2A type 1-A 131 0 9 3.23077846
173 H2B1C_HUMAN (P62807) Histone H2B type 1-C/E/F/G/I 126 0 11 3.48962935
174 ACTA_HUMAN (P62736) Actin, aortic smooth muscle 377 0 15 3.90067941

The expression levels of the 174 proteins were altered more than 2-fold as a result of lumican upregulation.

Differentially expressed proteins in lumican downregulated PANC-1 cells.

Spectral counting
No. ID Accession no. and description No. of amino acids NC siLum Fold-change (Rsc)
1 ACTG_HUMAN (P63261) Actin, cytoplasmic 2 375 19 0 −4.1933172
2 H2B1D_HUMAN (P58876) Histone H2B type 1-D 126 7 0 −2.8944219
3 H2A2A_HUMAN (Q6FI13) Histone H2A type 2-A 130 4 0 −2.2414896
4 HNRPU_HUMAN (Q00839) Heterogeneous nuclear ribonucleoprotein U 825 3 0 −1.9363502
5 H2B1M_HUMAN (Q99879) Histone H2B type 1-M 126 3 0 −1.9363502
6 KRT81_HUMAN (Q14533) Keratin, type II cuticular Hb1 505 3 0 −1.9363502
7 RL10_HUMAN (P27635) 60S ribosomal protein L10 214 3 0 −1.9363502
8 K2C6B_HUMAN (P04259) Keratin, type II cytoskeletal 6B 564 6 1 −1.8595343
9 CAPZB_HUMAN (P47756) F-actin-capping protein subunit β 277 2 0 −1.5490424
10 FUBP2_HUMAN (Q92945) Far upstream element-binding protein 2 711 2 0 −1.5490424
11 IPO7_HUMAN (O95373) Importin-7 1038 2 0 −1.5490424
12 K2C6C_HUMAN (P48668) Keratin, type II cytoskeletal 6C 564 2 0 −1.5490424
13 ML12A_HUMAN (P19105) Myosin regulatory light chain 12A 171 2 0 −1.5490424
14 NUCB1_HUMAN (Q02818) Nucleobindin-1 461 2 0 −1.5490424
15 EF1B_HUMAN (P24534) Elongation factor 1-β 225 2 0 −1.5490424
16 NDKA_HUMAN (P15531) Nucleoside diphosphate kinase A 152 2 0 −1.5490424
17 VINC_HUMAN (P18206) Vinculin 1134 7 2 −1.5155258
18 PDIA3_HUMAN (P30101) Protein disulfide-isomerase A3 505 4 1 −1.3933005
19 K2C5_HUMAN (P13647) Keratin, type II cytoskeletal 5 590 8 3 −1.2936552
20 K1C19_HUMAN (P08727) Keratin, type I cytoskeletal 19 400 11 5 −1.1429912
21 ECH1_HUMAN (Q13011) δ(3,5)-δ(2,4)-dienoyl-CoA isomerase, mitochondrial 328 5 2 −1.1144173
22 PAIRB_HUMAN (Q8NC51) Plasminogen activator inhibitor 1 RNA-binding protein 408 5 2 −1.1144173
23 RS3_HUMAN (P23396) 40S ribosomal protein S3 243 3 1 −1.0881611
24 CRIP1_HUMAN (P50238) Cysteine-rich protein 1 77 3 1 −1.0881611
25 RS28_HUMAN (P62857) 40S ribosomal protein S28 69 3 1 −1.0881611
26 RS13_HUMAN (P62277) 40S ribosomal protein S13 151 3 1 −1.0881611
27 RS27A_HUMAN (P62979) Ubiquitin-40S ribosomal protein S27a 156 3 1 −1.0881611
28 CAPG_HUMAN (P40121) Macrophage-capping protein 348 1 0 −1.0182433
29 CDC42_HUMAN (P60953) Cell division control protein 42 homolog 191 1 0 −1.0182433
30 CX6B1_HUMAN (P14854) Cytochrome c oxidase subunit 6B1 86 1 0 −1.0182433
31 GDIA_HUMAN (P31150) Rab GDP dissociation inhibitor α 447 1 0 −1.0182433
32 IQGA1_HUMAN (P46940) Ras GTPase-activating-like protein IQGAP1 1657 1 0 −1.0182433
33 RL12_HUMAN (P30050) 60S ribosomal protein L12 165 1 0 −1.0182433
34 RL35A_HUMAN (P18077) 60S ribosomal protein L35a 110 1 0 −1.0182433
35 SQSTM_HUMAN (Q13501) Sequestosome-1 440 1 0 −1.0182433
36 RL10L_HUMAN (Q96L21) 60S ribosomal protein L10-like 214 1 0 −1.0182433
37 RS14_HUMAN (P62263) 40S ribosomal protein S14 151 1 0 −1.0182433
38 AGR3_HUMAN (Q8TD06) Anterior gradient protein 3 homolog 166 1 0 −1.0182433
39 ALMS1_HUMAN (Q8TCU4) Alstrom syndrome protein 1 4167 1 0 −1.0182433
40 AP3D1_HUMAN (O14617) AP-3 complex subunit δ-1 1153 1 0 −1.0182433
41 BI2L2_HUMAN (Q6UXY1) Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 2 529 1 0 −1.0182433
42 CH041_HUMAN (Q6NXR4) Uncharacterized protein C8orf41 508 1 0 −1.0182433
43 CORO7_HUMAN (P57737) Coronin-7 925 1 0 −1.0182433
44 CSPG4_HUMAN (Q6UVK1) Chondroitin sulfate proteoglycan 4 2322 1 0 −1.0182433
45 CXL14_HUMAN (O95715) C-X-C motif chemokine 14 111 1 0 −1.0182433
46 DDX17_HUMAN (Q92841) Probable ATP-dependent RNA helicase DDX17 650 1 0 −1.0182433
47 DNJB1_HUMAN (P25685) DnaJ homolog subfamily B member 1 340 1 0 −1.0182433
48 EIF3C_HUMAN (Q99613) Eukaryotic translation initiation factor 3 subunit C 913 1 0 −1.0182433
49 FER_HUMAN (P16591) Tyrosine-protein kinase Fer 822 1 0 −1.0182433
50 GELS_HUMAN (P06396) Gelsolin 782 1 0 −1.0182433
51 INSRR_HUMAN (P14616) Insulin receptor-related protein 1297 1 0 −1.0182433
52 KRT85_HUMAN (P78386) Keratin, type II cuticular Hb5 507 1 0 −1.0182433
53 MT1X_HUMAN (P80297) MT-1X 61 1 0 −1.0182433
54 NALP6_HUMAN (P59044) NACHT, LRR and PYD domains-containing protein 6 892 1 0 −1.0182433
55 PLEC_HUMAN (Q15149) Plectin 4684 1 0 −1.0182433
56 PRS8_HUMAN (P62195) 26S protease regulatory subunit 8 406 1 0 −1.0182433
57 PUR2_HUMAN (P22102) Trifunctional purine biosynthetic protein adenosine-3 1010 1 0 −1.0182433
58 RFX6_HUMAN (Q8HWS3) DNA-binding protein RFX6 928 1 0 −1.0182433
59 RS17_HUMAN (P08708) 40S ribosomal protein S17 135 1 0 −1.0182433
60 RUNX1_HUMAN (Q01196) Runt-related transcription factor 1 453 1 0 −1.0182433
61 SEPT9_HUMAN (Q9UHD8) Septin-9 586 1 0 −1.0182433
62 SRSF4_HUMAN (Q08170) Serine/arginine-rich splicing factor 4 494 1 0 −1.0182433
63 SUMO3_HUMAN (P55854) Small ubiquitin-related modifier 3 103 1 0 −1.0182433
64 TIM13_HUMAN (Q9Y5L4) Mitochondrial import inner membrane translocase subunit Tim13 95 1 0 −1.0182433
65 UGDH_HUMAN (O60701) UDP-glucose 6-dehydrogenase 494 1 0 −1.0182433
66 WDHD1_HUMAN (O75717) WD repeat and HMG-box DNA-binding protein 1 1129 1 0 −1.0182433
67 ZZEF1_HUMAN (O43149) Zinc finger ZZ-type and EF-hand domain-containing protein 1 2961 1 0 −1.0182433
68 RL22_HUMAN (P35268) 60S ribosomal protein L22 128 1 0 −1.0182433
69 BASP1_HUMAN (P80723) Brain acid soluble protein 1 227 1 0 −1.0182433
70 SPSY_HUMAN (P52788) Spermine synthase 366 1 0 −1.0182433
71 RS25_HUMAN (P62851) 40S ribosomal protein S25 125 1 0 −1.0182433
72 RS9_HUMAN (P46781) 40S ribosomal protein S9 194 1 0 −1.0182433
73 HIP1R_HUMAN (O75146) Huntingtin-interacting protein 1-related protein 1068 1 0 −1.0182433
74 RL15_HUMAN (P61313) 60S ribosomal protein L15 204 1 0 −1.0182433
75 G6PI_HUMAN (P06744) Glucose-6-phosphate isomerase 558 1 0 −1.0182433
76 TERA_HUMAN (P55072) Transitional endoplasmic reticulum ATPase 806 1 4 1.05291534
77 RS5_HUMAN (P46782) 40S ribosomal protein S5 204 1 4 1.05291534
78 PCBP3_HUMAN (P57721) Poly(rC)-binding protein 3 371 1 4 1.05291534
79 K2C74_HUMAN (Q7RTS7) Keratin, type II cytoskeletal 74 529 4 11 1.0534109
80 CH60_HUMAN (P10809) 60 kDa heat shock protein, mitochondrial 573 7 20 1.19690092
81 RAN_HUMAN (P62826) GTP-binding nuclear protein Ran 216 0 2 1.20893401
82 ADT2_HUMAN (P05141) ADP/ATP translocase 2 298 0 2 1.20893401
83 CAZA1_HUMAN (P52907) F-actin-capping protein subunit α-1 286 0 2 1.20893401
84 G6PD_HUMAN (P11413) Glucose-6-phosphate 1-dehydrogenase 515 0 2 1.20893401
85 H2AV_HUMAN (Q71UI9) Histone H2A.V 128 0 2 1.20893401
86 H2B1H_HUMAN (Q93079) Histone H2B type 1-H 126 0 2 1.20893401
87 H2B1J_HUMAN (P06899) Histone H2B type 1-J 126 0 2 1.20893401
88 H2B1K_HUMAN (O60814) Histone H2B type 1-K 126 0 2 1.20893401
89 HCD2_HUMAN (Q99714) 3-hydroxyacyl-CoA dehydrogenase type-2 261 0 2 1.20893401
90 MT1A_HUMAN (P04731) Metallothionein-1A 61 0 2 1.20893401
91 RL18A_HUMAN (Q02543) 60S ribosomal protein L18a 176 0 2 1.20893401
92 RL21_HUMAN (P46778) 60S ribosomal protein L21 160 0 2 1.20893401
93 RS7_HUMAN (P62081) 40S ribosomal protein S7 194 0 2 1.20893401
94 SPT6H_HUMAN (Q7KZ85) Transcription elongation factor SPT6 1726 0 2 1.20893401
95 SRP14_HUMAN (P37108) Signal recognition particle 14 kDa protein 136 0 2 1.20893401
96 TBA4B_HUMAN (Q9H853) Putative tubulin-like protein α-4B 241 0 2 1.20893401
97 TCTP_HUMAN (P13693) Translationally-controlled tumor protein 172 0 2 1.20893401
98 UBB_HUMAN (P0CG47) Polyubiquitin-B 229 0 2 1.20893401
99 RL19_HUMAN (P84098) 60S ribosomal protein L19 196 0 2 1.20893401
100 FKB1A_HUMAN (P62942) Peptidyl-prolyl cis-trans isomerase FKBP1A 108 0 2 1.20893401
101 MDHM_HUMAN (P40926) Malate dehydrogenase, mitochondrial 338 0 2 1.20893401
102 NDE1_HUMAN (Q9NXR1) Nuclear distribution protein nudE homolog 1 346 0 2 1.20893401
103 PSA5_HUMAN (P28066) Proteasome subunit α type-5 241 0 2 1.20893401
104 H2B1B_HUMAN (P33778) Histone H2B type 1-B 126 0 2 1.20893401
105 HNRH2_HUMAN (P55795) Heterogeneous nuclear ribonucleoprotein H2 449 1 5 1.30464663
106 K2C1_HUMAN (P04264) Keratin, type II cytoskeletal 1 644 2 8 1.34002273
107 K1C9_HUMAN (P35527) Keratin, type I cytoskeletal 9 623 0 3 1.59614949
108 RLA0L_HUMAN (Q8NHW5) 60S acidic ribosomal protein P0-like 317 0 3 1.59614949
109 H2A1B_HUMAN (P04908) Histone H2A type 1-B/E 130 0 3 1.59614949
110 SRC8_HUMAN (Q14247) Src substrate cortactin 550 0 3 1.59614949
111 UBA1_HUMAN (P22314) Ubiquitin-like modifier-activating enzyme 1 1058 0 3 1.59614949
112 H2A1H_HUMAN (Q96KK5) Histone H2A type 1-H 128 0 3 1.59614949
113 H2A2B_HUMAN (Q8IUE6) Histone H2A type 2-B 130 0 3 1.59614949
114 HN1_HUMAN (Q9UK76) Hematological and neurological expressed 1 protein 154 0 3 1.59614949
115 HNRPK_HUMAN (P61978) Heterogeneous nuclear ribonucleoprotein K 463 0 3 1.59614949
116 K1C14_HUMAN (P02533) Keratin, type I cytoskeletal 14 472 0 3 1.59614949
117 K22O_HUMAN (Q01546) Keratin, type II cytoskeletal 2 oral 638 0 3 1.59614949
118 K6PP_HUMAN (Q01813) 6-phosphofructokinase type C 784 0 3 1.59614949
119 POTEJ_HUMAN (P0CG39) POTE ankyrin domain family member J 1038 0 3 1.59614949
120 RADI_HUMAN (P35241) Radixin 583 0 3 1.59614949
121 HS904_HUMAN (Q58FG1) Putative heat shock protein HSP 90-α A4 418 2 10 1.62280828
122 PROF1_HUMAN (P07737) Profilin-1 140 3 14 1.67515744
123 H90B3_HUMAN (Q58FF7) Putative heat shock protein HSP 90-β-3 597 1 7 1.70556987
124 TBB2A_HUMAN (Q13885) Tubulin β-2A chain 445 7 33 1.88806959
125 TIM50_HUMAN (Q3ZCQ8) Mitochondrial import inner membrane translocase subunit TIM50 353 0 4 1.90119651
126 RL4_HUMAN (P36578) 60S ribosomal protein L4 427 0 4 1.90119651
127 H2A1C_HUMAN (Q93077) Histone H2A type 1-C 130 0 4 1.90119651
128 K2C6A_HUMAN (P02538) Keratin, type II cytoskeletal 6A 564 0 4 1.90119651
129 NDK8_HUMAN (O60361) Putative nucleoside diphosphate kinase 137 0 4 1.90119651
130 TKT_HUMAN (P29401) Transketolase 623 0 4 1.90119651
131 H2B1O_HUMAN (P23527) Histone H2B type 1-O 126 0 5 2.15292781
132 H2B2F_HUMAN (Q5QNW6) Histone H2B type 2-F 126 0 5 2.15292781
133 ANXA5_HUMAN (P08758) Annexin A5 320 0 6 2.36724523
134 H2A2C_HUMAN (Q16777) Histone H2A type 2-C 129 0 6 2.36724523
135 H2B1L_HUMAN (Q99880) Histone H2B type 1-L 126 0 7 2.55385105
136 HSP76_HUMAN (P17066) Heat shock 70 kDa protein 6 643 0 8 2.71910308
137 TBA3E_HUMAN (Q6PEY2) Tubulin α-3E chain 450 0 8 2.71910308
138 TBA3C_HUMAN (Q13748) Tubulin α-3C/D chain 450 0 9 2.86739459
139 TBA4A_HUMAN (P68366) Tubulin α-4A chain 448 0 14 3.44154556
140 TBA1A_HUMAN (Q71U36) Tubulin α-1A chain 451 0 14 3.44154556
141 TBB8_HUMAN (Q3ZCM7) Tubulin β-8 chain 444 0 16 3.61971953
142 ACTC_HUMAN (P68032) Actin, α cardiac muscle 1 377 0 21 3.98789716
143 ACTS_HUMAN (P68133) Actin, α skeletal muscle 377 0 42 4.95088405

The expression levels of the 143 proteins were altered more than 2-fold as a result of lumican downregulation.

Correlation between lumican expression level and identified protein expression level.

Fold-change (Rsc)
ID Accession no. and description Lumican upregulation Lumican downregulation
ACTC_HUMAN (P68032) Actin, α cardiac muscle 1 −3.770661694 3.987897158
TBB2A_HUMAN (Q13885) Tubulin β-2A chain −2.989773612 1.888069587
H2B1H_HUMAN (Q93079) Histone H2B type 1-H −2.854729916 1.208934009
HS904_HUMAN (Q58FG1) Putative heat shock protein HSP 90-α A4 −2.705889054 1.622808285
TBA4A_HUMAN (P68366) Tubulin α-4A chain −2.705889054 3.441545557
H2B1O_HUMAN (P23527) Histone H2B type 1-O −1.885788034 2.152927808
ANXA5_HUMAN (P08758) Annexin A5 −1.580193134 2.367245226
H2A1H_HUMAN (Q96KK5) Histone H2A type 1-H −1.580193134 1.596149489
HNRPK_HUMAN (P61978) Heterogeneous nuclear ribonucleoprotein K −1.580193134 1.596149489
K22O_HUMAN (Q01546) Keratin, type II cytoskeletal 2 oral −1.580193134 1.596149489
K1C14_HUMAN (P02533) Keratin, type I cytoskeletal 14 −1.504094641 1.596149489
H2B1J_HUMAN (P06899) Histone H2B type 1-J −1.192430072 1.208934009
MDHM_HUMAN (P40926) Malate dehydrogenase, mitochondrial −1.192430072 1.208934009
NDK8_HUMAN (O60361) Putative nucleoside diphosphate kinase −1.192430072 1.901196513
HIP1R_HUMAN (O75146) Huntingtin-interacting protein 1-related protein 1.036399032 −1.018243251
RL22_HUMAN (P35268) 60S ribosomal protein L22 1.036399032 −1.018243251
SPSY_HUMAN (P52788) Spermine synthase 1.036399032 −1.018243251
RL10L_HUMAN (Q96L21) 60S ribosomal protein L10-like 1.106885931 −1.018243251
RL12_HUMAN (P30050) 60S ribosomal protein L12 1.106885931 −1.018243251
RS13_HUMAN (P62277) 40S ribosomal protein S13 1.106885931 −1.088161097
PAIRB_HUMAN (Q8NC51) Plasminogen activator inhibitor 1 RNA-binding protein 1.348681223 −1.114417304
IQGA1_HUMAN (P46940) Ras GTPase-activating-like protein IQGAP1 1.567756075 −1.018243251
MT1X_HUMAN (P80297) Metallothionein-1X 1.955622017 −1.018243251
H2B1M_HUMAN (Q99879) Histone H2B type 1-M 2.728671586 −1.936350191

Twenty-four proteins showed correlation between lumican expression level and their expression level.