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The role of microRNA in human lung squamous cell carcinoma

The role of microRNA in human lung squamous cell carcinoma
The role of microRNA in human lung squamous cell carcinoma

The role of microRNA in human lung squamous cell carcinoma

Ye Yang a ,Xiaofei Li a ,Qi Yang b ,Xiaoping Wang a ,Yongan Zhou a ,Tao Jiang a ,Qunfeng Ma c ,

Yun-Jie Wang a ,*

a

Department of Thoracic Surgery,Tangdu Hospital,Fourth Military Medical University,Xi’an 710038,Shaanxi Province,China b

Department of Digestion,Tangdu Hospital,Fourth Military Medical University,Xi’an 710038,Shaanxi Province,China c

Department of Cardiothoracic Surgery,Af?liated Hospital,Academy of Military Medical,Xi’an 710038,Shaanxi Province,China

Received 20August 2009;received in revised form 22March 2010;accepted 25March 2010

Abstract

MicroRNAs (miRNAs)are a group of small noncoding RNAs with modulator activity of gene expression.Deregulation of miRNA genes was found in several types of cancers.To explore the role of the miRNAs in Chinese lung squamous cell carcinoma (SCC),the expression pro?le of 711miRNAs in SCC was analyzed.Total RNAs were used for hybridization on a commercially available array (miRCURY LNA array v.10.0),which contains 1,200probes in tetramer,corre-sponding to 711human miRNA genes.The results of miRNA microarray analysis were con?rmed with quantitative real-time polymerase chain reaction.Seven human miRNAs (miR-126,miR-193a-3p,miR-30d,miR-30a,miR-101,let-7i,and miR-15a)were found to be signi?cantly downregulated in lung SCC (P !0.05),compared with normal lung tissues.The miRNAs miR-185*and miR-125a-5p were signi?cantly upregulated in lung SCC (P !0.05),compared with normal lung tissues.The miRNA let-7i was downregulated in 9of the 20SCC samples,and miR-126was down-regulated in 16of 20.The deregulation of some miRNAs in lung SCC suggests their possible involvement in the development and progression of SCC.ó2010Elsevier Inc.All rights reserved.

1.Introduction

Lung cancer is the most common cause of cancer mortality in the world [1],and its incidence is steadily increasing.The poor prognosis of this cancer is explained mainly by the fact that the diagnosis is generally made only at advanced stages.Identi?cation of early biomarkers is therefore needed [2].The subtypes of lung cancer,including adenocarcinoma (AD)and squamous cell carcinoma (SCC),present unique histopathological characteristics at distinct preferential anatomic locations,but their staging and treat-ment are similar.More effective systemic therapy is urgently needed.

The discovery of miRNAs has been a landmark event in molecular biology.miRNAs can posttranscriptionally regu-late the expressions of hundreds of their target genes,thereby controlling a wide range of biological functions,including cellular proliferation [3],differentiation [4],and apoptosis [5].Recent evidence indicates that miRNAs may function as tumor suppressors or oncogenes,and alteration in miRNA

expression may play a critical role in tumorigenesis and cancer progression [6,7].miRNAs have been found to be involved in known oncogenic pathways,including those of Tp53[8,9],BCL2[10],or KRAS [11].Finally,miRNAs seem to be very signi?cant prognostic factors in patients with different tumors [12e 15]and thus could be useful biomarkers for treatment [16].To date,however,comprehensive data regarding a miRNA signature of SCC in Han Chinese have been limited.

In this study,the miRNA pro?ling of three pairs of lung SCC tissues and normal lung tissues from Han Chinese subjects was analyzed,and nine miRNAs were found to express differentially in all three pairs.

2.Materials and methods 2.1.Patients and tissue specimens

A total of 23pairs of frozen samples were studied.Both tumor tissue and normal tissue were obtained from each patient who underwent surgical resection of SCC at our institution (Xijing Hospital,Fourth Military Medical University,Xi’an,China).The patients had not received

*Corresponding author.Tel.:t86-29-84777827.E-mail address:wangyjphd@https://www.doczj.com/doc/026771585.html, (Y .-J.Wang).

0165-4608/$e see front matter ó2010Elsevier Inc.All rights reserved.doi:10.1016/j.cancergencyto.2010.03.014

Cancer Genetics and Cytogenetics 200(2010)127e

133

adjuvant chemotherapy.This study was approved by the Institutional Review Boards of the hospitals.Written informed consent was obtained from all patients.

2.2.Analysis of miRNA microarray

Three pairs of specimens were analyzed by miRNA mi-croarray.Total RNAs were harvested with TRIzol(Invitro-gen,Carlsbad,CA)and RNeasy mini kit(Qiagen,Valencia, CA)according to the manufacturer’s instructions.After RNA measurement on a NanoDrop instrument(Thermo Scienti?c,Wilmington,DE),the samples were labeled using a miRCURY Hy3/Hy5Power labeling kit and were hybridized on a miRCURY LNA array(v.10.0;Exiqon, Vedbaek,Denmark).The samples were hybridized on a hybridization station.Scanning was performed with an Axon GenePix4000B microarray scanner(Axon Instru-ments e Molecular Devices,Union City,CA).GenePix pro v.6.0software was used to read the raw intensity of the image.The intensity of green signal was calculated after background subtraction;four replicated spots of each probe on the same slide were averaged.Median normalization was calculated as Normalized Data5(ForegroundàBack-ground)/Median,where Median is the50percent quantile of miRNA intensity O50in all samples after background correction.The statistical signi?cance of differentially expressed miRNA was analyzed by Student’s t-test.

2.3.Quantitative real-time polymerase chain reaction

Quantitative real-time polymerase chain reaction(qRT-PCR)was performed in duplicate,including negative reverse transcription(RT)controls to assess genomic DNA and non-template controls to ensure lack of signal in the assay back-ground.The RT reaction for miR-551b and miRNA-765 consisted of2m L10?RT buffer(Epicentre Biotechnologies, Madison,WI),2m L dNTPs0.25mmol/L each(HyTest,Turku, Finland),1m L RT Primer1m mol/L each(Applied Biosys-tems,Foster City,CA),0.3m L RNase inhibitor protein40 U/m L(Epicentre),2m L MMLV-RT10U/m L(Epicentre), and2m g total RNA,in a?nal volume of20m L.

Reactions were incubated at16 C for30minutes,42 C for42minutes,then85 C for5minutes.Following the RT step,1m L of the RT product was transferred into a25m L PCR consisting of2.5m L10?PCR buffer(Epicentre),1.5 m L25mmol/L MgCl2(Promega,Madison,WI),2.5m L dNTPs2.5mmol/L each(Ambion,Austin,TX),0.25?each 10,000?SYBR Green I(Invitrogen),1m L forward primer10 m mol/L,1m L reverse primer10m mol/L,and1unit Taq poly-merase(Promega)(Table1).The PCR cycling began with template denaturation at95 C for5minutes,then40cycles at95 C for10seconds,60 C for20seconds,72 C for20 seconds,and78 C for20seconds,performed on a Corbett Rotor-Gene3000real-time PCR system(Qiagen).Thresh-olds and baselines were manually determined,with

Table1

Sequences of reverse transcriptase e polymerase chain reaction primers

Primers Sequence

U6F50-GCTTCGGCAGCACATATACTAAAAT-30

U6R50-CGCTTCACGAATTTGCGTGTCAT-30

miR-551b GSP50-GGGCGACCCATACTTG-30

miR-551b R50-CAGTGCGTGTCGTGGAGT-30

miR-765GSP50-GGGTGGAGGAGAAGGAAG-30

miR-765R50-CAGTGCGTGTCGTGGAGT-30

Abbreviations:F,forward;R,reverse;GSP,gene-speci?c primer.

Table2

Statistical results,chromosomal location,and putative targets of miRNAs upregulated in lung SCC,compared with normal lung tissue

miRNA a Fold(SCC/Normal),

mean6SD P-value

Chromosomal

localization Putative targets b

hsa-miR-34a 1.58060.4120.2811p36.23BCL2,MET(alias c-Met),SIRT1,MYCN,CCND1

hsa-miR-637 3.10662.5260.05919p13.3RBM9,MNT,DAGLA,SGTA,GLP1R

hsa-miR-412 3.62262.4120.09014q32.31FREM2,PRKRIR,RALGPS1,SOX6,GNB4

ebv-miR-BART17-5p 1.50660.5210.289d d

kshv-miR-K12-6-3p 2.05761.0340.104d d

hsa-miR-185* 1.54360.0140.04222q11.2IKZF4(previously ZNFN1A4),AQP5,ESRRA,RAC3,RGS14 hsa-miR-338-5p 4.99862.8350.06817q25.3PHC3,FAM84A,NETO1,ST8SIA3,USP25

kshv-miR-K12-8 1.7596.8110.212d d

hsa-miR-22* 1.83661.0310.26617p13.3LCE5A,SPATA19,LCE2C,ABHD12,FKBP3

hsa-miR-509-5p 1.51760.6120.107Xq27.3FIGN,FOXP1,TET1,AFF3,SFRS11

sv40-miR-S1-5p 1.90761.2560.153d d

hsa-miR-125a-5p 1.55560.0080.00619q13.3STARD13,ZNF792,GCNT1,FUT4,NAIF1

hsa-miR-221* 2.71561.4390.104Xp11.3KIT(alias c-KIT),CDKN1B(alias P27KIP1),CDKN1C

(alias P57),RXFP4,FBXW2

hsa-miR-551b 1.76561.1910.1713q26.2HTR3B,BST2,ABCC3,TRIM41,CACNG6

hsa-miR-645 3.09861.5610.12920q13.13RAB22A,PHYHIPL,B3GALNT1,TNKS,SOX30 Abbreviations:ebv,Epstein e Barr virus;hsa,Homo sapiens;kshv,Kaposi’s sarcoma-associated herpesvirus;miRNA,micro-RNA;SCC,squamous cell carcinoma;sv40,simian virus40;SD,standard deviation.

a An asterisk is part of the miRNA nomenclature system and is not linked to any footnote speci?c to this table.

b For each row,the top?ve putative targets identi?ed with TargetScan are reported.

128Y.Yang et al./Cancer Genetics and Cytogenetics200(2010)127e133

thresholds typically set between 0.05to 0.1and paired with a baseline starting at 1e 3Ct and ?nishing at 15e 17Ct (where Ct is the threshold crossing point).The let-7i,miR-125a-5p,miR-126,and Run48were reversely transcribed and ampli?ed by ABI reaction (081006-H,0810007-B,0812017-G,and 0811271-H;Applied Biosystems).

2.4.qRT-PCR data analysis

For the target gene,changes were determined by relative quanti?cation [17].The change in ampli?cation of the target gene was normalized to U6.The fold change in the target gene for the results of quantitative real-time PCR

Table 3

Statistical results,chromosomal location,and putative targets of miRNAs downregulated in lung SCC,compared with normal lung tissue miRNA

a

Fold (SCC/Normal),mean 6SD P -value Chromosomal localization Putative targets b

hsa-miR-1260.41760.0330.0232q36.3CRK ,IRS1,VEGF ,PIK3R2(alias p85-b ),VCAM-1hsa-miR-6520.23960.0210.084Xq22.3EEF2,CCKAR ,USP47,XPOT ,PTPN4hsa-miR-193a-3p 0.51560.0420.04117q11.2ABI2,IL17RD ,ERBB4,FHDC1,SLC16A6hsa-miR-30d 0.22160.0190.0208q24.22No targets

hsa-miR-30a 0.20760.0090.0046q13KLHL28,NEDD4,TMEM170B ,STIM2,FAM160B1

hsa-miR-1430.38960.0910.0635q33.1KRAS ,ABL2,VASH1,HIPK2,ASAP3(previously DDEFL1)hsa-miR-7660.57460.1020.140Xq24ZNF763,NR3C2,POU2AF1,NUP210,ZNF609hsa-miR-491-3p 0.33360.0210.0529p21.3BNC2,PYROXD1,PCGF5,GABPA ,EEA1

hsa-miR-3200.63560.5920.2408p21.3ARPP19,MBD2,FTL ,CDK6,TMEM47(previously TM4SF10)hsa-miR-886-3p 0.56660.1660.4085q31.2RALGPS1,NLGN3,MARK4,SEPT5,PITX1hsa-let-7d*0.61660.1860.1249q22.32GPR98,PCDH8,CECR5,KRT15,GKAP1

hsa-miR-18a 0.45760.2120.37913q31.3ESR1(alias ERA ,ER-a )c ,NEDD9,GLRB ,PHC3hsa-miR-29b-1*0.49960.2020.2187q32.3SLC22A7,COL4A5,COL4A1,ROBO1,ADAMTS9

hsa-miR-1010.29160.0210.0121p31.3PTGS2(alias COX2),MCL1,TNPO1,GLTSCR1,FLRT3,EZH2hsa-let-7i

0.50660.0710.03912q14.1HMGA2,IGDCC3(previously PUNC ),ARID3B ,CLCN5,LIMD2hsa-miR-886-5p 0.53760.2310.3865q31.2KPNA6,CNGB1,BCAT2,TRIM54,CPNE7

hsa-miR-240.64260.2520.1959q22.32CALCR ,KDM5A (previously JARID1A ),TMEM50B ,CDV3,VCPIP1hsa-miR-7650.34560.1830.2391q23.1POU2F2,TIMP3,KCND1,PPP1R12B ,PTPRT hsa-miR-576-5p 0.62960.1990.1234q25ITGBL1,WDR72,NRIP1,ICA1L ,CUL3hsa-miR-220.54260.1860.17817p13.3FUT9,CCDC67,CBL ,TET2,H3F3B hsa-miR-299-5p 0.42460.1560.15814q32.31NAV3,IKZF2,ITIH5,SLC5A12,ROBO1

hsa-miR-106b 0.51960.2490.2387q22.1CDKN1A (alias P21),YOD1,ATL3,ACPL2,WNK3hsa-miR-20a 0.57960.1360.12613q31.3PDCD1LG2,CAMTA1,FAM129A ,TANC1,PRRG1hsa-miR-625*0.52260.3310.36014q23.3ESD ,DDX1,HIPK2,RFPL3,FRAS1

hsa-miR-1850.63760.0730.05122q11.21SLC16A2,PALM2,BSN ,ABCG4,PCDHAC1hsa-miR-483-5p 0.47960.3580.36411p15.5HLA-DOA ,FAM160B2,ELK1,AQP7,ELMO3hsa-miR-9390.64360.2880.2928q24.3SLC34A2,ZNRF1,MN1,CPLX2,LDOC1L

hsa-miR-26b 0.45460.0510.0872q35CHORDC1,POLR3G ,SLC2A13,TNRC6B ,TET3

hsa-miR-2220.47460.1290.133Xp11.3CDKN1B (alias P27KIP1),SNX4,RGS6,OSTM1,TCF12hsa-miR-369-3p 0.53360.2030.20714q32.31NF1,YOD1,RAB11FIP2,STK38L ,ZEB2hsa-miR-129-5p 0.58960.0610.0627q32.1TNRC6B ,HRNBP3,TCF4,CACNG2,LDB3hsa-miR-106a

0.56060.3860.230Xq26.2DOCK4,PFKP ,PTPN4,TLE4,FGD4kshv-miR-K12-4-3p 0.35860.2710.377d d

hsa-miR-26a 0.37160.0410.0573p22.2ATP11C ,B3GNT5,KLHDC5,STRADB (previously ALS2CR2),SLC7A11hcmv-miR-UL360.66160.4230.466d d

hsa-miR-574-3p 0.50160.2430.2504

RXRA ,KLF12,CUL2,DAB2IP ,NDUFA4L2hsa-miR-6340.47360.3010.35617q24.2PDIK1L ,ENAH ,BRWD1,KIAA1462,NRXN3hsa-miR-23a*0.58860.2640.32019p13.12NADSYN1,NFATC2,DYNLRB1,PYGM ,GPT hsa-miR-923

0.65960.2750.28317q12a frgament of the 28S rRNA ebv-miR-BHRF1-10.35160.1630.151d d ebv-miR-BART160.61060.2510.348d d

hsa-miR-363*0.34960.1990.223Xq26.2COPE ,PTCRA ,PDZD7,KANK3(previously ANKRD47),BIN3hsa-miR-15a 0.39360.0340.03113q14.3BCL2,KIF1B ,DCLK1,EDA ,ABL2

hsa-let-7e 0.44060.2430.34019q13.33XKR8,GALE ,TARBP2,CDC34,CYP4F8

hsa-miR-32*0.50260.2840.3329q31.3DIP2A ,UPP2,KRT78,LPAR6(previously P2RY5),RPS6KA6hsa-miR-8010.65560.1870.1821p35.3a fragment of U11spliceosomal RNA hsa-miR-17

0.544

60.263

0.271

13q31.3

ZNFX1,PKD2,MYT1L ,ITGB8,SCN1A

Abbreviations:ebv,Epstein e Barr virus;hsa,Homo sapiens ;hcmv,human cytomegalovirus;kshv,Kaposi’s sarcoma-associated herpesvirus;miRNA,microRNA;SCC,squamous cell carcinoma;SD,standard deviation.a

An asterisk is part of the miRNA nomenclature system and is not linked to any footnote speci?c to this table.b

For each row,the top ?ve putative targets identi?ed with TargetScan are reported.c

The software in use identi?ed ES -a as a gene distinct from ESR1;however,ES -a is an alias for ESR1,and the two symbols represent a single gene.Eliminating the duplication leaves four genes.

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was calculated for each sample using 2àDD Ct :DD Ct 5(Ct targetgene àCt U6)cancer à(Ct targetgene àCt U6)normal .Differentially expressed miRNA was de?ned by a 2àDD Ct value of O 1.5or !0.67.3.Results

3.1.Differentially expressed miRNAs in lung SCC The data from miRNA expression pro?ling indicated that 65miRNAs with O 1.5-fold change could be differentially expressed between the lung normal tissue and SCCs,with higher expression in SCC for 16miRNAs and lower expres-sion for 49miRNAs.The top ?ve putative targets identi?ed with TargetScan online software (version

4.1;Whitehead Institute for Biomedical Research;https://www.doczj.com/doc/026771585.html, )for each miRNA are listed in Tables 2and 3.Nine miR-NAs were detected to pass a Student’s t -test with statistical signi?cance (P !0.05):miR-185*,125a-5p,miR-126,miR-193a-3p,miR-30d,miR-30a,miR-101,let-7i,and miR-15a.

Hierarchical clustering analysis based on the miRNA array data led to two groupings for the samples,SCC and normal tissue,suggesting that the miRNA expression pro?le was consistent among the different SCC samples (Fig.1).The potential tumor suppressors were observed to be down-regulated and were clustered into one group,including miR-26a [18],miR-126[19],miR-17[20],miR-193a-3p [21],miR-320[22],let-7i [23],miR-15a [24],and miR-101[25].The potential oncogenes were observed to be upregu-lated and were clustered into another group,such as miR-185[26],miR-221*[27],and miR-338[28].3.2.Validation of miRNA microarray results by qRT-PCR in lung SCC

To validate the results of miRNA microarray from three pairs of lung SCCs and normal tissue,miR-551b and miR-765were selected and assayed by qRT-PCR in the same samples as used in the miRNA microarray experiment.The qRT-PCR results indicated that miR-551b was upregu-lated and miR-765was downregulated in each of the three lung SCCs samples used for validation,which was consis-tent with the results of miRNA microarray (Fig.2).3.3.Expression of let-7i,miR-125-5p,and miR-126in 20pairs of SCC samples

The miRNAs with O 1.5-fold changes were de?ned to be differentially expressed between the lung normal tissue and SCCs.We assayed the expression of let-7i,miR-125-5p,and miR-126from another 20pairs of samples

by

Fig.1.Hierarchical clustering of lung squamous cell carcinoma (SCC)samples.Samples are in columns,miRNAs in rows.The miRNA clustering tree is shown on the left,and the sample clustering tree appears at the top.The color scale along the top illustrates the relative expression level of a miRNA (red,high expression level;green,low expression level).

=

130Y.Yang et al./Cancer Genetics and Cytogenetics 200(2010)127e 133

qRT-PCR.For the20SCC samples,let-7i was upregulated in1and downregulated in9;miR-125-5p was upregulated in5and downregulated in5;and miR-126was upregu-lated in1and downregulated in16(Fig.3).

4.Discussion

Lung cancer is now the leading cause of cancer mortality worldwide[29].The current5-year survival rate for lung cancer is a discouraging15%,although there has been an incremental improvement in survival rate over the last several decades.The survival advances seen in other common malignancies have not been realized in lung cancer.A number of studies have directly pro?led miRNA expression in lung cancers,and unique groups of miRNAs were identi?ed to either characterize the neoplastic tissues or identify patients with poor prognosis[30e32].

We used miRNA expression arrays to determine the miRNA pro?les for lung SCC and normal lung tissue. The miRNA expression pro?les distinguished SCC from normal lung tissue,and the samples were classi?ed into two clusters:normal and SCC(Fig.1).The expression levels of miR-551b and miR-765determined by qRT-PCR were consistent with the results of miRNA microarray (Fig.2)in the same samples.A few of the miRNAs, including miR-30a,let-7i and miR-126,were found to be downregulated in lung SCCs;these results were consistent with?ndings for lung adenocarcinomas in Baltimore, Maryland[31],but were not consistent with?ndings from lung SCC in Michigan[33],suggesting the possibility of different miRNA expression for lung SCC in different ethnic groups.

The let-7miRNA,one of the best-studied miRNAs to date, is involved in inhibition of cancer growth.Reduced let-7i expression signi?cantly increased the resistance of ovarian and breast cancer cells to the chemotherapy drug cis-platinum, and was signi?cantly associated with shorter progression-free survival of patients with late-stage ovarian cancer[23].In the present study,let-7i,a member of the let-7miRNA family,was downregulated in7of the20samples.

MiR-126expression decreased in SCC,relative to paired uninvolved tissue(Fig.1and Fig.3C).MiR-126is located in chromosome9q34.3,within the host gene encoding for epidermal growth factor like-7(EGFL7)[34,35].MiR-126expression is the greatest within highly vascularized tissues,such as the lung,heart,and kidney[36].Recent studies indicate that miR-126might function as a tumor suppressor[19,37].A few genes targeted by miR-126are

involved in cancer growth,including CRK[37],IRS1 [21],VEGF[38],and PIK3R2(alias p85-b)[39].Upregula-tion of miR-126induced cell cycle G1arrest in a few cancer cell lines[19,38],suggesting that miR-126could be a promising treatment in anticancer therapy.

MiR-15a acts as a putative tumor suppressor by targeting the oncogenes BCL2[40]and CCND1and WNT3A[24].The miR-15a level is signi?cantly decreased in advanced prostate tumors,whereas the expression of BCL2,CCND1,and WNT3A is inversely upregulated[24],a?nding that is consis-tent with the present study(Table3).In line with our result of a downregulation of miR-101in lung SCC,miR-101has been observed to be decreased in human hepatocellular carcinoma [41]and colon cancer[42].Furthermore,downregulation

of Fig.2.Validation of miRNA microarray results by quantitative real-time polymerase chain reaction(qRT-PCR)in lung SCC samples for(A)miR-551b,(B)miR-765,and(C)miR-126in three pairs of samples checked by miRNA microarray and by qRT-PCR.

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miR-101that was associated with upregulation of PTGS2(alias COX2)and MCL1contributed to the growth,invasive-ness,and antiapoptotic character of tumor cells.

Finally,only miR-185*and miR-125-5p were signi?-cantly upregulated in three SCC samples.MiR-185was overexpressed in both kidney and bladder cancers [26].The present ?ndings demonstrate that some miRNAs are deregulated in lung SCC,suggesting the possible involve-ment of these genes in the development and progression of SCC.References

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