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Chinese Journal of Lung Cancer logoLink to Chinese Journal of Lung Cancer
. 2014 Jun 20;17(6):437–443. [Article in Chinese] doi: 10.3779/j.issn.1009-3419.2014.06.01

基因芯片筛选CD133+/CD133-肺腺癌细胞中新的耐药基因

Screening and Identification of Novel Drug-resistant Genes in CD133+ and CD133- Lung Adenosarcoma Cells Using cDNA Microarray

Hongyan WANG 1, Shaoqiu ZHENG 1, Yongsheng TU 2, Yajie ZHANG 1,*
PMCID: PMC6000102  PMID: 24949682

Abstract

Background and objective

Cancer stem cells (CSCs) are responsible for multi-drug resistance in tumors. CD133 is a known biomarker of CSCs. The aim of this study is to screen for drug-resistant differentially expressed genes in CD133+ and CD133- lung cancer cells and to identify novel lung tumor drug-resistant genes.

Methods

Magnetic activated cell sorting was used to isolate CD133+ and CD133- cells from human lung cancer cell line A549, and drug-resistant microarray was used to detect drug-resistant genes in the these cells. RT-qPCR was used to examine the expression of six lung tumor drug-resistant genes in pre-and post-chemotherapeutic A549 cells.

Results

A total of 31 differentially expressed genes were screened by microarray analysis. Of these genes, 30 were upregulated and one was downregulated in CD133+ cells compared with CD133- cells. Results were verified by RT-qPCR. CYP2C19, CYP2D6, CYP2E1, GSK3α, PPARα, and PPARβ/δ were significantly upregulated after the A549 cells were treated with 1.97 μg/mL DDP or 0.61 μg/mL doxorubicin for 48 h.

Conclusion

The drug resistance of lung adenosarcoma may be correlated with 31 differentially expressed genes screened by drug-resistant microarray. CYP2C19, CYP2D6, CYP2E1, GSK3α, PPARα, and PPARβ/δ might be novel lung adenosarcoma drug-resistant genes.

Keywords: CD133, Lung neoplasms, Multi-drug resistant, Drug-resistant microarray


肺癌是人类发病率和死亡率均居首位的恶性肿瘤。化学药物治疗是主要的治疗手段之一,但肿瘤细胞的耐药性却严重影响了抗肿瘤药物的治疗效果。肺癌细胞的耐药是多基因异常表达共同作用的结果,如P-糖蛋白(P-glycoprotein, P-gp)、多药耐药相关蛋白(mutidrug resistance protein, MRP)、乳腺癌耐药蛋白(breast cancer resistance protein, BCRP)和肺耐药相关蛋白(lung resistance-related protein, LRP)等基因的过表达,拓扑异构酶Ⅱ、谷胱甘肽-S-转移酶和蛋白激酶C的改变,另外,促进DNA修复和抑制细胞凋亡的基因表达改变以及某些癌基因的活化也可导致多药耐药[1]。但是有些肺癌耐药现象并不能用已知的耐药基因的表达来解释,还需要发现新的耐药相关基因。目前,国内外研究进行肿瘤耐药基因的筛选多利用生物芯片、差异显示PCR和抑制消减杂交等技术对肿瘤亲本细胞株和耐药细胞株的基因表达谱进行测定,寻找差异表达基因。肿瘤干细胞的发现使人们对肿瘤耐药的机制又有了许多新的认识,基于肿瘤干细胞理论对肺癌耐药的研究成了当今的热点。本研究以肿瘤干细胞分子标记CD133作为标志物,利用功能分类基因芯片技术对免疫磁珠分选后未经培养的CD133+和CD133-肺癌细胞的肿瘤耐药基因进行检测,筛选出差异表达基因,结合国内外文献,寻求新的肺癌耐药相关基因,为肺癌耐药的研究提供实验依据。

1. 材料与方法

1.1. 细胞培养

A549细胞培养在含10%新生牛血清的1640完全培养基(美国Gibco公司)中,放置在5%CO2、37 ℃饱和温度培养箱中培养。

1.2. CD133+和CD133-肺癌细胞的分离

收集对数生长期的A549细胞5×107个,离心后重悬于300 μL缓冲液(2%胎牛血清、2 mmol/L EDTA、0.01% PBS),再依次加入100 μL FCR阻断剂及100 μL CD133磁性微珠(德国Miltenyi Biotec公司),充分混悬后4 ℃暗处孵育30 min,续加缓冲液洗涤、离心、重悬。将细胞悬液移入已经安装在磁性分选架的MS阳性分选柱中,待细胞悬液流出,加入2倍体积的缓冲液洗涤分选柱(洗脱下来的含CD133-细胞)。待洗涤缓冲液流出后加入500 μL缓冲液,装上分选柱配套的柱芯,快速推柱芯,收集流出液为CD133+细胞。取LD阴性分选柱安装在磁性分选架上,将MS分选过程收集的流出液加入LD分选柱中,续用缓冲液洗涤,收集流出液为CD133-细胞。

1.3. CD133+和CD133-肺癌细胞差异基因的基因芯片筛选

MS柱分选获得CD133+细胞及LD柱分选获得CD133-细胞,不经培养,直接离心沉淀细胞,每5×106-10×106细胞加入1 mL TRIzol试剂(Invitrogen公司)。提取的RNA用RNeasy® MinElute™纯化试剂盒(Qiagen公司)纯化。用核酸定量仪检测纯化后的RNA的浓度及纯度并进行琼脂糖凝胶电泳。cDNA合成按RT-PCR Array First Strand Kit(美国SABiosciences公司)的说明书完成。合成后的cDNA加入SuperArray功能基因芯片RT2 Profiler™ PCR Array Human Cancer Drug Resistance & Metabolism(PAHS-004A,美国SABiosciences公司)中,经荧光定量PCR仪扩增。数据分析采用ΔΔCt方法。首先计算每个处理组中的每个耐药基因的ΔCt。ΔCt=平均值Ct-管家基因平均值Ct。然后计算2个PCR Array(或两组)中每个耐药基因的ΔΔCt。ΔΔCt =ΔCt(CD133+细胞组)-ΔCt(CD133-细胞组)。最后通过2-ΔΔCt计算CD133+细胞组与CD133-细胞组对应基因的表达差异。筛选出2-ΔΔCt≥2.0或≤0.5的基因作为差异表达基因。

1.4. RT-qPCR验证芯片中部分差异基因表达

随机选取基因芯片中耐药差异基因METIGF2RRARGPPARβ/δ进行RT-qPCR分析。同时检测筛选出的新的肺癌耐药相关基因CYP2C19CYP2D6CYP2E1GSK3αPPARα等的表达水平。根据RT-qPCR引物设计原则,利用Primer Premier5.0进行引物设计。各差异基因和内参照GAPDH引物均由TAKARA公司合成,具体见表 1。收集分选后培养的CD133+细胞及CD133-细胞,提取RNA,方法同1.3.1。cDNA合成按TAKARA公司PrimeScript RT Reagent kit说明书完成。RT-qPCR按照Roche公司RT-qPCR试剂盒说明书,于冰上配制反应体系:FastStart Universal SYGreen Master(ROX)12.5 µL,Forward primer(10 μM)0.75 µL,Reverse primer(10 μM)0.75 µL,cDNA 1 µL,ddH2O 10 µL。反应条件:50 ℃ 2 min,95 ℃预变性2 min,循环参数:95 ℃ 15 s,60 ℃ 60 s,共循环40次。每个样品设2个复孔,按上述条件置RT-qPCR仪上进行扩增反应,实验重复3次。采用ΔΔCt法进行相对定量分析,结果由ABI7500软件自动生成。

1.

RT-qPCR中各差异表达的耐药基因和内参基因GAPHD的引物序列

Primers for qPCR amplification

Gene Sense strand(5'to 3') Antisense strand(5'to 3')
GAPDH GCACCGTCAAGGCTGAGAAC TGGTGAAGACGCCAGTGGA
MET CTCCCATCCAGTGTCTCCAGAAG TGCAGCCCAAGCCATTCA
IGF2R CCGCTAAACAGTTCGCAAGGA CAGTTTGGGTTTCTGCCTCACA
RARG CCAGCCCTACATGTTCCCAAG CATCCTCAAACATTTCAGGGTTCTC
PPARβ/δ CTACGGTGTTCATGCATGTGAGG GCACTTCTGGAAGCGGCAGTA
CYP2C19 GGAAAACGGATTTGTGTGGGA GGTCCTTTGGGTCAATCAGAGA
CYP2D6 ACCAGGCTCACATGCCCTA TTCGATGTCACGGGATGTCAT
CYP2E1 ATGTCTGCCCTCGGAGTCA CGATGATGGGAAGCGGGAAA
GSK3α GGAAAGGCATCTGTCGGGG GAGTGGCTACGACTGTGGTC
PPARα ATGGTGGACACGGAAAGCC CGATGGATTGCGAAATCTCTTGG

1.5. A549细胞针对顺铂(cisplatin, DDP)和阿霉素的IC50浓度确立

将A549细胞密度调整至5×104个/mL,接种入96孔细胞培养板中,100 μL/孔,培养24 h后轻轻吸掉培养液,加入经RPMI1640培养液系列稀释的DDP或阿霉素(齐鲁制药有限公司),200 μL/孔,DDP终浓度分别为0.156 μg/mL、0.312, 5 μg/mL、0.625 μg/mL、1.25 μg/mL、2.5 μg/mL、5 μg/mL、10 μg/mL,阿霉素终浓度分别为0.062, 5 μg/mL、0.125 μg/mL、0.25 μg/mL、0.5 μg/mL、1 μg/mL、2 μg/mL、4 μg/mL,对照组不加药。各组设3个复孔,48 h后用CCK-8比色法检测细胞存活情况,测定波长为450 nm处各孔的吸光度(optical delnsity, OD)值,按以下公式计算细胞存活率:细胞存活率=(OD药物组/OD对照组)×100%。实验重复3次。通过线性拟合法计算出药物的半数有效抑制浓度(half inhibiting concentration, IC50)。

1.6. RT-qPCR检测肺癌耐药差异基因mRNA表达

收集A549细胞和DDP IC50和阿霉素IC50处理48 h后的A549细胞,抽提总RNA,cDNA合成,qPCR方法和相对定量分析同1.4。

2. 结果

2.1. 功能分类基因芯片结果

与CD133-细胞相比,CD133+肺腺癌细胞在84个检测的耐药基因中表达差异达两倍或以上的有31个,占36%(31/84),其中30个基因表达上调,1个基因表达下调,表达差异最为明显的基因是RARGESR2,它们的表达水平分别上调或下调了8.93倍和2.52倍(表 2)。这31个差异表达基因中,未被文献报道过的与肺癌耐药相关的基因有CYP2C19CYP2D6CYP2E1GSK3αPPARαPPARβ/δ

2.

CD133+与CD133-肺腺癌细胞表达差异2倍以上的肿瘤耐药基因

Differentially expressed drug-resistant genes between CD133+ and CD133- cells

RefSeq Gene symbol Gene description Chromosomal localization Fold change
If the fold change is positive, it means up-regulation. If the fold change is negative, it means down-regulation.
NM_000966 RARG Retinoic acid receptor, gamma 12q13 +8.93
NM_000367 TPMT Thiopurine S-methyltransferase 6p22.3 +7.39
NM_019884 GSK3α Glycogen synthase kinase 3 alpha 19q13.2 +5.66
NM_001800 CDKN2D Cyclin-dependent kinase inhibitor 2D 19p13 +5.17
NM_017458 MVP Major vault protein 16p11.2 +4.16
NM_006509 RELB V-rel reticuloendotheliosis viral oncogene homolog B 19q13.32 +4.04
NM_021976 RXRB Retinoid X receptor, beta 6p21.3 +3.59
NM_002503 NFKBIB Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta 19q13.1 +3.23
NM_005229 ELK1 ELK1, member of ETS oncogene family Xp11.2 +3.17
NM_006238 PPARβ/δ Peroxisome proliferator-activated receptor delta 6p21.2 +3.10
NM_000059 BRCA2 Breast cancer 2, early onset 13q12.3 +2.98
NM_001171 ABCC6 ATP-binding cassette, sub-family C (CFTR/MRP), member 6 16p13.1 +2.91
NM_000769 CYP2C19 Cytochrome P450, family 2, subfamily C, polypeptide 19 10q24 +2.91
NM_000122 ERCC3 Excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) 2q21 +2.81
NM_000106 CYP2D6 Cytochrome P450, family 2, subfamily D, polypeptide 6 22q13.1 +2.71
NM_002467 MYC V-myc myelocytomatosis viral oncogene homolog (avian) 8q24.21 +2.62
NM_000876 IGF2R Insulin-like growth factor 2 receptor 6q26 +2.54
NM_001437 ESR2 Estrogen receptor 2 (ER beta) 14q23.2 -2.52
NM_053056 CCND1 Cyclin D1 11q13 +2.45
NM_000546 TP53 Tumor protein p53 17p13.1 +2.43
NM_000038 APC Adenomatous polyposis coli 5q21-q22 +2.36
NM_000392 ABCC2 ATP-binding cassette, sub-family C (CFTR/MRP), member 2 10q24 +2.30
NM_000321 RB1 Retinoblastoma 1 13q14.2 +2.27
NM_004324 BAX BCL2-associated X protein 19q13.3-q13.4 +2.21
NM_005036 PPARα Peroxisome proliferator-activated receptor alpha 22q13.31 +2.15
NM_004996 ABCC1 ATP-binding cassette, sub-family C (CFTR/MRP), member 1 16p13.1 +2.14
NM_001668 ARNT Aryl hydrocarbon receptor nuclear translocator 1q21 +2.14
NM_138579 BCL2L1 BCL2-like 1 20q11.21 +2.13
NM_000245 MET Met proto-oncogene (hepatocyte growth factor receptor) 7q31 +2.11
NM_000773 CYP2E1 Cytochrome P450, family 2, subfamily E, polypeptide 1 10q24.3-qter +2.02
NM_003839 TNFRSF11A Tumor necrosis factor receptor superfamily, member 11a, NFKB activator 18q22.1 +2.01

2.2. 功能分类基因芯片中部分差异表达基因的验证

应用RT-qPCR检测了随机选取的RARGPPARβ/δIGF2RMET等四个差异基因和新发现的CYP2C19CYP2D6CYP2E1GSK3αPPARα等肺癌耐药基因在CD133+细胞与CD133-细胞中的表达,结果见图 1。与CD133-细胞比较,CD133+细胞RARGPPARβ/δIGF2RMETCYP2C19CYP2D6CYP2E1GSK3αPPARα等基因mRNA的表达均上调。该结果与功能分类基因芯片的检测结果一致。

1.

1

RT-qPCR验证部分差异表达基因在CD133+与CD133-细胞中的表达

Some drug-resistant genes expression between CD133+ and CD133- cells

2.3. A549细胞针对DDP和阿霉素的IC50浓度确立

不同浓度的DDP和阿霉素对A549细胞的增殖有明显的抑制作用,通过线性拟合法计算A549细胞的DDP IC50为1.97 μg/mL,阿霉素IC50为0.61 μg/mL(表 3)。

3.

不同浓度DDP和阿霉素对A549细胞的抑制率(Mean±SD)(%, n=3)

The survival rate of DDP and Doxorubicin on A549 cells (Mean±SD)(%, n=3)

DDP Doxorubicin
Concentration (μg/mL) Survival rate of cells Concentration (μg/mL) Survival rate of cells
Control 100 Control 100
0.156 95.50±2.06 0.062, 5 96.40±2.52
0.312, 5 88.60±2.09 0.125 87.56±2.71
0.625 80.25±1.98 0.25 79.20±2.91
1.25 66.01±1.29 0.5 53.97±3.30
2.5 40.32±3.15 1 34.86±4.33
5 24.70±1.54 2 21.3±2.06
10 11.17±1.63 4 7.06±3.02

2.4. RT-qPCR对部分肺癌耐药相关基因的检测结果

A549细胞经DDP IC50和阿霉素IC50分别作用48 h后,CYP2C19CYP2D6CYP2E1GSK3αPPARαPPARβ/δ等耐药相关基因表达均不同程度地上调(图 2)。

2.

2

DDP IC50(A)和阿霉素IC50(B)作用前后A549细胞中肺癌耐药基因表达的变化。IC50:半数有效抑制浓度。

Drug-resistant genes expression levels of A549 cells in pre-and post-chemotherapy

3. 讨论

CD133是目前使用较广泛的肿瘤干细胞标记物。研究发现,CD133+肺癌细胞具有干细胞样的特性,对化疗不敏感[2-5]。本研究以CD133作为标记物,分离CD133+和CD133-肺腺癌细胞,并筛选出二者之间的肿瘤耐药差异表达基因,为肺腺癌耐药的研究提供实验依据。

干细胞在体外培养过程中容易发生分化而失去干细胞的特性,为了维持CD133+细胞的未分化状态,我们将分选未经培养的CD133+和CD133-细胞直接用于后续实验。研究采用美国SuperArray公司生产的第二代功能分类基因芯片(RT2 Profiler™芯片),该芯片包含目前研究已证实与人类肿瘤耐药相关的84个基因。结果显示:在筛查的84个耐药基因中,有31个基因表达差异达两倍或两倍以上。与CD133-细胞相比,CD133+细胞有30个基因表达升高,1个基因表达降低。表达升高的基因按功能分类分别为:①药物转运蛋白相关基因,包括ABCC1ABCC2ABCC6MVP;②药物代谢酶类相关基因,包括ARNTCYP2C19CYP2D6CYP2E1GSK3αTPMT;③细胞增殖相关基因,包括IGF2RMETPPARαPPARβ/δRARGRXRB;④诱导凋亡相关基因,包括BAXBCL-XLRB1TP53;⑤转录因子,包括ELK1MYCNF-κBIBRELBTNFRSF11A;⑥DNA修复相关基因,包括APCBRCA2ERCC3;⑦细胞周期调控基因,包括CDKN2DCCND1。表达降低的基因是抑制细胞增殖的ESR2基因。这31个差异表达基因中,未被文献报道过的与肺癌耐药相关的基因有CYP2C19CYP2D6CYP2E1GSK3αPPARαPPARβ/δ

细胞色素P450(cytochrome P450, CYP450)属于血红蛋白超基因家族。作为重要的一相代谢酶,CYP450广泛参与人体内羟化、氧化、还原、水解等多种一相反应,对外源性药物、致癌化合物以及内源性物质如类固醇进行代谢。研究[6]表明,部分CYP450在肿瘤组织中高表达且与肿瘤的多药耐药相关。如CYP3A4/5在骨肉瘤中的高表达预示着不良的药物治疗效果[7]。CYP2C19、CYP2D6、CYP2E1在他莫西芬、吉非替尼、依托泊苷、长春新碱、沙利度胺、伊马替尼、环磷酰胺等多种常用抗癌药物的代谢中发挥重要作用[8]。现已证实CYP2C19在肝癌和结肠癌中高表达[9],CYP2D6在胃癌组织中表达也较相应正常组织高[10],CYP2E1在脑肿瘤、肝癌、乳腺癌、非小细胞肺癌中表达升高[11],但是这些基因的表达是否与肺癌耐药相关未见报道。本研究发现CD133+肺腺癌细胞较CD133-细胞高表达CYP2C19、CYP2D6、CYP2E1,提示它们可能在CD133+细胞耐药过程中发挥重要作用。这些CYP450可通过增强对抗肿瘤药物的代谢作用从而减弱药物的抗肿瘤作用甚至使其灭活,使肿瘤发生耐药现象。

糖原合成酶激酶3(glycogen synthase kinase 3, GSK3)是一种多功能的丝/苏氨酸磷酸激酶,有GSK3α和GSK3β两种亚型。GSK-3的基本功能是识别和磷酸化特定序列,GSK-3α第21位点上丝氨酸的磷酸化可造成GSK-3的失活,失活的GSK-3通过调控Wnt/β-catenin、PI3K/Akt和NF-κB等多种信号传导通路参与肿瘤细胞的增殖、分化和凋亡[12]。Fu等[13]报道GSK3α mRNA及蛋白在卵巢癌耐紫杉醇细胞株中表达明显较亲本株高,认为高表达的GSK3α可能与耐药有关。Piazza等[14]发现在多发性骨髓瘤细胞中敲除基因GSK3α后,瘤细胞对bortezomib诱导的凋亡敏感性增加。本研究发现CD133+肺腺癌细胞较CD133-细胞高表达GSK3α,提示GSK3可能参与CD133+肺腺癌细胞的耐药。

过氧化物酶体增殖因子激活受体(peroxisome proliferator activated receptors, PPARs)是一类由配体激活的转录因子,属于核激素受体超家族成员,有PPARα、PPARβ/δ和PPARγ三种亚型。目前研究提示PPARs与肿瘤具有相关性,但PPARα和PPARβ/δ在肿瘤发生发展中的作用一直存有争议。体外实验研究发现PPARα激动剂可诱导肿瘤细胞凋亡,抑制肿瘤新生血管形成,对人子宫内膜癌细胞、卵巢癌细胞、结肠癌细胞和黑色素瘤细胞均有不同程度的抗肿瘤活性[15]。但在NNK诱导的鼠肺癌模型上,激活PPARα可促进肺肿瘤的发生发展[16]。PPARβ在肺癌组织中表达降低,PPARβ激动剂可以下调Cyclin D1和PCNA,阻滞细胞周期G1期从而抑制肺腺癌细胞增殖[17]。但也有研究[18]报道PPARβ/δ激活剂可以促进肺癌细胞增殖,其机制涉及通过PI3K/AKT途径上调EP4的受体PGE2,下调PTEN和增加AKT磷酸化。本研究发现CD133+肺腺癌细胞较CD133-细胞高表达PPARα和PPARβ/δ,PPARα和PPARβ/δ在肺腺癌耐药中的确切作用究竟如何?这一课题值得深入研究。

肿瘤化疗耐药是一个多基因、多环节、多途径参与的过程,可能涉及影响不同生化途径的多种遗传因子表达的改变。本研究在CD133+/CD133-肺腺癌细胞中筛选出31个可能与肺癌多药耐药相关的基因,其中CYP2C19CYP2D6CYP2E1GSK3αPPARαPPARβ/δ为新发现的肺腺癌耐药相关基因,这些差异表达基因给肺腺癌耐药的研究提供了实验依据。进一步的研究将通过体内外试验证实这几个新颖的肺腺癌耐药相关基因在CD133+肺腺癌细胞耐药中的作用,以期为肺腺癌耐药的逆转提供新策略。

Funding Statement

本研究受教育部博士点基金(No.20134423110001)、广东省自然科学基金(No.S2012010010181)、广州市科技计划项目(No.2014Y2-00171)、广州市教育系统创新学术团队项目(No.13C06)和广州市属高校科研项目(No.2012C135)资助

This study was supported partly by the grants from Doctoral Fund of Ministry of Education of China (to Yajie ZHANG)(No.20134423110001), Guangdong Province Natural Science Foundation(to Yajie ZHANG)(No.S2012010010181), Science and Technology Program of Guangzhou (to Yajie ZHANG)(No.2014Y2-00171), Guangzhou Municipal Education Department Innavation team grant (to Yajie ZHANG)(No.13C06), and Guangzhou City-belonged Universities Scientific Research Program (to Hongyan WANG)(No.2012C135)

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