摘要:目的" 運(yùn)用生物信息學(xué)技術(shù)篩選膠質(zhì)母細(xì)胞替莫唑胺(GBM TMZ)耐藥差異表達(dá)基因(DEGs),探尋關(guān)鍵耐藥基因及發(fā)病機(jī)制,并預(yù)測相關(guān)作用中藥。方法" 在GBM、GEO2R和GPEIA等多種數(shù)據(jù)庫基礎(chǔ)上進(jìn)行生物學(xué)功能及通路富集分析,構(gòu)建蛋白互作網(wǎng)絡(luò)篩選關(guān)鍵基因,檢索關(guān)鍵基因在正常人、膠質(zhì)瘤患者組織中mRNA表達(dá)及生存率的影響。利用COREMINE平臺對關(guān)鍵耐藥基因構(gòu)建藥物-活性成分-作用靶點(diǎn)網(wǎng)絡(luò),篩選相關(guān)中藥活性成分。結(jié)果" 共篩選出293個DEGs,涉及FN1、CD44、CTGF、FOS等關(guān)鍵靶點(diǎn),其表達(dá)顯著高于正常人,影響患者總生存率,是GBM有害預(yù)后因素,但不會影響無復(fù)發(fā)生存率。影響細(xì)胞粘附、神經(jīng)系統(tǒng)發(fā)育、轉(zhuǎn)化生長因子β受體信號傳導(dǎo)和基因正向調(diào)節(jié)等生物學(xué)功能。經(jīng)COREMINE預(yù)測發(fā)現(xiàn),與FN1關(guān)系密切的干預(yù)藥物多歸屬肝經(jīng),性味多以清熱類和補(bǔ)虛類為主。結(jié)論" 篩選出12個與GBM TMZ耐藥相關(guān)的關(guān)鍵基因,F(xiàn)N1在TMZ耐藥發(fā)生發(fā)展中起重要作用,木香、青葉膽及蓖麻子的活性成分可能作為TMZ耐藥治療藥物來源。
關(guān)鍵詞:膠質(zhì)母細(xì)胞瘤;替莫唑胺;耐藥基因;生物信息學(xué);中藥預(yù)測
中圖分類號:R969" " " " " " " " " " " " " " " " " " " "文獻(xiàn)標(biāo)識碼:A" " " " " " " " " " " " " " "DOI:10.3969/j.issn.1006-1959.2024.19.002
文章編號:1006-1959(2024)19-0010-09
Drug Resistance Gene Screening and Therapeutic Drug Prediction of Glioblastoma
CHU Xiaoling1,WU Bo1,LAN Xiaohong1,YI Jianfeng2,LI Xuemei1,CHEN Xuqing1
(1.Department of Pharmacy,Eastern Theater Command General Hospital,Nanjing 210002,Jiangsu,China;
2.Research Center for Differentiation and Development of Basic Theories of TCM,Jiangxi University of Traditional Chinese Medicine,Nanchang 330004,Jiangxi,China)
Abstract:Objective" To screen differentially expressed genes (DEGs) of temozolomide (TMZ) resistance in glioblastoma cells (GBM) by bioinformatics technology, explore the key drug resistance genes and pathogenesis, and predict the related traditional Chinese medicine.Methods" Based on GBM, GEO2R, GPEIA and other databases, biological function and pathway enrichment analysis were carried out, and protein interaction network was constructed to screen key genes. The effects of key genes on mRNA expression and survival rate in normal human and glioma patients were searched. The COREMINE platform was further used to construct a drug-active ingredient-target network for key drug resistance genes, and the active ingredients of related Chinese medicines were screened.Results" A total of 293 DEGs were screened, involving key targets such as FN1, CD44, CTGF, and FOS. The expression was significantly higher than that of normal people, affecting the overall survival rate of patients, and was a harmful prognostic factor for GBM, but it did not affect the recurrence-free survival rate. While it affected biological functions such as cell adhesion, nervous system development, transforming growth factor β receptor signal transduction and gene positive regulation. It was predicted by COREMINE that the intervention drugs closely related to FN1 were mostly attributed to the liver meridian, and the nature and flavor were mainly heat-clearing and deficiency-tonifying.Conclusion" Twelve key genes related to TMZ resistance in GBM were screened out. FN1 plays an important role in the occurrence and development of TMZ resistance. The active components of Muxiang, Qingyedan and Bimazi may be used as the source of TMZ resistance drugs.
Key words:Glioblastoma;Temozolomide;Drug resistance genes;Bioinformatics;Traditional Chinese medicine prediction
膠質(zhì)母細(xì)胞瘤(glioblastoma, GBM)是常見的原發(fā)性顱內(nèi)惡性腫瘤(WHO IV級),其發(fā)病率占所有原發(fā)性中樞系統(tǒng)惡性腫瘤48%,盡管進(jìn)行了十多年大量的研究,但GBM的預(yù)后仍然很差[1-3]?,F(xiàn)階段,GBM標(biāo)準(zhǔn)治療以手術(shù)為主,輔以術(shù)后同步放化療。替莫唑胺(temozolomide, TMZ)因其口服吸收完全、生物利用度近乎100%、良好的血腦屏障通透性,以及突出的治療效果,已成為治療GBM首選藥物[4,5]。長期使用TMZ易產(chǎn)生耐受性,造成患者腫瘤復(fù)發(fā)率升高、中位生存期下降。因此,降低GBM TMZ耐藥是GBM臨床治療亟需解決問題。研究顯示[6],GBM TMZ耐藥機(jī)制與DNA損傷修復(fù)、細(xì)胞自噬及膠質(zhì)瘤干細(xì)胞等多途徑相關(guān),而耐藥性發(fā)生發(fā)展中參與調(diào)控的主要基因及干預(yù)藥物尚不完全清楚。生物信息學(xué)是由分子生物學(xué)和信息技術(shù)結(jié)合而成一門新興交叉學(xué)科,基因表達(dá)譜或其他高通量數(shù)據(jù)的生物信息學(xué)分析在研究人類疾病發(fā)病機(jī)制中發(fā)揮了關(guān)鍵作用。本研究應(yīng)用生物信息學(xué)技術(shù)篩選GBM TMZ耐藥關(guān)鍵基因,并對其進(jìn)行中藥預(yù)測,旨在為研究GBM TMZ耐藥發(fā)生發(fā)展的分子機(jī)制和實(shí)驗(yàn)研究提供理論依據(jù)。
1資料與方法
1.1數(shù)據(jù)來源" 基因數(shù)據(jù)庫:基因表達(dá)綜合數(shù)據(jù)庫(GEO)(https://www.ncbi.nlm.nih.gov/geo/)、STRING數(shù)據(jù)庫(https://cn.string-db.org/)、DAVID生物信息資源數(shù)據(jù)庫(https://david.ncifcrf.gov/)、UniProtKB蛋白質(zhì)數(shù)據(jù)庫(https://www.uniprot.org/help/uniprotkb)、TCMSP中藥系統(tǒng)藥理學(xué)分析平臺(https://old.tcmsp-e.com/tcmsp.php)、基因表達(dá)譜數(shù)據(jù)動態(tài)分析(http://gepia.cancer-pku.cn/)和Coremine Medical數(shù)據(jù)庫(https://www.coremine.com/)[7]。軟件工具包括:SangerBox生物醫(yī)學(xué)分析盒子(http://vip.sangerbox.com/login.html)和Cytoscape3.9.1(Network Analysis和cytoHubba插件)?;虮磉_(dá)譜芯片來源于GEO數(shù)據(jù)中GBM數(shù)據(jù)集,編號:GSE68029,平臺信息GPL570[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array由美國加州大學(xué)提供。
1.2 GBM/GBM-500 μM TMZ差異表達(dá)基因(DEGs)獲取及可視化處理" 利用GEO2R對GSE68029進(jìn)行分析(實(shí)驗(yàn)組為GBM-500 μM TMZ,對照組為GBM組),結(jié)果導(dǎo)出Excel文件,設(shè)置篩選參數(shù)(|log2FC|gt;0.5,Plt;0.05),得到DEGs[8]。利用Sanger Box中的工具模塊繪制DEGs火山圖及熱圖。
1.3 PPI網(wǎng)絡(luò)構(gòu)建及關(guān)鍵基因篩選" 將DEGs上傳至STRING數(shù)據(jù)庫中,選擇“Multiple proteins”模塊,物種選擇“Homo sapiens”,combined scoregt;0.7,排除孤立點(diǎn),導(dǎo)出CSV文件。將CSV文件導(dǎo)入Cytoscape3.9.1軟件行可視化處理,并用“Network Analysis”插件計算該網(wǎng)絡(luò)度值,設(shè)置篩選條件(關(guān)鍵基因度值gt;2倍平均度值),得到DEGs中的關(guān)鍵基因[9]。
1.4 DEGs功能富集分析" 將DEGs上傳到DAVID數(shù)據(jù)庫[10],選擇“OFFICEL GENE SYMBOL”模塊,物種選擇“Homo sapiens”提交,得到基因本體論(GO)功能注釋和京都基因百科全書(KEGG)信號通路。GO功能注釋包含生物過程(biological process, BP)、分子功能(molecular function, MF)和細(xì)胞成分(cell component, CC),篩選條件為Plt;0.05。
1.5關(guān)鍵基因在膠質(zhì)瘤中的表達(dá)及生存率影響" 在GPEIA數(shù)據(jù)庫中輸入關(guān)鍵基因,選擇“Single Gene Analysis”模塊,分析關(guān)鍵基因在正常人組織和膠質(zhì)瘤組織的差異性表達(dá);利用“Survival Analysis”模塊進(jìn)行總生存率分析。
1.6預(yù)測潛在中藥并構(gòu)建“中藥-活性成分-靶點(diǎn)”網(wǎng)絡(luò)" 依次在Coremine Medical數(shù)據(jù)平臺上輸入關(guān)鍵基因,檢索“Traditional Chinese medicine”模塊,設(shè)置篩選條件(Plt;0.05),得到潛在中藥并對其進(jìn)行性味歸經(jīng)分析。在TCMSP數(shù)據(jù)庫檢索中藥相關(guān)成分(設(shè)置篩選條件OB≥30%,DL≥0.18)及其對應(yīng)靶點(diǎn),用Cytoscape3.9.1行可視化處理。
2結(jié)果
2.1 GBM/GBM-500 μM TMZ差異表達(dá)基因獲取結(jié)果" 在GEO數(shù)據(jù)中檢索“glioblastoma”“temozolomide”“drug resistance”,獲得GSE68029芯片數(shù)據(jù)集(包括6例GBM和6例GBM-500 μM TMZ)。利用GEO2R在線分析軟件對其分組,用limma包分析該芯片基因表達(dá),并用SangBox軟件繪制火山圖和熱圖,見圖1。共獲得差異基因293個,其中上調(diào)基因199個,下調(diào)基因94個。
2.2耐藥關(guān)鍵基因獲取" 借助STRING數(shù)據(jù)庫構(gòu)建DEGs蛋白互作PPI網(wǎng)絡(luò)圖,下載分析結(jié)果,并用Cytoscape軟件可視化。排除孤立節(jié)點(diǎn)后,該網(wǎng)絡(luò)中有156個節(jié)點(diǎn)、273條邊,在DEGs蛋白互作(PPI)網(wǎng)絡(luò)圖中,形狀越大則連接度越大,見圖2A。隨后用“NetworkAnalyzer”插件分析該網(wǎng)絡(luò),其中FN1、CD44、CTGF、FOS、EGR1、ZEB1、AURKB、KITGL、ARF6、ITGA3、CHD4和NCAM1的度值高于平均值(見圖2B),該網(wǎng)絡(luò)中關(guān)鍵基因連接度排序,連接度越大,表示該基因在網(wǎng)絡(luò)中起主要橋梁作用。在網(wǎng)絡(luò)中起著中藥重要橋梁作用,可能為介導(dǎo)膠質(zhì)母細(xì)胞替莫唑胺耐藥關(guān)鍵靶點(diǎn)。
2.3基因本體論(GO)及KEGG信號通路富集分析結(jié)果" 將DEGs上傳至DAVID數(shù)據(jù)庫,進(jìn)行生物學(xué)功能及通路富集分析。GO分析共獲76個條目,其中生物過程主要涉及細(xì)胞粘附、神經(jīng)系統(tǒng)發(fā)育、細(xì)胞-基質(zhì)粘附、轉(zhuǎn)化生長因子β受體信號傳導(dǎo)途徑的調(diào)節(jié)和基因正向調(diào)節(jié)等;細(xì)胞組成成分涉及絲狀體膜、染色質(zhì)、膜和細(xì)胞表面等;分子功能涉及膠原蛋白結(jié)合、轉(zhuǎn)錄輔助因子結(jié)合和DNA結(jié)合等,見表1。KEGG信號通路主要富集在癌癥、細(xì)胞外基質(zhì)受體相互作用、造血細(xì)胞系和磷脂酰肌醇3激酶信號通路等,見圖3。
2.4關(guān)鍵基因在正常組織和膠質(zhì)瘤中的表達(dá)差異及總生存率(overall survival, OS)影響" 為探明關(guān)鍵基因參與調(diào)控GBM,借助GEPIA數(shù)據(jù)庫分析其在正常人、GBM患者組織mRNA表達(dá)及OS影響。GBM患者FN1、CD44、CTGF、FOS、EGR1和ZEB1表達(dá)明顯高于正常人(Plt;0.05),見圖4A~4F;GPEIA數(shù)據(jù)庫中FN1、CD44、CTGF、FOS、EGR1和ZEB1在正常組織與腫瘤組織中mRNA表達(dá),左側(cè)方塊示腫瘤組織,右側(cè)方塊示正常組織。圖4G、圖4H顯示了高、低表達(dá)FN1對患者總生存率、無復(fù)發(fā)生率的影響:高表達(dá)的FN1顯著影響其總生存率,是GBM有害預(yù)后因素,但不會影響無復(fù)發(fā)生存率(Plt;0.05)。
2.5相關(guān)中藥及主要作用靶點(diǎn)預(yù)測分析" 在COREMINE平臺上檢索關(guān)鍵基因,得到密切關(guān)聯(lián)中藥(Plt;0.05)見表2。與FN1相關(guān)的中藥有木香(P=0.001 11)、蘄蛇(P=0.005 43)、蓖麻子(P=0.0188)和青葉膽(P=0.0195);與CD44相關(guān)中藥有蔓荊子(P=0.001 06)、挖耳草(P=0.007 52);與CTGF相關(guān)中藥是蘆莖(P=0.000 499)、關(guān)木通(P=0.000 511)和鵝不食草(P=0.003 07);與FOS相關(guān)中藥有甜石榴(P=0.004)、梔子花(P=0.009 91);與EGR1相關(guān)中藥有黃絲郁金(P=0.0111)、姜黃(P=0.0112)、新疆雪蓮(P=0.016)和黃連(P=0.0172);與ZEB1相關(guān)中藥有挖耳草(P=0.001 68)、旋覆金沸草(P=0.006 24)、旋覆花(P=0.006 24);與AURKB相關(guān)中藥有夏天無(P=0.001 26)、川貝母(P=0.003 01);與KITLG相關(guān)中藥有羊腎(P=0.006 38);與ARF6相關(guān)中藥是朝鮮淫羊藿(P=0.002 82);與ITGA3相關(guān)中藥有金錢草(P=0.000 12);與NCAM1相關(guān)中藥是沙苑子(P=0.009 37)。為探明中藥作用于FN1潛在活性化合物及主要靶點(diǎn),在TCMSP數(shù)據(jù)庫檢索中藥成分及作用靶點(diǎn),并構(gòu)建“中藥-活性成分-作用靶點(diǎn)”網(wǎng)絡(luò),符合篩選條件的化合物有21個,作用于70個靶點(diǎn),見圖5A。該網(wǎng)絡(luò)主要靶點(diǎn)分別是MAOB、MAOA、HTR3A、DRD2、SLC6A4、HTR2A、ESR1和HSP90AA1。將預(yù)測中藥進(jìn)行性味及歸經(jīng)分析,結(jié)果顯示作用于關(guān)鍵基因中藥主要?dú)w屬肝經(jīng),性味則偏苦、溫,以清熱類和補(bǔ)虛類為主,見圖5B和圖5C;主要靶點(diǎn)見圖5D。
3討論
近年來GBM TMZ耐藥相關(guān)報道呈逐漸上升趨勢,TMZ耐藥性受多基因、多通路介導(dǎo)[11-13],尋找影響TMZ耐藥的關(guān)鍵基因、功能及干預(yù)藥物對于分子水平上揭示耐藥發(fā)生發(fā)展機(jī)制具有重要意義,也可為GBM的早期診斷及新治療策略的制定提供依據(jù)。本研究通過GEO數(shù)據(jù)庫篩選合適的基因芯片,對GBM和500 μM TMZ處理后GBM組織樣本進(jìn)行DEGs分析,篩選出293個DEGs,包括上調(diào)基因199個和下調(diào)基因94個。DEGs的GO富集主要生物學(xué)過程集中在細(xì)胞粘附、神經(jīng)系統(tǒng)發(fā)育、細(xì)胞-基質(zhì)粘附、轉(zhuǎn)化生長因子β受體信號傳導(dǎo)途徑的調(diào)節(jié)和基因正向調(diào)節(jié)等。既往研究發(fā)現(xiàn)[14],腫瘤細(xì)胞周圍微環(huán)境對化療藥物的反應(yīng)有重大影響,細(xì)胞外基質(zhì)蛋白賦予細(xì)胞粘附介導(dǎo)耐藥性產(chǎn)生,側(cè)面驗(yàn)證了生物信息分析的可靠性。TGF-β1過表達(dá)導(dǎo)致MGMT啟動子低甲基化膠質(zhì)母細(xì)胞瘤細(xì)胞在體外和體內(nèi)中出現(xiàn)替莫唑胺耐藥性[11]。KEGG通路主要富集在癌癥、細(xì)胞外基質(zhì)受體相互作用、造血細(xì)胞系和磷脂酰肌醇3激酶信號通路。多種生長因子、激素及細(xì)胞外基質(zhì)等物質(zhì)構(gòu)成了腫瘤微環(huán)境,環(huán)境穩(wěn)態(tài)改變影響腫瘤細(xì)胞活力、增殖、侵襲及對藥物敏感性[15]。因此,研究上述信號通路有助于探明GBM進(jìn)展及其對TMZ的敏感性。
通過蛋白網(wǎng)絡(luò)互作得到關(guān)鍵基因,分別是FN1、CD44、CTGF、FOS、EGR1、ZEB1、AURKB、KITGL、ARF6、ITGA3、CHD4和NCAM1。表達(dá)上調(diào)的有FN1、CD44、CTGF、FOS、EGR1、ZEB1、AURKB、ARF6、ITGA3、CHD4和NCAM1,表達(dá)下調(diào)的是KITGL。GPEIA數(shù)據(jù)庫分析得出,F(xiàn)N1、CD44、CTGF、FOS、EGR1和ZEB1表達(dá)顯著高于正常人,可能參與調(diào)控GBM發(fā)生發(fā)展,直接或間接影響TMZ耐藥性。FN1顯著影響患者總生存率,是GBM有害預(yù)后因素,但不會影響無復(fù)發(fā)生率;其他基因?qū)颊呖偵媛薀o明顯影響,但目前尚不能排除毫無作用。 FN1存在于細(xì)胞外膜蛋白,是細(xì)胞外基質(zhì)和基底膜中的主要非膠原性糖蛋白,在細(xì)胞黏附中起著重要作用,可調(diào)節(jié)腫瘤細(xì)胞生長、繁殖和浸潤。近年來,研究報道[16,17],F(xiàn)N1可誘導(dǎo)PTPRM甲基化通過STAT3信號促進(jìn)GBM發(fā)生發(fā)展,且過表達(dá)FN1是GBM患者獨(dú)立的不良預(yù)后因素。黏附分子CD44(cd44 molecular, CD44)分布細(xì)胞表面跨膜糖蛋白,主要參與異質(zhì)性粘附,即腫瘤細(xì)胞與宿主細(xì)胞和宿主基質(zhì)的粘附,異質(zhì)性粘附在腫瘤細(xì)胞侵襲轉(zhuǎn)移中起促進(jìn)作用。結(jié)締組織生長因子(connective tissue growth factor, CTGF)是一種可刺激成纖維細(xì)胞增殖和膠原沉積生長因子,是高度保守CCN多肽家族中成員,高表達(dá)GTGF可誘導(dǎo)GBM細(xì)胞增殖、遷移和侵襲[18]。細(xì)胞致癌基因(cellular oncogene fos, FOS)作為一類核蛋白轉(zhuǎn)錄因子,在調(diào)控細(xì)胞生長、分裂、增殖、分化及程序死亡等方面具有重要作用。早期生長反應(yīng)蛋白1(early growth response protein 1, EGR1)為早期反應(yīng)基因家族最為重要一員,在組織損傷修復(fù)及腫瘤發(fā)生發(fā)展中扮演重要角色。Knudsen AM等[19]對207個GBM進(jìn)行了EGR1/EGR3免疫染色和定量,EGR1表達(dá)隨著WHO等級增加而增加,EGR1沒有預(yù)后價值,但可能參與MGMT甲基化。Chen L等[20]采用呋喃二烯酮(FUR)體外抑制TMZ耐藥的GBM細(xì)胞,免疫熒光和雙熒光素酶結(jié)果示,抑制EGR1介導(dǎo)轉(zhuǎn)錄可能有助于FUR依懶性阻斷硫酸軟骨素蛋白多糖4(CSPG4)信號和GBM細(xì)胞存活。鋅指E盒結(jié)合蛋白1(zinc finger e-box-binding homeobox 1, ZEB1)是鋅指結(jié)構(gòu)轉(zhuǎn)錄因子家族中的重要一員,可通過直接或間接抑制E粘附蛋白或極性蛋白表達(dá),促使相互連接的上皮細(xì)胞轉(zhuǎn)化為可在細(xì)胞基質(zhì)間移動的間質(zhì)細(xì)胞,增加腫瘤侵襲和轉(zhuǎn)移能力。研究發(fā)現(xiàn),ZEB1優(yōu)先在侵襲性GBM細(xì)胞中表達(dá),其中ZEB1-miR-200反饋回路通過下游效應(yīng)子ROBO1、c-MYB和MGMT將這些過程相互連接。此外,膠質(zhì)母細(xì)胞瘤患者中的ZEB1表達(dá)預(yù)示著較短的生存期和較差的替莫唑胺反應(yīng)[21]。由此可見,通過生物信息學(xué)分析出的關(guān)鍵基因,對于研究GBM TMZ耐藥機(jī)制意義重大,并有可能成為新的潛在治療靶點(diǎn)。
為了挖掘潛在治療GBM TMZ耐藥中藥及其活性成分,從而達(dá)到精準(zhǔn)治療目的。本研究將核心基因映射到Coremine Medical數(shù)據(jù)庫,篩選相關(guān)中藥并對其歸經(jīng)和功效分析,發(fā)現(xiàn)藥物多歸屬肝經(jīng),多以清熱類和補(bǔ)虛類為主,與中醫(yī)對腦膠質(zhì)瘤用藥基本一致。FN1在PPI網(wǎng)絡(luò)中起著主要橋梁作用,可能作為介導(dǎo)TMZ耐藥關(guān)鍵靶點(diǎn)。進(jìn)而構(gòu)建“中藥-活性成分-作用靶點(diǎn)”網(wǎng)絡(luò),木香、青葉膽及蓖麻子的活性成分參與調(diào)控MAOB、MAOA、HTR3A、DRD2、SLC6A4、HTR2A、ESR1及HSP90AA1等基因,可能成為治療TMZ耐藥潛在中藥及候選靶點(diǎn)。
本研究利用生物信息學(xué)方法對于GBM TMZ耐藥機(jī)制進(jìn)行分析,并預(yù)測耐藥關(guān)鍵基因所涉及的中藥,對于GBM TMZ機(jī)制研究及臨床用藥具有參考意義。本研究局限之處在于數(shù)據(jù)分析依賴于GEO數(shù)據(jù)庫,其中所納入樣本數(shù)量有限,對于結(jié)果分析可能造成偏倚,需要進(jìn)一步實(shí)驗(yàn)驗(yàn)證。
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收稿日期:2023-10-18;修回日期:2023-10-25
編輯/肖婷婷
基金項(xiàng)目:國家自然科學(xué)基金項(xiàng)目(編號:82060739)
作者簡介:初曉玲(1981.11-),女,山東萊州人,本科,主管藥師,主要從事醫(yī)院藥學(xué)、中藥藥理研究
通訊作者:陳旭青(1981.6-),女,江蘇南京人,本科,主管藥師,主要從事醫(yī)院藥學(xué)、中藥藥理研究