孫楠,樊粵光,李鵬飛,曾意榮,曾建春
(1廣州中醫(yī)藥大學(xué),廣州510405;2廣州中醫(yī)藥大學(xué)第一附屬醫(yī)院)
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激素性股骨頭壞死患者血漿microRNA表達(dá)譜及生物信息分析
孫楠1,樊粵光1,李鵬飛1,曾意榮2,曾建春2
(1廣州中醫(yī)藥大學(xué),廣州510405;2廣州中醫(yī)藥大學(xué)第一附屬醫(yī)院)
摘要:目的分析激素性股骨頭壞死(SONFH)患者血漿microRNA表達(dá)譜變化及生物信息內(nèi)容,并探討其意義。方法選取SONFH患者(觀察組)和健康志愿者(對(duì)照組)各6例,采用Real-time PCR法檢測(cè)其血漿microRNA相對(duì)表達(dá)量,篩選差異表達(dá)的microRNA。采用TargetScan、mirBase及miRanda三個(gè)在線數(shù)據(jù)庫(kù)預(yù)測(cè)交集靶基因,分別進(jìn)行功能富集性分析和信號(hào)轉(zhuǎn)導(dǎo)通路富集(Pathway)分析。結(jié)果共檢測(cè)768個(gè)microRNA,兩組差異表達(dá)的microRNA 16 個(gè),其中觀察組上調(diào)10個(gè),比較明顯的是hsa-miR-1207-5p和hsa-miR-887(觀察組/對(duì)照組>3);下調(diào)6個(gè),比較明顯的是hsa-miR-96-5p、hsa-miR-576-5p(觀察組/對(duì)照組<0.5)。三個(gè)在線數(shù)據(jù)庫(kù)共篩選出交集靶基因887個(gè),其中上調(diào)microRNA 483個(gè),hsa-miR-1207-5p未檢出交集靶基因,hsa-miR-887檢出交集靶基因?yàn)镚SK3A和CASK;下調(diào)microRNA 404個(gè),hsa-miR-96-5p檢出交集靶基因114個(gè),hsa-miR-576-5p檢出59個(gè)。功能富集性分析顯示,兩組差異表達(dá)microRNA調(diào)控的靶基因功能主要包括解剖結(jié)構(gòu)形態(tài)、間充質(zhì)細(xì)胞增殖、細(xì)胞代謝過(guò)程等,Pathway分析顯示靶基因明顯富集于各種信號(hào)通路。結(jié)論SONFH患者血漿microRNA明顯上調(diào)的是hsa-miR-1207-5p和hsa-miR-887,明顯下調(diào)的是hsa-miR-96-5p、hsa-miR-576-5p,microRNA異常表達(dá)可能通過(guò)各信號(hào)通路參與SONFH的發(fā)病。
關(guān)鍵詞:股骨頭壞死;糖皮質(zhì)激素;微小RNA;基因表達(dá)譜
股骨頭壞死(ONFH)主要發(fā)生于青壯年[1],包括創(chuàng)傷性和非創(chuàng)傷性,后者又分為激素性、酒精性。其中激素性股骨頭壞死(SONFH)發(fā)病隱匿,常在出現(xiàn)股骨頭塌陷后才表現(xiàn)出髖部、腹股溝中點(diǎn)處疼痛,關(guān)節(jié)活動(dòng)受限等,嚴(yán)重影響患者的生活質(zhì)量[2,3]。目前SONFH發(fā)病機(jī)制仍不明確。microRNA是一類長(zhǎng)18~25 nt的內(nèi)源性小分子非編碼RNA,通過(guò)堿基互補(bǔ)配對(duì)的方式識(shí)別特定編碼序列的mRNA,影響其翻譯過(guò)程,從而起到調(diào)控基因表達(dá)的作用[4]。microRNA 廣泛參與一系列生命活動(dòng)的調(diào)控,包括細(xì)胞增殖和分化、細(xì)胞凋亡、器官形成和發(fā)育、脂肪代謝等[5]。研究發(fā)現(xiàn),microRNA在SONFH患者壞死骨組織中異常表達(dá)[6],說(shuō)明microRNA參與其病理過(guò)程,可作為SONFH的生物學(xué)標(biāo)記物,但其在血漿中的表達(dá)情況少見(jiàn)報(bào)道。本研究通過(guò)microRNA芯片技術(shù)篩選出SONFH患者血漿中異常表達(dá)的microRNA,并對(duì)其生物信息學(xué)內(nèi)容進(jìn)行分析。
1資料與方法
1.1臨床資料選擇2014年7月~2015年2月廣州中醫(yī)藥大學(xué)第一附屬醫(yī)院關(guān)節(jié)科收治的SONFH患者6例作為觀察組,其中男2例、女4例,年齡26~37歲,發(fā)病時(shí)間9~34個(gè)月、平均23.2個(gè)月;原發(fā)病為濕疹1例、系統(tǒng)性紅斑狼瘡4例、銀屑病1例。納入標(biāo)準(zhǔn):①符合ONFH診斷標(biāo)準(zhǔn)[7];②有明確的長(zhǎng)期大量糖皮質(zhì)激素應(yīng)用史;③原發(fā)病治愈或處于穩(wěn)定期。排除標(biāo)準(zhǔn):①原發(fā)病尚未得到有效控制或處于疾病活動(dòng)期;②伴隨長(zhǎng)期大量飲酒史或既往股骨頭、股骨頸創(chuàng)傷史。選取同期廣州中醫(yī)藥大學(xué)在校健康志愿者6例作為對(duì)照組,其中男5例、女1例,年齡23~35歲。兩組性別、年齡具有可比性。本研究均獲得受試者的知情同意,并通過(guò)廣州中醫(yī)藥大學(xué)第一附屬醫(yī)院倫理委員會(huì)倫理審查。
1.2血漿中異常表達(dá)microRNA的篩選
1.2.1材料Nuclease free water、miRNA PCR ARRAY、SYBRTMGreen master mix(Exiqon公司,丹麥),cDNA模板、ROX (Invitrogen公司,美國(guó)),Gene Amp PCR System 7900(ABI公司,美國(guó)),紫外分光光度計(jì)(Thermo Scientific公司,美國(guó)),緩沖液(Reaction Buffer Exiqon公司,丹麥)。
1.2.2RNA提取及質(zhì)量檢測(cè)兩組采用一次性真空EDTA抗凝采血管采集靜脈血約6 mL,4 ℃、2 000 g離心10 min,取上層血漿。將血漿轉(zhuǎn)移至滅菌2 mL EP管中,-80 ℃超低溫冰箱凍存?zhèn)溆?。樣品化凍? 000 g離心5 min,轉(zhuǎn)移上清至新的1.5 mL EP管中,加入TRIzol-LS試劑750 μL,劇烈震蕩5 s,根據(jù)TRIzol試驗(yàn)步驟進(jìn)行RNA沉淀、清洗、再溶解、沉淀及抽提,得到總RNA。采用NanoDrop? ND-1000微量紫外分光光度計(jì)進(jìn)行紫外分光,總RNA蛋白A260/A280為1.48~1.62視為合格。
1.2.3microRNA相對(duì)表達(dá)量檢測(cè)采用Real-time PCR法。按照miRCURYTM Hy3TM/Hy5TM試劑盒說(shuō)明書(shū)進(jìn)行操作:將試劑置于冰上于室溫下融化,取微量離心管,用移液器取1.0 μg RNA樣品,加入3.0 μL去RNA酶水稀釋,加入0.5 μL緩沖液充分混合。將混合液離心,置于42 ℃溫育60 min,于95 ℃溫育5 min以失活逆轉(zhuǎn)錄酶,完成cDNA逆轉(zhuǎn)錄。合成的cDNA移入硅化的tube管中備用。將制備的cDNA模板、nuclease-free 水和SYBRTMGreen master mix置于冰上溶解15~20 min。將反應(yīng)獲得的cDNA模板用nuclease-free 水稀釋110倍,與Greenmaster mix充分混合,加入miRNA PCR ARRAY。PCR反應(yīng)條件: 95 ℃ 10 min, 95 ℃ 10 s,60 ℃ 1 min,40 個(gè)循環(huán),降溫速度1.6 ℃/s。每孔重復(fù)3 次,取平均Ct 值。選取hsa-miR-423-5p為內(nèi)參,試驗(yàn)重復(fù)3次,取平均值?;蛳鄬?duì)表達(dá)量以2-ΔΔCt表示。以相對(duì)表達(dá)量觀察組/對(duì)照組>2且P<0.05為顯著上調(diào),觀察組/對(duì)照組<0.7且P<0.05為顯著下調(diào)。
1.3差異表達(dá)microRNA的生物信息分析通過(guò)TargetScan、mirBase及miRanda三個(gè)在線數(shù)據(jù)庫(kù)預(yù)測(cè)差異表達(dá)microRNA的靶基因,TargetScan采用保守microRNA家族的保守位點(diǎn)、mirBase采用哺乳動(dòng)物、miRanda采用mirSVR分值不超過(guò)-0.1的保守microRNA進(jìn)行預(yù)測(cè)。選取三個(gè)在線數(shù)據(jù)庫(kù)預(yù)測(cè)的交集靶基因,分別進(jìn)行功能富集性分析和信號(hào)轉(zhuǎn)導(dǎo)通路富集(Pathway)分析。
2結(jié)果
2.1兩組microRNA差異表達(dá)情況本研究共檢測(cè)了768個(gè)microRNA,兩組差異表達(dá)microRNA共16個(gè)。上調(diào)的10個(gè)microRNA中,觀察組與對(duì)照組hsa-miR-424-5p相對(duì)表達(dá)量分別為0.000 9±0.000 1、0.000 5±0.000 3,hsa-miR-31-5p分別為0.001 9±0.001 0、0.000 9±0.001 3,hsa-miR-190b分別為0.000 9±0.003 9、0.000 5±0.002 1,觀察組/對(duì)照組分別為1.97、1.96、1.68,P均<0.05;其余7個(gè)microRNA均顯著上調(diào),其中hsa-miR-1207-5p和hsa-miR-887相對(duì)表達(dá)量觀察組/對(duì)照組>3,見(jiàn)表1。下調(diào)的6個(gè)microRNA中,4個(gè)microRNA(hsa-miR-96-5p、hsa-miR-576-5p、hsa-miR-15b-3p、hsa-miR-624-5p)顯著下調(diào),其中hsa-miR-96-5p、hsa-miR-576-5p下調(diào)比較明顯(觀察組/對(duì)照組<0.5),見(jiàn)表2。
表1 SONFH患者血漿顯著上調(diào)的microRNA(相對(duì)表達(dá)量,±s)
注:與對(duì)照組比較,*P<0.05。
表2 SONFH患者血漿下調(diào)的microRNA(相對(duì)表達(dá)量,
注:與對(duì)照組比較,*P<0.05,#P<0.01。2.2差異表達(dá)microRNA的生物信息分析結(jié)果三個(gè)在線數(shù)據(jù)庫(kù)共篩選出交集靶基因887個(gè),其中上調(diào)microRNA 483個(gè),hsa-miR-1207-5未檢出交集靶基因,hsa-miR-887檢出交集靶基因?yàn)镚SK3A和CASK;下調(diào)microRNA 404個(gè),hsa-miR-96-5p檢出交集靶基因114個(gè),hsa-miR-576-5p檢出59個(gè)。功能富集性分析顯示,兩組差異表達(dá)microRNA調(diào)控的靶基因功能主要包括:解剖結(jié)構(gòu)形態(tài)、間充質(zhì)細(xì)胞增殖、細(xì)胞代謝過(guò)程、細(xì)胞內(nèi)信號(hào)轉(zhuǎn)導(dǎo)、系統(tǒng)發(fā)生、質(zhì)膜蛋白質(zhì)的定位、解剖結(jié)構(gòu)的發(fā)展、神經(jīng)系統(tǒng)發(fā)育、質(zhì)膜組織;Pathway分析顯示,靶基因明顯富集于各種信號(hào)通路:肌動(dòng)蛋白細(xì)胞調(diào)控通路、胰島素信號(hào)通路、鈣離子信使通路、雌激素受體信號(hào)轉(zhuǎn)導(dǎo)通路、促性腺激素信號(hào)通路等。
3討論
microRNA能夠穩(wěn)定存在于外周血中,具有耐RNA 酶的特點(diǎn),在血漿中結(jié)構(gòu)比較穩(wěn)定,不易被降解。通過(guò)對(duì)差異表達(dá)microRNA的研究及靶基因功能、信號(hào)通路的預(yù)測(cè),可以揭示疾病的發(fā)生、發(fā)展機(jī)制,并將特異性microRNA作為疾病的標(biāo)記物[8~10]。目前血漿microRNA在骨科領(lǐng)域的研究重點(diǎn)為骨腫瘤,在SONFH中的研究較少[11]。SONFH的發(fā)病機(jī)制目前尚不明確,但普遍認(rèn)為是由于應(yīng)用糖皮質(zhì)激素后引起骨內(nèi)穩(wěn)態(tài)失衡、細(xì)胞損傷,致使局部供血障礙,最終導(dǎo)致ONFH[12]。研究證實(shí),大量使用糖皮質(zhì)激素可以導(dǎo)致細(xì)胞凋亡,從而引起SONFH[13]。在美國(guó),每年有10 000~20 000人因服用糖皮質(zhì)激素導(dǎo)致ONFH而需進(jìn)行人工髖關(guān)節(jié)置換,占據(jù)了美國(guó)人工髖關(guān)節(jié)置換數(shù)量的10%[14]。因此,研究SONFH患者血漿中的microRNA表達(dá)譜變化,探索其靶基因與生物學(xué)功能,對(duì)SONFH的診斷與治療有重要意義。
本研究發(fā)現(xiàn),SONFH患者血漿中有16 個(gè)microRNA 表達(dá)與正常人有顯著差異,上調(diào)的microRNA有10個(gè),其中上調(diào)2倍以上的有7個(gè),上調(diào)3倍以上的是hsa-miR-887、hsa-miR-1207-5p;下調(diào)的有6個(gè),hsa-miR-96-5p、hsa-miR-576-5p下調(diào)比較明顯(觀察組/對(duì)照組<0.5)。 hsa-miR-1207-5p是從8q24染色體的PVT1基因進(jìn)行轉(zhuǎn)錄[15],PVT1在糖尿病腎病、乳腺癌、結(jié)腸癌、淋巴瘤等疾病中均有特異表達(dá)[16]。hsa-miR-96-5p作用位點(diǎn)在7#染色體,能夠顯著抑制胰腺癌細(xì)胞的遷移和侵襲[17]。hsa-miR-887、hsa-miR-576-5p在疾病差異表達(dá)microRNA中尚無(wú)報(bào)道,因此本研究是首次在SONFH患者血漿中發(fā)現(xiàn)差異表達(dá)的hsa-miR-887、hsa-miR-576-5p,其可能成為SONFH診斷、治療的新目標(biāo)。本研究中SONFH患者血漿hsa-miR-15b-3p表達(dá)顯著上調(diào)。hsa-miR-15b-3p屬于hsa-miR-15家族,在細(xì)胞凋亡過(guò)程中具有重要作用。Bcl-2是hsa-miR-15的直接作用靶點(diǎn),其上調(diào)可降低Bcl-2水平,還可以誘導(dǎo)SGC7901/VCR細(xì)胞凋亡[18]。因此,hsa-miR-15b-3p表達(dá)上調(diào)而誘導(dǎo)細(xì)胞凋亡程序啟動(dòng)可能與SONFH的發(fā)病有關(guān)。
本研究對(duì)靶基因進(jìn)行生物信息分析,結(jié)果發(fā)現(xiàn)hsa-miR-887對(duì)應(yīng)交集靶基因?yàn)镚SK3A和CASK,主要調(diào)控解剖結(jié)構(gòu)形態(tài);hsa-miR-96-5p檢出交集靶基因114個(gè)、hsa-miR-576-5p檢出59個(gè),主要調(diào)控間充質(zhì)細(xì)胞增殖、細(xì)胞代謝過(guò)程、細(xì)胞內(nèi)信號(hào)轉(zhuǎn)導(dǎo)等生物學(xué)過(guò)程;Pathway分析顯示,靶基因明顯富集于各種信號(hào)通路。吳興凈等[19]對(duì)SONFH患者的壞死區(qū)骨組織microRNA進(jìn)行檢測(cè),發(fā)現(xiàn)靶基因功能涉及信號(hào)轉(zhuǎn)導(dǎo)、轉(zhuǎn)錄調(diào)控。由此可見(jiàn),SONFH患者血漿差異表達(dá)的microRNA可能通過(guò)對(duì)靶基因的調(diào)控影響分子信號(hào)的轉(zhuǎn)導(dǎo)和基因轉(zhuǎn)錄過(guò)程,從而引起SONFH。
綜上所述,SONFH患者血漿microRNA上調(diào)明顯的是hsa-miR-1207-5p和hsa-miR-887,下調(diào)明顯的是hsa-miR-96-5p、hsa-miR-576-5p,microRNA異常表達(dá)可能通過(guò)各信號(hào)通路參與SONFH的發(fā)病。目前關(guān)于SONFH患者血漿microRNA差異表達(dá)的研究較少,大多數(shù)血漿microRNA的功能和作用機(jī)制尚不十分明確,同時(shí)血漿中microRNA作用的發(fā)揮受內(nèi)環(huán)境影響,在骨細(xì)胞和外周循環(huán)中的作用可能并不相同。本研究為進(jìn)一步研究SONFH的發(fā)病提供了依據(jù),但差異表達(dá)microRNA的調(diào)控機(jī)制尚不明確,仍需進(jìn)一步研究。
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·論著·
Bioinformatic analysis of miRNA expression profile in plasma of patients with
steroid-induced osteonecrosis of the femoral head
SUNNan1,FANYue-guang,LIPeng-fei,ZENGYi-rong,ZENGJian-chun
(1GuangzhouUniversityofChineseMedicine,Guangzhou510405,China)
Abstract:ObjectiveTo analyze the changes of plasma microRNA expression profile and the content of bioinformatics in patients with steroid-induced osteonecrosis of the femoral head (SONFH) and to explore its significance. MethodsSONFH patients (observation group) and healthy volunteers (control group) were selected with 6 cases in each group. The real-time PCR was used to detect the relative expression of microRNA in the plasma to screen the differential expression of microRNA. TargetScan, mirBase and miRanda databases were used to predict the target genes which were analyzed by gene ontology (GO) and signal transduction pathway analysis. ResultsTotally 768 microRNAs were detected by microRNA chip detection. Sixteen microRNAs were different and significant in plasma of SONFH patients. Compared with the control group, 10 were up-regulated (significantly: hsa-miR-1207-5p and hsa-miR-887), and 6 were down-regulated (significantly: hsa-miR-96-5p and hsa-miR-576-5p). Totally 887 target genes were screened for the intersection by using TargetScan, mirBase and miRanda three databases. During which, 483 genes were up-regulated, 404 were down-regulated. No target genes of hsa-miR-1207-5p were detected, and the target genes of hsa-miR-887 were GSK3A and CASK. Totally 404 microRNAs were down-regulated, 114 Hsa-miR-96-5p-related target genes and 59 hsa-miR-576-5p-related target genes were found. GO and pathway analysis revealed that some differential expression of microRNAs, along with their target genes, were found to be involved in anatomical structure morphogenesis, mesenchymal cell proliferation, positive regulation of metabolic process and significantly enriched in the signal pathway. ConclusionsIn the plasma of SONFH patients, hsa-miR-1207-5p and hsa-miR-887 were significantly up-regulated, and hsa-miR-96-5p and hsa-miR-576-5p were significantly down-regulated. The abnormal expression of microRNAs in plasma of patients may be involved in the pathogenesis of SONFH through various signal pathways.
Key words:osteonecrosis of the femoral head; glucocorticoids; microRNA; gene expression profiling
收稿日期:(2015-11-10)
中圖分類號(hào):R681.8
文獻(xiàn)標(biāo)志碼:A
文章編號(hào):1002-266X(2015)48-0001-04
doi:10.3969/j.issn.1002-266X.2015.48.001
通信作者簡(jiǎn)介:樊粵光(1954-),男,教授,研究方向?yàn)轶y膝關(guān)節(jié)疾病,曾獲中華中醫(yī)藥學(xué)會(huì)科學(xué)技術(shù)二等獎(jiǎng)。E-mail: 925324600@qq.com
作者簡(jiǎn)介:第一孫楠(1986-),男,博士研究生,研究方向?yàn)轶y膝關(guān)節(jié)疾病。E-mail: sunnan.524@163.com
基金項(xiàng)目:國(guó)家自然科學(xué)基金資助項(xiàng)目(81373652)。