周明旺,李盛華,鄧昶,付志斌,吉星,陳彥同,胡星榮,劉一飛,王鵬志,趙秋玥
血瘀質(zhì)非創(chuàng)傷性股骨頭壞死m(xù)iRNA差異表達(dá)篩選及生物信息學(xué)分析
周明旺1,李盛華1,鄧昶2,付志斌1,吉星1,陳彥同2,胡星榮2,劉一飛2,王鵬志2,趙秋玥2
1.甘肅省中醫(yī)院,甘肅 蘭州 730050;2.甘肅中醫(yī)藥大學(xué)中醫(yī)臨床學(xué)院,甘肅 蘭州 730000
篩選血瘀質(zhì)、非血瘀質(zhì)非創(chuàng)傷性股骨頭壞死(NONFH)患者與健康人外周血中差異表達(dá)的miRNA,建立miRNA表達(dá)譜,分析其生物學(xué)信息,為血瘀質(zhì)NONFH的防治提供依據(jù)。選取血瘀質(zhì)、非血瘀質(zhì)NONFH患者各10例(NONFH組)和健康志愿者8例(正常組),采用RT-PCR檢測其血漿miRNA相對表達(dá)量,篩選差異表達(dá)的miRNA。應(yīng)用實(shí)時(shí)熒光定量PCR對差異表達(dá)的hsa-miR-365a-3p、hsa-miR-483-3p進(jìn)行驗(yàn)證。采用TargetScan、microRNAorg、PITA在線數(shù)據(jù)庫對差異miRNA進(jìn)行靶基因預(yù)測,并進(jìn)行靶基因生物信息學(xué)分析。與正常組比較,NONFH組有差異表達(dá)的miRNA 50個(gè),其中上調(diào)21個(gè),下調(diào)29個(gè)。與非血瘀質(zhì)NONFH組比較,血瘀質(zhì)NONFH組有差異表達(dá)的miRNA 33個(gè),其中上調(diào)10個(gè),下調(diào)23個(gè)。經(jīng)篩選,最終確定血瘀質(zhì)NONFH差異表達(dá)miRNA 5個(gè)。實(shí)時(shí)熒光定量PCR驗(yàn)證結(jié)果與miRNA芯片結(jié)果相符。3個(gè)在線數(shù)據(jù)庫共篩選出交集靶基因11個(gè),僅表達(dá)下調(diào)miRNA中hsa-miR-365a-3p檢出交集靶基因11個(gè),余未檢測出交集靶基因。GO分析顯示,差異表達(dá)miRNA主要與受體結(jié)合、蛋白及酶的活性有關(guān)。Pathway分析顯示,血瘀質(zhì)NONFH差異表達(dá)miRNA靶基因主要富集于軸突導(dǎo)向、Rap1、賴氨酸降解、Fc epsilon RI、甘油磷脂代謝、T細(xì)胞受體、血小板活化、成骨細(xì)胞分化等多個(gè)信號(hào)通路。血瘀質(zhì)NONFH差異表達(dá)miRNA可能通過調(diào)控Rap1、賴氨酸降解、甘油磷脂代謝、血小板活化、成骨細(xì)胞分化、Ras、PI3K-Akt等信號(hào)通路參與NONFH發(fā)生發(fā)展過程。
血瘀質(zhì);非創(chuàng)傷性股骨頭壞死;miRNA;基因芯片;生物信息學(xué)
非創(chuàng)傷性股骨頭壞死(non-traumatic osteonecrosis of femoral head,NONFH)主要由血液供應(yīng)的破壞和凝血纖溶系統(tǒng)紊亂引起,最終導(dǎo)致股骨頭塌陷,為骨科難治性疾病[1]。由于發(fā)病較隱匿,缺乏早期臨床癥狀,對其早期檢測尚存困難,因此闡明其病因病機(jī)成為當(dāng)今研究主要方向。中醫(yī)藥重視辨析體質(zhì)狀態(tài),對NONFH的治療有積極作用。本課題組前期研究顯示,血瘀質(zhì)是NONFH的高發(fā)體質(zhì)類型之一[2]。miRNA是一類非編碼RNA,近年來,越來越多數(shù)據(jù)表明,其參與破骨細(xì)胞的形成、分化、凋亡和吸收[3-4],在NONFH的發(fā)病中扮演了極為重要的角色[5]?;诖耍菊n題組通過miRNA芯片技術(shù)篩選出血瘀質(zhì)NONFH患者血漿中異常表達(dá)的miRNA,并對其進(jìn)行生物信息學(xué)分析,探討血瘀質(zhì)及相關(guān)miRNA異常表達(dá)與NONFH發(fā)病的相關(guān)性,以期為中醫(yī)藥調(diào)體干預(yù)NONFH提供新的思路和依據(jù)。
參照《股骨頭壞死臨床診療規(guī)范》[6]、《中藥新藥臨床研究指導(dǎo)原則》[7]、《成人股骨頭壞死診療標(biāo)準(zhǔn)專家共識(shí)(2012年版)》[8]制定診斷標(biāo)準(zhǔn)。
依據(jù)《中醫(yī)體質(zhì)分類與判定》[9]制定血瘀體質(zhì)NONFH相關(guān)miRNA組學(xué)分析及其靶基因調(diào)控網(wǎng)絡(luò)研究調(diào)查表。按照轉(zhuǎn)化分對中醫(yī)體質(zhì)類型進(jìn)行判斷,分為平和質(zhì)、氣虛質(zhì)、陽虛質(zhì)、陰虛質(zhì)、痰濕質(zhì)、濕熱質(zhì)、血瘀質(zhì)、氣郁質(zhì)、特稟質(zhì)共9種類型。平和質(zhì):轉(zhuǎn)化分≥60分,其他8種體質(zhì)轉(zhuǎn)化分均小于30分,判斷為“是”;轉(zhuǎn)化分≥60分,其他8種體質(zhì)轉(zhuǎn)化分均小于40分,判斷為“基本是”;不滿足上述條件者判斷為“否”。偏頗體質(zhì):轉(zhuǎn)化分≥40分判斷為“是”,轉(zhuǎn)化分30~39分判斷為“傾向是”,轉(zhuǎn)化分<30分判斷為“否”。
①NONFH組符合上述診斷標(biāo)準(zhǔn)及中醫(yī)體質(zhì)判定標(biāo)準(zhǔn);②年齡18~70歲;③受試者對本研究知情。
①創(chuàng)傷性股骨頭壞死者;②強(qiáng)直性脊柱炎、骨腫瘤、髖臼發(fā)育不良、類風(fēng)濕關(guān)節(jié)炎者;③合并嚴(yán)重內(nèi)臟病變或嚴(yán)重代謝異常疾病者;④妊娠期婦女;⑤精神疾病或智力障礙者;⑥正在參加其他臨床試驗(yàn)者。
選擇2016年6月-2017年6月甘肅省中醫(yī)院骨科經(jīng)問卷調(diào)查判定為血瘀質(zhì)NONFH患者及非血瘀質(zhì)NONFH患者各10例作為NONFH組,選取同期于甘肅省中醫(yī)院體檢的健康志愿者8例作為正常組,3組性別(2=0.223,=0.890)、年齡(=0.102,=0.903)比較差異無統(tǒng)計(jì)學(xué)意義,具有可比性。本研究經(jīng)甘肅省中醫(yī)院倫理委員會(huì)審查批準(zhǔn)(2015-018-01)。10例血瘀質(zhì)NONFH患者為從前期數(shù)據(jù)庫篩選出的典型單純血瘀體質(zhì),經(jīng)過反復(fù)體質(zhì)判定,不存在偏頗體質(zhì)。
對調(diào)查者進(jìn)行相關(guān)理論知識(shí)、調(diào)查方法及試驗(yàn)方法培訓(xùn)。因NONFH分布不集中,故指定專職調(diào)查者進(jìn)行病例收集。取患者空腹外周血3 mL,置入裝有EDTA抗凝劑的無菌管,混勻,于1 h內(nèi)室溫下3000 r/min離心10 min,分離血漿,收集上層淡黃色血漿,移至2 mL凍存管內(nèi),標(biāo)記患者信息后置于甘肅省中醫(yī)院中心實(shí)驗(yàn)室-80 ℃冰箱保存。
TRIzol試劑(Ambion公司)、Gene Expression Wash Pack、miRNA complete Labeling and Hyb Kit(24×)、miRNA Spike In Kit、Package 20 backings(8 HD arrays per slide)、Package 20 backings(4 arrays per slide)、Chip(Agilent公司,美國),miScript Ⅱ Reverse Transcription Kit(Qiagen公司,德國),QuantiFast?SYBR?Green PCR Kit(Qiagen公司,德國),Micro Bio-Spin 6(Bio-RAD公司,美國),熒光定量PCR儀(Roche公司,瑞士),引物由Agilent公司提供。
1.8.1 RNA提取及質(zhì)量檢測
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??俁NA采用NanoDrop RND-2000微量紫外分光光度計(jì)進(jìn)行檢測并經(jīng)Agilent Bioanalyzer 2100(Agilent Technologies)檢測RNA完整性。
1.8.2 Agilent microRNA芯片操作及數(shù)據(jù)分析
RNA質(zhì)檢合格后,按照流程進(jìn)行樣本的標(biāo)記、芯片雜交及洗脫。首先,總RNA經(jīng)過去磷酸化,變性,再進(jìn)一步用Cyanine-3-CTP標(biāo)記。標(biāo)記好的RNA純化后和芯片雜交,洗脫后利用Agilent Scanner G2505C(Agilent Technologies)掃描得到原始圖像。采用Feature Extraction(version10.7.1.1,Agilent Technologies)處理原始圖像提取原始數(shù)據(jù),利用Genespring(version13.1,Agilent Technologies)進(jìn)行quantile標(biāo)準(zhǔn)化和后續(xù)處理。對標(biāo)準(zhǔn)化后的數(shù)據(jù)進(jìn)行過濾,用于比較的每組樣本中至少有1組100%標(biāo)記為Detected的探針留下進(jìn)行后續(xù)分析。利用檢驗(yàn)的值和倍數(shù)變化值進(jìn)行差異miRNA篩選,篩選標(biāo)準(zhǔn)為上調(diào)或下調(diào)倍數(shù)變化值≥2.0且≤0.05。
1.8.3 實(shí)時(shí)熒光定量PCR驗(yàn)證差異表達(dá)miRNA
利用miScript Ⅱ Reverse Transcription Kit將待測RNA反轉(zhuǎn)錄成cDNA。反轉(zhuǎn)錄體系:總RNA 0.5 μg,5×miScript HiSpec Buffer 2 μL,10×Nucleics Mix 1 μL,miScript Reverse Transcriptase Mix 0.5 μL,Nuclease-free H2O加至10 μL。反應(yīng)程序:37 ℃、60 min,95 ℃、5 min。反轉(zhuǎn)錄完畢后加入90 μL Nuclease-free H2O儲(chǔ)存在-20 ℃冰箱備用。以此cDNA為模板,用QuantiFast?SYBR?Green PCR Kit進(jìn)行實(shí)時(shí)熒光定量PCR。反應(yīng)體系:2×QuantiFast?SYBR?Green PCR Master Mix 5 μL,10 μmol/L Universal primer 0.2 μL,10 μmol/L microRNA-specific primer 0.2 μL,cDNA 1 μL,Nuclease-free H2O 3.6 μL。PCR程序:95 ℃、5 min,95 ℃、10 s,60 ℃、30 s,40個(gè)循環(huán)。以2-ΔΔCt值表示miRNA的相對表達(dá)水平。重復(fù)3次。
1.8.4 差異表達(dá)miRNA生物信息學(xué)分析
通過TargetScan(http://www.targetscan.org/)、microRNAorg(http://www.microrna.org/microrna/home. do)及PITA(http://www.pita.org.fj/)在線數(shù)據(jù)庫預(yù)測差異表達(dá)miRNA的靶基因,TargetScan采用保守miRNA家族的保守位點(diǎn)、PITA采用Scaled Score分值不超過-9.73、microRNAorg采用mirSVR分值不超過-0.1的保守miRNA進(jìn)行預(yù)測。選取3個(gè)在線數(shù)據(jù)庫預(yù)測的交集靶基因,進(jìn)行信號(hào)轉(zhuǎn)導(dǎo)通路(Pathway)富集分析,以判定差異miRNA主要影響的信號(hào)通路。
與正常組相比,NONFH組有差異表達(dá)的miRNA 50個(gè)。上調(diào)21個(gè),其中hsa-miR-4739、hsa-miR-3610、hsa-miR-134-5p是表達(dá)前3位的miRNA,差異倍數(shù)(FC)值分別為18.452 68、7.215 677、6.312 345;下調(diào)29個(gè),其中hsa-miR-6834-3p、hsa-miR-631、hsa-miR-6892-5p是表達(dá)前3位的miRNA,F(xiàn)C值分別為7.900 493、6.327 500、6.299 431。與非血瘀質(zhì)NONFH組相比,血瘀質(zhì)NONFH組有差異表達(dá)的miRNA 33個(gè)。上調(diào)10個(gè),其中hsa-miR-6786-5p、hsa-miR-550a-5p、hsa-miR-4788是表達(dá)前3位的miRNA,F(xiàn)C值分別為3.598 814、3.477 553、3.325 008;下調(diào)23個(gè),其中hsa-let-7b-5p、hsa-miR-25-3p、hsa-miR-16-5p是表達(dá)前3位的miRNA,F(xiàn)C值分別為9.518 297、8.887 547、6.615 946。經(jīng)篩選,最終確定血瘀質(zhì)NONFH差異表達(dá)miRNA 5個(gè),其中表達(dá)上調(diào)miRNA為has-miR-4270,表達(dá)下調(diào)為hsa-miR-129-1-3p、hsa-miR-365a-3p、hsa-miR-483-3p、hsa-miR-6731-3p,詳見表1。
表1 miRNA差異表達(dá)篩選結(jié)果
miRNA名稱FC值P值差異表達(dá) has-miR-42705.067 789 0.016 611上調(diào) hsa-miR-129-1-3p5.918 068 9.16E-04下調(diào) hsa-miR-365a-3p6.746 917 0.004 935下調(diào) hsa-miR-483-3p9.078 883 0.013 898下調(diào) hsa-miR-6731-3p7.225 763 0.001 938下調(diào)
實(shí)時(shí)熒光定量PCR結(jié)果顯示,與正常組比較,血瘀質(zhì)NONFH組hsa-miR-365a-3p、hsa-miR-483-3p表達(dá)水平明顯下調(diào)(<0.05),與miRNA芯片檢測結(jié)果一致。見表2。
表2 實(shí)時(shí)熒光定量PCR驗(yàn)證結(jié)果(2-ΔΔCt)
組別has-miR-365a-3phas-miR-483-3p 正常組 1.000 0 1.000 0 血瘀質(zhì)NONFH組 0.230 0* 0.240 0*
注:與正常組比較,*<0.05
采用GeneSpring13.1軟件,通過TargetScan、PITA、microRNAorg在線數(shù)據(jù)庫對差異miRNA進(jìn)行靶基因預(yù)測。結(jié)果顯示,hsa-miR-365a-3p檢出交集靶基因11個(gè),余未檢測出交集靶基因,結(jié)果見圖1。
圖1 靶基因預(yù)測結(jié)果
針對差異表達(dá)miRNA進(jìn)行GO分析,共得到111條相關(guān)注釋描述,包括分子功能(MF)23條、生物學(xué)過程(BP)65條和細(xì)胞組分(CC)23條。進(jìn)一步針對分子功能分析,發(fā)現(xiàn)差異表達(dá)miRNA主要與受體結(jié)合、蛋白與酶的活性有關(guān)。見圖2。
Pathway分析顯示,靶基因主要富集于軸突導(dǎo)向、Rap1、賴氨酸降解、Fc epsilon RI、甘油磷脂代謝、T細(xì)胞受體、血小板活化、成骨細(xì)胞分化等多個(gè)信號(hào)通路。見表3。
圖2 差異表達(dá)miRNA GO分析分子功能結(jié)果
表3 差異表達(dá)miRNA信號(hào)通路及靶基因預(yù)測
KEGG IDGeneSymbols hsa04360:Axon guidanceSEMA6D;EFNA3 hsa04015:Rap1 signaling pathwayLCP2;EFNA3 hsa00310:Lysine degradationKMT2D hsa04664:Fc epsilon RI signaling pathwayLCP2 hsa00564:Glycerophospholipid metabolismETNK1 hsa04660:T cell receptor signaling pathwayLCP2 hsa04611:Platelet activationLCP2 hsa04380:Osteoclast differentiationLCP2 hsa04650:Natural killer cell mediated cytotoxicityLCP2 hsa04014:Ras signaling pathwayEFNA3 hsa05206:miRNAs in cancerEFNA3 hsa04151:PI3K-Akt signaling pathwayEFNA3 hsa01100:Metabolic pathwaysETNK1
本研究顯示,血瘀質(zhì)NONFH差異表達(dá)miRNA共5個(gè),其中表達(dá)上調(diào)為has-miR-4270,表達(dá)下調(diào)為hsa-miR-129-1-3p、hsa-miR-365a-3p、hsa-miR-483-3p、hsa-miR-6731-3p。隨后對hsa-miR-365a-3p、hsa-miR-483-3p進(jìn)行實(shí)時(shí)熒光定量PCR驗(yàn)證,結(jié)果與芯片數(shù)據(jù)高度一致。研究表明,miR-483可抑制胰島素生長因子1表達(dá)[10-12],促進(jìn)血管內(nèi)皮細(xì)胞凋亡[13]。研究發(fā)現(xiàn),miR-483與急性心室缺血、血管腔形成及成骨分化有關(guān)[14-15]。多項(xiàng)研究表明,miR-365與骨代謝、冠狀動(dòng)脈粥樣硬化有關(guān)[16-18],這可能是NONFH的發(fā)生途徑。
Pathway分析顯示,靶基因主要富集于軸突導(dǎo)向、Rap1、賴氨酸降解、Fc epsilon RI、甘油磷脂代謝、T細(xì)胞受體、血小板活化、成骨細(xì)胞分化等多個(gè)信號(hào)通路。其中多條通路參與了骨代謝、脂代謝、血管新生及血小板活化等可能導(dǎo)致NONFH發(fā)生的調(diào)控。研究表明,Rap1是一氧化氮產(chǎn)生和內(nèi)皮功能調(diào)節(jié)的關(guān)鍵物質(zhì),而一氧化氮系血管穩(wěn)態(tài)的關(guān)鍵決定因素[19-20]。Rap1是血小板活化、血管新生和血栓形成關(guān)鍵[21]。Ras信號(hào)通路被證實(shí)與血管內(nèi)皮細(xì)胞增殖及血管形態(tài)有關(guān)[22-23]。而PI3K/Akt信號(hào)通路是細(xì)胞內(nèi)重要的信號(hào)通路,是一條從細(xì)胞膜到細(xì)胞核的快速通路轉(zhuǎn)導(dǎo)系統(tǒng),其與細(xì)胞凋亡、血管再生密切相關(guān),若受到抑制將導(dǎo)致血管缺血[24]。
綜上所述,本研究采用miRNA芯片技術(shù)研究血瘀質(zhì)NONFH差異表達(dá)miRNA,并對這些miRNA進(jìn)行生物信息學(xué)分析。結(jié)果表明,血瘀質(zhì)NONFH差異表達(dá)miRNA可能通過調(diào)控Rap1、賴氨酸降解、甘油磷脂代謝、血小板活化、成骨細(xì)胞分化、Ras、PI3K-Akt等信號(hào)通路參與NONFH的發(fā)生發(fā)展過程。本研究是對NONFH的miRNA基因表達(dá)譜的初步探討,僅觀察了NONFH患者及健康志愿者外周血中miRNA的表達(dá)情況。今后需擴(kuò)大樣本進(jìn)一步針對NONFH高發(fā)中醫(yī)體質(zhì)類型探討miRNA與靶基因的關(guān)系。
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Screening and Bioinformatics Analysis of Differentially Expressed MicroRNAs in Non-traumatic Osteonecrosis of Femoral Head with Blood Stasis
ZHOU Mingwang1, LI Shenghua1, DENG Chang2, FU Zhibin1, JI Xing1, CHEN Yantong2,HU Xingrong2, LIU Yifei2, WANG Pengzhi2, ZHAO Qiuyue2
To establish the miRNA expression profile and analyze its biological information by screening the miRNA differentially expressed in the peripheral blood of the patients with and without blood stasis and non-traumatic osteonecrosis of femoral head (NONFH); To provide a basis for the prevention and treatment of NONFH with blood stasis.Totally 10 cases of NONFH with out blood stasis (NONFH group), 10 cases of NONFH with blood stasis and 8 cases of healthy volunteers (normal group) were selected. The relative expression of miRNA in plasma was detected by RT-PCR, and the miRNA with different expression was screened. The differential expression of hsa-miR-365a-3p and hsa-miR-483-3p was verified by real-time fluorescence quantitative PCR. Three online databases, TargetScan, microRNAorg, PITA were used to predict the target genes of different miRNAs, and the target genes were analyzed by bioinformatics.Compared with the normal group, 50 miRNAs were differentially expressed, 21 up-regulated and 29 down-regulated in NONFH groups. Compared with the NONFH without blood stasis group, 33 miRNAs were differentially expressed, 10 up-regulated and 23 down-regulated in NONFH with blood stasis group. After screening, five miRNAs with different expression of NONFH with blood stasis group were identified. The results of real-time fluorescent quantitative PCR were consistent with those of miRNA microarray. In the three online databases, 11 cross target genes were screened out; only 11 cross target genes were detected in hsa-miR-365a-3p expression down regulated miRNA; the rest were not detected. GO analysis showed that the differential expression of miRNA was mainly related to receptor binding, protein and enzyme activity. Pathway analysis showed that the differentially expressed miRNA target genes of NONFH with blood stasis were mainly enriched in axon guidance, Rap1, lysine degradation, Fc epsilon RI, glycerophospholipid metabolism, T cell receptor, platelet activation, osteoblast differentiation and other signaling pathways.The different expressions miRNA of NONFH with blood stasis are obtained. These differentially expressed miRNAs may be involved in the development of NONFH by regulating the signal pathways of Rap1, lysine degradation, glycerophospholipid metabolism, platelet activation, osteoblast differentiation, RAS, PI3K-Akt and so on.
blood stasis; non-traumatic osteonecrosis of femoral head; microRNA; gene chip; bioinformatics
R272.968
A
1005-5304(2020)08-0036-05
10.3969/j.issn.1005-5304.201910076
國家自然科學(xué)基金(81473712、81560782)
李盛華,E-mail:820512343@qq.com
(2019-10-08)
(2020-01-20;編輯:季巍巍)