李潔, 劉彩瑩, 嚴文文, 沈玉芹, 徐金媛, 徐國彤, 呂立夏, 宋浩明△
動脈型肺動脈高壓分子標志基因的篩選與鑒定*
李潔1, 劉彩瑩2, 嚴文文1, 沈玉芹1, 徐金媛2, 徐國彤3, 呂立夏2, 宋浩明1△
(1同濟大學附屬同濟醫院心內科,上海 200065;2同濟大學醫學院生物化學與分子生物學系,上海 200092;3同濟大學醫學院藥學院,上海 200092)
本研究旨在篩選和鑒定參與動脈型肺動脈高壓(pulmonary arterial hypertension, PAH)發病的關鍵基因及相關信號通路,為進一步的轉化醫學研究提供新靶點。從美國國立生物技術信息中心的GEO (Gene Expression Omnibus)數據庫中獲取人GSE113439、GSE117261、GSE48149和GSE53408基因芯片數據集,經過數據篩選后確定PAH組103例和對照組56例進行比較分析。采用NetworkAnalyst軟件篩選差異基因(differentially expressed genes, DEGs),Enrichr和Metascape進行基因本體論(gene ontology, GO)和京都基因和基因組數據庫(Kyoto Encyclopedia of Genes and Genomes, KEGG)分析,STRING和Cytoscape建立蛋白質-蛋白質相互作用(protein-protein interaction, PPI)網絡確定潛在的樞紐基因。采用野百合堿構建PAH大鼠模型,通過測量血液動力學參數與組織形態學觀察造模是否成功,RT-qPCR驗證肺組織中候選基因的mRNA表達。共獲得2 048個差異基因,其中1480個上調,568個下調,主要涉及炎癥與細胞增殖等方面的信號通路,例如單純皰疹病毒1感染通路、人乳頭瘤病毒感染通路以及腫瘤通路等。其中最顯著的DEGs依次為、、、和,樞紐基因為、、、和。野百合堿誘導4周后,PAH組大鼠右心室收縮壓(right ventricular systolic pressure, RVSP)和平均肺動脈壓(mean pulmonary arterial pressure, mPAP)與對照組相比顯著升高(<0.05),肺組織蘇木精-伊紅(hematoxylin-eosin, HE)染色顯示肺小動脈管壁明顯增厚(<0.01),證明PAH模型建立成功。RT-qPCR結果表明,、、和的mRNA表達在PAH組顯著上調(<0.05),而、、、和的mRNA表達在PAH組顯著下調(<0.05),、、和的mRNA表達在兩組間無顯著差異(>0.05)。本研究篩選并驗證了參與PAH發生的關鍵基因,有望為進一步的轉化醫學研究提供新靶點。
動脈型肺動脈高壓;生物信息學;炎癥;細胞增殖
動脈型肺動脈高壓(pulmonary arterial hypertension, PAH)的特點是肺小動脈病變引起的肺血管阻力和肺動脈壓力升高,最終導致右心室重構甚至右心衰竭和死亡。PAH對人類健康的危害極大,據統計,成人PAH人群發病率約2.4/百萬人年,患病率約15/百萬。未接受靶向藥物治療的PAH患者的中位生存期平均為2.8年,5年生存率僅為34%[1]。PAH的發病機制很復雜,鈣、鋅等離子通道和血管活性物質的失衡都參與了PAH的發展。此外,Hippo信號通路、骨形態發生蛋白7(bone morphogenetic protein-7, BMP-7)/Smads信號通路等也參與了PAH的發展[2-3]。雖然近年來對PAH的認識逐漸加深,但是目前PAH尚缺乏全面有效的治療方法。因此,鑒定PAH關鍵的分子標記基因對于深入理解PAH的發病機制和開發新型治療方法尤為重要。
近幾年,隨著基因測序技術的發展,基因表達總庫提供了許多獨立的基因表達數據集,而薈萃分析可以整合多個數據集,確定在單個數據集無法識別的分子特征,從而進一步揭示疾病深層的分子機制。目前雖有研究對GSE113439與GSE117261數據集進行生物信息學分析[4],但在本研究中整合的數據集更完整,可能揭示的分子機制也更加深入和全面。
6~7周齡SPF級雄性Sprague-Dawley大鼠40只,體重(260±10) g,購于上海斯萊克實驗動物有限公司。大鼠飼養環境溫度為(22±2) ℃,明暗時間為12 h/12 h,可自由飲水攝食。
野百合堿、生理鹽水和多聚甲醛(Sigma-Aldrich);無水乙醇(湖北佰智昂生物化工有限公司);PCR試劑盒[天根生化科技(北京)有限公司];引物(上海生工生物技術有限公司);戊巴比妥鈉(上海思域化工科技有限公司);逆轉錄酶試劑盒(Thermo Fisher)。
低溫高速離心機(Eppendorf);實時熒光定量PCR儀(Bio-Rad);NanoDrop 2000超微量分光光度儀(Thermo Fisher);逆轉錄PCR儀(東勝創新公司);聚乙烯(PE)-50導管(American Health & Medical Supply International Corp.);Powerlab 8/30系統和壓力傳感器(AD Instruments);電子天平(上海舜宇恒平科學儀器有限公司)。
4.1數據來源和處理從美國國立生物技術信息中心的GEO (gene expression omnibus)數據庫(www.ncbi.nlm.nih.gov/geo)中獲取4個mRNA表達數據集:GSE113439、GSE117261、GSE48149和GSE53408,樣本均來源于人肺組織。將納入的數據分為PAH組和正常對照(normal control, NC)組,各個數據集的特征見表1。經過log2轉換和基因名注釋后,將數據集上傳到NetworkAnalyst(https://www.networkanalyst.ca/)[5]進行薈萃分析。將納入的數據進行背景整合,歸一化處理和數據質量檢查后,使用主成分分析對結果進行去批次效應處理。用Fisher法選擇差異基因(differentially expressed genes, DEGs),篩選條件為整合值<0.05。

表1 四個數據集的詳細信息
4.2功能注釋和通路富集分析采用Enrichr(https://maayanlab.cloud/Enrichr/)和Metascape(https://metascape.org/gp/index.html#/main/step1)[6-7]進行基因本體論(gene ontology, GO)和京都基因和基因組數據庫(Kyoto Encyclopedia of Genes and Genomes, KEGG)富集分析。
4.3蛋白質-蛋白質相互作用(protein-protein interaction, PPI)網絡的構建和關鍵基因的篩選本研究中,在STRING數據庫(https://string-db.org/)[8]中對前2 000個DEGs進行蛋白質-蛋白質相互作用網絡構建,并應用分子整合檢測(molecular complex detection, MCODE)對DEGs進行網絡成分分析,篩選degree>10的基因構建優化PPI網絡。之后在Cytoscape[9]中用CytoHubba的betweenness算法篩選樞紐基因。
4.4動物分組以及干預大鼠適應1周后,分為NC組和PAH組,每組20只。操作前,將乙醇和生理鹽水按2∶8的體積比混合,并將野百合堿溶于乙醇鹽水中,制備野百合堿溶液。NC組大鼠在后頸部接受單次乙醇生理鹽水溶液注射,PAH組大鼠接受單次野百合堿皮下注射(50 mg/kg)。兩組大鼠均在同濟醫院特定的清潔級動物房中飼養4周,實驗所涉及的大鼠操作均得到同濟大學附屬同濟醫院動物倫理委員會的審批,實驗方案許可編號為2020-DW-002。
4.5血流動力學的測量4周后,大鼠禁食10 h,腹腔注射2%戊巴比妥鈉(40 mg/kg)麻醉大鼠。將PE-50導管插入右心室后,用Powerlab 8/30系統和壓力傳感器測量右心室收縮壓(right ventricular systolic pressure, RVSP)和平均肺動脈壓(mean pulmonary artery pressure, mPAP)。
4.6動物處死和留取樣本壓力測量后,將大鼠脫頸處死,摘除肺和心臟并保存于-80 ℃冰箱。解剖左心室(left ventricle, LV)、室間隔(interventricular septum, S)及右心室(right ventricle, RV)并分別稱重,計算右心室肥厚指數(right ventricular hypertrophy index, RVHI):RVHI=RV/(LV+S)。
4.7組織形態學分析大鼠左肺和心臟組織用4%多聚甲醛固定24 h,然后入石蠟切成5 μm厚的切片,進行蘇木精-伊紅(hematoxylin-eosin, HE)染色。通過使用Image-Pro Plus軟件選取直徑在50~200 μm之間的10條肺小動脈測量其血管壁面積(wall area, WA)和血管總面積(vessel total area, TA),用WA占TA的百分率(WA%)來評價肺血管重塑情況:WA%=WA/TA×100%。
4.8RT-qPCR用Trizol提取肺組織的總RNA后逆轉錄合成cDNA,并使用qPCR試劑盒和引物擴增待選基因的cDNA。每個樣本進行3次重復并求取平均數,以GAPDH為內參照,采用2-??Ct方法進行數據分析。引物序列見表2。

表2 RT-qPCR引物序列
動物實驗數據用GraphPad Prism 8進行統計分析。結果用均數±標準差(mean±SD)表示。NC組和PAH組之間的差異采用檢驗。以<0.05為差異有統計學意義。
經過數據篩選后納入159例患者,其中PAH組103例,NC組56例。數據處理流程,見圖1A;主成分分析結果,見圖1B;各個數據集的詳細信息,見表1。

Figure 1. Data processing flowchart and principal component analysis. A: four datasets were downloaded from NCBI-GEO, in which 26 patients were excluded for they were not PAH; B: each point represents a sample, and the farther the distance between two samples, the greater the difference between these two samples, and the closer the distance, the smaller the difference.
差異基因表達分析篩選出2 048個DEGs,其中1 480個上調,568個下調。前50個DEGs的熱圖,見圖2。對前5個DEGs進行功能分析并進行動物驗證,其中除GATA結合蛋白2(GATA-binding protein 2,)外,其他基因在PAH中報道較少,見表3。

Figure 2. Heatmap of the top 50 DEGs. Each grid represents the expression of a gene in a sample, where red represents genes up-regulated in PAH group, and green represents genes down-regulated in PAH group compared with NC group.

表3 前5個差異基因的功能
Positive values of the combined T stat indicate the of down-regulation genes in PAH group compared with NC group, and negative values indicate the up-regulation of genes in PAH group compared with NC group.
利用Enrichr和Metascape對DEGs進行的功能注釋和通路富集分析。總體DEGs主要富集在單純皰疹病毒1(herpes simplex virus 1, HSV-1)感染、人乳頭瘤病毒(human papillomavirus, HPV)感染及腫瘤等通路中,見圖3A;在生物過程方面主要涉及轉錄與DNA復制的調控、蛋白質磷酸化和RNA聚合酶Ⅱ啟動子的調控,見圖3B;在分子功能方面主要涉及RNA結合、鈣黏蛋白結合及蛋白激酶活化,見圖3C;在細胞組分方面主要涉及細胞核和中心體,見圖3D。值得注意的是,本研究發現HSV-1感染通路在PAH中高度富集,然而它在PAH中的功能少有報道,因此本研究擬對HSV-1感染通路相關基因——含桿狀病毒IAP重復序列蛋白2(baculoviral IAP repeat-containing protein 2,)、骨髓基質細胞抗原2(bone marrow stromal cell antigen 2,)、蛋白酪氨酸磷酸酶非受體型11(protein tyrosine phosphatase non-receptor type 11,)、(transporter associated with antigen processing 1)和進行RT-qPCR驗證。

Figure 3. KEGG pathway and GO analysis of total DEGs in Enrichr. A: KEGG pathway analysis; B: GO biological process analysis; C: GO molecular function analysis; D: GO cellular component analysis. The length of the red band represents the significant degree of differential enrichment results.
上調的DEGs主要在內質網中的蛋白質加工和HSV-1感染等通路明顯富集,見圖4A;在GO功能方面主要涉及有絲分裂細胞周期的調控及細胞對應激的反應,見圖4B。

Figure 4. KEGG pathway and GO analysis of up-regulated DEGs in Metascape. A: KEGG pathway; B: GO analysis enrichment. The different colors in the graph represent the significance of the enrichment results, and the size of the dots represents the number of enriched genes.
下調的DEGs主要在Th17細胞分化信號通路、細胞黏附分子相關通路等富集,見圖5A;在GO功能方面細胞主要與對生長因子刺激的反應及血管生成相關,見圖5B。

Figure 5. KEGG pathway and GO analysis of down-regulated DEGs in Metascape. A: KEGG pathway; B: GO analysis enrichment. The different colors in the graph represent the significance of enrichment results, and the size of the dots represents the number of enriched genes.
通過STRING和Cytoscape對DEGs構建PPI網絡并篩選出樞紐基因,分別為鼠雙微體蛋白2(murine double minute 2,)、熱休克蛋白90α家族A類成員1(heat shock protein 90 alpha family class A member 1,)、核仁素(nucleolin,)、β-連環素(β-catenin/catenin beta 1,)和蛋白磷酸酶2催化亞基α(protein phosphatase 2 catalytic subunit alpha,),對其進行功能分析并進行動物實驗驗證,見圖6、表4。

Figure 6. Protein-protein interaction (PPI) network of the top 2 000 DEGs. The figure shows the PPI network of the top 2 000 DEGs screened for degree greater than 10. The darker the color of the dots in the network, the greater the degree value, the more linkage with other proteins and the more important the function.

表4 Betweenness算法中排名前5位的hub基因
4周后,與對照組相比,PAH組的大鼠出現厭食、行動遲緩、體重增長減少和呼吸急促,實驗結束前均無大鼠死亡。如表5所示,PAH組所有大鼠與NC組相比,RVSP、mPAP及RVHI均顯著增高(<0.05),提示造模成功。

表5 動物模型參數
*<0.05,**<0.01NC group.
于光鏡下觀察兩組大鼠肺組織HE染色,NC組大鼠肺小動脈內皮細胞的連續性好,管壁薄,管腔面積大;PAH大鼠的肺小動脈管壁厚度明顯增厚,管腔面積明顯縮小,見圖7。

Figure 7. Pathomorphological changes of rat lung tissues in each group (HE staining, scale bar=20 μm).
與NC組比較,PAH組大鼠肺小動脈WA%明顯增高(0.01),出現明顯的血管重構,見表5。
通過RT-qPCR檢測差異基因在大鼠肺組織中的表達,數據顯示,PAH組、、和的mRNA表達在明顯上調(<0.05),而線粒體核糖體蛋白L11(mitochondrial ribosomal protein L11,)、腎上腺素受體α1A(adrenoceptor alpha 1A,)、、和的mRNA表達在PAH組明顯下調(<0.05),其余基因的mRNA表達無顯著差異,見圖8。

Figure 8. Relative mRNA expression of key genes in PAH group and NC group. The rats in PAH group received a single injection of monocrotaline, while those in NC group received a single injection of ethanol saline solution, and then lung tissue was obtained after 4 weeks for RT-qPCR. Mean±SD. n=20. *P<0.05,**P<0.01 vs NC group.
既往大量研究已探討過PAH的潛在機制以及內皮功能障礙、血管旁細胞增生和炎癥在PAH發生發展過程中的作用,但PAH的發病機制仍未完全闡明。本研究通過生物信息學分析篩選出2 048個DEGs,并用野百合堿誘導的PAH大鼠的肺組織對15個關鍵基因進行檢測,其中、、和的mRNA表達在PAH組中顯著上調,、、、和的mRNA表達在PAH組中顯著下調,大部分關鍵基因功能與細胞增殖及能量代謝的轉變有關。此外HSV-1感染、HPV感染、Th17細胞分化信號通路、細胞黏附分子通路等炎癥和免疫相關信號通路的明顯富集,提示免疫炎癥參與了PAH的發病機制。因此本研究將從細胞增殖和免疫紊亂相關機制方面予以闡述。
MRPL11是MRP家族的成員。研究表明,下調可以導致線粒體翻譯缺陷,從而引起線粒體編碼蛋白的合成減少以及氧化磷酸化亞基的合成受損,最終導致細胞能量代謝的轉變,抑制細胞的遷移與增殖[10-11]。既往研究提示,線粒體功能障礙通過多種途徑參與PAH的發生發展,Ryan等[12]發現PAH患者的線粒體DNA缺失和線粒體ATP產生增加等會促進PAH患者的肺動脈平滑肌細胞(pulmonary artery smooth muscle cells, PASMCs)的增殖,從而導致血管松弛功能受損。在本研究中,的表達在PAH組中顯著下調,同時通過對野百合堿誘導的PAH大鼠的肺組織進行檢測,我們證實的表達在PAH大鼠中也明顯下調。因此我們推測MRPL11可能通過調節線粒體編碼蛋白的合成及細胞的糖酵解代謝狀態來參與PAH的發生發展。
ADRA1A是G蛋白偶聯受體超家族的成員其中的一個亞型,可調節細胞生長和增殖。研究表明,下調可能促進成纖維細胞的增殖和膠原蛋白的產生[13]。在本研究中的下調說明其可能通過調節肺小動脈成纖維細胞等細胞的增殖,在PAH的形成中起到作用。
GATA2是鋅指轉錄因子GATA家族的成員,在調節細胞增殖相關基因的轉錄方面起著重要作用。唐思鋒等[14]的研究結果表明干擾或的表達可以抑制基因的表達從而降低細胞自噬水平,促進細胞凋亡。本研究中的下調與既往的研究結果一致[15],說明在PAH的發生形成中,GATA2可能通過調節部分細胞的自噬從而促進PAH的發生和發展。
MDM2是一種E3泛素蛋白連接酶,在調節細胞的增殖與凋亡發揮重要作用。研究表明,抑制的表達能夠負向調控血管內皮生長因子(vascular endothelial growth factor, VEGF)的表達從而抑制肺高壓小鼠肺血管內皮細胞的增殖[16]。此外,抑制的表達可使線粒體中活性氧的產生增加,導致線粒體DNA損傷,最終促進細胞凋亡[17]。在本研究中,在PAH組中顯著上調可能說明其可通過調節內皮細胞的增殖參與PAH的發展。
NCL位于真核細胞核仁中,可由VEGF和細胞外基質協同介導從細胞核轉移到細胞表面,參與核糖體的生物合成、成熟以及細胞增殖等生物過程。對內皮細胞表面NCL的表達進行功能性阻斷或下調可明顯抑制內皮細胞的增殖、遷移以及血管的生成[18]。在本研究中,在PAH組中顯著上調,提示NCL可能通過促進內皮細胞等細胞的增殖與遷移從而影響PAH的發展。
HSP90AA1是HSP90家族的一員。有研究表明,HSP90可以在PAH大鼠的PASMCs線粒體中過表達,通過維持線粒體DNA的完整性減少PASMCs的氧化損傷,促進PASMC的增殖[19]。此外,HSP90通過核因子κB(nuclear factor-κB, NF-κB)通路和NOD樣受體蛋白3(NOD-like receptor protein 3, NLRP3)通路激活炎癥因子,如腫瘤壞死因子α(tumor necrosis factor-α, TNF-α)、白細胞介素6(interleukin-6, IL-6)和IL-1β[20]。在本研究中在肺組織中的上調,表明HSP90AA1可能通過線粒體相關通路以及NLRP3等炎癥通路加重細胞氧化損傷以及炎癥反應參與PAH的發生和發展。
β-catenin/是Wnt/β-catenin通路的核心成分。目前認為抑制Wnt/β-catenin通路的激活能夠降低細胞周期蛋白D1、VEGF和c-Myc的表達從而抑制PASMCs的增殖,減輕PAH[21-22]。同時Wnt/β-catenin信號對T細胞的分化、效應功能和遷移至關重要[23]。因此,我們推測β-catenin/可能通過Wnt/β-catenin通路調節細胞的增殖以及T細胞的功能,從而在PAH中起到重要作用。
本研究中DEGs的富集分析結果顯示PAH組的Th17細胞分化信號通路、細胞黏附分子通路和趨化因子信號通路都存在明顯富集[24-26],這些信號通路與既往研究結果報道一致。其中HSV-1感染通路富集明顯,而其在PAH中的功能目前則知之甚少。HSV-1是一種常見的人類病原體,其參與了多種心血管疾病的發展[27]。HSV-1感染可通過增加細胞間黏附分子1(intercellular adhesion molecule-1, ICAM-1)和一氧化氮水平導致內皮功能紊亂,從而使白細胞經過淋巴細胞功能相關抗原1(lymphocyte function-associated antigen 1, LFA-1)/ICAM-1復合體通過內皮屏障[28]。此外,HSV-1還可以通過增強三酰甘油和飽和膽固醇酯在血管平滑肌細胞(vascular smooth muscle cells, VSMCs)中的累積以介導VSMCs的增殖[29-30]。目前認為PAH的發生是由內皮屏障的破壞而啟動的,因此我們認為HSV-1可能通過病毒的感染,增加ICAM-1水平引發內皮屏障功能障礙,同時導致PASMCs的增殖,從而最終促進PAH的發生和發展。在本研究中,我們也驗證了HSV-1感染通路的相關基因,其中和在PAH組顯著下調,其余基因沒有顯著性差異,但有降低趨勢。研究表明,PTPN11能夠通過與腺嘌呤核苷酸轉運酶1(adenine nucleotide translocase 1, ANT1)結合激活caspase-1從而抑制NLRP3的過度激活[31],而抑制能夠通過Akt和STAT3通路抑制PASMCs的遷移和增殖,改善肺小動脈的重塑[32]。BST2能夠作為細胞黏附分子參與內皮細胞對單核細胞的招募[33],并通過激活EGFR以及NF-κB通路從而調節細胞周期蛋白cyclin A和cyclin D1,以及凋亡蛋白Bax、Bcl2與caspas-3的表達,促進細胞增殖,抑制細胞凋亡[34-35]。在本研究中,和在PAH組中顯著下調,說明與可能通過對炎癥的激活以及細胞周期的調節參與PAH的發生與發展。
綜上所述,本研究采用生物信息學的方法對GEO數據庫中的PAH基因芯片數據進行整合分析,篩選差異基因并經GO及KEGG富集分析,得到比單個數據集更加全面可靠的差異基因和信號通路。其中,HSV-1感染通路等新通路的發現可為深入研究PAH發生機制提供方向。此外,、、和等新的關鍵基因的發現,可能為PAH的轉化醫學相關研究提供新的靶點。
[1]中華醫學會呼吸病學分會肺栓塞與肺血管病學組,中國醫師協會呼吸醫師分會肺栓塞與肺血管病工作委員會,全國肺栓塞與肺血管病防治協作組,等. 中國肺動脈高壓診斷與治療指南(2021版)[J]. 中華醫學雜志, 2021, 101(1):11-51.
Pulmonary Embolism and Pulmonary Vascular Disease Group of the Chinese Medical Association, Pulmonary Embolism and Pulmonary Vascular Disease Working Committee of the Respiratory Physicians Branch of the Chinese Medical Association, National Pulmonary Embolism and Pulmonary Vascular Disease Prevention and Treatment Collaborative Group, et al. Guidelines for the diagnosis and treatment of pulmonary hypertension in China (2021 edition)[J]. Natl Med J Chin, 2021, 101(1):11-51.
[2]朱寧,陳皓,趙旭勇,等. 野百合堿誘導的大鼠肺動脈高壓對大鼠肺Hippo信號通路相關分子表達的影響[J]. 中國病理生理雜志, 2019, 35(7):1333-1338.
Zhu N, Chen H, Zhao XY, et al. Effects of monocrotaline-induced pulmonary hypertension on expression of Hippo signaling pathway-related molecules in rat lung[J]. Chin J Pathophysiol, 2019, 35(7):1333-1338.
[3]張晶晶,武垣伶,黃丹娜,等. BMP-7/Smads通路參與EndoMT在大鼠HHPH中的作用[J]. 中國病理生理雜志, 2020, 36(2):316-322.
Zhang JJ, Wu YL, Huang DN, et al. Role of BMP-7/Smads pathway in regulation of EndoMT in rats with HHPH[J]. Chin J Pathophysiol, 2020, 36(2):316-322.
[4]仲紅艷,唐珊,趙飛飛,等. 肺動脈高壓關鍵基因的篩選及生物信息學分析[J]. 中國循環雜志, 2020, 35(8):793-800.
Zhong HY, Tang S, Zhao FF, et al. Key genes for pulmonary arterial hypertension screened with bioinformatics analysis[J]. Chin Circ J, 2020, 35(8):793-800.
[5] Zhou G, Soufan O, Ewald J, et al. NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis[J]. Nucleic Acids Res, 2019, 47(W1):W234-W241.
[6] Kuleshov MV, Jones MR, Rouillard AD, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update[J]. Nucleic Acids Res, 2016, 44(W1):W90-W97.
[7] Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets[J]. Nat Commun, 2019, 10(1):1523.
[8] Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks[J]. Genome Res, 2003, 13(11):2498-2504.
[9] Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage,supporting functional discovery in genome-wide experimental datasets[J]. Nucleic Acids Res, 2019, 47(D1): D607-D613.
[10] Huang G, Li H, Zhang H. Abnormal expression of mitochondrial ribosomal proteins and their encoding genes with cell apoptosis and diseases[J]. Int J Mol Sci, 2020, 21(22):8879.
[11] Besse A, Brezavar D, Hanson J, et al. LONP1 de novo dominant mutation causes mitochondrial encephalopathy with loss of LONP1 chaperone activity and excessive LONP1 proteolytic activity[J]. Mitochondrion, 2020, 51:68-78.
[12] Ryan J, Dasgupta A, Huston J, et al. Mitochondrial dynamics in pulmonary arterial hypertension[J]. J Mol Med (Berl), 2015, 93(3):229-242.
[13] Drummond PD, Dawson LF, Wood FM, et al. Up-regulation of α1-adrenoceptors in burn and keloid scars[J]. Burns, 2018, 44(3):582-588.
[14] 唐思鋒,王德友,趙偉. 從GATA2、GATA6探究環狀RNA調控胃癌自噬和凋亡的機制[J]. 中華實驗外科雜志, 2020, 37(9):1655-1657.
Tang SF, Wang DY, Zhao W. Mechanism of autophagy and apoptosis regulated by cyclic RNA in gastric cancer from GATA2 and GATA6[J]. Chin J Exp Sur, 2020, 37(9):1655-1657.
[15] Marciano BE, Olivier KN, Folio LR, et al. Pulmonary manifestations of GATA2 deficiency[J]. Chest, 2021, 160(4):1350-1359.
[16] Shen H, Zhang J, Wang C, et al. MDM2-mediated ubiquitination of angiotensin-converting enzyme 2 contributes to the development of pulmonary arterial hypertension[J]. Circulation, 2020, 142(12):1190-1204.
[17] Elkholi R, Abraham-Enachescu I, Trotta AP, et al. MDM2 integrates cellular respiration and apoptotic signaling through NDUFS1 and the mitochondrial network[J]. Mol Cell, 2019, 74(3):452-465.
[18] Huang Y, Shi H, Zhou H, et al. The angiogenic function of nucleolin is mediated by vascular endothelial growth factor and nonmuscle myosin[J]. Blood, 2006, 107(9):3564-3571.
[19] Boucherat O, Peterlini T, Bourgeois A, et al. Mitochondrial HSP90 accumulation promotes vascular remodeling in pulmonary arterial hypertension[J]. Am J Respir Crit Care Med, 2018, 198(1):90-103.
[20] Li F, Song X, Su G, et al. AT-533, a Hsp90 inhibitor, attenuates HSV-1-induced inflammation[J]. Biochem Pharmacol, 2019, 166:82-92.
[21] Wande Y, Jie L, Aikai Z, et al. Berberine alleviates pulmonary hypertension through Trx1 and β-catenin signaling pathways in pulmonary artery smooth muscle cells[J]. Exp Cell Res, 2020, 390(1):111910.
[22] Yu XM, Wang L, Li JF, et al. Wnt5a inhibits hypoxia-induced pulmonary arterial smooth muscle cell proliferation by downregulation of β-catenin[J]. Am J Physiol Lung Cell Mol Physiol, 2013, 304(2):L103-L111.
[23] Li X, Xiang Y, Li F, et al. WNT/β-catenin signaling pathway regulating T cell-inflammation in the tumor microenvironment[J]. Front Immunol, 2019, 10:2293.
[24] Szulcek R, Happé CM, Rol N, et al. Delayed microvascular shear adaptation in pulmonary arterial hypertension. Role of platelet endothelial cell adhesion molecule-1 cleavage[J]. Am J Respir Crit Care Med, 2016, 193(12):1410-1420.
[25] Bhagwani A, Thompson AAR, Farkas L. When innate immunity meets angiogenesis-the role of toll-like receptors in endothelial cells and pulmonary hypertension[J]. Front Med (Lausanne), 2020, 7:352.
[26] Hashimoto-Kataoka T, Hosen N, Sonobe T, et al. Interleukin-6/interleukin-21 signaling axis is critical in the pathogenesis of pulmonary arterial hypertension[J]. Proc Natl Acad Sci U S A, 2015, 112(20):E2677-E2686.
[27] Rauff B, Malik A, Bhatti YA, et al. Association of viruses in the development of cardiovascular diseases[J]. Curr Pharm Des, 2021, 27(37):3913-3923.
[28] Liu H, Qiu K, He Q, et al. Mechanisms of blood-brain barrier disruption in herpes simplex encephalitis[J]. J Neuroimmune Pharmacol, 2019, 14(2):157-172.
[29] Hajjar DP, Pomerantz KB, Falcone DJ, et al. Herpes simplex virus infection in human arterial cells. Implications in arteriosclerosis[J]. J Clin Invest, 1987, 80(5):1317-1321.
[30] Skelly CL, He Q, Spiguel L, et al. Modulating vascular intimal hyperplasia using HSV-1 mutant requires activated MEK[J]. Gene Ther, 2013, 20(2):215-224.
[31] Guo W, Liu W, Chen Z, et al. Tyrosine phosphatase SHP2 negatively regulates NLRP3 inflammasome activation via ANT1-dependent mitochondrial homeostasis[J]. Nat Commun, 2017, 8(1):2168.
[32] Cheng Y, Yu M, Xu J, et al. Inhibition of Shp2 ameliorates monocrotaline-induced pulmonary arterial hypertension in rats[J]. BMC Pulm Med, 2018, 18(1):130.
[33] Yoo H, Park SH, Ye SK, et al. IFN-γ-induced BST2 mediates monocyte adhesion to human endothelial cells[J]. Cell Immunol, 2011, 267(1):23-29.
[34] Liu W, Cao Y, Guan Y, et al. BST2 promotes cell proliferation,migration and induces NF-κB activation in gastric cancer[J]. Biotechnol Lett, 2018, 40(7):1015-1027.
[35] Jin H, Zhang L, Wang S,et al. BST2 promotes growth and induces gefitinib resistance in oral squamous cell carcinoma via regulating the EGFR pathway[J]. Arch Med Sci, 2021, 17(6):1772-1782.
Screening and identification of molecular marker genes for pulmonary arterial hypertension
LI Jie1, LIU Cai-ying2, YAN Wen-wen1, SHEN Yu-qin1, XU Jin-yuan2, XU Guo-tong3, Lü Li-xia2, SONG Hao-ming1△
(1,,,,200065,;2,,,200092,;3,,,200092,)
To identify the key genes and related signaling pathways involved in the pathogenesis of pulmonary arterial hypertension (PAH), which can provide new targets for translational medicine research.GSE113439, GSE117261, GSE48149 and GSE53408 gene microarray datasets were extracted from Gene Expression Omnibus (GEO) database, and then 103 cases of PAH and 56 cases of healthy controls were identified after data screening for comparison analysis. NetworkAnalyst was used to screen differentially expressed genes (DEGs), and Enrichr and Metascape were used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Moreover, protein-protein interaction (PPI) network was established using STRING and Cytoscape to identify the hub genes. Rat PAH model was constructed using monocrotaline, which was determined by measuring haemodynamic parameters and histomorphological observations. Changes in mRNA levels of candidate DEGs in lung tissues were validated by RT-qPCR.A total of 2 048 DEGs were obtained, in which 1 480 were up-regulated and 568 were down-regulated. These genes were mainly relevant to inflammation and proliferation, such as herpes simplex virus 1 infection, human papillomavirus infection and pathways in cancer.,,,andwere the most significant DEGs, and hub genes including,,,andwere also identified. Four weeks after the injection of monocrotaline, right ventricular systolic pressure (RVSP) and mean pulmonary arterial pressure (mPAP) of rats in PAH group were significantly higher compared to the control group (<0.05), and hematoxylin-eosin (HE) staining of lung tissues showed that the walls of small pulmonary arteries were significantly thickened (<0.01), which indicated PAH model was established successfully. The up-regulation of,,and, and down-regulation of,,andin PAH group were verified by RT-qPCR (<0.05), while the expression of,,andwere not significantly different (>0.05).Key genes involved in the development of PAH were identified, which were expected to provide new targets for translational medicine research.
Pulmonary arterial hypertension; Bioinformatics; Inflammation; Cell proliferation
R563; R363.2
A
10.3969/j.issn.1000-4718.2022.06.014
1000-4718(2022)06-1063-12
2021-12-13
2022-02-10
國家自然科學基金青年基金資助項目(No. 81700316)
Tel: 13004113931; E-mail: songhao-ming@163.com
(責任編輯:余小慧,宋延君)