摘要
胰腺癌具有高度迁移性和侵袭性的特点,预后不良,但癌基因的突变及分子调控关系等的改变会影响胰腺癌的恶性生物学行为。泛素/ISG15结合酶E2L6(UBE2L6)在泛癌中的表达及胰腺癌中的生物学功能依然不清楚。本研究拟通过生物信息学分析及实验验证,探讨UBE2L6对胰腺癌增殖、迁移侵袭能力的影响及可能的分子机制。
从UCSC Xena下载TCGA和GTEx的RNA-seq数据,用R(4.0.2)软件的“limma”包分析UBE2L6在泛癌中的差异表达。利用从GEO数据集下载数据及qRT-PCR分别验证UBE2L6在胰腺癌组织及细胞中的差异表达。胰腺癌细胞转染靶向UBE2L6的siRNA后用CCK-8细胞增殖、克隆形成、Transwell迁移和侵袭实验分析UBE2L6对胰腺癌细胞生物学功能的影响。利用UBE2L6的分子相关性、蛋白相互作用及基因富集分析(GSEA)探讨其可能的作用机制。进一步利用TCGA数据库的胰腺癌临床数据,分析UBE2L6的表达与其临床病理特征的关系及临床应用价值。
表达差异分析提示UBE2L6在泛癌中表达增高,在胰腺癌组织及BxPC-3(t=33.82,P<0.000 1)、PANC-1(t=7.36,P=0.001 8)、AsPC-1(t=9.61,P=0.000 7)、SW1990(t=10.26,P=0.000 5)及MIA PaCa-2(t=12.65,P=0.000 2)等胰腺癌细胞系中亦高表达。细胞功能实验显示,UBE2L6可促进胰腺癌PANC-1和AsPC-1细胞的增殖、迁移及侵袭。Spearman相关性分析提示BCL2A1蛋白与UBE2L6的相关性最大(r=0.442)。蛋白相互作用分析显示,其可能与HERC6、RPS27A、HERC5、UBA52、ISG15、UBA7、DDX58、UBC、UBB、ARIH1等蛋白有相互作用。同时,GSEA富集分析提示UBE2L6与肿瘤免疫微环境等密切相关。而临床病理相关性分析显示,UBE2L6高表达与胰腺癌组织病理学分级密切相关(
胰腺癌是全球癌症相关性死亡的主要原因之一,排在美国患者癌症相关性死亡的第3
泛素/ISG15结合酶E2L6(ubiquitin/ISG15-conjugating enzyme E2 L6,UBE2L6)是编码E2泛素结合酶家族的成员,也是翻译后蛋白修饰的关键酶,有证据显示其可以促进干扰素刺激基因15(ISG15)与底物蛋白的共价连接,在白血病细胞分化过程中发挥重要作
从UCSC Xena(https://xenabrowser.net/datapages)下载泛癌数据,将经过Toil流程统一处理的TCGA和GTEx的TPM格式的RNA-seq数据进行Log2转换,用R(4.0.2)软件的“limma”包分析UBE2L6在泛癌中的差异表达,“ggplot2”包可视化其差异表达。进一步在GEO数据集(Gene Expression Omnibus DataSets,http://www.ncbi.nlm.nih.gov/geo)下载GPL570文件,及GSE15471(包含39例胰腺癌组织及相应的癌旁组织)和GSE16515(包含36例胰腺癌组织和16例癌旁组织)数据集,利用perl软件将探针名转换为基因名后,选取UBE2L6的表达数据用GraphPad Prism 8绘制散点图。
所有胰腺癌细胞株BxPC-3、PANC-1、AsPC-1、SW1990、MIA PaCa-2及正常胰腺导管上皮细胞HPDE均购自美国ATCC细胞库。PANC-1、MIA PaCa-2、SW1990和HPDE、BxPC-3、AsPC-1细胞分别用含10%胎牛血清(Gbico,美国)的DMEM(Gbico,美国)和RPMI 1640(Gbico,美国)培养基置于37 ℃的5% CO2培养箱培养。采用Lipofectamine 2000 (Invitrogen,美国)将UBE2L6的siRNA(Ribobio,中国)及阴性对照(negative control,NC)转染入PANC-1和AsPC-1细胞内,48 h后进行实时荧光定量PCR检测或细胞功能实验。
用RNA-easy Isolation Reagent试剂盒(Vazyme,中国)提取总RNA,并用分光光度计测定产物纯度及浓度。然后用HiScript III 1st Strand cDNA Synthesis Kit(+gDNA wiper)逆转录试剂盒(Vazyme,中国)和Cham
用CCK-8试剂盒(Bosterbio,中国)检测胰腺癌细胞的增殖能力。PANC-1和AsPC-1细胞转染入siRNA 48 h后以2×1
将siRNA转染入PANC-1及AsPC-1细胞48 h后,消化重悬细胞并按800/孔接种于6孔板中,加入含10%胎牛血清的培养基2 mL,置于培养箱中培养12~14 d,磷酸盐缓冲液漂洗后以4%多聚甲醛室温下固定30 min,然后以0.1%结晶紫染色30 min后在显微镜下拍照。
PANC-1及AsPC-1细胞转染入siRNA 48 h后,细胞消化重悬并以无血清培养基200 μL稀释后按5×1
分子相关性分析:将TCGA数据库中UBE2L6的表达按中位数分为高表达组和低表达组,Spearman相关性分析寻找高风险组中相关性最大的基因,并用R(4.0.2)软件的“ggplot2”包进行可视化。蛋白互作分析:利用string数据库(https://www.string-db.org/)构建UBE2L6的蛋白相互作用网络图。GSEA富集分析:根据TCGA数据库中UBE2L6的mRNA表达中位数,将其分为高表达组和低表达组,使用GSEA 3.0软件中的KEGG基因集GeneSetsDebates:C2.CP.KEGG.V6.2.Symbols.gmt(Curated)进行GSEA富集分析,设定循环次数为1 000次。以错误发现率(false discovery rate,FDR)<0.25,P<0.05为显著富集的基因集合,进一步筛选与UBE2L6密切相关的基因集用“ggplot2”进行多基因富集分析及可视化。
从TCGA数据库(https://portal.gdc.cancer.gov)下载胰腺癌的转录组、基因表达量、HTSeq-FPKM及临床数据,数据集截止到2021年4月20日。胰腺癌临床数据纳入标准:⑴ 病理确诊为胰腺腺癌(pancreatic adenocarcinoma,PAAD);⑵ 临床相关资料完整。除去部分信息缺失的个体,将168例胰腺癌纳入本研究。根据UBE2L6的表达平均值分为高表达组和低表达组,用SPSS 26.0软件分析其与临床病理的相关性。用R(4.0.2)软件的“Survival”包对患者的年龄、性别、分级、肿瘤分期、淋巴结转移、UBE2L6表达水平等指标进行单因素和多因素Cox回归分析,探讨其对胰腺癌预后的影响。同时,提取TCGA(胰腺癌)和GTEx(正常组织)的RNA-seq数据(需要Log2转换),用R(4.0.2)软件的“pROC”包绘制受试者工作特征曲线(receiver operating characteristic curve,ROC),分析UBE2L6对胰腺癌的潜在诊断价值。利用基因表达谱交互式分析数据库(Gene Expression Profiling Interactive Analysis,GEPIA)(http://gepia.cancer-pku.cn)的Kaplan-Meier生存分析评估UBE2L6对胰腺癌的预后价值。
分析来自TCGA及GTEx数据库的数据,发现UBE2L6在胰腺癌、膀胱尿路上皮癌、乳腺浸润癌、宫颈鳞癌和腺癌、胆管癌、结肠癌、弥漫性大B细胞淋巴瘤、食管癌、多形成性胶质细胞瘤、头颈鳞状细胞癌、肾嫌色细胞癌、肾透明细胞癌、肾乳头状细胞癌、急性髓细胞样白血病、脑低级别胶质瘤、肝细胞肝癌、卵巢浆液性囊腺癌、前列腺癌、直肠腺癌、皮肤黑色素瘤、胃癌、睾丸癌、甲状腺癌、胸腺癌等24种癌症中表达增高(

图1 UBE2L6在泛癌中的表达
Figure 1 Expressions of UBE2L6 in pan-cancer
为了探讨UBE2L6在胰腺癌组织中的表达情况,分析其在GEO数据集中的表达,发现UBE2L6在胰腺癌组织中的表达水平相较于癌旁组织显著增高(GSE15471:t=6.549,P<0.001,GSE16515:t=4.502,P<0.001)(

图2 UBE2L6在胰腺癌组织及细胞系中的表达 A:UBE2L6在GSE15471中的表达水平;B:UBE2L6在GSE16515中的表达水平;C:胰腺癌细胞中UBE2L6的相对mRNA表达
Figure 2 Expressions of UBE2L6 in pancreatic cancer tissues and cell lines A: Expression of UBE2L6 in GSE15471; B: Expression of UBE2L6 in GSE16515; C: Relative mRNA expression of UBE2L6 in pancreatic cancer cell lines
为探讨UBE2L6对胰腺癌增殖、迁移及侵袭等生物学功能的影响,设计了针对UBE2L6靶序列的siRNA(GCT GGT GAA TAG ACC GAA T)。qRT-PCR检测提示,在PANC-1及AsPC-1细胞中转染UBE2L6的siRNA能明显下调其表达水平(t=39.18,P<0.000 1;t=47.87,P<0.000 1)(

图3 UBE2L6对胰腺癌细胞PANC-1和AsPC-1的增殖、迁移及侵袭的影响 A:在UBE2L6敲低的PANC-1和AsPC-1细胞中UBE2L6的相对mRNA表达水平;B:CCK-8检测PANC-1和AsPC-1细胞的增殖;C:克隆平板实验检测PANC-1和AsPC-1细胞的克隆形成;D:Transwell迁移实验检测PANC-1和AsPC-1细胞的迁移;E:Transwell侵袭实验检测PANC-1和AsPC-1细胞的侵袭
Figure 3 Influences of UBE2L6 on proliferation, migration, and invasion of pancreatic cancer PANC-1 and AsPC-1 cells A: Relative mRNA expression of UBE2L6 in UBE2L6-knockdown PANC-1 and AsPC-1 cells; B: The proliferation of PANC-1 and AsPC-1 cells detected by CCK-8 assay; C: The colony-forming capacity of PANC-1 and AsPC-1 cells detected by colony formation assay; D: The migration of PANC-1 and AsPC-1 cells detected by Transwell migration assay; E: The invasion of PANC-1 and AsPC-1 cells detected by Transwell invasion assay
为进一步探讨UBE2L6的分子机制,Spearman相关性分析提示,B细胞淋巴瘤2相关蛋白A1(BCL2A1)与UBE2L6的相关性最大(r=0.442)(

图4 UBE2L6的分子相关性、蛋白相互作用及多基因GSEA富集分析 A:UBE2L6分子相关性热图;B:UBE2L6的蛋白相互作用网络图;C:UBE2L6的多基因GSEA富集分析
Figure 4 Molecular correlation heatmap, protein interaction, and multi-gene sets enrichment analysis of UBE2L6 A: Molecular correlation heatmap of UBE2L6; B: Protein interaction network of UBE2L6; C: Multi-gene sets enrichment analysis of UBE2L6
临床病理相关性分析结果显示,UBE2L6的高表达与胰腺癌组织病理学分级相关(

图5 UBE2L6与胰腺癌的关系 A:UBE2L6富集于胰腺癌通路;B:UBE2L6的ROC曲线;C:UBE2L6的生存曲线
Figure 5 Relationship between UBE2L6 and pancreatic cancer A: Enrichment of UBE2L6 in pancreatic cancer signaling pathway; B: ROC curve of UBE2L6; C: Kaplan-Meier survival curve of UBE2L6
根据国际癌症研究中心的数
UBE2L6作为一种翻译后修饰的关键酶参与了蛋白质的泛素化修
目前,生物信息学技术已广泛应用于生物医学领域,为分子生物学机制研究提供了新的见
为了探索,笔者通过GSEA富集分析发现,UBE2L6在胰腺癌中显著富集(FDR<0.05),说明UBE2L6参与胰腺癌的病理生理过程,有一定的临床研究价值。另外,ROC曲线分析显示UBE2L6的AUC>0.9,提示其在胰腺癌中具有较高的诊断效能,而Kaplan-Meier生存分析也发现其表达水平与胰腺癌的不良预后紧密相关(P<0.05),预示着UBE2L6表达量高的患者的中位生存时间可能更短。UBE2L6与胰腺癌的临床病理相关性分析进一步提示,虽然UBE2L6的表达水平与患者的年龄、性别、淋巴结转移和TNM临床分期等无关(P>0.05),但却与胰腺癌的组织病理学分级显著相关(P<0.05),意味着有血管浸润等组织病理学分级晚的胰腺癌患者其UBE2L6的表达水平也更高。并且,后续的单因素Cox回归分析亦发现UBE2L6的低表达可以改善胰腺癌患者的预后,这些结果都表明UBE2L6在胰腺癌的进展中可能扮演着癌基因的角色,开发靶向抑制UBE2L6表达的药物可能具有治疗胰腺癌的潜力。遗憾的是,受到TCGA数据库样本量的限制,本研究的多因素Cox回归分析显示UBE2L6不是胰腺癌的独立预后因素,这可能与本次纳入的样本量较少有关,有待进一步的大数据库整合研究证实。
综上,本研究确定了UBE2L6在泛癌中普遍高表达,其高表达与胰腺癌的发生发展关系密切,并与其诊断及预后显著相关。同时,UBE2L6可促进胰腺癌细胞的增殖、迁移及侵袭,其分子机制可能与细胞凋亡、泛素化修饰、MAPK信号通路以及对肿瘤免疫微环境的调节等有关。未来,需要收集更多的临床数据并增加生物学实验进一步探索UBE2L6在胰腺癌中的功能及分子机制。
利益冲突
所有作者均声明不存在利益冲突。
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