CN112266958A - 胃癌检测用的内参miRNA、应用及试剂盒 - Google Patents

胃癌检测用的内参miRNA、应用及试剂盒 Download PDF

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CN112266958A
CN112266958A CN202011015916.6A CN202011015916A CN112266958A CN 112266958 A CN112266958 A CN 112266958A CN 202011015916 A CN202011015916 A CN 202011015916A CN 112266958 A CN112266958 A CN 112266958A
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陈璇
柴可群
费宝莹
吴人照
余志红
朱佳杰
任泽明
童晔玲
陈思思
薛晓敏
李毓
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Zhejiang Academy of Traditional Chinese Medicine
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Abstract

本发明公开了一种胃癌检测用的内参miRNA、应用及试剂盒。胃癌检测用的内参miRNA为miRNA rno‑let‑7g‑5p或rno‑miR‑429,其中,rno‑let‑7g‑5p的序列为:5’‑UGAGGUAGUAGUUUGUACAGUU‑3’,rno‑miR‑429的序列为:5’‑UAAUACUGUCUGGUAAUGCCGU‑3’。本发明胃癌检测用的内参miRNA是通过高通量测序能在全基因组范围内筛选到相对最稳定的内参,并经过了RT‑qPCR验证,可以用于作为RT‑qPCR检测时的内参。

Description

胃癌检测用的内参miRNA、应用及试剂盒
技术领域
本发明涉及生物技术检测技术领域,特别是涉及一种胃癌检测用的内参 miRNA、应用及试剂盒。
背景技术
胃癌属于消化系统常见病,无论在全球还是在我国,胃癌发病率和致死率在所有恶性肿瘤中均排名第五和第三,严重威胁人类健康。虽然我国胃癌病人的五年生存率已经提升到35.9%,仍远低于韩国的68.9%的五年生存率(Claudia Allemani,TomohiroMatsuda,Veronica Di Carlo,Rhea Harewood,Melissa Matz, Maja
Figure RE-GDA0002849062960000011
etal.Global surveillance of trends in cancer survival 2000–14 (CONCORD-3):analysis of individual records for 37513025patients diagnosed with one of18cancers from 322population-based registries in 71countries.The Lancet,2018,391(10125):1023-1075.)。我国胃癌高发,占全球新发病例总数的近一半。胃癌的治疗困难重重,但其发生及进展经历一个漫长的过程,其诊断和早期治疗是降低胃癌死亡率的关键。
高通量测序技术又称深度测序技术,近十余年来逐渐兴起,在基础研究和临床研究领域得到广泛应用。该技术测序通量大,可实现在全基因组范围内检测基因的表达的目的。
miRNA是一类约22个核苷酸的非编码RNA,通过在转录后水平调控基因的表达参与诸多关键的生理和病理过程,具有高度保守性、时序性和组织特异性,在很多疾病的诊断和治疗中发挥重要作用(Benjamin P.Lewis,Christopher B. Burge,DavidP.Bartel.Conserved Seed Pairing,Often Flanked by Adenosines, Indicates thatThousands of Human Genes are MicroRNA Targets[J].cell,2005, 120(1):0-20.),是胃癌发病机理及其治疗药物候选靶标研究中的重要环节。
荧光定量PCR(RT-qPCR)技术广泛应用于基因表达研究中(Livak KJ andSchmittgen TD.(2001)Analysis of relative gene expression data using real-timequantitative PCR and the 2-ΔΔCT method.Methods,25,402-408.)。基因表达水平的标准化对于准确的表达分析至关重要(
Figure RE-GDA0002849062960000012
A,Thulke S,Mackay IM,Landt O,SiegertW and Nitsche A.(2004)Guideline to reference gene selection for quantitativereal-time PCR.Biochemical and Biophysical Research Communications,313,856-862.)。许多假定稳定表达的所谓管家基因在某些实验条件下或某些器官中可能不稳定。因此,在实验中筛选表达恒定的内参 miRNA,是准确比较目的miRNA表达水平差异的前提。
大鼠1-甲基-3-硝基-1-亚硝基胍(MNNG)诱导胃癌模型能模拟人正常胃组织到慢性胃炎、慢性萎缩性胃炎、肠化生、上皮内瘤变、胃癌、死亡全过程,目前该模型已被广泛应用(陈泽慧,魏玥,安静,彭继升,黄大未,贾云飞,杨晋翔. 胃癌及胃癌前病变大鼠造模方法的文献研究.天津中医药,2019,36(9): 850-855.)。然而,目前这一模型中的表达稳定的miRNA内参基因的筛选和检测尚未见报道。
发明内容
本发明针对现有技术中存在的上述不足,提供了一种胃癌检测用的内参 miRNA、应用及试剂盒。
本申请通过利用高通量测序技术在全基因组范围内对该模型中的内参基因进行了筛选,并用RT-qPCR技术进一步验证筛选,获得了2个表达最稳定的内参miRNA。
胃癌检测用的内参miRNA,为miRNA rno-let-7g-5p或rno-miR-429,其中, rno-let-7g-5p的序列为:5’-UGAGGUAGUAGUUUGUACAGUU-3’,rno-miR-429 的序列为:5’-UAAUACUGUCUGGUAAUGCCGU-3’。
本发明又提供了miRNA rno-let-7g-5p或rno-miR-429在作为非疾病诊断为目的的、胃癌检测用的内参miRNA中的应用。本申请中作为内参的miRNA在用于胃癌检测时,可以适用于筛选治疗胃癌的药物,通过药物作用和未施加药物作用组中相关可作为分子标记的miRNA量的检测,检测时用本申请的内参 miRNA,从而可以得出药物是否有效。
所述的应用中检测方法为RT-qPCR或高通量测序。
所述的应用中检测对象为大鼠胃组织。
本发明又提供了一种用于检测胃癌的试剂盒,包括用于检测内参miRNA rno-let-7g-5p或rno-miR-429的引物,
其中,rno-let-7g-5p的序列为:5’-UGAGGUAGUAGUUUGUACAGUU-3’, rno-miR-429的序列为:5’-UAAUACUGUCUGGUAAUGCCGU-3’。
所述的试剂盒中用于检测内参rno-let-7g-5p的上游引物序列为 5’-TGAGGTAGTAGTTTGTACAGTT-3’,用于检测内参rno-miR-429的上游引物序列为5’-TAATACTGTCTGGTAATGCCGT-3’。
本发明还提供了一种非疾病诊断为目的的、检测胃癌的方法,使用所述的试剂盒,使用RT-qPCR方法检测作为胃癌分子标记的miRNA,并使用miRNA rno-let-7g-5p或rno-miR-429作为内参miRNA。
优选的,作为胃癌分子标记的miRNA为rno-miR-542-3p。用于检测 rno-miR-542-3p的上游引物序列为5’-TGTGACAGATTGATAACTGAAA-3’。
本发明胃癌检测用的内参miRNA是通过高通量测序能在全基因组范围内筛选到相对最稳定的内参,并经过了RT-qPCR验证,可以用于作为RT-qPCR检测时的内参。
附图说明
图1为本发明高通量筛选的流程图。
图2为rno-let-7g-5p和rno-miR-429熔解曲线图,其中A为rno-let-7g-5p, B为rno-miR-429,同一图中多条曲线表示多次重复。
图3为不同内参对RNA-Seq和RT-qPCR结果中rno-miR-542-3p组间表达变化的校准结果图,其中A为RNA-Seq结果,B为RT-qPCR结果。
具体实施方式
实施例1
(1)试剂和仪器
MNNG:日本东京化成工业株式会社生产,批号:75F71-TF;
总RNA提取试剂盒:Trizol(invitrogen,美国);
反转录试剂盒:PrimeScriptTM RT Master Mix(TaKaRa,日本);
qPCR试剂盒:SYBR Premix Ex Taq TMⅡ(TaKaRa,日本);
引物:上海生工生物工程有限公司设计合成;
荧光定量PCR仪:StepOnePlusTM(ABI,美国);
分光光度计:NanoDrop ND2000(Thermo,美国)。
(2)动物实验Wistar大鼠,6周龄,体重约200g,均饲养于浙江省中医药研究院的屏障实验室内,每12h光照明暗交替。动物实验经过浙江省立同德医院伦理委员会论证和批准[No.(2016)040]。
分为自然对照组、模型组(MNNG溶液167μg/ml,自由饮用),连续造模 36周。最后1天,戊巴比妥钠麻醉大鼠后,解剖胃部及其上游0.5cm食管和下游1.5cm十二指肠。每个胃样品垂直平均分为2部分:一部分于液氮中速冻,提取总RNA后进行高通量测序;另一部分用10%福尔马林固定,用于病理观察。
(3)病理检测
胃组织用10%福尔马林固定,经石蜡包埋后,切4μm厚度切片。切片随后进行HE染色,或AB-PAS染色,光镜下检测。检测者对实验设计和结果评估均为单盲检测。
(4)高通量测序和生物信息学分析
图1为本发明高通量筛选的流程图。
总RNA提取:取全程胃组织,使用Trizol试剂,按照说明书实验流程提取总RNA,并用分光光度计检测总RNA质量和浓度。送样深圳华大基因科技服务有限公司进行高通量测序。高通量测序:文库制备、质检、测序和数据分析等流程按照Illumina公司的标准步骤进行。
统计方法:采用SPSS17.0统计软件进行统计,所有数据以均数±标准差
Figure RE-GDA0002849062960000041
的形式表示,组间比较采用t-检验方法检验,P<0.05为有统计学意义,差异显著。
内参筛选方法:geNorm软件筛选出相对最稳定内参miRNA(1、 Vandesompele J,DePreter K,Pattyn F,Poppe B,Van Roy N,De Paepe A,et al. Accurate normalizationof real-time quantitative RT-PCR data by geometric averaging of multipleinternal control genes.Genome Biology,2002,3: research0034.1.;2、Andersen CL,Jensen JL,and
Figure RE-GDA0002849062960000042
TF.Normalization of real-time quantitative reversetranscription-PCR data:A model-based variance estimation approach to identifygenes suited for normalization,applied to bladder and colon cancer datasets.Cancer Research,2004,64,5245-5250.)。
通过高通量测序,得到在模型与正常组均表达的miRNA共580个。由于内参基因的表达量要求在高度或中度表达,排除太高或低表达,因此选择RPKM 值在1000以上的miRNA。模型组表达量大于1000,有111个miRNA基因,针对这111个基因,利用geNorm软件在正常组和模型组之间筛选出最稳定的两个内参miRNA,为rno-let-7g-5p(序列:5’-UGAGGUAGUAGUUUGUACAGUU-3’),rno-miR-429(序列:5’- UAAUACUGUCUGGUAAUGCCGU-3’)。let-7g-5p在大鼠和人的基因组中高度保守,序列完全相同;人的hsa-miR-429序列信息为:UAAUACUGUCUGGUAAAACCGU,miR-429在大鼠和人中有2个碱基不同。
(5)RT-qPCR
RNA提取(Trizol)、反转(Takara)和qPCR(Takara)实验按照说明书进行。qPCR实验在StepOnePlus system(ABI)仪器上运行。引物序列:
用于检测rno-let-7g-5p的上游引物:5’-TGAGGTAGTAGTTTGTACAGTT-3’;用于检测rno-mir-429的上游引物:5’-TAATACTGTCTGGTAATGCCGT-3’。
合成内参基因的引物序列,用RT-qPCR方法(使用加尾法miRNA的 RT-qPCR方法,上述引物序列为上游引物,下游引物由反转录试剂盒中统一提供。)检测其熔解曲线,结果获得了单峰(图2),说明2个内参基因的引物扩增的产物单一,特异性高。
实施例2
rno-let-7g-5p和rno-miR-429作内参基因的检测与应用。
我们在高通量测序结果中筛选出rno-miR-542-3p的绝对表达量(RPKM值) 在模型组显著高于正常对照组。然后我们分别用rno-let-7g-5p和rno-miR-429作为内参基因,分析高通量测序结果中rno-miR-542-3p相对表达水平,结果如图 3A所示;然后我们用RT-qPCR技术进行验证(使用反转录试剂盒:PrimeScriptTM RT Master Mix(TaKaRa,日本)),其中,用于检测rno-miR-542-3p的上游引物序列为5’-TGTGACAGATTGATAACTGAAA-3’,下游引物为反转录试剂盒中自带的通用型引物,实验数据如图3B所示,支持上述结果。说明rno-let-7g-5p和 rno-miR-429做内参基因校准后,高通量测序结果和RT-qPCR结果一致,即基因相对表达水平与绝对表达水平表现出的组间差异一致。
序列表
<110> 浙江省中医药研究院
<120> 胃癌检测用的内参miRNA、应用及试剂盒
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Claims (9)

1.胃癌检测用的内参miRNA,其特征在于,为miRNA rno-let-7g-5p或rno-miR-429,其中,rno-let-7g-5p的序列为:5’-UGAGGUAGUAGUUUGUACAGUU-3’,rno-miR-429的序列为:5’-UAAUACUGUCUGGUAAUGCCGU-3’。
2.miRNA rno-let-7g-5p或rno-miR-429在作为非疾病诊断为目的的、胃癌检测用的内参miRNA中的应用。
3.如权利要求2所述的应用,其特征在于,检测方法为RT-qPCR。
4.如权利要求2或3所述的应用,其特征在于,检测对象为大鼠胃组织。
5.一种用于检测胃癌的试剂盒,其特征在于,包括用于检测内参miRNA rno-let-7g-5p或rno-miR-429的引物,
其中,rno-let-7g-5p的序列为:5’-UGAGGUAGUAGUUUGUACAGUU-3’,rno-miR-429的序列为:5’-UAAUACUGUCUGGUAAUGCCGU-3’。
6.如权利要求5所述的试剂盒,其特征在于,用于检测内参rno-let-7g-5p的上游引物序列为5’-TGAGGTAGTAGTTTGTACAGTT-3’,用于检测内参rno-miR-429的上游引物序列为5’-TAATACTGTCTGGTAATGCCGT-3’。
7.一种非疾病诊断为目的的、检测胃癌的方法,其特征在于,使用如权利要求5或6任一所述的试剂盒,使用RT-qPCR方法检测检测作为胃癌分子标记的miRNA,并使用miRNA rno-let-7g-5p或rno-miR-429作为内参miRNA。
8.如权利要求7所述的方法,其特征在于,作为胃癌分子标记的miRNA为rno-miR-542-3p。
9.如权利要求8所述的方法,其特征在于,用于检测rno-miR-542-3p的上游引物序列为5’-TGTGACAGATTGATAACTGAAA-3’。
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Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100216139A1 (en) * 2008-11-10 2010-08-26 Battelle Memorial Institute METHODS, COMPOSITIONS, AND DEVICES UTILIZING MicroRNA TO DETERMINE PHYSIOLOGICAL CONDITIONS
CN109609630A (zh) * 2018-12-03 2019-04-12 哈尔滨医科大学 用于早期胃癌诊断的分子标志物及其应用

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CN109609630A (zh) * 2018-12-03 2019-04-12 哈尔滨医科大学 用于早期胃癌诊断的分子标志物及其应用

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