云南地区宫颈癌组织中人乳头瘤病毒18型LCR基因变异特征分析

Characterization of the Polymorphisms of Human Papillomavirus Type-18 LCR in Cervical Cancer in Yunnan,China

研究云南地区人乳头瘤病毒18型LCR基因在宫颈癌组织中的变异特点,通过系统发生分析探讨HPV-18变异株的分子流行特征,并通过转录因子结合位点的预测分析LCR变异对病毒感染可能造成的影响。本研究提取了云南地区74例女性宫颈癌组织样本中的DNA,通过PCR、测序、序列比对,分析了9个HPV-18LCR完整DNA序列的基因变异信息,并用Mega 7.0软件使用邻接法进行进化分析,使用JASPAR数据库对可能的转录因子结合位点进行预测。HPV-18LCR序列中发现T7258A、C7529A、G7563A、A7567C、T7592C、A7670T、T7736G、C7764T、C7857T、A41G、C54T、A89C和T104C13个核苷酸点突变,其中最常见变异位点是T7592C,其次是C7857T,突变频率分别为100%和44.4%。9个HPV-18LCR完整DNA序列分属于4个HPV-18LCR变异体,进化树分析显示云南地区流行的HPV-18主要为A系变异体(8个A1亚系,1个A4亚系),HPV-18LCR中T7592C、C7857T变异位于转录因子TBP、HOXA5的结合区域内。云南地区宫颈癌组织中主要流行的HPV-18为A系变异体,T7592C、C7857T是HPV-18LCR中主要变异位点。

We wished to explore the gene polymorphisms and identify the potential binding sites for the transcription factors of human papillomavirus type-18 long control region(LCR)in cervical cancer in Yunnan,China.The DNA samples were extracted from 74 cervical cancer tissues collected from women in Yunnan,China.Nine entire LCRs of HPV-18 were amplified,sequenced and aligned with the HPV-18 reference sequence.Phylogenetic tree was generated by Mega 7.0 using the neighbor-joining method.The transcription factor binding sites in HPV-18 LCR were predicted using the JASPAR database.Thirteen nucleotide substitution sites were identified:T7258 A,C7529 A,G7563 A,A7567 C,T7592 C,A7670 T,T7736 G,C7764 T,C7857 T,A41 G,C54 T,A89 Cand T104 C.T7592 Cand C7857 Twere the most variable sites identified in 100% and 44.4% of samples,respectively.Combinations of all single nucleotide polymorphisms resulted in four HPV-18 LCR variants.Phylogenetic analysis based on the HPV-18 LCR sequences showed that all the samples were clustered into the A lineage(eight belonged to the A1 sub-lineage,one belonged to the A4 sub-lineage).T7592 Cand C7857 Tcould be the potential binding sites for the transcription factors TBP and HOXA5,respectively.These data showed that HPV-18 variants in Yunnan were clustered into the A lineage,and that the most variable sites in the HPV-18 LCR were T7592 C and C7857 T.