基于转录组测序的急性B淋巴细胞白血病IKZF1转录本分型和定量分析

Transcriptome sequencing-based classification and quantification of IKZF1 transcript isoforms in B-cell acute lymphoblastic leukemia

目的通过转录组测序(RNA-seq)和生物信息分析对急性B淋巴细胞白血病(B-ALL)患者IKZF1基因突变型转录本进行分型和定量分析。方法选择2018年9月至2020年9月河北燕达陆道培医院263例B-ALL患者为研究对象。设计一套用RNA-seq数据进行IKZF1转录本分型和定量分析的生物信息分析流程,并应用于这些患者的测序数据分析。将用RNA-seq分析得到的IKZF1突变型转录本与反转录聚合酶链反应(RT-PCR)法的结果进行比较。结果在263例B-ALL患者中,RT-PCR结合Sanger测序鉴定出53例患者存在IKZF1突变转录本,其中IK6和IK10转录本分别占67.9%(36/53)和28.3%(15/53),有2例患者IK6和IK10转录本双阳性。RNA-seq分析共鉴定出51例患者存在IKZF1突变转录本。以RT-PCR结果为参考,RNA-seq分析IKZF1突变转录本的敏感度为94.3%(50/53),特异度为99.5%(209/210)。在50例RNA-seq和RT-PCR分析IKZF1突变均阳性的患者中,有6例患者的突变型转录本占IKZF1总表达量的比值(psi值)[M(Q1,Q3)]为0.14(0.11,0.35),低于其他44例患者的0.88(0.35,0.97),差异有统计学意义(Z=-3.945,P<0.001)。IKZF1突变多发生于以JAK-STAT通路异常为特征的Ph+和Ph样B-ALL,以及伴PAX5易位的B-ALL。结论通过优化的生物信息分析流程设计,可以用RNA-seq数据对B-ALL的IKZF1转录本进行分型和定量分析,并且发现了IKZF1突变型转录本的表达量分群现象和IKZF1突变与PAX5易位的伴随现象。

Objective To classify and quantify IKZF1 mutant transcripts in B-cell acute lymphoblastic leukemia(B-ALL)by RNA sequencing(RNA-seq)and bioinformatics analysis.Methods A cohort of 263 B-ALL cases was enrolled at Hebei Yanda Ludaopei Hospital from September 2018 to September 2020.An integrated bioinformatics pipeline was developed to adapt the classification and quantification of IKZF1 transcripts from RNA-seq and was applied to sequencing data of these cases.The IKZF1 mutant transcripts classified by RNA-seq analysis were compared with the qualitative reverse transcription PCR(RT-PCR).Results IKZF1 mutant transcripts were identified in 53 B-ALL patients by RT-PCR and Sanger sequencing,among which IK6 and IK10 transcripts accounted for 67.9%(36/53)and 28.3%(15/53)respectively.Additionally,2 patients were double positive for IK6 and IK10.RNA-seq analysis identified 51 patients with IKZF1 mutant transcripts.Compared with the RT-PCR result,the detection sensitivity and specificity of RNA-seq analysis reached 94.3%(50/53)and 99.5%(209/210),respectively.Among the 50 patients with IKZF1 mutant transcripts both in RNA-seq and RT-PCR analysis,the ratio of mutant transcripts to total IKZF1 transcripts in 6 patients was 0.14(0.11,0.35),which was significantly lower than that of the other 44 patients[0.88(0.35,0.97),Z=-3.945,P<0.001].IKZF1 mutations mostly occurred in Ph+and Ph-like B-ALL,characterized by abnormal JAK-STAT pathway,and B-ALL with PAX5 translocation.Conclusions Through the optimized bioinformatics analysis process,RNA-seq data can be used to classify and quantitatively analyze IKZF1 transcripts in B-ALL.Furthermore,the relative expression of mutant IKZF1 transcripts was found to cluster into two groups,and IKZF1 mutation was found often accompanied with PAX5 translocations.