Whole-Exome Sequencing of ETV6/RUNX1 in Four Childhood Acute Lymphoblastic Leukaemia Cases

Identification of a novel MEF2C::SS18L1 fusion in childhood acute B-lymphoblastic leukemia

PURPOSE

Leukemia-associated fusion genes are closely related to the occurrence, development, diagnosis, and treatment of leukemia. DNA microarrays and second-generation sequencing have discovered multiple B-ALL fusion genes. We identified a novel MEF2C::SS18L1 fusion gene in a child diagnosed with B-ALL. This study investigates the oncogenicity and prognosis of this fusion gene in B-ALL.

METHODS

A child with B-ALL who has a MEF2C::SS18L1 fusion is reported as a newly discovered case. Compared the breakpoints, structural domains, clinical phenotypes, and differential expression genes of MEF2C::SS18L1 and MEF2D::SS18.Using "ONCOFUSE" software, the carcinogenicity of MEF2C::SS18L1 is predicted. Using whole transcriptome sequencing, we analyze the breakpoints and the secondary structure of the fusion protein. Further, we compared the structures, differentially expressed genes, and clinical phenotypes of MEF2D and MEF2C fusion genes by DESeq, GO functional enrichment, and flow cytometry immunophenotyping analysis.

RESULTS

Whole transcriptome sequencing identified a MEF2C::SS18L1 fusion transcript in a 3-year-old child with B-ALL. The MADS box, MEF structural domain, HJURP_C structural domain, and TAD I structural domain of MEF2C, and the QPGY structural domain of SS18L1, make up the fusion protein. "Oncofuse" found a 0.99 Bayesian probability that the fusion gene drives cancer. The breakpoint positions, fusion protein secondary structures, differentially expressed genes, and clinical characteristics of this patient were identical to those with MEF2D::SS18 fusion gene.

CONCLUSION

We identified a novel MEF2C::SS18L1 fusion gene in childhood ALL, which shares similar structural and clinical characteristics with MEF2D::SS18. Further studies with more samples should be conducted in future.

[Clinical features and prognosis of ETV6-RUNX1-positive childhood B-precursor acute lymphocyte leukemia]

目的

探讨ETV6-RUNX1融合基因阳性儿童急性前体B淋巴细胞白血病（B-ALL）的临床特征及预后。

方法

回顾性分析2011年4月至2020年5月福建医科大学附属协和医院小儿血液科收治的927例初诊B-ALL患儿的临床资料。根据ETV6-RUNX1检测结果，分为ETV6-RUNX1⁺组及ETV6-RUNX1⁻组，对比两组的临床特征及预后；182例ETV6-RUNX1⁺患儿规范治疗，其中144例接受中国儿童白血病协作组（CCLG）-ALL 2008方案治疗（CCLG-ALL 2008方案组），38例接受中国儿童癌症协作组（CCCG）-ALL 2015方案治疗（CCCG-ALL 2015方案组），对比两种方案的疗效、严重不良反应（SAE）发生率及治疗相关死亡（TRM）率。

结果

927例B-ALL患儿中，189例（20.4%）ETV6-RUNX1阳性。ETV6-RUNX1⁺组初诊时有危险因素（年龄≥10岁或<1岁，WBC≥50×10⁹/L）的患者比例均显著低于ETV6-RUNX1⁻组（P值分别为0.000和0.001），而泼尼松诱导试验反应良好、诱导化疗第15天或第19天微小残留病（MRD）<1%，以及诱导化疗第33天或第46天MRD<0.01%的患者比例显著高于ETV6-RUNX1⁻组（P值分别为0.001、0.028和0.004）。ETV6-RUNX1⁺组的5年无事件生存（EFS）及总生存（OS）率均显著高于ETV6-RUNX1⁻组（EFS：89.8%对83.2%，P＝0.003；OS：90.2%对86.3%，P＝0.030）。CCLG-ALL 2008组感染相关SAE发生率显著高于CCCG-ALL 2015组（27.1%对5.3%，P＝0.004），TRM发生率也高于CCCG-ALL 2015组，但差异无统计学意义（4.9%对0，P＝0.348）。

结论

ETV6-RUNX1⁺儿童B-ALL初诊危险因素较少，早期治疗反应较好，复发率低，总体预后良好；适当减低化疗强度，可降低感染相关SAE及TRM发生率，并进一步提高该亚型ALL患儿的OS率。

[Clinical characteristics and gene expression profiles in children with ETV6-RUNX1 acute lymphoblastic leukemia]

目的

通过基因表达谱研究儿童ETV6-RUNX1阳性急性淋巴细胞白血病（ALL）异质性，探索不同聚类分组临床特征，为临床个性化诊疗及利用测序技术探索预后相对不良组预测模型提供可行性参考。

方法

应用改进的基因片段分析技术对2016年8月至2019年6月北京儿童医院收治的264例初诊ALL患儿的骨髓标本进行57个分型基因检测和聚类分析，重点分析56例ETV6-RUNX1阳性患者的基因表达谱与临床特点、免疫表型和早期化疗反应的关系。

结果

基因分型聚类显示ETV6-RUNX1阳性ALL被分为两组：E/R-1组（45例，80.4%）和E/R-2组（11例，19.6%）。E/R-2聚类离散度大于E/R-1，spearman相关系数分别为0.788、0.901；E/R-2、E/R-1组初诊PLT中位数分别为104（27～644）×10⁹/L、50（8～390）×10⁹/L（P<0.01），初诊骨髓原始幼稚细胞比例分别为0.830（0.270～0.975）、0.935（0.445～0.990）（P<0.05）；CD22⁺CD34⁺CD20⁻CD117⁻CD56⁻免疫组合在E/R-2组占比更高（P<0.001）；E/R-2和E/R-1组化疗第33天流式细胞术检测的微小残留病（MRD）转阴例数分别为5例（55.6%）和32例（88.9%）（P＝0.064），去除临界值病例敏感性分析转阴例数分别为5例（55.6%）和32例（91.4%）（P＝0.035）；第33天PCR检测的MRD转阴例数分别为7例（77.8%）和36例（100.0%）（P＝0.047）。

结论

ETV6-RUNX1阳性ALL患儿在基因表达谱层面存在异质性，符合E/R-2表达特征的患儿可能初诊时血小板减少倾向小但早期化疗反应相对不良。

Association of ARID5B Genetic Variants with Risk of Childhood B Cell Precursor Acute Lymphoblastic Leukaemia in Latvia

Background: Acute lymphoblastic leukaemia (ALL) is the most common malignancy in childhood. Despite numerous investigations very little is still known about its aetiology. However, in one genome wide association study conducted to identify the possible genetic risk factors, two allelic variations rs10821936 and rs10994982 in the 3rd intron of the ARID5B gene were identified as possible ALL risk alleles. Association between ARID5B gene variants and ALL risk was also been confirmed for different ethnic groups. Materials and Methods: Eight genetic variants in the gene ARID5B were genotyped - rs10994982, rs7908445, rs7923074, rs10821936, rs10821937, rs7896246, rs10821938 and rs7089424 in 77 ALL patients in remission and in 122 age and gender matched controls; parental samples were also genotyped in 50 cases. Results: Six out of the eight (rs7908445, rs7923074, rs10821936, rs10821937, rs7896246 and rs7089424) analysed allelic variations were identified in the case-control analysis as statistically significant risk alleles for ALL development. In the family study and using hybrid analysis, all allelic variations were significantly associated with ALL. During the study, risk haplotype was identified rs10994982/rs7908445/rs7923074/ rs10821936/ rs10821937/rs7896246/rs10821938/rs7089424 – ATACCAAG – with a frequency in cases of 0.17 and in the control group at 0.29 (chi square = 6.69, p value = 0.009). In the family association study the same haplotype showed statistical significance (chi squared = 10.3, p value = 0.001). Conclusions: Results of the study replicate and extend previously published findings for ARID5B localized allelic variants, but do not explain the mechanism of action related to the pathogenesis of ALL.