Characterisation of the genomic landscape of CRLF2 deregulated acute lymphoblastic leukaemia. Homo sapiens

Deregulated expression of the type I cytokine receptor, CRLF2 (CRLF2-d), is observed in 5-15% of B-cell precursor acute lymphoblastic leukaemia (BCP-ALL), is associated with activation of the JAK/STAT pathway and has an inferior outcome compared to those with good risk cytogenetics. We aimed to determine the clinical and genetic landscape of CRLF2-d ALL using genomic approaches including karyotyping, fluorescence in situ hybridisation, whole genome and whole exome sequencing. The clinical and demographic features of CRLF2-d patients were characteristic of BCP-ALL. Patients with IGH-CRLF2 were older than those with P2RY8-CRLF2 (4yrs v 14yrs, p<0.001), while the incidence of CRLF2-d among Down syndrome patients was high (31%). CRLF2-d co-occurred with established primary chromosomal rearrangements but the majority (72%) had B-other ALL. The copy number alteration (CNA) profile was similar to B-other ALL, although CRLF2-d patients harboured higher frequencies of IKZF1 (43% v 23%) and BTG1 deletions (15% v 2%). There were differences in the CNA profile between IGH-CRLF2 and P2RY8-CRLF2 patients: deletions of IKZF1 (71% v 33% p<0.001), BTG1 (31% v 9%, p=0.004) and ADD3 (46% v 13%, p=0.008). A novel gene fusion, USP9X-DDX3X was discovered in 18% of CRLF2-d ALL. Pathway analysis of the mutational profile revealed novel involvement of the focal adhesion pathway. In conclusion, CRLF2-d defines a discrete subtype of B-other ALL, characterised by a distinctive profile of cooperating abnormalities, which drive leukaemogenesis in conjunction with CRLF2-d. Although the functional relevance of many of these abnormalities are unknown, they likely activate alternative pathways, which may represent novel therapeutic targets. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or remission bone marrow. Overall design: DNA copy number analysis of 26 acute lymphoblastic leukaemia samples (11 diagnostic only, 15 matched diagnostic and remission samples) was perform using the Affymetrix Genome-Wide Human SNP6.0 Array.

在5%-15%的B细胞前体急性淋巴细胞白血病（B-cell precursor acute lymphoblastic leukaemia, BCP-ALL）患者中，可观察到I型细胞因子受体CRLF2的异常表达（CRLF2-d）。该异常与JAK/STAT通路激活相关，且相较于细胞遗传学风险良好的患者，其预后更差。本研究旨在通过核型分析（karyotyping）、荧光原位杂交（fluorescence in situ hybridisation, FISH）、全基因组测序及全外显子组测序等基因组学手段，解析CRLF2-d阳性急性淋巴细胞白血病的临床与遗传学特征谱。CRLF2-d患者的临床及人口学特征符合BCP-ALL的典型表现：携带IGH-CRLF2融合的患者年龄大于P2RY8-CRLF2融合患者（14岁 vs 4岁，p<0.001）；而唐氏综合征（Down syndrome）患者中CRLF2-d的发生率高达31%。CRLF2-d可与已明确的原发性染色体重排共存，但多数（72%）患者被归类为B-other ALL。其拷贝数变异（copy number alteration, CNA）谱与B-other ALL相似，但CRLF2-d患者中IKZF1缺失（43% vs 23%）与BTG1缺失（15% vs 2%）的检出频率更高。此外，IGH-CRLF2与P2RY8-CRLF2患者的CNA谱存在显著差异：IKZF1缺失（71% vs 33%，p<0.001）、BTG1缺失（31% vs 9%，p=0.004）及ADD3缺失（46% vs 13%，p=0.008）的检出率均存在统计学差异。本研究在18%的CRLF2-d ALL患者中发现了一种新型基因融合USP9X-DDX3X。对突变谱的通路分析显示，黏着斑通路（focal adhesion pathway）存在新的异常激活。综上，CRLF2-d定义了一类独立的B-other ALL亚型，其特征为存在独特的协同异常谱，这些异常可与CRLF2-d共同驱动白血病发生。尽管目前多数此类异常的功能相关性尚不明确，但它们可能通过激活替代通路发挥作用，有望成为新型治疗靶点。本研究按照制造商操作说明，对冻存的诊断期骨髓或缓解期骨髓提取的DNA进行了Affymetrix SNP芯片检测。整体实验设计：采用Affymetrix Genome-Wide Human SNP6.0芯片对26例急性淋巴细胞白血病样本（11例仅为诊断期样本，15例为匹配的诊断期与缓解期样本）进行DNA拷贝数分析。