INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (SNP data). Homo sapiens

Using high-resolution genomic microarray analysis, a distinct genomic profile was defined in 114 samples from patients with splenic marginal zone lymphoma (SMZL). Notably, deletion or uniparental disomy of chromosome 7q were detected in 39% of SMZLs but in only 9 of 170 (5%) mature B-cell lymphomas (p<10-6). The presence of unmutated IgVH genes, genomic complexity, 17p13-P53 deletion and 8q gain including MYC gene, but not 7q deletion, were correlated with shorter overall survival. Extensive mapping analyses narrowed down the commonly deleted region to 2.7 Mb. in 7q32.1-q32.2 from SND1 to COPG2 genes. High-throughput sequencing analysis of the 7q32 deleted segment in SMZL cells did not identify bi-allelic deletions, insertions or clear pathogenic mutations, but detected six single nucleotide changes in IRF5 (n=2), TMEM209 (n=2), CALU (n=1) and ZC3HC1 (n=1). Comparative expression analysis found that IRF5, TMEM209 and CALU genes had down-regulated expression in lymphomas with 7q32 deletion vs. non-deleted tumors. Ectopic expression of IRF5 in marginal-zone lymphoma cells decreased cell proliferation and induced apoptosis. These results indicate that small deletions, insertions and/or point mutations inactivating genes within 7q32 are not common events in SMZL. Further studies are required to evaluate the putative role of IRF5 in SMZL pathogenesis. Overall design: Affymetrix GeneChip 50k-XbaI and/or 250-NspI/StyI SNP microarrays were performed for 59 SMZL samples and 4 Marginal Zone cell lines according to the manufacturer's directions.

本研究通过高分辨率基因组微阵列分析（high-resolution genomic microarray analysis），明确了114例脾边缘区淋巴瘤（splenic marginal zone lymphoma, SMZL）患者样本的特征性基因组特征。值得注意的是，39%的SMZL病例检测到7号染色体长臂（7q）缺失或单亲二体（uniparental disomy），而在170例成熟B细胞淋巴瘤中仅9例（5%）存在该异常（p<10⁻⁶）。未突变的免疫球蛋白重链可变区（immunoglobulin heavy chain variable region, IgVH）基因、基因组复杂性升高、17p13-P53缺失以及包含MYC基因的8q扩增（而非7q缺失）与较短的总生存期相关。通过大范围定位分析，将该常见缺失区域缩小至7q32.1-q32.2区间内2.7 Mb的片段，其覆盖的基因范围为SND1至COPG2基因。对SMZL细胞中7q32缺失片段的高通量测序分析（high-throughput sequencing analysis）未发现双等位基因缺失、插入或明确的致病性突变，但在IRF5（n=2）、TMEM209（n=2）、CALU（n=1）及ZC3HC1（n=1）基因中检测到6个单核苷酸变异。比较表达分析显示，与未发生7q32缺失的肿瘤相比，存在7q32缺失的淋巴瘤中IRF5、TMEM209及CALU基因的表达水平显著下调。在边缘区淋巴瘤细胞中异位表达IRF5可抑制细胞增殖并诱导细胞凋亡。上述结果表明，7q32区域内导致基因失活的小片段缺失、插入及/或点突变在SMZL中并非常见事件。未来需开展进一步研究以评估IRF5在SMZL发病机制中的潜在作用。整体实验设计：按照制造商提供的操作指南，对59例SMZL样本及4株边缘区淋巴瘤细胞系进行了Affymetrix GeneChip 50k-XbaI及/或250-NspI/StyI单核苷酸多态性（single nucleotide polymorphism, SNP）微阵列检测。