Amplified Genes May Be Overexpressed, Unchanged, or Downregulated in Cervical Cancer Cell Lines

Several copy number-altered regions (CNAs) have been identified in the genome of cervical cancer, notably, amplifications of 3q and 5p. However, the contribution of copy-number alterations to cervical carcinogenesis is unresolved because genome-wide there exists a lack of correlation between copy-number alterations and gene expression. In this study, we investigated whether CNAs in the cell lines CaLo, CaSki, HeLa, and SiHa were associated with changes in gene expression. On average, 19.2% of the cell-line genomes had CNAs. However, only 2.4% comprised minimal recurrent regions (MRRs) common to all the cell lines. Whereas 3q had limited common gains (13%), 5p was entirely duplicated recurrently. Genome-wide, only 15.6% of genes located in CNAs changed gene expression; in contrast, the rate in MRRs was up to 3 times this. Chr 5p was confirmed entirely amplified by FISH; however, maximum 33.5% of the explored genes in 5p were deregulated. In 3q, this rate was 13.4%. Even in 3q26, which had 5 MRRs and 38.7% recurrently gained SNPs, the rate was only 15.1%. Interestingly, up to 19% of deregulated genes in 5p and 73% in 3q26 were downregulated, suggesting additional factors were involved in gene repression. The deregulated genes in 3q and 5p occurred in clusters, suggesting local chromatin factors may also influence gene expression. In regions amplified discontinuously, downregulated genes increased steadily as the number of amplified SNPs increased (pPARP1 in 1q, TNFSF10 and ECT2 in 3q and CLPTM1L, AHRR, PDCD6, and DAP in 5p. Overall, gene expression and copy-number profiles reveal factors other than gene dosage, like epigenetic or chromatin domains, may influence gene expression within the entirely amplified genome segments.

目前已在宫颈癌基因组中鉴定出多个拷贝数变异区域（copy number-altered regions, CNAs），其中尤以3号染色体长臂（3q）与5号染色体短臂（5p）的扩增最为显著。然而，拷贝数变异对宫颈癌发生的具体贡献仍未明确，这是因为全基因组范围内拷贝数变异与基因表达之间缺乏显著相关性。本研究针对细胞系CaLo、CaSki、HeLa及SiHa中的CNAs是否与基因表达变化相关展开了探究。平均而言，各细胞系基因组中有19.2%的区域携带CNAs，但其中仅2.4%属于所有细胞系共有的最小复发性区域（minimal recurrent regions, MRRs）。3q仅存在有限的共扩增区域（占比13%），而5p则呈现出完全重复性的扩增。全基因组范围内，仅15.6%位于CNAs中的基因出现了表达变化；与之相比，MRRs中该比例最高可达前者的3倍。5号染色体短臂（Chr 5p）的完全扩增已通过荧光原位杂交（Fluorescence in situ hybridization, FISH）得到验证，但5p中仅最高33.5%的被检测基因出现了表达失调。在3q中该比例仅为13.4%；即便在包含5个MRRs且有38.7%复发性获得单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）的3号染色体长臂2区6带（3q26）区域，该比例也仅为15.1%。值得注意的是，5p中多达19%的失调基因、3q26中多达73%的失调基因均出现了表达下调，这提示存在其他因子参与了基因沉默过程。3q与5p中的失调基因呈簇状分布，这表明局部染色质因子同样可能对基因表达产生影响。在非连续性扩增区域中，随着扩增的单核苷酸多态性位点数量增加，下调基因的比例呈稳步上升趋势（p<0.001），相关基因包括1号染色体上的PARP1、3号染色体上的TNFSF10与ECT2，以及5号染色体上的CLPTM1L、AHRR、PDCD6和DAP。综上，基因表达与拷贝数谱分析结果显示，除基因剂量外，表观遗传调控或染色质结构域等其他因素，同样可能影响完全扩增基因组片段内的基因表达。