Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA.
Nature. 2013 Aug 8;500(7461):207-11. doi: 10.1038/nature12064.
The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks. This was the first successful attempt to immortalize human-derived cells in vitro. The robust growth and unrestricted distribution of HeLa cells resulted in its broad adoption--both intentionally and through widespread cross-contamination--and for the past 60 years it has served a role analogous to that of a model organism. The cumulative impact of the HeLa cell line on research is demonstrated by its occurrence in more than 74,000 PubMed abstracts (approximately 0.3%). The genomic architecture of HeLa remains largely unexplored beyond its karyotype, partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain, examined point- and indel-mutation variations, mapped copy-number variations and loss of heterozygosity regions, and phased variants across full chromosome arms. We also investigated variation and copy-number profiles for HeLa S3 and eight additional strains. We find that HeLa is relatively stable in terms of point variation, with few new mutations accumulating after early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24.21 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis. We combined these maps with RNA-seq and ENCODE Project data sets to phase the HeLa epigenome. This revealed strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome approximately 500 kilobases upstream, and enabled global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes.
海拉细胞系于 1951 年从一位名叫 Henrietta Lacks 的宫颈癌患者的癌细胞中建立。这是首次成功尝试在体外使人类来源的细胞永生化。海拉细胞的旺盛生长和不受限制的分布导致其广泛采用--无论是有意的还是通过广泛的交叉污染--并且在过去的 60 年里，它一直扮演着类似模式生物的角色。海拉细胞系对研究的累积影响体现在其在超过 74000 篇 PubMed 摘要中出现（约 0.3%）。除了其核型之外，海拉细胞的基因组结构在很大程度上仍未被探索，部分原因是像许多癌症一样，其广泛的非整倍体使此类分析具有挑战性。我们对海拉细胞系 CCL-2 株进行了单倍型解析全基因组测序，检测了点突变和插入缺失突变、映射了拷贝数变异和杂合性丢失区域，并对整条染色体臂进行了单倍型相位变异检测。我们还研究了海拉 S3 和另外 8 个细胞株的变异和拷贝数谱。我们发现，海拉细胞在点突变方面相对稳定，早期传代后很少积累新的突变。单倍型解析有助于重建高度重排的 8q24.21 染色体区域，该区域整合了人乳头瘤病毒 18 型（HPV-18）基因组，这很可能是引发肿瘤发生的事件。我们将这些图谱与 RNA-seq 和 ENCODE 项目数据集相结合，对海拉细胞的表观基因组进行了相位分析。这揭示了整合的 HPV-18 基因组在大约 500kb 上游强烈、单倍型特异性地激活原癌基因 MYC，并且能够对基因剂量和表达之间的关系进行全局分析。这些数据为过去和未来依赖于海拉细胞的实验提供了一个广泛相位、高质量的参考基因组，并证明了单倍型解析在表征癌症基因组和表观基因组方面的价值。
