The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

Haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain shows that HeLa is relatively stable in terms of point variation; integration of several data sets reveals strong, haplotype-specific activation of the proto-oncogene MYC by the human papilloma virus type 18 genome, and enables the relationship between gene dosage and expression to be examined. The first genomic characterization of the HeLa cancer cell line, the longest-serving and arguably most commonly used human cell line in biomedical research, reveals a genome that is surprisingly stable with respect to both point-mutation and copy-number alterations. The point-mutation rate may be no higher than the somatic mutation rate of normal tissue, and very few copy-number alterations distinguish the genomes of different HeLa strains that were split from one another in the mid-1950s. The authors examine the relationship between gene dosage and expression by integrating several data sets, including those from the ENCODE project, and find strong activation of the MYC proto-oncogene by the human papilloma virus type 18 (HPV-18) integration at chromosome 8q24.21. 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 vitro1. The robust growth and unrestricted distribution of HeLa cells resulted in its broad adoption—both intentionally and through widespread cross-contamination2—and for the past 60 years it has served a role analogous to that of a model organism3. 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 karyotype4, partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing5 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-seq6 and ENCODE Project7 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.