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

Abstract

SummaryThe HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks, marking the first successful attempt to continually culture human-derived cells in vitro1. HeLa’s robust growth and unrestricted distribution resulted in its broad adoption – both intentionally and through widespread cross-contamination2 – and for the past sixty years it has served a role analogous to that of a model organism3. Its cumulative impact is illustrated by the fact that HeLa is named in >74,000 or ~0.3% of PubMed abstracts. The genomic architecture of HeLa remains largely unexplored beyond its karyotype4, in part because like many cancers, its extensive aneuploidy renders such analyses challenging. We performed haplotype-resolved whole genome sequencing5 of the HeLa CCL-2 strain, discovering point and indel variation, mapping copy-number and loss of heterozygosity (LOH), and phasing variants across full chromosome arms. We further investigated variation and copy-number profiles for HeLa S3 and eight additional strains. Surprisingly, HeLa is relatively stable with respect to point variation, accumulating few new mutations since early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region at chromosome 8q24.21 at which the HPV-18 viral genome integrated as the likely initial event underlying tumorigenesis. We combined these maps with RNA-Seq6 and ENCODE Project7 datasets to phase the HeLa epigenome, revealing strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome ~500 kilobases upstream, and permitting 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.

PRC 1‐labeled microtubule bundles and kinetochore pairs show one‐to‐one association in metaphase

“…In HeLa cells, both the number of chromosomes and their structure show abnormalities 27, 28, 29. The number of chromosomes has been shown to vary between 56 and 179 30, 31, 32, 33.…”

Long-distance interaction of the integrated HPV fragment with MYC gene and 8q24.22 region upregulating the allele-specific MYC expression in HeLa cells

“…3 a ). In addition, the integrated structure also contains a non‐coding regulatory region of HPV genome 7. Considering the complexity of the HPV integration, we deigned dual gRNAs which targeted HPV18 genome at nucleotide 5,790 and 2,057, respectively (NCBI Reference Sequence: NC_001357.1; Fig.…”

“…Considering the long distance between the two elements, previous studies mainly focused on the effect of HPV E6 and E7 proteins on the expression of MYC gene 11, 12. However, a recent study demonstrated that the highly expressed MYC was almost exclusively from the HPV‐integrated haplotype (mean ratio, 95:1) by RNA‐seq data, which implicated that the integration of viral genome, as a strong activator of MYC expression, acted in cis rather than trans manor 7. Therefore, they hypothesized that there is maybe a long‐range chromatin interaction between integrated HPV fragment and the HPV‐integrated haplotype MYC gene, but it still needed further evidence.…”

CIN and Aneuploidy: Different Concepts, Different Consequences

“…For instance, 61% of all cancerous mouse cell lines tested were aneuploid, [49] and most human cancer cell lines are aneuploid as well. [50][51][52] While single chromosome trisomies can act as tumor suppressors (in the euploid HCT 116 colorectal cancer cell line and in mouse xenografts), spontaneous karyotype evolution in these cell lines leads to selection for karyotypes that grow better than their euploid counterparts. [42] Indeed, the frequency of aneuploidy among tumors and cancer cell lines shows that aneuploidy in a cancer setting is quite well tolerated, with certain aneuploidies even being beneficial to cancer cell growth.…”