Multi-omic measurements of heterogeneity in HeLa cells across laboratories
Open accessAbstract
Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 international laboratories. We cultured cells in uniform conditions and profiled genome-wide copy numbers, mRNAs, proteins and protein turnover rates in each cell line. We discovered substantial heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto varieties, and observed progressive divergence within a specific cell line over 50 successive passages. Genomic variability has a complex, nonlinear effect on transcriptome, proteome and protein turnover profiles, and proteotype patterns explain the varying phenotypic response of different cell lines to Salmonella infection. These findings have implications for the interpretation and reproducibility of research results obtained from human cultured cells.
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Epigenetic changes happened immediately after treatment (2 hrs H2O2) and lasted for at least 1-2 cell divisions.
“the epigenetic changes happened immediately after the treatment (2 hrs incubation with H2O2) and lasted for at least 1 – 2 cell divisions (cell-doubling time: 17.5 – 32.3 hours for HeLa cells58) (Extended Data Fig. 4).”
From Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability (2025) · cites this paper as [58]
Previously described hallmark genomic events characteristic of PDAC lesions were observed in pseudo-bulk summary, in some cases only in a subset of genomic subclones for each line.
“In this “pseudo-bulk” summary, previously described hallmark genomic events characteristic of PDAC lesions1–6 were readily observed, albeit in some cases only in a subset of genomic subclones for each line.”
From Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution (2022) · cites this paper as [5]
Microsatellite assays typically used for confirmation of cell identity provide minimal insights into genomic and transcriptomic variabilities that might arise when the apparently identical line is propagated at different laboratories or in disparate culture conditions.
“the microsatellite assays typically used for confirmation of cell identity provide minimal insights into genomic and transcriptomic variabilities that might arise when the apparently identical line is propagated at different laboratories5 or in disparate culture conditions”
From Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution (2022) · cites this paper as [5]
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- Authors
- Liu, Y., Mi, Y., Mueller, T., Kreibich, S., Williams, E. G., Van Drogen, A., Borel, C., Frank, M., Germain, P.-L., Bludau, I., Mehnert, M., Seifert, M., Emmenlauer, M., Sorg, I., Bezrukov, F., Bena, F. S., Zhou, H., Dehio, C., Testa, G., Saez-Rodriguez, J., Antonarakis, S. E., Hardt, W.-D., & Aebersold, R.
- Affiliations
- Yale University (US)
- ETH Zurich (CH)
- University of Geneva (CH)
- European Institute of Oncology (IT)
- Nationales Centrum für Tumorerkrankungen Dresden (DE)
- University of Basel (CH)
- University Hospital of Geneva (CH)
- Chinese Academy of Sciences (CN)
- University of Milan (IT)
- University of Zurich (CH)
- Corresponding author
- Liu, Yansheng
- Aebersold, Ruedi
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2019-02-18
- Volume
- 37
- Issue
- 3
- Pages
- 314-322
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2912937988
- Cited by
- 338
- References
- 15
- Citations by year
- 2026: 22 · 2025: 41 · 2024: 36 · 2023: 55 · 2022: 44 · 2021: 52 · 2020: 55 · 2019: 31
- FWCI
- 18.08
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, other-oa)
- edoc (University of Basel) (submittedVersion)
- Open Repository and Bibliography (University of Luxembourg) (submittedVersion, cc-by-nc-sa)
- RWTH Publications (RWTH Aachen) (submittedVersion)
- ETH Zürich Research Collection
- Funders
- National Science Foundation
- Bayer
- Johns Hopkins University
- Universität Basel
- European Molecular Biology Laboratory
- Cancer Research UK
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (107679, 163180, 3100A0)
- Eidgenössische Technische Hochschule Zürich
- Ministero della Salute
- Universität Zürich
- Universitätsspital Zürich
- Regione Lombardia
- National Institutes of Health
- National Institute of General Medical Sciences (F32GM119190)
- H2020 European Research Council (670821)
- FP7 Ideas: European Research Council (616441, 249968)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Viral Infectious Diseases and Gene Expression in Insects
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- HeLa cells, cell line heterogeneity, biological variation, reproducibility, copy number variation, transcriptome, proteome, protein turnover, multi-omics
- MeSH terms
- HeLa Cells, Humans, Reproducibility of Results, Genome, Human, Proteome, Genomics, DNA Copy Number Variations, Transcriptome
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