Available online 27 June 2025

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Cancer cell lines are valuable models for studying tumor biology, yet their genomic evolution during culture can compromise experimental reproducibility. We conducted a detailed genomic analysis of the triple-negative breast cancer cell line MDA-MB-231-luc-GFP, examining sublines obtained from different sources, at various time points, and across distinct passages. We introduce the concept of intraline heterogeneity (ILH) to highlight the genomic variability observed among these sublines. Our analyses revealed extensive genomic diversity, including differences in single-nucleotide variants (SNVs) and copy number alterations (CNAs). In particular, CNAs exhibited remarkable heterogeneity, with pronounced chromosomal gains and losses between sublines, underscoring the impact of genomic instability on ILH. These findings suggest that ILH may influence experimental outcomes, emphasizing the importance of considering passage-specific genomic characterization to ensure consistency and reliability in cancer research.

Graphical abstractDownload: Download high-res image (230KB)Download: Download full-size imageKeywords

MDA-MB-231-luc-GFP

breast cancer

cell lines evolution

intraline heterogeneity

passage-specific genomic characterization

genomic heterogeneity

sublines

cancer genomics

karyotype

experimental reproducibility

Data availabilityExonic DNA sequencing data have been deposited at the Sequence Read Archive (www.ncbi.nlm.nih.gov/sra) under the BioProject PRJNA1225476. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

© 2025 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.