Reproducibility in cancer research

Kasan, Merve (2024): Reproducibility in cancer research: a study of the (epi)genomic, transcriptomic, and phenotypic stability in chromosomal translocation-driven pediatric sarcoma cell lines. Dissertation, LMU München: Medizinische Fakultät

Abstract

Since decades, human cell lines serve as indispensable tools in cancer research (1). While these research models are widely recognized and favorable due to their relatively easy usage and capability to provide invaluable insight into cancer biology, recent studies raised questions about their reliability (2–5). Over the past decade, researchers have identified significant challenges with the genomic stability of cancer cell lines in unnatural culture environments and the reproducibility of results obtained using these models (2,3,6,11). In the late 2010s, two pioneering studies have shed light on the genomic and phenotypic instability of highly mutated adult carcinoma cell lines: HeLa and MCF-7 (2,3). These studies revealed a remarkable diversity of the respective same cancer cell line across different laboratories, along with the instability of a cell line in prolonged cell culture leading to genomic and transcriptomic heterogeneity and consequential phenotypic variations (2,3). These findings underscored the limitations in reproducibility associated with using human cell line models in cancer research. Nevertheless, while the implications of these observations on adult carcinoma cell lines are becoming increasingly apparent, the generalizability of such conclusions to other cancer cell lines remains largely unexplored. This thesis aimed to investigate the level of variation in cancer cell lines with a lower mutational burden (oligomutated). To achieve this goal, Ewing sarcoma (EwS), a malignant pediatric bone cancer, was selected as a representative model due to its reputation for harboring minimal somatic mutation (7–9). EwS is caused by a chromosomal rearrangement that results in a chimeric oncogenic transcription factor (COTF), which plays a crucial role in regulating the transcription and biology of the tumor (8,10). The hypothesis was that EwS cell lines would exhibit greater genetic and phenotypic stability than adult carcinoma cell lines. Analyzing the molecular and phenotypic traits of 11 EwS cell line A-673 strains from various laboratories showed remarkable genomic and phenotypic uniformity, contrasting control groups of adult carcinoma HeLa and MCF-7 strains. Additionally, newly purchased A-673, HeLa and MCF-7 cell lines were subjected to a 12-months continuous cell culture for a longitudinal analysis. Notably, EwS cell line A-673 exhibited exceptional stability in terms of genomic and transcriptomic levels as well as drug sensitivity, when compared to adult carcinoma cell lines. Further, four additional EwS cell lines were included in the longitudinal analysis to investigate the observed stability in the A-673 cell line. The analysis revealed that although all five EwS cell lines showed higher stability than their adult carcinoma counterparts, varying degrees of (epi)genomic, transcriptomic, and phenotypic alterations were observed after 12 months of continuous passaging. This indicated that cell line stability is a spectrum even within the same cancer entity. The observed remarkable stability of COTF-driven pediatric sarcoma cells underscores their potential as faithful models for cancer research and therapeutic drug testing. Since these cell line models could offer more consistent and reproducible outcomes, this discovery may have profound implications for preclinical studies, which may aid in the translation of research findings into clinical applications. Moreover, this thesis sheds light on the spectrum of reproducibility in in vitro scientific results, emphasizing the importance of carefully considering cell line characteristics in experimental design and result interpretation, even within the same tumor entity.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: reproducibility, cancer research, cell lines
• Themengebiete: 600 Technik, Medizin, angewandte Wissenschaften ; 600 Technik, Medizin, angewandte Wissenschaften > 610 Medizin und Gesundheit
• Fakultäten: Medizinische Fakultät
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 12. Dezember 2024
• 1. Bericht­erstatter:in: Grünewald, Thomas