Genomic profiling of cell lines reveals hidden research bias and caveats

AbstractCancer cell lines are extremely valuable tools for carcinoma research. Biodiversity of cell lines and continuous random mutation in cell lines during passage, however, might result in phenotypic inconsistency and lead to biased experimental conclusions. Using statistics based on known and inferred protein interaction networks, as well as public research literature database, our study shows that essential driver genotypes of cell lines might have hidden impact on research results. Furthermore, by comprehensive genomic profiling of 8 most common used urothelial cell lines and comparing them to previous publications, we found that regardless of similar short tandem repeat (STR) profile, driver gene loss in cell lines could happen by random mutation. Our results suggest that clinical research using urothelial carcinoma cell lines might be influenced by cell line genotypes which could only be determined by next-generation sequencing. Meanwhile, this study indicates that the conditionally reprogrammed cells (CRCs), which closely resemble original tumor tissue, might represent a better alternative for in vitro research, which may be better used for personalized medicine.

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Comprehensive genomic profiling of urothelial carcinoma cell lines reveals hidden research bias and caveats

Clinical and Translational Medicine ◽

10.1002/ctm2.36 ◽

2020 ◽

Vol 10 (1) ◽

pp. 294-296 ◽

Cited By ~ 2

Author(s):

Yongwen Luo ◽

Lingao Ju ◽

Gang Wang ◽

Chen Chen ◽

Yejinpeng Wang ◽

...

Keyword(s):

Urothelial Carcinoma ◽

Cell Lines ◽

Carcinoma Cell ◽

Genomic Profiling ◽

Carcinoma Cell Lines ◽

Research Bias ◽

Comprehensive Genomic Profiling ◽

Urothelial Carcinoma Cell

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Synthesis and Antitumor Activity Evaluation of New Phenanthrene-Based Tylophorine Derivatives

Letters in Organic Chemistry ◽

10.2174/1570178615666181025115513 ◽

2019 ◽

Vol 16 (6) ◽

pp. 462-467

Author(s):

Songtao Li ◽

Hongling Zhao ◽

Zhifeng Yin ◽

Shuhua Deng ◽

Yang Gao ◽

...

Keyword(s):

Antitumor Activity ◽

Cell Lines ◽

Antitumor Activities ◽

Human Carcinoma ◽

Carcinoma Cell Lines ◽

Structure Activity ◽

Human Carcinoma Cell ◽

Ic50 Values ◽

Relationship Of

A series of new phenanthrene-based tylophorine derivatives (PBTs) were synthesized in good yield and their structures were characterized by 1H-NMR spectroscopy and ESI MS. In vitro antitumor activity of these compounds against five human carcinoma cell lines, including HCT116 (colorectal), BGC-823 (gastric), HepG-2 (hepatic), Hela (cervical) and H460 (lung) cells, was evaluated by MTT assay. Among these PBTs, compound 6b showed the highest antitumor activities against HCT116 and HepG-2 cell lines with IC50 values of 6.1 and 6.4 μM, respectively, which were comparable to that of adriamycin hydrochloride. The structure-activity relationship of these compounds was also discussed based on the results of their antitumor activity.

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Progression and Differentiation of Alveolar Rhabdomyosarcoma Is Regulated by PAX7 Transcription Factor—Significance of Tumor Subclones

Cells ◽

10.3390/cells10081870 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1870

Author(s):

Klaudia Skrzypek ◽

Grażyna Adamek ◽

Marta Kot ◽

Bogna Badyra ◽

Marcin Majka

Keyword(s):

Transcription Factor ◽

Cell Lines ◽

Migration Activity ◽

Id Proteins ◽

Rh30 Cell ◽

Str Profile ◽

And Migration

Rhabdomyosarcoma (RMS), is the most frequent soft tissue tumor in children that originates from disturbances in differentiation process. Mechanisms leading to the development of RMS are still poorly understood. Therefore, by analysis of two RMS RH30 cell line subclones, one subclone PAX7 negative, while the second one PAX7 positive, and comparison with other RMS cell lines we aimed at identifying new mechanisms crucial for RMS progression. RH30 subclones were characterized by the same STR profile, but different morphology, rate of proliferation, migration activity and chemotactic abilities in vitro, as well as differences in tumor morphology and growth in vivo. Our analysis indicated a different level of expression of adhesion molecules (e.g., from VLA and ICAM families), myogenic microRNAs, such as miR-206 and transcription factors, such as MYOD, MYOG, SIX1, and ID. Silencing of PAX7 transcription factor with siRNA confirmed the crucial role of PAX7 transcription factor in proliferation, differentiation and migration of RMS cells. To conclude, our results suggest that tumor cell lines with the same STR profile can produce subclones that differ in many features and indicate crucial roles of PAX7 and ID proteins in the development of RMS.

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