Research Article: Investigation of Cross-Contamination and Misidentification of 278 Widely Used Tumor Cell Lines

Date Published: January 20, 2017

Publisher: Public Library of Science

Author(s): Yaqing Huang, Yuehong Liu, Congyi Zheng, Chao Shen, Patricia Talamas-Rohana.

http://doi.org/10.1371/journal.pone.0170384

Abstract

In recent years, biological research involving human cell lines has been rapidly developing in China. However, some of the cell lines are not authenticated before use. Therefore, misidentified and/or cross-contaminated cell lines are unfortunately commonplace. In this study, we present a comprehensive investigation of cross-contamination and misidentification for a panel of 278 cell lines from 28 institutes in China by using short tandem repeat profiling method. By comparing the DNA profiles with the cell bank databases of ATCC and DSMZ, a total of 46.0% (128/278) cases with cross-contamination/misidentification were uncovered coming from 22 institutes. Notably, 73.2% (52 out of 71) of the cell lines established by the Chinese researchers were misidentified and accounted for 40.6% of total misidentification (52/128). Further, 67.3% (35/52) of the misidentified cell lines established in laboratories of China were HeLa cells or a possible hybrid of HeLa with another kind of cell line. Furthermore, the bile duct cancer cell line HCCC-9810 and degenerative lung cancer Calu-6 exhibited 88.9% match in the ATCC database (9-loci), indicating that they were from the same origin. However, when we used 21-loci to compare these two cell lines with the same algorithm, the percent match was only 48.2%, indicating that these two cell lines were different. The SNP profiles of HCCC-9810 and Calu-6 also revealed that they were different cell lines. 150 cell lines with unique profiles demonstrated a wide range of in vitro phenotypes. This panel of 150 genomically validated cancer cell lines represents a valuable resource for the cancer research community and will advance our understanding of the disease by providing a standard reference for cell lines that can be used for biological as well as preclinical studies.

Partial Text

Although cell line authentication has been widely recommended for many years, misidentification, including cross-contamination, remains an unresolved issue [1, 2]. With the development of biomedical research, more and more scientific reports involving human cell lines have been published by researchers in China. However, authentication has been neglected by many researchers [3]. Until recently, many major journals and research agencies recommended that cell lines should be verified for authenticity before publication or inclusion in grant applications. Although there are many new methods for cell line authentication [4, 5], DNA profiling based on short tandem repeat (STR) is still proposed as a gold standard method. Our lab started using STR for cell line authentication from 2009 with 16/20-loci STR and found about 25% cross-contamination or misidentification among 380 cell lines from 2009 to 2013 [6]. In this study, we provided 21-loci STR for 278 cancer cell lines (data collected from 2014 to 2016), in accordance with the major cell repository’ recommendation for the testing of cell line identity. We observed examples of cross-contamination and misidentification of cell lines, and provided reference STR profiles for cancer cell lines that are currently unavailable in the STR database of major cell repositories. Additionally, we have extended the number of genetic loci for STR profiles currently available in public databases.

We presented a panoptic survey of cell line cross-contamination among human tumor cell lines using molecular genetic methods. The STR profiling technique uses fluorescence and multiplex PCR based technology to detect STR loci with overlapping size range. The specificity and polymorphism advantages make it method of choice for the authentication of human cell lines.

 

Source:

http://doi.org/10.1371/journal.pone.0170384

 

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