A silver lining in cell line authentication: Short tandem repeat analysis of 1373 cases in China from 2010 to 2019

Misspellings or "miscellings"-Non-verifiable and unknown cell lines in cancer research publications

Reproducible laboratory research relies on correctly identified reagents. We have previously described gene research papers with wrongly identified nucleotide sequence(s), including papers studying miR-145. Manually verifying reagent identities in 36 recent miR-145 papers found that 56% and 17% of papers described misidentified nucleotide sequences and cell lines, respectively. We also found 5 cell line identifiers in miR-145 papers with misidentified nucleotide sequences and cell lines, and 18 cell line identifiers published elsewhere, that did not represent indexed human cell lines. These 23 identifiers were described as non-verifiable (NV), as their identities were unclear. Studying 420 papers that mentioned 8 NV identifier(s) found 235 papers (56%) that referred to 7 identifiers (BGC-803, BSG-803, BSG-823, GSE-1, HGC-7901, HGC-803, and MGC-823) as independent cell lines. We could not find any publications describing how these cell lines were established. Six cell lines were sourced from cell line repositories with externally accessible online catalogs, but these cell lines were not indexed as claimed. Some papers also stated that short tandem repeat (STR) profiles had been generated for three cell lines, yet no STR profiles could be identified. In summary, as NV cell lines represent new challenges to research integrity and reproducibility, further investigations are required to clarify their status and identities.

Investigation of the mixed origins of the MGC-803 cell line reveals that it is a hybrid cell line derived from HeLa

Human cancer cell lines have an essential role in cancer research, but only authentic cell lines should be used as biological models. Authentication testing using short tandem repeat (STR) loci has shown that MGC-803 cells, which were reported to come from gastric adenocarcinoma, are similar to HeLa. In this study, we confirmed that the MGC-803 cell line contains genetic material from HeLa, including genetic sequence from human papilloma virus 18 (HPV18). Additional alleles were present on STR analysis that remained stable after extensive passaging and generation of mono-clones. This behavior is consistent with a hybrid cell line arising from cell-cell fusion. Further genetic analysis revealed that MGC-803 originated from donors with different genetic ancestries, one African (HeLa) and the other Asian. Transcriptomic analysis demonstrated that MGC-803 closely resembles HeLa and another nasopharyngeal-HeLa hybrid cell line CNE-2. Based on these findings, we conclude that MGC-803 is a hybrid cell line derived from HeLa and other cells, the latter derived from a different patient with Asian genetic ancestry.

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay

We report an amplification-free genotyping method to determine the number of human short tandem repeats (STRs). DNA-based STR profiling is a robust method for genetic identification purposes such as forensics and biobanking and for identifying specific molecular subtypes of cancer. STR detection requires polymerase amplification, which introduces errors that obscure the correct genotype. We developed a new method that requires no polymerase. First, we synthesized perylene-nucleoside reagents and incorporated them into oligonucleotide probes that recognize five common human STRs. Using these probes and a bead-based hybridization approach, accurate STR detection was achieved in only 1.5 h, including DNA preparation steps, with up to a 1000-fold target DNA enrichment. This method was comparable to PCR-based assays. Using standard fluorometry, the limit of detection was 2.00 ± 0.07 pM for a given target. We used this assay to accurately identify STRs from 50 human subjects, achieving >98% consensus with sequencing data for STR genotyping.

Using short tandem repeat profiling to validate cell lines in biobanks

Aim. To approve the COrDIS kit (Gordiz, Russia) for the authenticity of cell lines from the Bioresource Collection of the N.N. Blokhin National Medical Research Center of Oncology by the short tandem repeat (STR) profiling.

Material and methods. The chosen method proved to be a reliable and reproducible option. With this approach, a number of polymorphic STR loci are amplified using commercially available primer sets. Polymerase chain reaction (PCR) products are analyzed simultaneously with size standards using automated fluorescent detection methods. The results are presented as a simple number code corresponding to the lengths of the PCR products amplified at each locus. By applying this method to cell lines, the laboratory can both authenticate commercial cell lines and build a database of their lines. In the work, we used the COrDIS EXPERT 26 kit (Gordiz, Russia), validated for molecular genetic identification of personality based on multiplex PCR analysis of 26 highly polymorphic loci of human genomic deoxyribonucleic acid. PCR results were analyzed by capillary electrophoresis using an automatic genetic analyzer with laser-induced fluorescence detection (Applied Biosystems 3500xL).

Results. When testing the method, profiling of 37 cell lines was carried out, of which 18 were announced in international databases and 19 were unique, obtained at the N. N. Blokhin National Medical Research Center of Oncology, as well as a cell line mixture in order to determine the limits of contamination detection. The obtained results showed the correspondence of commercial cell lines with the data in international databases. Within the framework of this work, profiles of unique lines were obtained and the foundation of own genetic database was laid. Studies to identify the limit of contamination detection by another line have shown that even 4% of the contaminant culture in the total pool can be used to identify its individual alleles.

Conclusion. The results obtained indicate the possibility of using the method to identify samples of the collection and detect intraspecific contamination.

Cell line authentication: a necessity for reproducible biomedical research

Immortalized or continuous cell lines are invaluable tools in basic and preclinical research. However, the widespread use of misidentified cell lines is a serious threat to scientific reproducibility. Based on the experiences of mandatory cell line authentication at the International Journal of Cancer (IJC), we provide an overview of the issues pertinent to misidentified cell lines and discuss available solutions. We also summarize the lessons learned, revealing that at least 5% of the human cell lines used in manuscripts considered for peer review are misidentified. About 4% of the considered manuscripts are rejected for severe cell line problems, and most are subsequently published in other journals. In order to diminish such malpractice and its consequences for the scientific record, we postulate that strict multi-layered quality control is essential. Besides journals and publishers, we encourage scientists, research institutions, and funders to take action on the matter and revise their respective policies. Hence, we provide concrete recommendations on introducing regular authentication schemes and staff training, and discuss future steps for enhancing good cell culture practices.