A novel TE distribution-based authentication protocol for Drosophila cell lines

Drosophila cell lines are used by researchers to investigate various cell biological phenomena. It is crucial to exercise good cell culture practice. Poor handling can lead to both inter- and intraspecies cross-contamination as well as the introduction of large- and small-scale genomic changes. These factors, therefore, make it imperative that methods to authenticate Drosophila cell lines are developed. Mammalian cell line authentication is reliant on short tandem repeat (STR) profiling. In Drosophila cell lines, low STR mutation rates and the extremely low STR allelic diversity, key requirements for STR profiling, preclude the value of this technique. In contrast, transposable elements (TE) are highly polymorphic among individual flies and abundant in Drosophila cell lines. Therefore, we investigated the utility of TE insertions as useful markers to discriminate Drosophila cell lines derived from different/same donor genotypes, including divergent sub-lines of the same cell line. We developed a PCR-based next-generation sequencing enabled protocol to cluster cell lines based on the genome-wide distribution a limited number of active TE families. We determined the distribution of TE families in S2R+, S2-DRSC, S2-DGRC, Kc167, ML-DmBG3-c2, mbn2, CME W1 Cl.8+, and OSS Drosophila cell lines. Two independent downstream analyses of the NGS data yielded similar clustering of these cell lines. Double-blind testing of the protocol reliably identified various Drosophila cell lines. In addition, our data indicate minimal changes with respect to the genome-wide distribution of these six TE families when cells are passaged for at least 50 times. The protocol developed can accurately identify and distinguish the numerous Drosophila cell lines available to the research community, thereby aiding reproducible Drosophila cell culture research.