Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

Abstract

Cell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabelling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here we leverage the classical observation that transposable elements (TEs) proliferate in cultured Drosophila cells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance of Drosophila cell lines. We identify multiple cases where TE profiles clarify the origin of Drosophila cell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of LTR retrotransposon families are necessary to mark Drosophila cell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome sequencing data (called ngs_te_mapper2), which revealed loss of heterozygosity as a mechanism shaping the unique TE profiles that identify Drosophila cell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines in Drosophila and other organisms.

A novel transposable element-based authentication protocol for Drosophila cell lines

“…Six TE families shown by Han et al . (2021) to be sufficient to identify Drosophila cell lines based on whole genome sequencing (WGS) data were used as initial candidates for primer design.…”

“…WGS data from Zhang et al (2010) , Lee et al (2014) , and Han et al (2021) for all focal cell lines were mapped against TE canonical sequences and merged into a single BAM file.…”

“…These properties, together with the large number of potential insertion sites across the genome and stability of TE insertions at individual loci, suggest that TE insertions should theoretically be useful markers to simultaneously discriminate Drosophila cell lines made from different donor genotypes as well as from the same donor genotype, including divergent sub-lines of the same cell line. Han et al . (2021) recently tested this prediction and demonstrated that genome-wide TE insertion profiles can reliably cluster different Drosophila cell lines from the same donor genotypes and discriminate cell lines from different donor genotypes, while also preserving information about the laboratory of origin.…”

“…(2021) recently tested this prediction and demonstrated that genome-wide TE insertion profiles can reliably cluster different Drosophila cell lines from the same donor genotypes and discriminate cell lines from different donor genotypes, while also preserving information about the laboratory of origin. A minimal subset of six active TE families ( 297 , copia , mdg3 , mdg1 , roo , and 1731 ) was also determined to have essentially the same discriminative power as the genome-wide dataset ( Han et al 2021 ). These six TE families are all long terminal repeat (LTR) retrotransposons, which are the most abundant type of TE in Drosophila cell lines ( Rahman et al 2015 ) and are typically composed of recently active insertions with highly similar sequences ( Bergman and Bensasson 2007 ), features which potentially enhance their use as markers.…”

Bergerac Strains of C. elegans Revisited: Expansion of Tc1 elements Impose a Significant Genomic and Fitness Cost

“…McClintock v2.0.0 provides an estimate of normalized mean coverage. Five callers were chosen from the McClintock pipeline to estimate Tc1 copynumber based on the absolute difference from the normalized mean coverage and ddPCR copy-number estimate: ngs_te_mapper2 (Han et al 2021), RelocaTE (Robb et al 2013), TEMP2 (Yu et al 2021), RetroSeq (Keane et al 2013), andTEFLoN (Adrion et al 2017).…”