scholarly journals Genome-wide silencing screen in mesothelioma cells reveals that loss of function of BAP1 induces chemoresistance to ribonucleotide reductase inhibition: implication for therapy

2018 ◽  
Author(s):  
Agata Okonska ◽  
Saskja Bühler ◽  
Vasundhara Rao ◽  
Manuel Ronner ◽  
Maxime Blijlevens ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Ribonucleotide Reductase ◽  
Genetically Engineered ◽  
Whole Genome ◽  
Loss Of Function ◽  
Functional Studies ◽  
Genome Wide ◽  
Sirna Screens ◽  
Gemcitabine Treatment

ABSTRACTIntroductionLoss of function of BRCA1 associated protein 1 (BAP1) is observed in about 50% of malignant pleural mesothelioma (MPM) cases. The aim of this study was to investigate whether this aspect could be exploited for targeted therapy.MethodsA genetically engineered model was established expressing either functional or nonfunctional BAP1 and whole-genome siRNA screens were performed assessing impaired survival between the two cell lines. Cytotoxity induced by gemcitabine and hydroxyurea were assessed in a panel of BAP1-WT and BAP1-mut/del cell lines. Functional studies were carried out in BAP1 mut/del cell line reconstituted with BAP1 WT or BAP1 C91A (catalytically dead mutant) and in BAP1 WT cell line upon siRNA-mediated knock-down of BAP1.ResultsThe whole-genome siRNA screen unexpectedly revealed 11 hits (FDR<0.05) more cytotoxic for BAP1-proficient cells. Two actionable targets, RRM1 and RRM2, were validated and their inhibition mediated by gemcitabine or hydroxyurea respectively, was more cytotoxic in BAP1-proficient cell lines. Upregulation of RRM2 upon gemcitabine and hydroxyurea was more profound in BAP1 mut/del cell lines. Increased lethality mediated by gemcitabine and hydroxyurea was observed in NCI-H2452 cells reconstituted with BAP1 WT but not with C91A mutant and upregulation of RRM2 in NCI-H2452-BAP1 WT spheroids was modest compared to control or C91A mutant. Finally, the opposite was observed after BAP1 knockdown in BAP1-proficient SPC111 cell line.ConclusionWe found that BAP1 is involved in the regulation of RRM2 levels during replication stress. These observations reveal a potential therapeutic approach where MPM patients to be stratified depending on BAP status for gemcitabine treatment.

scholarly journals A Genome-Wide CRISPR Screen Implicates MYC Dysregulation in TCF3-PBX1 B-ALL

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3915-3915
Author(s):  
Ruth E Cranston ◽  
Paul B Sinclair ◽  
Matthew Bashton ◽  
Matthew P Selby ◽  
Christine J Harrison
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Pathway Analysis ◽  
P Value ◽  
Whole Genome ◽  
Gene Set Enrichment ◽  
Data Set ◽  
Genome Wide

Abstract Introduction: Acute lymphoblastic leukaemia (ALL) is the most common paediatric cancer, of which, precursor B-cell ALL (B-ALL) accounts for approximately 80% of diagnoses. B-ALL is a heterogeneous disease, with patients characterised and risk stratified according to their cytogenetic profile. TCF3-PBX1 B-ALL was associated with a poor prognosis, but on current therapies outcome has greatly improved. However, approximately 10% of these patients relapse with their disease and at this stage have a dismal prognosis (Moorman et. al. Lancet Oncology 2010). Thus, this subset of patients pose a clinical challenge, and further understanding of disease mechanisms in relapsed TCF3-PBX1 is required to aid the discovery of novel targets for therapy. Methods: Clustered regularly-interspaced short palindromic repeats (CRISPR) technology was utilised as a whole genome CRISPR knockout (GeCKO) screen (Sanjana et. al. Nature Methods 2014) for genome-wide identification of candidate oncogene and tumour suppressor genes (TSGs) in B-ALL cell lines, including 697 (relapsed TCF3-PBX1), REH (ETV6-RUNX1), NALM16 (hypodiploid) and HAL-01 (TCF3-HLF). The GeCKO screens were performed at 300-fold library coverage, with transduced and selected cells harvested at day 0, weeks 2, 4, 6 and 8. DNA was sequenced across the integrated sgRNA region. The abundance of sgRNA constructs was analysed over time using the model-based analysis of genome-wide CRISPR-Cas9 knockout (MAGeCK) program (Li et. al. Genome Biology 2014) to identify candidate oncogenes and TSGs. Pathway analysis was performed for the identification of significantly dysregulated pathways in TCF3-PBX1 using the 697 data set and the MaGeCK Gene Set Enrichment Analysis pathway program. Results: Whole genome CRISPR screening in the 697 cell line successfully identified 2213 candidate oncogenes (false discovery rate (FDR) <0.05, p value <0.012) and 5 candidate TSGs (FDR <0.3, p value < 6.7x10-5). Amongst the significant candidate oncogenes was MYC (FDR = 3.0x10-6, p value = 2.3x10-8, rank 16) and MaGeCK Gene Set Enrichment pathway analysis using the Molecular Signatures Database (MSigDB) Hallmarks data set, identified HALLMARK_MYC_TARGETS_V1 and HALLMARK_MYC_TARGETS_V2 as the two most significant negatively regulated pathways within the knockout screen (FDR of 1.79x10-55 and 9.876x10-21, respectively). These data indicate a role for MYC dysregulation in TCF3-PBX1 B-ALL. Additionally, the identification of the intriguing TSG candidates CREBBP (FDR = 0.059, p value = 5.5x10-6, rank 2), MLXIP (FDR = 0.24, p value = 3.4x10-5, rank 3), HIF1A (FDR = 0.29, p value = 6.7x10-5, rank 4) and ARNT (FDR = 0.02, p value = 1x10-6, rank 1) further highlighting the importance of MYC signalling in TCF3-PBX1 B-ALL. HIF1A inhibits MYC by direct interaction, induction of the repressor MXI1 and by coordinating the degradation of MYC by the proteasome (Zhang et. al. Cancer Cell 2007, Corn et. al. Cancer Biol. Ther. 2005, Gordan et. al. Cancer Cell 2007). ARNT dimerises with HIF1A and is responsible for the recruitment of transcriptional coactivators for the transcriptional output of HIF1A (Partch et. al. Proc Natl Acad Sci USA 2011), while CREBBP has been reported to have a role in MYC inhibition in G1, preventing the progression from G1 to S phase (Rajabi et. al. J. Biol. Chem. 2005), in addition to interaction with the candidate TSG, HIF1A (Ema et. al. EMBO J. 1999, Bhattacharya et. al. Genes Dev. 1999, Park et. al. Mol. Pharmacol. 2008). Despite the role of MLXIP in glycolysis in B-ALL (Wernicke et. al. Leuk Res. 2012), and MLXIP knockout being synthetic lethal in MYC-overexpressing neuroblastoma cell lines (Carroll et. al. Cancer Cell 2015), CRISPR mediated knockout of MLXIP in the 697 TCF3-PBX1 cell line promoted growth. This may be because knockout of MLXIP reduces the number of MLXIP-MLX heterodimers to compete with MYC-MAX heterodimers at E-box sequences, permitting transcriptional activation of MYC-target genes (Carroll et. al. Cancer Cell 2015). This study has identified a number of potential mechanisms by which MYC deregulation can occur in TCF3-PBX1 B-ALL, highlighting the essential role of MYC in disease maintenance. MYC inhibition offers a potential avenue for targeted therapy in relapsed TCF3-PBX1 B-ALL, which warrants further investigation. Disclosures No relevant conflicts of interest to declare.

scholarly journals Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11

2021 ◽  
Vol 22 (11) ◽  
pp. 5798
Author(s):  
Shoko Tokumoto ◽  
Yugo Miyata ◽  
Ruslan Deviatiiarov ◽  
Takahiro G. Yamada ◽  
Yusuke Hiki ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Desiccation Tolerance ◽  
Expression Profiles ◽  
Insect Cell Line ◽  
Gene Expression Profiles ◽  
Late Embryogenesis Abundant ◽  
Heat Shock Factor 1 ◽  
Genome Wide ◽  
A Genome

The Pv11, an insect cell line established from the midge Polypedilum vanderplanki, is capable of extreme hypometabolic desiccation tolerance, so-called anhydrobiosis. We previously discovered that heat shock factor 1 (HSF1) contributes to the acquisition of desiccation tolerance by Pv11 cells, but the mechanistic details have yet to be elucidated. Here, by analyzing the gene expression profiles of newly established HSF1-knockout and -rescue cell lines, we show that HSF1 has a genome-wide effect on gene regulation in Pv11. The HSF1-knockout cells exhibit a reduced desiccation survival rate, but this is completely restored in HSF1-rescue cells. By comparing mRNA profiles of the two cell lines, we reveal that HSF1 induces anhydrobiosis-related genes, especially genes encoding late embryogenesis abundant proteins and thioredoxins, but represses a group of genes involved in basal cellular processes, thus promoting an extreme hypometabolism state in the cell. In addition, HSF1 binding motifs are enriched in the promoters of anhydrobiosis-related genes and we demonstrate binding of HSF1 to these promoters by ChIP-qPCR. Thus, HSF1 directly regulates the transcription of anhydrobiosis-related genes and consequently plays a pivotal role in the induction of anhydrobiotic ability in Pv11 cells.

Chromosome-mediated gene transfer of hydroxyurea resistance and amplification of ribonucleotide reductase activity

1983 ◽  
Vol 3 (6) ◽  
pp. 1053-1061
Author(s):  
W H Lewis ◽  
P R Srinivasan
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Ribonucleotide Reductase ◽  
Chinese Hamster ◽  
Fold Increase ◽  
Resistant Cell ◽  
Plating Efficiency ◽  
Wild Type Cell ◽  
Wild Type ◽  
Metaphase Chromosomes

Metaphase chromosomes purified from a hydroxyurea-resistant Chinese hamster cell line were able to transform recipient wild-type cells to hydroxyurea resistance at a frequency of 10(-6). Approximately 60% of the resulting transformant clones gradually lost hydroxyurea resistance when cultivated for prolonged periods in the absence of drug. One transformant was subjected to serial selection in higher concentrations of hydroxyurea. The five cell lines generated exhibited increasing relative plating efficiency in the presence of the drug and a corresponding elevation in their cellular content of ribonucleotide reductase. The most resistant cell line had a 163-fold increase in relative plating efficiency and a 120-fold increase in enzyme activity when compared with the wild-type cell line. The highly hydroxyurea-resistant cell lines had strong electron paramagnetic resonance signals characteristic of an elevated level of the free radical present in the M2 subunit of ribonucleotide reductase. Two-dimensional electrophoresis of cell-free extracts from one of the resistant cell lines indicated that a 53,000-dalton protein was present in greatly elevated quantities when compared with the wild-type cell line. These data suggest that the hydroxyurea-resistant cell lines may contain an amplification of the gene for the M2 subunit of ribonucleotide reductase.

scholarly journals Comprehensive Analysis of SWI/SNF Inactivation in Lung Adenocarcinoma Cell Models

Cancers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3712
Author(s):  
Paola Peinado ◽  
Alvaro Andrades ◽  
Marta Cuadros ◽  
Maria Isabel Rodriguez ◽  
Isabel F. Coira ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Genetic Alterations ◽  
Cell Models ◽  
Functional Studies ◽  
Cellular Models ◽  
Mutational Status

Mammalian SWI/SNF (SWitch/Sucrose Non-Fermentable) complexes are ATP-dependent chromatin remodelers whose subunits have emerged among the most frequently mutated genes in cancer. Studying SWI/SNF function in cancer cell line models has unveiled vulnerabilities in SWI/SNF-mutant tumors that can lead to the discovery of new therapeutic drugs. However, choosing an appropriate cancer cell line model for SWI/SNF functional studies can be challenging because SWI/SNF subunits are frequently altered in cancer by various mechanisms, including genetic alterations and post-transcriptional mechanisms. In this work, we combined genomic, transcriptomic, and proteomic approaches to study the mutational status and the expression levels of the SWI/SNF subunits in a panel of 38 lung adenocarcinoma (LUAD) cell lines. We found that the SWI/SNF complex was mutated in more than 76% of our LUAD cell lines and there was a high variability in the expression of the different SWI/SNF subunits. These results underline the importance of the SWI/SNF complex as a tumor suppressor in LUAD and the difficulties in defining altered and unaltered cell models for the SWI/SNF complex. These findings will assist researchers in choosing the most suitable cellular models for their studies of SWI/SNF to bring all of its potential to the development of novel therapeutic applications.

Biological and Molecular Characterization by Integrative Genomics Approach of CMA-03/06, a Newly Established Interleukin-6 Independent Variant of the CMA-03 Human Myeloma Cell Line.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1814-1814
Author(s):  
Donata Verdelli ◽  
Lucia Nobili ◽  
Katia Todoerti ◽  
Laura Mosca ◽  
Sonia Fabris ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Cell Line ◽  
Molecular Characterization ◽  
Cell Lines ◽  
Stromal Cells ◽  
Interleukin 6 ◽  
Myeloma Cell ◽  
Growth And Survival ◽  
Genome Wide

Abstract Abstract 1814 Poster Board I-840 Background The growth and survival of multiple myeloma (MM) cells in the bone marrow microenvironment is regulated by functional complex interactions between the tumor cells and the surrounding bone marrow stromal cells mediated by adhesion molecules and the production of several cytokines of which interleukin-6 (IL-6) has been identified as the most important. Major advances in the investigation of MM biology were made possible by the availability of human myeloma cell lines (HMCLs). The IL-6-dependent CMA-03 cell line was established in our laboratory from a peritoneal effusion of a refractory relapsed MM patient. By gradually decreasing the IL-6 added to the culture, an IL-6-independent variant, CMA-03/06, could be obtained. Aims. To perform a biological and molecular characterization of this novel cell line, and to provide insights into the signaling pathways and target genes involved in the growth and survival of CMA-03/06. Methods. The growth, immunophenotypic, cytogenetic and fluorescence in situ hybridization (FISH) characterization of CMA-03/06 cell line was performed by means of standard procedures. IL-6 production into the culture media was determined using a high sensitivity IL-6 specific ELISA. Genome-wide profiling data were generated by means of Affymetrix GeneChip® Human Mapping 250K Nsp arrays; copy number (CN) alterations were calculated using the DNAcopy Bioconductor package, based on circular binary segmentation method. Global gene expression profiling (GEP) was performed by means of the GeneChip® Human Gene 1.0 ST Arrays (Affymetrix); the supervised analyses were done using the SAM software version 3.0. Results Unlike CMA-03, the addition of IL-6 to the culture medium of CMA-03/06 cells or co-culture with multipotent mesenchymal stromal cells did not induce an increase in CMA-03/06 proliferation. IL-6 was not detected in the supernatants from either CMA-03 or CMA-03/06 cell lines within 48 h, suggesting that the IL-6 independence of CMA03/06 cells is not a result of the development of an autocrine IL-6 loop. Nevertheless, IL-6 induced the activation of STAT3 and STAT1 in both cell lines, even if a slight constitutive STAT3 phosphorylation was found in CMA-03/06. The immunophenotypic analysis showed a significant difference in the expression of three antigens in the 2 cell lines: CD45 was considerably reduced in CMA-03/06 cells, whereas they were found positive for both chains of IL-6 receptor, CD126 and CD130, almost undetectable in CMA-03. Conventional cytogenetic and FISH analyses did not reveal differences between the 2 HMCLs. The genome-wide analysis allowed the identification of about 100 altered chromosomal regions common to both HMCLs, mostly DNA gains. Comparison of CMA-03/06 and CMA-03 cells evidenced a different CN in only 15 small chromosomal regions, 8 of which did not contain any transcript, whereas few genes were located on the other ones. GEP analysis of CMA-03/06 compared with CMA-03 identified 21 upregulated and 47 downregulated genes, many of which particularly relevant for MM biology, mainly involved in cellular signaling, cell cycle, cell adhesion, cell development, regulation of transcription, immunologic, inflammatory or defense activity, apoptosis. None of the genes differentially expressed in CMA-03/06 compared with CMA-03 except 1 were positioned on the chromosomal regions showing a different CN. Finally, CMA-03/06 cell line showed a lower susceptibility to camptothecin-induced apoptosis compared to CMA-03 cells. Conclusions Our data show the IL-6 independence of CMA-03/06 cell line in the absence of an autocrine IL-6 loop; the cells, however, maintain the IL-6 signaling pathway responsiveness. A consistent number of genes particularly relevant for MM biology were found deregulated in CMA-03/06 cell line compared with CMA-03. Furthermore, CMA-03/06 cell line shows an increased resistance to apoptosis. The novel CMA03/06 cell line may thus represent a suitable model for studies investigating molecular mechanisms involved in clonal evolution towards IL-6 and/or stroma-independent growth and survival of myeloma cells. Disclosures No relevant conflicts of interest to declare.

scholarly journals Conditionally immortalized human proximal tubular epithelial cells isolated from the urine of a healthy subject express functional calcium-sensing receptor

2015 ◽  
Vol 308 (11) ◽  
pp. F1200-F1206 ◽  
Author(s):  
Annarita Di Mise ◽  
Grazia Tamma ◽  
Marianna Ranieri ◽  
Maria Svelto ◽  
Bert van den Heuvel ◽  
...  
Keyword(s):  
Healthy Subject ◽  
Cell Line ◽  
Cell Lines ◽  
Cyclopiazonic Acid ◽  
Cytosolic Calcium ◽  
Epithelial Cell Line ◽  
Loss Of Function ◽  
Calcium Sensing Receptor ◽  
Calcium Sensing ◽  
Proximal Tubular

The calcium-sensing receptor (CaSR) is a G protein-coupled receptor, which plays an essential role in regulating Ca2+ homeostasis. Here we show that conditionally immortalized proximal tubular epithelial cell line (ciPTEC) obtained by immortalizing and subcloning cells exfoliated in the urine of a healthy subject expresses functional endogenous CaSR. Immunolocalization studies of polarized ciPTEC revealed the apical localization of the receptor. By Western blotting of ciPTEC lysates, both monomeric and dimeric forms of CaSR at 130 and ∼250 kDa, respectively, were detected. Functional studies indicated that both external calcium and the positive CaSR allosteric modulator, NPS-R568, induced a significant increase in cytosolic calcium, proving a high sensitivity of the endogenous receptor to its agonists. Calcium depletion from the endoplasmic reticulum using cyclopiazonic acid abolished the increase in cytosolic calcium elicited by NPS-R568, confirming calcium exit from intracellular stores. Activation of CaSR by NPS-R significantly reduced the increase in cAMP elicited by forskolin (FK), a direct activator of adenylate cyclase, further confirming the functional expression of the receptor in this cell line. CaSR expressed in ciPTEC was found to interact with Gq as a downstream effector, which in turn can cause release of calcium from intracellular stores via phospholipase C activation. We conclude that human proximal tubular ciPTEC express functional CaSR and respond to its activation with a release of calcium from intracellular stores. These cell lines represent a valuable tool for research into the disorder associated with gain or loss of function of the CaSR by producing cell lines from patients.

scholarly journals An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs

2021 ◽  
Author(s):  
Ashley L Cook ◽  
Nicolas Wyhs ◽  
Surojit B Sur ◽  
Blair Ptak ◽  
Maria Popoli ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
High Throughput ◽  
High Throughput Screening ◽  
Growth Inhibitor ◽  
Suppressor Gene ◽  
Loss Of Function ◽  
Cancer Pathways ◽  
Isogenic Cell Line ◽  
Cell Line Panel

We describe the creation and characterization of an isogenic cell line panel representing common cancer pathways, with multiple features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cells were generated using CRISPR-technologies. Surprisingly, we discovered most of these lines did not result in complete gene inactivation, despite integration of sgRNA at the desired genomic site. However, a subset of the lines harbored true, biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterize lines covering 19 pathways frequently subject to loss of function in cancers. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a multiplexed high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of TP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena.

scholarly journals Brain and Breast Cancer Cells with PTEN Loss of Function Reveal Enhanced Durotaxis and RHOB Dependent Amoeboid Migration Utilizing 3D Scaffolds and Aligned Microfiber Tracts

Cancers ◽  
2021 ◽  
Vol 13 (20) ◽  
pp. 5144
Author(s):  
Annalena Wieland ◽  
Pamela L. Strissel ◽  
Hannah Schorle ◽  
Ezgi Bakirci ◽  
Dieter Janzen ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Tumor Cells ◽  
Cell Lines ◽  
Essential Role ◽  
Brain Structures ◽  
Loss Of Function ◽  
Pten Loss ◽  
Tumor Cell Migration ◽  
Functional Studies ◽  
Tnbc Cell

Background: Glioblastoma multiforme (GBM) and metastatic triple-negative breast cancer (TNBC) with PTEN mutations often lead to brain dissemination with poor patient outcome, thus new therapeutic targets are needed. To understand signaling, controlling the dynamics and mechanics of brain tumor cell migration, we implemented GBM and TNBC cell lines and designed 3D aligned microfibers and scaffolds mimicking brain structures. Methods: 3D microfibers and scaffolds were printed using melt electrowriting. GBM and TNBC cell lines with opposing PTEN genotypes were analyzed with RHO-ROCK-PTEN inhibitors and PTEN rescue using live-cell imaging. RNA-sequencing and qPCR of tumor cells in 3D with microfibers were performed, while scanning electron microscopy and confocal microscopy addressed cell morphology. Results: In contrast to the PTEN wildtype, GBM and TNBC cells with PTEN loss of function yielded enhanced durotaxis, topotaxis, adhesion, amoeboid migration on 3D microfibers and significant high RHOB expression. Functional studies concerning RHOB-ROCK-PTEN signaling confirmed the essential role for the above cellular processes. Conclusions: This study demonstrates a significant role of the PTEN genotype and RHOB expression for durotaxis, adhesion and migration dependent on 3D. GBM and TNBC cells with PTEN loss of function have an affinity for stiff brain structures promoting metastasis. 3D microfibers represent an important tool to model brain metastasizing tumor cells, where RHO-inhibitors could play an essential role for improved therapy.

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

Genetics ◽  
2021 ◽  
Author(s):  
Shunhua Han ◽  
Preston J Basting ◽  
Guilherme B Dias ◽  
Arthur Luhur ◽  
Andrew C Zelhof ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cell Line ◽  
Loss Of Heterozygosity ◽  
Cell Lines ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Drosophila Cell ◽  
Genome Wide ◽  
Cell Culture Systems ◽  
Cell Line Identity

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.

Sign in / Sign up

Export Citation Format

Share Document