{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14730"],"description":["RNA-seq profiling of HeLa GFP cells treated with a Cas9 bearing either a scramble or a GFP guide to study the activation of inflammatory pathways 3 days after Cas9 delivery"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Maxwell® RSC simplyRNA Tissue Kit (Promega) was used to isolate total RNA from cells, according to the manufacturer’s instructions. DNase I (Qiagen) treatment was performed to remove any potential residual contamination of genomic DNA.","Sample Collection - HeLa GFP cells were generated by infecting HeLa WT cells with the pLenti-CMV-MCS-GFP-SV-puro plasmid (#73582, Addgene), previously depleted of the promoter and enhancer regions to generate a stable cell line that does not express the GFP protein. HeLa GFP cells were grown under standard tissue culture conditions (37°C, 5% CO2) in DMEM, supplemented with 10% FBS, 2mM L-Glutamine and 1% Penicillin/Streptomycin.","Library Construction - Illumina stranded mRNA prep Ligation kit for polyA transcripts","Sequencing - For RNA-seq, RNA from HeLa GFP cells was quantified with Qubit fluorimeter and checked for integrity on Agilent Bioanalyzer 2100; the library was then prepared with the Illumina stranded mRNA prep Ligation kit for polyA transcripts and cells treated with Cas9 carrying either the scramble or the GFP guide were sequenced with the GU_NextSeq550 sequencer, following the manifacturer’s instructions"],"figure_sub":["MINSEQE Score","Assays and Data","organisation","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 550"],"pubmed_abstract":["The CRISPR/Cas9 technology is a powerful and versatile tool to disrupt genes' functions by introducing sequence-specific DNA double-strand breaks (DSBs). Here, we repurpose this technology to eradicate aberrant cells by specifically targeting silent and non-functional genomic sequences present only in target cells to be eliminated. Indeed, an intrinsic challenge of most current therapies against cancer and viral infections is the non-specific toxicity that they can induce in normal tissues because of their impact on important cellular mechanisms shared, to different extents, between unhealthy and healthy cells. The CRISPR/Cas9 technology has potential to overcome this limitation; however, so far effectiveness of these approaches was made dependent on the targeting and inactivation of a functional gene product. Here, we generate proof-of-principle evidence by engineering HeLa and RKO cells with a promoterless Green Fluorescent Protein (GFP) construct. The integration of this construct simulates either a genomic alteration, as in cancer cells, or a silent proviral genome. Cas9-mediated DSBs in the GFP sequence activate the DNA damage response (DDR), reduce cell viability and increase mortality. This is associated with increased cell size, multinucleation, cGAS-positive micronuclei accumulation and the activation of an inflammatory response. Pharmacological inhibition of the DNA repair factor DNA-PK enhances cell death. These results demonstrate the therapeutic potential of the CRISPR/Cas9 system in eliminating cells with an aberrant genome, regardless of the expression or the function of the target DNA sequence."],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Weaponizing CRISPR/Cas9 for selective elimination of cells with an aberrant genome"],"additional_accession":["ERP167413"],"pubmed_authors":["Sara Tavella, Alessia di Lillo, Anastasia Conti, Fabio Iannelli, Alexandra Mancheno-Ferris, Valentina Matti, Raffaella Di Micco, Fabrizio d'Adda di Fagagna","Data Submission IFOM - ETS","Alexandra Mancheno-Ferris","Fabrizio d'Adda di Fagagna","Sara Tavella","Fabio Iannelli"]},"is_claimable":false,"name":"Weaponizing CRISPR/Cas9 for selective elimination of cells with an aberrant genome","description":"RNA-seq profiling of HeLa GFP cells treated with a Cas9 bearing either a scramble or a GFP guide to study the activation of inflammatory pathways 3 days after Cas9 delivery","dates":{"release":"2025-05-06T00:00:00Z","modification":"2026-06-06T00:10:30.982Z","creation":"2024-12-24T17:01:08.893Z"},"accession":"E-MTAB-14730","cross_references":{"ENA":["ERP167413"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"],"doi":["10.1016/j.dnarep.2025.103840"]}}