biostudies-arrayexpressAmy WebbHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16128Functional lysosomes are essential for tumor growth. CQ, a widely used lysosome inhibitor, has been combined with various other therapeutics for testing in cancer patients. However, no studies have reported enhanced antitumor effects from these treatments. To investigate how tumor cells survive CQ-mediated lysosome inhibition, we conducted transcriptome analysis using RNA sequencing (RNA-seq) on an adenocarcinoma NSCLC patient-derived xenograft (PDX #72-1001) to compare gene expression changes between control (vehicle) and CQ treatment groups.biostudies-arrayexpressLibrary Construction - RNA libraries for RNA-seq were prepared using SMARTER Mrna-SEQ Library Prep Kit following manufactures's protocols.Sequencing - Sequenced on Illumina NovaSeq X Plus at Genome Sequencing Facility at Ohio State UniversitySample Treatment - For drug treatment: lysosome inhibitor CQ (50 mg/kg/day, i.p.) was formulated with PBS, and administrated to the mice after implantation for 2 weeks. After 2 weeks of drug treatment, all mice were euthanized, and the tissue were collected for RNA-seq.Nucleic Acid Extraction - RNA was harvested using Rneasy mini plus kit (Qiagen), 2 µg of total RNA was used for the construction of sequencing libraries.Sample Collection - Th lung cancer patient-derived xenograft (PDX) models were used to measure the efficacy of the drug combination. PDX #72-1001 were established by transplanting freshly removed tumor tissue into NSG female mouse flank subcutaneously following the protocol . Anesthetized NSG mice were inoculated with small pieces of tumor tissues (~1 mm3). Animals were treated with buprenorphine at 0.1 mg/kg for pain management. Tumor sizes were measured using a vernier caliper and the tumor volumes were calculated. Tumor size around 1200 mm3 considered as the end point for all experiments and no tumor exceeded the size in this study. At the end point, animals were sacrificed, tumors were excised and stored in liquid nitrogen with Serum-Free Cell freezing buffer.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Reads normalized using variance stabilizing transformation from deseq2Sequence Alignment - Raw fastq was uploaded to Qiagen RNAseq analysis portal for QC trimming and mapping. Options set to use QIAseq FastSelect RNA Lib Kit (N6-T RT + ODT-T RT primers) and mapped to Homo sapiens (GRCh38.noalt.106).UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAHomo sapiensYaogang ZhongDeliang GuoAmy WebbfalseRNA sequencing of non–small cell lung cancer (NSCLC) patient-derived xenograft (PDX) tissues following chloroquine (CQ) treatmentFunctional lysosomes are essential for tumor growth. CQ, a widely used lysosome inhibitor, has been combined with various other therapeutics for testing in cancer patients. However, no studies have reported enhanced antitumor effects from these treatments. To investigate how tumor cells survive CQ-mediated lysosome inhibition, we conducted transcriptome analysis using RNA sequencing (RNA-seq) on an adenocarcinoma NSCLC patient-derived xenograft (PDX #72-1001) to compare gene expression changes between control (vehicle) and CQ treatment groups.2025-12-05T00:00:00Z2025-12-05T20:21:46.915Z2025-11-14T13:27:30.338ZE-MTAB-16128ERP184449EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969