Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing of non–small cell lung cancer (NSCLC) patient-derived xenograft (PDX) tissues following chloroquine (CQ) treatment

ABSTRACT: Functional 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.

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Homo sapiens

SUBMITTER: Amy Webb

PROVIDER: E-MTAB-16128 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA sequencing of non–small cell lung cancer (NSCLC) cell line H1299 following chloroquine (CQ) treatment

Project description:Functional 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 a NSCLC H1299 cell line to compare gene expression changes between control (vehicle) and CQ treatment groups.

2025-12-05 | E-MTAB-16126 | biostudies-arrayexpress

RNA sequencing of luminal breast cancer patient-derived xenografts (PDX) library to capture tumor heterogeneity and explore the mechanisms of resistance to CDK4/6 inhibitors

Project description:Combining CDK4/6 inhibitors (CDK4/6i) with endocrine therapy has proven clinically effective and represents now the first-line treatment for advanced Luminal Breast Cancer (LBC) patients. However, resistance to CDK4/6i almost invariably arises in these patients, emphasising the critical need to comprehend these mechanisms and develop new strategies to overcome resistance. We report on the generation and characterisation of a LBC PDX displaying acquired resistance to CDK4/6i palbociclib. Treating a sensitive luminal BC PDX with the CDK4/6i palbociclib revealed that, despite initial tumour shrinkage, some tumours might eventually regrow under drug treatment. RNA sequencing, followed by gene set enrichment analyses, unveiled that this PDX have become refractory to CDK4/6i, both at biological and molecular level.

2024-11-18 | E-MTAB-14085 | biostudies-arrayexpress

Whole transcriptome profiling of 79 patient derived xenograft (PDX) models

Project description:RNA-Seq and a species-specific mapping strategy were used to profile the human and mouse transcriptomes of tumour samples taken from 79 PDX models representing multiple cancer types (19 x breast, 37 x lung, 8 x colorectal, 7 x ovarian, 3 x endometrial, 2 x pancreatic, 2 x ampullary, 1 x leukaemia).

2016-03-01 | E-MTAB-3980 | biostudies-arrayexpress

Pharmacological inhibition of TREM1 attenuates patient derived xenograft models

Project description:To characterize the transcriptional changes in PDX tumors during TREM1 inhibition by microarray

2023-09-27 | E-MTAB-13257 | biostudies-arrayexpress

Medulloblastoma Patient-Derived Xenograft Proteomics

Project description:Proteomic and phosphoproteomic characterization of 20 orthotopic patient-derived xenograft models of medulloblastoma

2022-09-01 | PXD035070 | Pride

Melatonin mitigates Chloroquine-induced defects in porcine immature Sertoli cells

Project description:Chloroquine (CQ) could function as a lysosomotropic inhibitor to impair the autophagy-lysosome pathway, and is widely used to treat malarial, tumor and recently COVID-19. However, the effect of CQ treatment on porcine immature Sertoli cells (iSCs) remains unclear.;Here we showed that CQ treatment reduced iSCs viability in a dose-dependent manner. CQ treatment (20µM) of iSCs for 36h could elevate oxidative stress, damage mitochondrial function and promote apoptosis. Melatonin (MT) (10nM) could partially rescue CQ-induced phenotypic defects. Transcriptome profiling (RNA-seq) identified 1611 differentially expressed genes (DEGs) (776 up- and 835 down-regulated) (20µM CQ vs. DMSO control group), mainly involved in MAPK cascade, cell proliferation/apoptosis, HIF-1, PI3K-Akt and lysosome signaling pathways. In contrast, MT addition identified only 467 (224 up- and 243 down-regulated) DEGs (CQ+MT vs. DMSO), enriched in cell cycle, regulation of apoptotic process, lysosome and reproduction, respectively.Collectively, CQ treatment could impair porcine iSC viability by deranging apoptosis- and autophagy related signaling pathways, which could be partially rescued by MT supplementation.

2024-07-06 | GSE180995 | GEO

Affymetrix GeneChip Human Genome U133 Plus 2.0 array expression analysis of patient-derived xenografts in NSG mice

Project description:To provide a snapshot of gene expression for the cancer models distributed by The Jackson Laboratory as assayed using the Affymetrix HU133 platform.

2021-12-17 | E-MTAB-9063 | biostudies-arrayexpress

RNA-seq of subcutaneous patient-derived neuroblastoma xenografts (LU-NB-1) - Comparison of Prochlorperazine + Pitavastatin (PCZ+PIT) combination alone to one combined with standard-of-care COJEC protocol (PCZ+PIT+COJEC)

Project description:Neuroblastoma (NB) is a pediatric cancer characterized by significant heterogeneity and poor prognosis, specially in high-risk cases with MYCN amplification. Understanding the molecular response of neuroblastoma to different treatments can provide insights into potential therapeutic strategies. The aim of this experiment as to asses in vivo response of combination of Prochlorperazine and Pitavastatin alone or along standard of care chemotherapy COJEC. Neuroblastoma in vivo model was obtained via subcutaneous injection of human high-risk, MYCN-amplified neuroblastoma organoids in NSG mice (PDX, LU-NB-1). When tumors reached 200-300 mm3, mice were randomized into treatment groups: control (n=7), PCZ + PIT combination (n=7), and PCZ + PIT combination + COJEC (n=6). PCZ + PIT (total volume 50 μl; 5 mg/kg of each drug) was administered i.t. daily five times per week. COJEC treatment was given i.p. and consisted of five different chemotherapies distributed in cycles over one week; Day 1 – cisplatin (1mg/kg) + vincristine (0,25mg/kg), Day 3 – etoposide (4mg/kg) + cyclophosphamide (75mg/kg), Day 5 – carboplatin (25mg/kg). All COJEC drugs were dissolved in saline and combination treatment was suspended in vehicle consisting of 2.5% DMSO, 2.5% Tween 80, 40% PEG, 55% PBS solution. Control mice were treated with i.t. injections of the vehicle used for PCZ+PIT and i.p injections of saline. Treatment was administered for 10 days, after which mice were euthanized, tumor pieces were collected snap-frozen. Mouse weights and tumor volumes were measured three times per week throughout the study. RNA was extracted from snap-frozen tumor pieces and RNA sequencing was conducted.

2025-07-30 | E-MTAB-14902 | biostudies-arrayexpress

RNA-seq expression analysis of patient-derived xenografts in NSG mice

Project description:To provide a snapshot of gene expression for the cancer models distributed by The Jackson Laboratory.

2021-12-17 | E-MTAB-9153 | biostudies-arrayexpress

Stranded RNA-seq expression analysis of patient-derived xenografts in NSG mice

Project description:To provide a snapshot of gene expression for the cancer models distributed by The Jackson Laboratory.

2021-12-17 | E-MTAB-9204 | biostudies-arrayexpress