Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Upregulated stromal EGFR and vascular remodeling in human NSCLC murine models (xenografts) of VEGF inhibitor resistance

ABSTRACT: The mechanisms by which tumors develop resistance to angiogenesis inhibitors, and the relative contributions of tumor cells and stroma to resistance, are not completely understood. We developed three human lung adenocarcinoma murine models of resistance to the VEGF inhibitor bevacizumab and, using species-specific profiling, separately investigated tumor cell and stromal molecules associated with resistance. Gene expression changes associated with acquired resistance occurred predominantly in stromal (mouse) and not tumor (human) cells. Components of the EGFR and FGFR2 pathways were significantly upregulated in stroma, but not in tumor cells. Increased activated EGFR was detected on pericytes of xenografts that acquired resistance and on endothelium of tumors with relative primary resistance. Acquired resistance was associated with a pattern of pericyte-covered, normalized revascularization, whereas tortuous, uncovered vessels were observed in relative primary resistance. Dual targeting of VEGF and EGFR pathways with bevacizumab and erlotinib, or the VEGFR/EGFR inhibitor vandetanib, reduced pericyte coverage and increased progression-free survival. These findings demonstrate that alterations in tumor stromal pathways, including EGFR and FGFR2, are associated with, and may contribute to VEGF inhibitor resistance and that targeting these pathways may improve therapeutic efficacy. Understanding stromal signaling may be critical for developing biomarkers for angiogenesis inhibitors and improving combination regimens. To identify changes in stromal and tumor gene expression associated with acquired resistance to anti-VEGF therapy, we performed RNA microarray analyses comparing H1975 control (vehicle-treated) and BV-resistant (bevacizumab-treated until progression) xenografts (n=3 biologic replicates per group of treatment) using Illumina mouse (WG-6 v2) and human (WG-6 v3)-specific expression arrays. Probes in these arrays have been designed to minimize cross-species reactivity and consistent with this essentially no cross reactivity was observed in experiments mixing human and mouse cell lines.Total RNA was extracted from snap-frozen tissues using the mirVanaTM miRNA Isolation Kit (Ambion, Austin, TX) according to manufacturer’s protocol. Biotin labeled cRNA samples for hybridization were prepared by using Illumina Total Prep RNA Amplification Kit (Ambion Inc., Austin, TX). One microgram of total RNA was used for the synthesis of cDNA and followed by an amplification and biotin labeling. Each of 1.5 μg of biotinylated cRNAs was hybridized to both mouseWG-6 v2 and human WG-6v3 Expression BeadChips (Illumina®, San Diego, CA) at the same time, for analysis of murine and human transcriptomes. Signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Health care Bio-Sciences, Little Chalfont, UK). Gene expression data were collected by using Illumina bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina Inc.). Data were analyzed using the BRB-ArrayTools Version 3.7.0 Beta platform developed by Dr. Richard Simon and the BRB-Array Tools development team. A log base 2 transformation was applied to the data set prior to data normalization. A median array was selected as the reference array for normalization and statistical significance was set using a p<0.01. Genes differentially expressed between groups were determined applying univariate t-test with estimation of the false discovery rate (FDR). Genes were determined using selection criteria of a p<0.005 and a fold-change ≥1.5.

ORGANISM(S): Homo sapiens

SUBMITTER: Tina Cascone

PROVIDER: E-GEOD-26644 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Bevacizumab induces glioblastoma resistance in two in vivo xenograft models. Two cell lines were developed with acquired resistance to bevacizumab. Gene expression difference were analyzed between treated and untreated tumors. Purpose: Antiangiogenic therapy reduces vascular permeability and delays progression but may ultimately promote an aggressive treatment-resistant phenotype. The aim of the present study was to identify mechanisms responsible for glioblastoma resistance to antiangiogenic therapy. Experimental Design: Glioma stem cell (GSC) NSC11 and U87 cell lines with acquired resistance to bevacizumab were developed from orthotopic xenografts in nude mice treated with bevacizumab. Genome-wide analyses were used to identify changes in tumor subtype and specific factors associated with resistance. Results: Mice with established parental NSC11 and U87 cells responded to bevacizumab, whereas glioma cell lines derived at the time of acquired resistance to anti-VEGF therapy were resistant to bevacizumab and did not have prolongation of survival compared to untreated controls. Gene expression profiling comparing anti-VEGF therapy-resistant cell lines to untreated controls demonstrated an increase in genes associated with a mesenchymal origin, cellular migration/invasion, and inflammation. Gene Set Enrichment Analysis (GSEA) demonstrated that bevacizumab-treated tumors showed a highly significant correlation to published mesenchymal gene signatures. Mice bearing resistant tumors showed significantly greater infiltration of myeloid cells in NSC11 and U87 resistant tumors. Invasion-related genes were also upregulated in both NSC11 and U87 resistant cells, which had higher invasion rates in vitro compared with their respective parental cell lines. Conclusions: Our studies identify multiple pro-inflammatory factors associated with resistance and identify a proneural-to-mesenchymal transition (PMT) in tumors resistant to antiangiogenic therapy. Glioma cell lines were injected into the caudate of nude mice and were allowed to grow untreated (samples labeled control) or were treated with 10 mg/kg IP twice weekly with bevacizumab (samples labeled Avastin). At the time of animal death, tumor tissue from the mouse was removed, and RNA was isolated and analyzed using gene expression. U87R and NSC11R represent cells resistant to bevacizumab (Avastin).

Project description:Background. Bevacizumab, an antibody neutralizing Vascular Endothelial Growth Factor (VEGF), is licensed for the management of patients with advanced colon cancer. However, tumor biomarkers identifying the molecular tumor subsets most amenable to angiogenesis modulation are lacking. Patients and Methods. We profiled expession of 24526 genes by means of whole genome 24K DASL (c-DNA-mediated, Annealing, Selection and Ligation) arrays, (Illumina, CA) in 16 bevacizumab-treated patients with advanced colon cancer (Test set). Genes with correlation to 8-month Progression-free status were studied by means of qPCR in two independent colon cancer cohorts: 49 patients treated with bevacizumab+chemotherapy (Bevacizumab qPCR set) and 72 patients treated with chemotherapy only (Control qPCR set). Endpoints were best tumor response before metastasectomy (ORR) and progression-free survival (PFS). Results. Five genes were significantly correlated to 8-month progression-free status in the Test set: overexpression of KLF12 and downregulation of AGR2, ALDH6A1, MCM5, TFF2. In the two independent datasets, irinotecan- or oxaliplatin-based chemotherapy was administered as first-line treatment and metastasectomies were subsequently applied in 8-14% of patients. No prognostically significant gene classifier encompassing all five genes could be validated in the Bevacizumab or Control qPCR sets. The complex gene expression profile of all-low tumor (ALDH6A1+TFF2+MCM5) was strongly associated with ORR in the Bevacizumab qPCR set (ORR 85.7%, p=0.007), but not in the Control set (ORR 36.4%, p=0.747). The Odds Ratio for response for the all-low tumor (ALDH6A1+TFF2+MCM5) profile versus any other ALDH6A1+TFF2+MCM5 profile was 15 (p=0.018) in the Bevacizumab qPCR set but only 0.72 (p=0.63) in the Control set. The tumor expression profile of (KLF12-high+TFF2-low) was significantly associated with PFS only in the Bevacizumab qPCR set: bevacizumab-treated patients with (KLF12-high + TFF2-low) tumors had superior PFS (median 14 months, 95% CI 2-21) compared to patients with any other (KLF12+TFF2) expression profile (median PFS 7 months, 95% CI 5-10, p=0.021). The Hazard Ratio for disease progression for (KLF12-high + TFF2-low) versus any other KLF12+TFF2 expression profile was 2.92 (p=0.03) in the Validation and 1.29 (p=0.39) in the Control set. Conclusions. Our <three-stage> hypothesis-generating study failed to validate the prognostic significance of a five-gene classifier in mCRC patients. Exploratory analyses suggest two gene signatures that are potentially associated with bevazicumab benefit in patients with advanced colon cancer. 18 tumor tissue samples were analysed, no replicates

Dataset Information

Upregulated stromal EGFR and vascular remodeling in human NSCLC murine models (xenografts) of VEGF inhibitor resistance

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets