ArticleGenome medicine2009
Networking of differentially expressed genes in human cancer cells resistant to methotrexate.
Article in Genome medicine, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 72 citations in OpenAlex.
- BMI-dependent prognostic role of EEF1G in breast cancer: A 15-year follow-up of the Guangzhou Breast Cancer Cohort Study.Cancer medicine · 2025Article
- Citrus flavonoids for overcoming breast cancer resistance to methotrexate: identification of potential targets of nobiletin and sinensetin.Discover oncology · 2025Article
- Identifying squalene epoxidase as a metabolic vulnerability in high-risk osteosarcoma using an artificial intelligence-derived prognostic index.Clinical and translational medicine · 2024Article
- Identification of Prognostic Markers and Potential Therapeutic Targets using Gene Expression Profiling and Simulation Studies in Pancreatic Cancer.Current computer-aided drug design · 2024Article
- A targetable pathway to eliminate TRA-1-60+/TRA-1-81+ chemoresistant cancer cells.Journal of molecular cell biology · 2023Article
- Blood-Based Diagnosis and Risk Stratification of Patients with Pancreatic Intraductal Papillary Mucinous Neoplasm (IPMN).Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Article
- Identification of the methotrexate resistance-related diagnostic markers in osteosarcoma via adaptive total variation netNMF and multi-omics datasets.Frontiers in genetics · 2023Article
- Chemotherapy induces ACE2 expression in breast cancer via the ROS-AKT-HIF-1α signaling pathway: a potential prognostic marker for breast cancer patients receiving chemotherapy.Journal of translational medicine · 2022Article
- Arylamine N-acetyltransferase 1 deficiency inhibits drug-induced cell death in breast cancer cells: switch from cytochrome C-dependent apoptosis to necroptosis.Breast cancer research and treatment · 2022Article
- BOSO: A novel feature selection algorithm for linear regression with high-dimensional data.PLoS computational biology · 2022Article
- The role of lncRNA H19 in tumorigenesis and drug resistance of human Cancers.Frontiers in genetics · 2022Review
- Single-cell sequencing reveals the potential oncogenic expression atlas of human iPSC-derived cardiomyocytes.Biology open · 2021Article
- The advances of methotrexate resistance in rheumatoid arthritis.Inflammopharmacology · 2020Review
- Article
- Trimodal distribution of arylamine N-acetyltransferase 1 mRNA in breast cancer tumors: association with overall survival and drug resistance.BMC genomics · 2018Article
- Exploring the key genes and pathways of side population cells in human osteosarcoma using gene expression array analysis.Journal of orthopaedic surgery and research · 2018Article
- Curcumin may serve an anticancer role in human osteosarcoma cell line U-2 OS by targeting ITPR1.Oncology letters · 2018Article
- Enhanced and Selective Antiproliferative Activity of Methotrexate-Functionalized-Nanocapsules to Human Breast Cancer Cells (MCF-7).Nanomaterials (Basel, Switzerland) · 2018Article
- Comparative proteomics analysis of human osteosarcoma by 2D DIGE with MALDI-TOF/TOF MS.Journal of bone oncology · 2016Article
- Vascular endothelial growth factor A as predictive marker for mTOR inhibition in relapsing high-grade serous ovarian cancer.BMC systems biology · 2016Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe need for an integrated view of data obtained from high-throughput technologies gave rise to network analyses. These are especially useful to rationalize how external perturbations propagate through the expression of genes. To address this issue in the case of drug resistance, we constructed biological association networks of genes differentially expressed in cell lines resistant to methotrexate (MTX).
methodsSeven cell lines representative of different types of cancer, including colon cancer (HT29 and Caco2), breast cancer (MCF-7 and MDA-MB-468), pancreatic cancer (MIA PaCa-2), erythroblastic leukemia (K562) and osteosarcoma (Saos-2), were used. The differential expression pattern between sensitive and MTX-resistant cells was determined by whole human genome microarrays and analyzed with the GeneSpring GX software package. Genes deregulated in common between the different cancer cell lines served to generate biological association networks using the Pathway Architect software.
resultsDikkopf homolog-1 (DKK1) is a highly interconnected node in the network generated with genes in common between the two colon cancer cell lines, and functional validations of this target using small interfering RNAs (siRNAs) showed a chemosensitization toward MTX. Members of the UDP-glucuronosyltransferase 1A (UGT1A) family formed a network of genes differentially expressed in the two breast cancer cell lines. siRNA treatment against UGT1A also showed an increase in MTX sensitivity. Eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) was overexpressed among the pancreatic cancer, leukemia and osteosarcoma cell lines, and siRNA treatment against EEF1A1 produced a chemosensitization toward MTX.
conclusionsBiological association networks identified DKK1, UGT1As and EEF1A1 as important gene nodes in MTX-resistance. Treatments using siRNA technology against these three genes showed chemosensitization toward MTX.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.