ArticleExperimental biology and medicine (Maywood, N.J.)2017
Whole transcriptome analysis identifies differentially regulated networks between osteosarcoma and normal bone samples.
Article in Experimental biology and medicine (Maywood, N.J.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 1 of them a synthesis that pooled it.
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Who cites it
78 citing papers in PubMed, 1 synthesis or guideline pooled it, 111 citations in OpenAlex.
- Meta-analysis of integrated ChIP-seq and transcriptome data revealed genomic regions affected by estrogen receptor alpha in breast cancer.BMC medical genomics · 2023Pooled it
- Immunoglobulin Superfamily Protein BTNL9 Functions as a Non-Canonical Transcriptional Regulator to Suppress NSCLC Through Cell Cycle and p53 Pathways.International journal of molecular sciences · 2026Article
- 5-hydroxymethylcytosine profiles in circulating cell-free DNA associate with disease status in patients with osteosarcoma.NPJ precision oncology · 2026Article
- Single-cell and multi-omics integrative modeling identifies mitochondrial gene HSPE1 as a therapeutic target in osteosarcoma.Journal of translational medicine · 2026Article
- SLC7A5 serves as a potential therapeutic target for osteosarcoma: a comprehensive analysis based on bioinformatics and experimental validation.American journal of cancer research · 2026Article
- Heterogeneity-based stratification identifies CKMT2 as a prognostic marker in osteosarcoma.Frontiers in cell and developmental biology · 2026Article
- UpregulatedImmunoTargets and therapy · 2026Article
- Establishment and Characterization of OS-MET-R-092: A Novel Patient-Derived Cell Culture from an Osteosarcoma Bone Metastasis.International journal of molecular sciences · 2025Article
- Single-cell sequencing uncovers sensory neuron-mediated CGRP signaling as a driver of sarcoma progression.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Osteosarcoma: A Comprehensive Morphological and Molecular Review with Prognostic Implications.Biology · 2025Review
- 5-hydroxymethylcytosine profiles in circulating cell-free DNA associate with disease status in patients with osteosarcoma.Research square · 2025Article
- Molecular and Glycosylation Pathways in Osteosarcoma: Tumor Microenvironment and Emerging Strategies Toward Personalized Oncology.Current issues in molecular biology · 2025Review
- BTNL9 exerts anti-cancer effects by inhibiting CDC20 to induce G2/M arrest in pancreatic cancer.World journal of gastrointestinal oncology · 2025Article
- Article
- Comparison of Differentially Expressed Genes in Human and Canine Osteosarcoma.Life (Basel, Switzerland) · 2025Article
- Causal effect of gut microbiota metabolic pathways on CSAG1 expression in chondrosarcoma: a mendelian randomization analysis.BMC cancer · 2025Article
- Article
- Role of arachidonic acid metabolism in osteosarcoma prognosis by integrating WGCNA and bioinformatics analysis.BMC cancer · 2025Article
- The Role of Radiosensitizing Drugs in Osteosarcoma Treatment: Mechanisms and Clinical Perspectives.Drug design, development and therapy · 2025Review
- Article
18 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We performed whole transcriptome analysis of osteosarcoma bone samples. Initially, we sequenced total RNA from 36 fresh-frozen samples (18 tumoral bone samples and 18 non-tumoral paired samples) matching in pairs for each osteosarcoma patient. We also performed independent gene expression analysis of formalin-fixed paraffin-embedded samples to verify the RNAseq results. Formalin-fixed paraffin-embedded samples allowed us to analyze the effect of chemotherapy. Data were analyzed with DESeq2, edgeR and Reactome packages of R. We found 5365 genes expressed differentially between the normal bone and osteosarcoma tissues with an FDR below 0.05, of which 3399 genes were upregulated and 1966 were downregulated. Among those genes, BTNL9, MMP14, ABCA10, ACACB, COL11A1, and PKM2 were expressed differentially with the highest significance between tumor and normal bone. Functional annotation with the reactome identified significant changes in the pathways related to the extracellular matrix degradation and collagen biosynthesis. It was suggested that chemotherapy may induce the modification of ECM with important collagen biosynthesis. Taken together, our results indicate that changes in the degradation of extracellular matrix seem to be an important mechanism of osteosarcoma and efficient chemotherapy induces the genes related to bone formation. Impact statement Osteosarcoma is a rare disease but it is of interest to many scientists all over the world because the current standard treatment still has poor results. We sequenced total RNA from 36 fresh-frozen paired samples (18 tumoral bone samples and 18 non-tumoral paired samples) from osteosarcoma patients. We found that differences in the gene expressions between the normal and affected bones reflected the changes in the regulation of the degradation of collagen and extracellular matrix. We believe that these findings contribute to the understanding of OS and suggest ideas for further studies.
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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.