ArticlePLoS computational biology2010
Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 2 of them syntheses that pooled it.
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Who cites it
40 citing papers in PubMed, 2 syntheses or guidelines pooled it, 81 citations in OpenAlex.
- Identification of Candidate Biomarkers for Transplant Rejection from Transcriptome Data: A Systematic Review.Molecular diagnosis & therapy · 2019Pooled it
- A Computational Gene Expression Score for Predicting Immune Injury in Renal Allografts.PloS one · 2015Pooled it
- CCR7 and CD48 as Predicted Targets in Acute Rejection Related to M1 Macrophage after Pediatric Kidney Transplantation.Journal of immunology research · 2024Article
- Uncovering a novel role of focal adhesion and interferon-gamma in cellular rejection of kidney allografts at single cell resolution.Frontiers in immunology · 2023Article
- Identification of PDCD1 as a potential biomarker in acute rejection after kidney transplantationFrontiers in immunology · 2022Article
- Preliminary Investigation of the Biomarkers of Acute Renal Transplant Rejection Using Integrated Proteomics Studies, Gene Expression Omnibus Datasets, and RNA Sequencing.Frontiers in medicine · 2022Article
- Early-pregnancy prediction of risk for pre-eclampsia using maternal blood leptin/ceramide ratio: discovery and confirmation.BMJ open · 2021Article
- Imaging alloreactive T cells provides early warning of organ transplant rejection.JCI insight · 2021Article
- Computational Prediction of Biomarkers, Pathways, and New Target Drugs in the Pathogenesis of Immune-Based Diseases Regarding Kidney Transplantation Rejection.Frontiers in immunology · 2021Article
- Advanced Genomics-Based Approaches for Defining Allograft Rejection With Single Cell Resolution.Frontiers in immunology · 2021Review
- Approaches for Controlling Antibody-Mediated Allograft Rejection Through Targeting B Cells.Frontiers in immunology · 2021Review
- Precision annotation of digital samples in NCBI's gene expression omnibus.Scientific data · 2017Article
- Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data.Microbiome · 2017Article
- Tissue Non-Specific Genes and Pathways Associated with Diabetes: An Expression Meta-Analysis.Genes · 2017Article
- Assessment of Circulating Protein Signatures for Kidney Transplantation in Pediatric Recipients.Frontiers in medicine · 2017Article
- Advances in diagnostics for transplant rejection.Expert review of molecular diagnostics · 2016Review
- Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long-Term Outcomes.American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons · 2016Article
- Data standards can boost metabolomics research, and if there is a will, there is a way.Metabolomics : Official journal of the Metabolomic Society · 2016Review
- Antibody-mediated rejection in pediatric kidney transplantation: pathophysiology, diagnosis, and management.Drugs · 2015Review
- Computational Models for Transplant Biomarker Discovery.Frontiers in immunology · 2015Review
Corrections and comments
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Authors and funding
14 authors at 2 institutions in 1 country.
Funding
Abstract
Serum proteins are routinely used to diagnose diseases, but are hard to find due to low sensitivity in screening the serum proteome. Public repositories of microarray data, such as the Gene Expression Omnibus (GEO), contain RNA expression profiles for more than 16,000 biological conditions, covering more than 30% of United States mortality. We hypothesized that genes coding for serum- and urine-detectable proteins, and showing differential expression of RNA in disease-damaged tissues would make ideal diagnostic protein biomarkers for those diseases. We showed that predicted protein biomarkers are significantly enriched for known diagnostic protein biomarkers in 22 diseases, with enrichment significantly higher in diseases for which at least three datasets are available. We then used this strategy to search for new biomarkers indicating acute rejection (AR) across different types of transplanted solid organs. We integrated three biopsy-based microarray studies of AR from pediatric renal, adult renal and adult cardiac transplantation and identified 45 genes upregulated in all three. From this set, we chose 10 proteins for serum ELISA assays in 39 renal transplant patients, and discovered three that were significantly higher in AR. Interestingly, all three proteins were also significantly higher during AR in the 63 cardiac transplant recipients studied. Our best marker, serum PECAM1, identified renal AR with 89% sensitivity and 75% specificity, and also showed increased expression in AR by immunohistochemistry in renal, hepatic and cardiac transplant biopsies. Our results demonstrate that integrating gene expression microarray measurements from disease samples and even publicly-available data sets can be a powerful, fast, and cost-effective strategy for the discovery of new diagnostic serum protein biomarkers.
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