ArticleTransplantation2011
Gene expression changes are associated with loss of kidney graft function and interstitial fibrosis and tubular atrophy: diagnosis versus prediction.
Article in Transplantation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it, 29 citations in OpenAlex.
- Evaluation of gene expression classification studies: factors associated with classification performance.PloS one · 2014Pooled it
- Discovery of Biomarkers Related to Interstitial Fibrosis and Tubular Atrophy among Kidney Transplant Recipients by mRNA-Sequencing.Journal of personalized medicine · 2023Article
- Biopsy-Controlled Non-Invasive Quantification of Collagen Type VI in Kidney Transplant Recipients: A Post-Hoc Analysis of the MECANO Trial.Journal of clinical medicine · 2020Article
- N-Octanoyl-Dopamine inhibits cytokine production in activated T-cells and diminishes MHC-class-II expression as well as adhesion molecules in IFNγ-stimulated endothelial cells.Scientific reports · 2019Article
- Effects of DNA Methylation on Progression to Interstitial Fibrosis and Tubular Atrophy in Renal Allograft Biopsies: A Multi-Omics Approach.American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons · 2017Article
- Urinary MicroRNA as Biomarker in Renal Transplantation.American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons · 2017Review
- Meta-analysis approach as a gene selection method in class prediction: does it improve model performance? A case study in acute myeloid leukemia.BMC bioinformatics · 2017Article
- Article
- Epigenetics in Kidney Transplantation: Current Evidence, Predictions, and Future Research Directions.Transplantation · 2016Review
- Factors affecting the accuracy of a class prediction model in gene expression data.BMC bioinformatics · 2015Article
- Dendritic cells and macrophages in the kidney: a spectrum of good and evil.Nature reviews. Nephrology · 2014Review
- The urine microRNA profile may help monitor post-transplant renal graft function.Kidney international · 2014Article
- Identification of biomarkers to assess organ quality and predict posttransplantation outcomes.Transplantation · 2012Article
- Renal interstitial fibrosis: mechanisms and evaluation.Current opinion in nephrology and hypertension · 2012Review
- Upregulation of miR-142-3p in peripheral blood mononuclear cells of operationally tolerant patients with a renal transplant.Journal of the American Society of Nephrology : JASN · 2012Article
- Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes.Kidney international · 2011Article
- MicroRNA profiles in allograft tissues and paired urines associate with chronic allograft dysfunction with IF/TA.American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons · 2011Article
Corrections and comments
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
Abstract
backgroundLoss of kidney graft function due to interstitial fibrosis (IF) and tubular atrophy (TA) is the most common cause of kidney allograft loss.
methodsOne hundred one allograft tissues (26 samples with IF/TA, 17 normal allografts, and an independent biopsy group collected at 3 month [n=34] posttransplantation) underwent microarray analysis to identify early detection/diagnostic biomarkers of IF/TA. Profiling of 24 allograft biopsies collected at or after 9-month posttransplantation (range 9-18 months) was used for validation. Three-month posttransplantation biopsies were classified as IF/TA nonprogressors (group 1) or progressors (group 2) using graft function and histology at 9-month posttransplantation.
resultsWe identified 2223 differentially expressed probe sets between IF/TA and normal allograft biopsies using a Bonferroni correction. Genes up-regulated in IF/TA were primarily involved in pathways related to T-cell activation, natural killer cell-mediated cytotoxicity, and programmed cell death. A least absolute shrinkage and selection operator model was derived from the differentially expressed probe sets, resulting in a final model that included 10 probe sets and had 100% training set accuracy. The N-fold crossvalidated error was 2.4% (sensitivity 95.8% and specificity 100%). When 3-month biopsies were tested using the model, all the samples were classified as normal. However, evaluating gene expression of the 3-month biopsies and fitting a new penalized model, 100% sensitivity was observed in classifying the samples as group1 or 2. This model was evaluated in the sample set collected at or after 9-month posttransplantation.
conclusionsAn IF/TA gene expression signature was identified, and it was useful for diagnosis but not prediction. However, gene expression profiles at 3 months might predict IF/TA progression.
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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.