Dataset Information

Comparison of different normalization strategies for the analysis of glomerular microRNAs in IgA nephropathy.

ABSTRACT: Small nucleolar RNAs (snoRNAs) have been used for normalization in glomerular microRNA (miRNA) quantification without confirmation of validity. Our aim was to identify glomerular reference miRNAs in IgA nephropathy. We compared miRNAs in human paraffin-embedded renal biopsies from patients with cellular-crescentic IgA-GN (n?=?5; crescentic IgA-GN) and non-crescentic IgA-GN (n?=?5; IgA-GN) to mild interstitial nephritis without glomerular abnormalities (controls, n?=?5). Laser-microdissected glomeruli were used for expression profiling of 762 miRNAs by low-density TaqMan arrays (cards A and B). The comparison of different normalization methods (GeNormPlus, NormFinder, global mean and snoRNAs) in crescentic IgA-GN, IgA-GN and controls yielded similar results. However, levels of significance and the range of relative expression differed. In median, two normalization methods demonstrated similar results. GeNormPlus and NormFinder gave different top ranked reference miRNAs. Stability ranking for snoRNAs varied between cards A and B. In conclusion, we suggest the geometric mean of the most stable reference miRNAs found in GeNormPlus (miR-26b-5p), NormFinder (miR-28-5p) and snoRNAs (RNU44) as reference. It should be considered that significant differences could be missed using one particular normalization method. As a starting point for glomerular miRNA studies in IgA nephropathy we provide a library of miRNAs.

SUBMITTER: Bockmeyer CL

PROVIDER: S-EPMC4995590 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparison of different normalization strategies for the analysis of glomerular microRNAs in IgA nephropathy.

Bockmeyer Clemens L CL Säuberlich Karen K Wittig Juliane J Eßer Marc M Roeder Sebastian S SS Vester Udo U Hoyer Peter F PF Agustian Putri A PA Zeuschner Philip P Amann Kerstin K Daniel Christoph C Becker Jan U JU

Scientific reports 20160824

Small nucleolar RNAs (snoRNAs) have been used for normalization in glomerular microRNA (miRNA) quantification without confirmation of validity. Our aim was to identify glomerular reference miRNAs in IgA nephropathy. We compared miRNAs in human paraffin-embedded renal biopsies from patients with cellular-crescentic IgA-GN (n = 5; crescentic IgA-GN) and non-crescentic IgA-GN (n = 5; IgA-GN) to mild interstitial nephritis without glomerular abnormalities (controls, n = 5). Laser-microdissected glom ...[more]

PMID: 27553688

Similar Datasets

Project description:Background: In a previous study of patients with assumed benign IgA nephropathy (IgAN), we have shown that 18.6% develop a progressive clinical course, which was not predicted by any known clinical nor histopathological parameters (Knoop 2017). We aim to differentiate between future progressors and non-progressors with assumed benign IgAN by using glomerular transcriptomics from diagnostic kidney biopsies and to investigate whether this can identify drugs to be used in those patients. Methods: We included adult progressors (n=15) and patients with clinical remission (non-progressors, n=21) from our previously reported IgAN cohort. Glomerular cross-sections were obtained through laser-capture microdissection from 10µm archival kidney biopsy sections for mRNA sequencing, using the SMARTer Stranded Total RNA-Seq kit – Pico Input Mammalian (Clontech Laboratories, California, USA). Key results were validated in external cohorts and on the protein level with immunohistochemistry in the discovery cohort and an internal validation cohort. We also compared our transcriptomic findings with an external genome-wide association study (GWAS) dataset (Kiryluk 2021). Results: For the statistical analyses, we studied 8 progressors and 9 non-progressors. Based on the 1,240 differentially expressed glomerular genes from the initial kidney biopsies, we were able to identify future IgAN progressors and non-progressors using a two-component classifier. The classifier predicted disease progression with 88% accuracy, 75% sensitivity and 100% specificity (AUC=0.875), more accurate than the recommended International IgAN Prediction Tool in this specific patient cohort. Among our differentially expressed genes, 10 were also found in the GWAS dataset (Kiryluk 2021). We identified 45 drug targets in the DrugBank database, including angiotensinogen, a target of sparsentan, currently investigated as therapy in IgAN (NCT03762850 and NCT04663204). The findings on upregulation of angiotensinogen, which was independent of blood pressure, were validated in an internal IgAN validation cohort. Interestingly, complement activation did not play a major role in our data. Our work suggests that LXR, FXR and macrophage activation pathways could be critically involved in the inhibition of the progression of low-risk ccRCC. Furthermore, a 10-component classifier could support an early identification of apparently low-risk ccRCC patients.

Project description:BackgroundGlomerular deposition of C4d is a widely used biomarker for activation of the lectin pathway in the complement system and is reported to be associated with kidney progression in immunoglobulin A nephropathy (IgAN). The aim of this study was to evaluate whether glomerular C4d deposition, as a new biomarker, improves the prediction of kidney prognosis in IgAN.Study designSystematic review and meta-analysis.Setting & populationPatients with biopsy-proven primary IgAN without age limitations.Selection Criteria for Studies: Cross-sectional or cohort studies reporting the prevalence of glomerular C4d deposition or evaluating its association with IgAN progression.PredictorGlomerular C4d deposition.OutcomeComposite progression event of a >30% decline in estimated glomerular filtration rate or end-stage kidney disease.Results12 studies with 1,251 patients were included. The prevalence of glomerular C4d deposition was 34% (95% CI, 27%-41%), with large heterogeneity (I 2 = 86%; P < 0.001). Patients with C4d deposition had lower estimated glomerular filtration rates (mean difference [MD], -11.48; 95% CI, -18.27 to -4.70; P < 0.001) as well as higher urinary protein-creatinine ratios (MD, 0.87; 95% CI, 0.53-1.21; P < 0.001) or 24-hour urinary protein excretion (MD, 0.99; 95% CI, 0.50-1.47; P < 0.001) and higher risk for hypertension (relative risk [RR], 1.45; 95% CI, 1.06-1.99; P = 0.02) than patients without C4d deposition. Glomerular C4d deposition was associated with a high Oxford classification score, including M1, E1, S1, and T1/2 lesions (all P ≤ 0.006). Patients with C4d deposition had higher rates of use of renin-angiotensin system blockers and immunosuppressants. Glomerular C4d was found to be a risk factor for the composite kidney event (RR, 3.17; 95% CI, 2.29-4.40; P < 0.001; adjusted HR, 2.05; 95% CI, 1.53-2.76; P < 0.001) and end-stage kidney disease (RR, 4.37; 95% CI, 3.15-6.07; P < 0.001) without evidence of heterogeneity.LimitationsThe definition of positive C4d was not uniform and not all studies provided data about kidney outcomes.ConclusionsGlomerular C4d deposition is associated with an adverse prognosis and may be a useful biomarker of disease prediction in IgAN.

Dataset Information

Comparison of different normalization strategies for the analysis of glomerular microRNAs in IgA nephropathy.

Publications

Comparison of different normalization strategies for the analysis of glomerular microRNAs in IgA nephropathy.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure