A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds

BACKGROUND: Microarrays provide a means to simultaneously examine the gene expression of the entire transcriptome in a single sample. Many studies have highlighted the need for novel software and statistical approaches to assess the measured gene expression. Less attention has been directed toward whether genes considered undetectable by microarray can be detected by other strategies or whether these genes can provide accurate gene expression determinations. In the kidney this is a concern for genes such as cytokines which dramatically influence the immune response but are often considered low abundance genes produced by a small number of cells. RESULTS: Using both publicly available and our own microarray datasets we analyzed the detection p-value and detection call values for 81 human kidney samples run on the U133A or U133Plus2.0 Affymetrix microarrays (Affymetrix, Santa Clara, CA). For the cytokine genes, the frequency of detection in each sample group (normal, transplant and renal cell carcinoma) was examined and revealed that a majority of cytokine related genes are not detectable in human kidney by microarray. Using a subset of 29 Mayo transplant samples, a group of seven transplant-related cytokines and eight non-cytokine genes were evaluated by real-time PCR (rt-PCR). For these 15 genes we compared the impact of decreasing microarray detection frequency with the changes in gene expression observed by both microarray and rt-PCR. We found that as microarray detection frequency decreased the correlation between microarray and rt-PCR data also decreased. CONCLUSION: We conclude that, when analyzing microarray data from human kidney samples, genes generally expressed at low abundance (i.e. cytokines) should be evaluated with more sensitive approaches such as rt-PCR. In addition, our data suggest that the use of detection frequency cutoffs for inclusion or exclusion of microarray data may be appropriate when comparing microarray and rt-PCR gene expression data and p-value calculations

Factors at de novo donorâ specific antibody initial detection associated with allograft loss: a multicenter study

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149234/1/tri13395-sup-0001-FigS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149234/2/tri13395_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149234/3/tri13395.pd

Determinants of Discard of Expanded Criteria Donor Kidneys: Impact of Biopsy and Machine Perfusion

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73820/1/j.1600-6143.2008.02157.x.pd

Clinical and kidney structural characteristics of living kidney donors with nephrolithiasis and their long-term outcomes

Background: Nephrolithiasis in living kidney donors is concerning due to the potential impact on long-term postdonation kidney function. Methods: We performed a cohort study of living kidney donors from 2 centers with a baseline computed tomography scan and implantation renal biopsy. Donors (\u3e5 y since donation) completed a follow-up survey or underwent chart review to assess eGFR and incident hypertension. Stone formers were classified as symptomatic if they had a past symptomatic episode or asymptomatic if only incidental radiographic kidney stones were identified during donor evaluation. We compared baseline clinical, imaging, and biopsy characteristics by stone former status including review of metabolic evaluations in stone formers. Long-term risks of renal complications (low eGFR and hypertension) by stone former status were evaluated. Results: There were 12 symptomatic and 76 asymptomatic stone formers among 866 donors. Overall, baseline clinical characteristics and implantation biopsy findings were similar between stone formers and non-stone formers. After a median follow-up of 10 y, stone former status was not associated with eGFR \u3c60 mL/min/1.73 m2, eGFR \u3c45 mL/min/1.73 m Conclusions: Both asymptomatic and symptomatic SF have favorable histology findings at baseline. Long-term kidney outcomes were favorable in select stone formers with no evident increased long-term risk for decreased kidney function or hypertension after donation

Race-free estimated glomerular filtration rate equation in kidney transplant recipients:development and validation study

OBJECTIVE: To compare the performance of a newly developed race-free kidney recipient specific glomerular filtration rate (GFR) equation with the three current main equations for measuring GFR in kidney transplant recipients.DESIGN: Development and validation study SETTING: 17 cohorts in Europe, the United States, and Australia (14 transplant centres, three clinical trials).PARTICIPANTS: 15 489 adults (3622 in development cohort (Necker, Saint Louis, and Toulouse hospitals, France), 11 867 in multiple external validation cohorts) who received kidney transplants between 1 January 2000 and 1 January 2021.MAIN OUTCOME MEASURE: The main outcome measure was GFR, measured according to local practice. Performance of the GFR equations was assessed using P 30 (proportion of estimated GFR (eGFR) within 30% of measured GFR (mGFR)) and correct classification (agreement between eGFR and mGFR according to GFR stages). The race-free equation, based on creatinine level, age, and sex, was developed using additive and multiplicative linear regressions, and its performance was compared with the three current main GFR equations: Modification of Diet in Renal Disease (MDRD) equation, Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) 2009 equation, and race-free CKD-EPI 2021 equation. RESULTS: The study included 15 489 participants, with 50 464 mGFR and eGFR values. The mean GFR was 53.18 mL/min/1.73m 2 (SD 17.23) in the development cohort and 55.90 mL/min/1.73m 2 (19.69) in the external validation cohorts. Among the current GFR equations, the race-free CKD-EPI 2021 equation showed the lowest performance compared with the MDRD and CKD-EPI 2009 equations. When race was included in the kidney recipient specific GFR equation, performance did not increase. The race-free kidney recipient specific GFR equation showed significantly improved performance compared with the race-free CKD-EPI 2021 equation and performed well in the external validation cohorts (P 30 ranging from 73.0% to 91.3%). The race-free kidney recipient specific GFR equation performed well in several subpopulations of kidney transplant recipients stratified by race (P 30 73.0-91.3%), sex (72.7-91.4%), age (70.3-92.0%), body mass index (64.5-100%), donor type (58.5-92.9%), donor age (68.3-94.3%), treatment (78.5-85.2%), creatinine level (72.8-91.3%), GFR measurement method (73.0-91.3%), and timing of GFR measurement post-transplant (72.9-95.5%). An online application was developed that estimates GFR based on recipient's creatinine level, age, and sex (https://transplant-prediction-system.shinyapps.io/eGFR_equation_KTX/). CONCLUSION: A new race-free kidney recipient specific GFR equation was developed and validated using multiple, large, international cohorts of kidney transplant recipients. The equation showed high accuracy and outperformed the race-free CKD-EPI 2021 equation that was developed in individuals with native kidneys.TRIAL REGISTRATION: ClinicalTrials.gov NCT05229939.</p

The Banff 2019 Kidney Meeting Report (I): Updates on and clarification of criteria for T cell– and antibody-mediated rejection

The XV. Banff conference for allograft pathology was held in conjunction with the annual meeting of the American Society for Histocompatibility and Immunogenetics in Pittsburgh, PA (USA) and focused on refining recent updates to the classification, advances from the Banff working groups, and standardization of molecular diagnostics. This report on kidney transplant pathology details clarifications and refinements to the criteria for chronic active (CA) T cell–mediated rejection (TCMR), borderline, and antibody-mediated rejection (ABMR). The main focus of kidney sessions was on how to address biopsies meeting criteria for CA TCMR plus borderline or acute TCMR. Recent studies on the clinical impact of borderline infiltrates were also presented to clarify whether the threshold for interstitial inflammation in diagnosis of borderline should be i0 or i1. Sessions on ABMR focused on biopsies showing microvascular inflammation in the absence of C4d staining or detectable donor-specific antibodies; the potential value of molecular diagnostics in such cases and recommendations for use of the latter in the setting of solid organ transplantation are presented in the accompanying meeting report. Finally, several speakers discussed the capabilities of artificial intelligence and the potential for use of machine learning algorithms in diagnosis and personalized therapeutics in solid organ transplantation

Computational Biology: Modeling Chronic Renal Allograft Injury

New approaches are need to develop more effective interventions to prevent long-term rejection of organ allografts. Computational biology provides a powerful tool to assess the large amount of complex data that is generated in longitudinal studies in this area. This manuscript outlines how our two groups are using mathematical modeling to analyze predictors of graft loss using both clinical and experimental data and how we plan to expand this approach to investigate specific mechanisms of chronic renal allograft injury

A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds

Abstract Background Microarrays provide a means to simultaneously examine the gene expression of the entire transcriptome in a single sample. Many studies have highlighted the need for novel software and statistical approaches to assess the measured gene expression. Less attention has been directed toward whether genes considered undetectable by microarray can be detected by other strategies or whether these genes can provide accurate gene expression determinations. In the kidney this is a concern for genes such as cytokines which dramatically influence the immune response but are often considered low abundance genes produced by a small number of cells. Results Using both publicly available and our own microarray datasets we analyzed the detection p-value and detection call values for 81 human kidney samples run on the U133A or U133Plus2.0 Affymetrix microarrays (Affymetrix, Santa Clara, CA). For the cytokine genes, the frequency of detection in each sample group (normal, transplant and renal cell carcinoma) was examined and revealed that a majority of cytokine related genes are not detectable in human kidney by microarray. Using a subset of 29 Mayo transplant samples, a group of seven transplant-related cytokines and eight non-cytokine genes were evaluated by real-time PCR (rt-PCR). For these 15 genes we compared the impact of decreasing microarray detection frequency with the changes in gene expression observed by both microarray and rt-PCR. We found that as microarray detection frequency decreased the correlation between microarray and rt-PCR data also decreased. Conclusion We conclude that, when analyzing microarray data from human kidney samples, genes generally expressed at low abundance (i.e. cytokines) should be evaluated with more sensitive approaches such as rt-PCR. In addition, our data suggest that the use of detection frequency cutoffs for inclusion or exclusion of microarray data may be appropriate when comparing microarray and rt-PCR gene expression data and p-value calculations.</p

Identification and characterization of kidney transplants with good glomerular filtration rate at 1 year but subsequent progressive loss of renal function

Background. After the first year after kidney transplantation, 3% to 5% of grafts fail each year but detailed studies of how grafts progress to failure are lacking. This study aimed to analyze the functional stability of kidney transplants between 1 and 5 years after transplantation and to identify initially well-functioning grafts with progressive decline in allograft function. Methods. The study included 788 adult conventional kidney transplants performed at the Mayo Clinic Rochester between January 2000 and December 2005 with a minimum graft survival and follow-up of 2.6 years. The modification of diet in renal disease equation for estimating glomerular filtration rate (eGFR(MDRD)) was used to calculate the slope of renal function over time using all available serum creatinine values between 1 and 5 years after transplantation. Results. Most transplants demonstrated good function (eGFR(MDRD) &amp;gt;= 40 mL/min) at 1 year with positive eGFR(MDRD) slope between 1 and 5 years after transplantation. However, a subset of grafts with 1-year eGFR(MDRD) &amp;gt;= 40 mL/min exhibited strongly negative eGFR(MDRD) slope between 1 and 5 years suggestive of progressive loss of graft function. Forty-one percent of this subset reached graft failure during follow-up, accounting for 69% of allograft failures occurring after 2.5 years after transplantation. This pattern of progressive decline in estimated glomerular filtration rate despite good early function was associated with but not fully attributable to factors suggestive of enhanced antidonor immunity. Conclusions. Longitudinal analysis of serial estimated glomerular filtration ratemeasurements identifies initially well-functioning kidney transplants at high risk for subsequent graft loss. For this subset, further studies are needed to identify modifiable causes of functional decline