DNA expression analysis: serial analysis of gene expression, microarrays and kidney disease

Analysis of the gene expression profile of curcumin-treated kidney on endotoxin-induced renal inflammation

Acute or chronic kidney inflammation is closely related to the progress of kidney diseases. Curcumin, a yellow pigment present in the rhizome of turmeric (Curcuma longa L. Zingiberaceae), was found to be a potential anti-inflammatory agent. The present study aimed to investigate the effects and explore the protective mechanism of curcumin on lipopolysaccharide (LPS)-induced kidney inflammation in mice using gene chip and pathological technology. Nine SPF Kunming mice (aged 6-8 weeks, weighing 20-25 g) were divided into three groups. Saline and LPS were injected intraperitoneally in a normal control group and a model group, respectively. Mice in the treatment group were first injected with curcumin (5 mg/kg) for 3 days before being injected with LPS (5 mg/kg). Kidney tissues were harvested at 6 h after treatment. Parts of kidney were fixed with 10 % formaldehyde for HE, Periodic acid-Schiff staining, and immunohistochemistry. Affymetrix gene chips (mouse 430 chip) were used to detect the renal gene expression profile, and the results were analyzed using bioinformatics methods. The renal gene expression profile showed that there are 148 Affy IDs (up-down group) whose levels of gene expression were increased after LPS stimulation and decreased by curcumin treatment and that there are 133 Affy IDs (down-up group) exhibiting the opposite trend. In the differentially expressed genes of the up-down group, 21 Gene Ontology (GO) genes were selected by screening function (P ≤ 0.01). In the biological processes, most of the genes were found to be related to the genes of regulation of macrophage activation and macrophage activation-associated genes. In the cellular localization, there were four functional GO genes (P ≤ 0.01); in the molecular structure, there were seven functional GO genes (P ≤ 0.01). In the down-up group, there were functional GO genes (P ≤ 0.01) and one functional GO gene (P ≤ 0.01) in the biological process and the cellular localization, respectively. Macrophage infiltration could be observed as early as 6 h after LPS stimulation. Pretreatment with 5 mg/kg of curcumin significantly decreased the macrophage infiltration. At 6 h after LPS injection, significant decreased expression of M6PRBP-1 and NEDD-4 was observed in renal tissue. On the other hand, pretreatment with curcumin significantly increased renal M6PRBP-1 and NEDD-4 expression. In this study, we also found the signaling pathway and the possible target gene of the protective effects of curcumin on endotoxin-induced renal inflammation. The kidney gene expression profile in the inflammatory state was clarified by using gene chip technology. Furthermore, we confirmed that curcumin treatment can change the gene expression profile.

Gene expression profiling in organ transplantation

Aim of Review. Huge effort is being made among the transplant community investigating novel biomarkers that enable transplant clinicians to identify patients at risk for allograft rejection or those who will develop tolerance so that immunosuppression could be safely minimized or even ideally withdrawn. Despite the important advances achieved in the identification of several potential biomarkers of tolerance, rejection, or both, validation and demonstration of their clinical utility still needs to be tested, which will need international cooperative networks. It is important to note that the reproducibility of differently expressed genes might be affected by many factors such as gene ranking and selection methods, inherent differences between types, and the choice of thresholds. However, because microarray analyses are expensive and time consuming and their statistical evaluation is often very difficult, gene expression analysis using the RTPCR method is nowadays recommended. Conclusions. In the field of organ transplantation, gene-expression-based decision might help in improving patient and graft outcome and there are a multitude of studies showing that gene-expression profiling is feasible.

Experimental approaches to the human renal transcriptome

The sum of RNA transcripts of a cell, organ structure, or organism can be referred to as transcriptome. An increasing number of studies report on specific and common alterations in the renal transcriptome in human nephropathies. In this review several challenges in transcriptomic analyses of the human kidney are discussed. This includes ways to approach the heterogeneity of the kidney itself as well as the diversity of renal diseases. Conventional and upcoming techniques for transcriptional profiling of minute tissue samples are presented, including so-called next generation sequencing and microRNA detection. Different tools to integrate transcriptomic data in a systematic context are discussed beside the current challenge to combine such results with data sets from other integrative biology technologies.

Functional genomic analysis of peripheral blood during early acute renal allograft rejection

BACKGROUND

Acute graft rejection is an important clinical problem in renal transplantation and an adverse predictor for long-term graft survival. Peripheral blood biomarkers that provide evidence of early graft rejection may offer an important option for posttransplant monitoring, optimize the utility of graft biopsy, and permit timely and effective therapeutic intervention to minimize the graft damage.

METHODS

In this feasibility study (n=58), we have used gene expression profiling in a case-control design to compare whole blood samples between normal subjects (n=20) and patients with (n=11) or without (n=22) biopsy-confirmed acute rejection (BCAR) or borderline changes (n=5).

RESULTS

A total of 183 probe sets representing 160 genes were differentially expressed (false discovery rate [FDR] <0.01) between subjects with or without BCAR, from which linear discriminant analysis and cross-validation identified an initial gene signature of 24 probe sets, and a more refined set of 11 probe sets found to classify subject samples correctly. Cross-validation suggested an out-of-sample sensitivity of 73% and specificity of 91% for identification of samples with or without BCAR. An increase in classifier gene expression correlated closely with acute rejection during the first 3 months posttransplant. Biological evaluation indicated that the differentially expressed genes encompassed processes related to immune response, signal transduction, and cytoskeletal reorganization.

CONCLUSION

Preliminary evidence indicates that gene expression in the peripheral blood may yield a relevant measure for the occurrence of BCAR and offer a potential tool for immunologic monitoring. These results now require confirmation in a larger cohort.

Urinary proteomics: a tool to discover biomarkers of kidney diseases

There is intense interest in applying proteomics to urine analysis in order to promote a better understanding of kidney disease processes, develop new biomarkers for diagnosis and detect early factors that contribute to end-stage renal diseases. This interest creates numerous opportunities as well as challenges. To fulfill this task, proteomics requires, in its different stages of realization, various technological platforms with high sensitivity, high throughput and large automation ability. In this review, we will give an overview of promising proteomic methods that can be used for analyzing urinary proteome and detecting biomarkers for different kidney diseases. Furthermore, we will focus on the current status and future directions in investigating kidney diseases using urinary proteomics.

Profiling gene expression in kidney development

Rapid determination of the expression levels of all genes can be achieved with microarrays. This technology is beginning to revolutionize the study of kidney development. Genome-wide expression studies of the developing rat, mouse and human kidneys have found thousands of expressed genes, with many hundreds showing changes in expression as a function of developmental time. The resulting gene expression profiles provide an important discovery function, identifying new genes and pathways not previously implicated in kidney organogenesis. In combination with microdissection techniques, microarrays further extend global gene expression analysis to discrete components or cell types within the kidney. The resulting detailed molecular portrait of normal kidney development provides a baseline for studies of the many mouse mutants available with abnormal kidney development.

Gene expression profiling of anti-GBM glomerulonephritis model: the role of NF-kappaB in immune complex kidney disease

BACKGROUND

Immune complexes may cause an irreversible onset of chronic renal disease. Most patients with chronic renal disease undergo a final common pathway, marked by glomerulosclerosis and interstitial fibrosis. We attempted to draw a molecular map of anti-glomerular basement membrane (GBM) glomerulonephritis in mice using oligonucleotide microarray technology.

METHODS

Kidneys were harvested at days 1, 3, 7, 11, and 16 after inducing glomerulonephritis by using anti-GBM antibody. In parallel with examining the biochemical and histologic changes, gene expression profiles were acquired against five pooled control kidneys. Gene expression levels were cross-validated by either reverse transcription-polymerase chain reaction (RT-PCR), real-time PCR, or immunohistochemistry.

RESULTS

Pathologic changes in anti-GBM glomerulonephritis were confirmed in both BALB/c and C57BL/6 strains. Among the 13,680 spotted 65mer oligonucleotides, 1112 genes showing significant temporal patterns by permutation analysis of variance (ANOVA) with multiple testing correction [false discovery ratio (FDR) < 0.05] were chosen for cluster analysis. From the expression profile, acute inflammatory reactions characterized by the elevation of various cytokines, including interleukin (IL)-1 and IL-6, were identified within 3 days of disease onset. After 7 days, tissue remodeling response was prominent with highly induced extracellular-matrix (ECM) genes. Although cytokines related to lymphocyte activation were not detected, monocyte or mesangial cell proliferation-related genes were increased. Tumor necrosis factor-alpha (TNF-alpha) and nuclear factor-kappaB (NF-kappaB) pathway were consistently activated along the entire disease progression, inducing various target genes like complement 3, IL-1b, IL-6, Traf1, and Saa1.

CONCLUSION

We made a large-scale gene expression time table for mouse anti-GBM glomerulonephritis model, providing a comprehensive overview on the mechanism governing the initiation and the progression of inflammatory renal disease.

A comparative analysis of transcript abundance using SAGE and Affymetrix arrays

A number of methods are currently used for gene expression profiling. They differ in scale, economy and sensitivity. We present the results of a direct comparison between serial analysis of gene expression (SAGE) and the Barley1 Affymetrix GeneChip. Both technology platforms were used to obtain quantitative measurements of transcript abundance using identical RNA samples and assessed for their ability to quantify differential gene expression. For SAGE, a total of 82,122 tags were generated from two independent libraries representing whole developing barley caryopsis and dissected embryos. The Barley1 GeneChip contains 22,791 probe sets. Results obtained from both methods are generally comparable, indicating that both will lead to similar conclusions regarding transcript levels and differential gene expression. However, excluding singletons, 24.4% of the unique SAGE tags had no corresponding probe set on the Barley1 array indicating that a broader snapshot of gene expression was obtained by SAGE. Discrepancies were observed for a number of "genes" and these are discussed.