Repuncturing the renal biopsy: strategies for molecular diagnosis in nephrology

Probing Renal Microstructure and Function with Advanced Diffusion MRI: Concepts, Applications, Challenges, and Future Directions

Diffusion measurements in the kidney are affected not only by renal microstructure but also by physiological processes (i.e., glomerular filtration, water reabsorption, and urine formation). Because of the superposition of passive tissue diffusion, blood perfusion, and tubular pre-urine flow, the limitations of the monoexponential apparent diffusion coefficient (ADC) model in assessing pathophysiological changes in renal tissue are becoming apparent and motivate the development of more advanced diffusion-weighted imaging (DWI) variants. These approaches take advantage of the fact that the length scale probed in DWI measurements can be adjusted by experimental parameters, including diffusion-weighting, diffusion gradient directions and diffusion time. This forms the basis by which advanced DWI models can be used to capture not only passive diffusion effects, but also microcirculation, compartmentalization, tissue anisotropy. In this review, we provide a comprehensive overview of the recent advancements in the field of renal DWI. Following a short introduction on renal structure and physiology, we present the key methodological approaches for the acquisition and analysis of renal DWI data, including intravoxel incoherent motion (IVIM), diffusion tensor imaging (DTI), non-Gaussian diffusion, and hybrid IVIM-DTI. We then briefly summarize the applications of these methods in chronic kidney disease and renal allograft dysfunction. Finally, we discuss the challenges and potential avenues for further development of renal DWI. LEVEL OF EVIDENCE: 5 TECHNICAL EFFICACY: Stage 2.

Molecular architecture of proliferative lupus nephritis as elucidated using 50-plex imaging mass cytometry proteomics

Due to unique advantages that allow high-dimensional tissue profiling, we postulated imaging mass cytometry (IMC) may shed novel insights on the molecular makeup of proliferative lupus nephritis (LN). This study interrogates the spatial expression profiles of 50 target proteins in LN and control kidneys. Proliferative LN glomeruli are marked by podocyte loss with immune infiltration dominated by CD45RO+, HLA-DR+ memory CD4 and CD8 T-cells, and CD163+ macrophages, with similar changes in tubulointerstitial regions. Macrophages are the predominant HLA-DR expressing antigen presenting cells with little expression elsewhere, while macrophages and T-cells predominate cellular crescents. End-stage sclerotic glomeruli are encircled by an acellular fibro-epithelial Bowman's space surrounded by immune infiltrates, all enmeshed in fibronectin. Proliferative LN also shows signs indicative of epithelial to mesenchymal plasticity of tubular cells and parietal epithelial cells. IMC enabled proteomics is a powerful tool to delineate the spatial architecture of LN at the protein level.

Using Imaging Mass Cytometry to Define Cell Identities and Interactions in Human Tissues

In the evolving landscape of highly multiplexed imaging techniques that can be applied to study complex cellular microenvironments, this review characterizes the use of imaging mass cytometry (IMC) to study the human kidney. We provide technical details for antibody validation, cell segmentation, and data analysis specifically tailored to human kidney samples, and elaborate on phenotyping of kidney cell types and novel insights that IMC can provide regarding pathophysiological processes in the injured or diseased kidney. This review will provide the reader with the necessary background to understand both the power and the limitations of IMC and thus support better perception of how IMC analysis can improve our understanding of human disease pathogenesis and can be integrated with other technologies such as single cell sequencing and proteomics to provide spatial context to cellular data.

Kidney Injury Monitoring in Tobramycin-Treated Rhesus Monkeys: Supplementing Urinary Kidney Biomarkers With Kidney Biopsy Gene Expression Profiling

Kidney biopsies are used sparingly to diagnose kidney injury in the clinic. Here we have conducted a small exploratory study to directly compare the low-grade kidney injury monitoring performance of serum safety biomarkers, novel urine safety biomarkers, microscopic histopathology and targeted gene expression alterations in kidney biopsy specimens in rhesus monkeys treated with tobramycin. Targeted gene expression increases were observed in the kidney biopsy samples and whole kidney sections for kidney injury molecule 1 (KIM-1), clusterin (CLU), osteopontin (OPN) messenger RNA transcripts. In addition, increases of the urinary kidney safety protein biomarkers including KIM-1, CLU, OPN were also observed. These increases in gene expression and urinary protein end point were in concordance with the eventual low-grade kidney lesions seen in terminal tissue sections. In contrast, conventional serum biomarkers blood urea nitrogen and serum creatinine were not as sensitive in monitoring kidney injury. Although these data do not support routinely adding kidney biopsies to regular toxicology studies, they provide evidence on the value and limitations of incorporating gene expression profiling on kidney biopsy specimens, further underscore the value of urinary kidney safety biomarkers for improved low-grade kidney injury monitoring, and open the door for future definitive studies.

Feasibility of quantitative susceptibility mapping (QSM) of the human kidney

Objective

To evaluate the feasibility of in-vivo quantitative susceptibility mapping (QSM) of the human kidney.

Methods

An axial single-breath-hold 3D multi-echo sequence (acquisition time 33 s) was completed on a 3 T-MRI-scanner (Magnetom Prisma, Siemens Healthineers, Erlangen, Germany) in 19 healthy volunteers. Graph-cut-based unwrapping combined with the T₂*-IDEAL approach was performed to remove the chemical shift of fat and to quantify QSM of the upper abdomen. Mean susceptibility values of the entire, renal cortex and medulla in both kidneys and the liver were determined and compared. Five subjects were measured twice to examine the reproducibility. One patient with severe renal fibrosis was included in the study to evaluate the potential clinical relevance of QSM.

Results

QSM was successful in 17 volunteers and the patient with renal fibrosis. Anatomical structures in the abdomen were clearly distinguishable by QSM and the susceptibility values obtained in the liver were comparable to those found in the literature. The results showed a good reproducibility. Besides, the mean renal QSM values obtained in healthy volunteers (0.04 ± 0.07 ppm for the right and − 0.06 ± 0.19 ppm for the left kidney) were substantially higher than that measured in the investigated fibrotic kidney (− 0.43 ± − 0.02 ppm).

Conclusion

QSM of the human kidney could be a promising approach for the assessment of information about microscopic renal tissue structure. Therefore, it might further improve functional renal MR imaging.

Electronic supplementary material

The online version of this article (10.1007/s10334-020-00895-9) contains supplementary material, which is available to authorized users.

Urinary expression of long non-coding RNA TUG1 in non-diabetic patients with glomerulonephritides

Metabolic alterations serve a significant role in the pathogenesis of kidney disease. Long non-coding RNA (lncRNA) taurine upregulated gene 1 (TUG1) is a known regulator of podocyte health and mitochondrial biogenesis. Although TUG1 protects against podocyte loss in models of diabetic nephropathy, it is unknown if urinary TUG1 expression is associated with clinical and histopathological findings in non-diabetic patients diagnosed with glomerulonephritides. In the present study, the expression of TUG1, podocyte-specific markers (nephrin and podocin) and mitochondrial biogenesis-associated mRNAs (transcription factor A mitochondrial, cytochrome C oxidase subunit 5A and peroxisome proliferator-activated receptor γ coactivator 1α) were examined in urinary sediment of non-diabetic patients with biopsy-confirmed glomerulonephritides and healthy controls. Urinary expression of TUG1 was significantly lower in patients with glomerulonephritides, particularly those diagnosed with Focal Segmental Glomerulosclerosis (FSGS). Furthermore, TUG1 levels were associated with urinary expression of podocyte-specific markers and mRNAs associated with mitochondrial biogenesis. Loss of TUG1 expression in urinary sediment was strongly associated with FSGS, highlighting the potential of this lncRNA and its mitochondrial biogenesis-associated targets as non-invasive biomarkers of assessing podocytopathy.

Diagnostic, Prognostic, and Therapeutic Value of Non-Coding RNA Expression Profiles in Renal Transplantation

End-stage renal disease is a public health problem responsible for millions of deaths worldwide each year. Although transplantation is the preferred treatment for patients in need of renal replacement therapy, long-term allograft survival remains challenging. Advances in high-throughput methods for large-scale molecular data generation and computational analysis are promising to overcome the current limitations posed by conventional diagnostic and disease classifications post-transplantation. Non-coding RNAs (ncRNAs) are RNA molecules that, despite lacking protein-coding potential, are essential in the regulation of epigenetic, transcriptional, and post-translational mechanisms involved in both health and disease. A large body of evidence suggests that ncRNAs can act as biomarkers of renal injury and graft loss after transplantation. Hence, the focus of this review is to discuss the existing molecular signatures of non-coding transcripts and their value to improve diagnosis, predict the risk of rejection, and guide therapeutic choices post-transplantation.

Utility of Genomic Testing after Renal Biopsy

BACKGROUND

Renal biopsy is the mainstay of renal pathological diagnosis. Despite sophisticated diagnostic techniques, it is not always possible to make a precise pathological diagnosis. Our aim was to identify a genetic cause of disease in patients who had undergone renal biopsy and determine if genetic testing altered diagnosis or treatment.

METHODS

Patients with suspected familial kidney disease underwent a variety of next-generation sequencing (NGS) strategies. The subset of these patients who had also undergone native kidney biopsy was identified. Histological specimens were reviewed by a consultant pathologist, and genetic and pathological diagnoses were compared.

RESULTS

Seventy-five patients in 47 families underwent genetic sequencing and renal biopsy. Patients were grouped into 5 diagnostic categories based on pathological diagnosis: tubulointerstitial kidney disease (TIKD; n = 18); glomerulonephritis (GN; n = 15); focal segmental glomerulosclerosis and Alport Syndrome (n = 11); thrombotic microangiopathy (TMA; n = 17); and nonspecific pathological changes (n = 14). Thirty-nine patients (52%) in 21 families (45%) received a genetic diagnosis; 13 cases (72%) with TIKD, 4 (27%) with GN, 6 (55%) with focal segmental glomerulosclerosis/Alport syndrome, and 10 (59%) with TMA and 6 cases (43%) with nonspecific features. Genetic testing resulted in changes in understanding of disease mechanism in 21 individuals (54%) in 12 families (57%). Treatment would have been altered in at least 26% of cases (10/39).

CONCLUSIONS

An accurate genetic diagnosis can result in changes in clinical diagnosis, understanding of pathological mechanism, and treatment. NGS should be considered as a complementary diagnostic technique to kidney biopsy in the evaluation of patients with kidney disease.

Development of a 2-dimensional atlas of the human kidney with imaging mass cytometry

An incomplete understanding of the biology of the human kidney, including the relative abundances of and interactions between intrinsic and immune cells, has long constrained the development of therapies for kidney disease. The small amount of tissue obtained by renal biopsy has previously limited the ability to use patient samples for discovery purposes. Imaging mass cytometry (IMC) is an ideal technology for quantitative interrogation of scarce samples, permitting concurrent analysis of more than 40 markers on a single tissue section. Using a validated panel of metal-conjugated antibodies designed to confer unique signatures on the structural and infiltrating cells comprising the human kidney, we performed simultaneous multiplexed imaging with IMC in 23 channels on 16 histopathologically normal human samples. We devised a machine-learning pipeline (Kidney-MAPPS) to perform single-cell segmentation, phenotyping, and quantification, thus creating a spatially preserved quantitative atlas of the normal human kidney. These data define selected baseline renal cell types, respective numbers, organization, and variability. We demonstrate the utility of IMC coupled to Kidney-MAPPS to qualitatively and quantitatively distinguish individual cell types and reveal expected as well as potentially novel abnormalities in diseased versus normal tissue. Our studies define a critical baseline data set for future quantitative analysis of human kidney disease.

Switching renal transplant recipients to belatacept therapy: results of a real-life gradual conversion protocol

Conversion to belatacept immunosuppression is a therapeutic option for renal-transplant recipients with calcineurin inhibitors (CNI) toxicity, but it associates with high risk of acute rejection. Gradual conversion and serial immune monitoring with urinary chemokine CXCL9 may allow increasing safety of this maneuver. We converted kidney transplant recipients with signs of toxicity to CNI or other immunosuppressive drugs to belatacept over a 2-month period. We monitored renal function, metabolic profile, and circulating lymphocyte subsets. We also quantified urinary CXCL9 over a 12-month follow-up period. Between September 2016 and March 2017, 35 patients were successfully switched to belatacept immunosuppression at 3.3 (1.3-7.2) years after transplant. Two patients had a reversible rise in serum creatinine, associated with acute rejection in one case. Urinary CXCL9 increased before serum creatinine. After conversion, blood pressure and HbA1c significantly declined while eGFR and proteinuria remained stable. The percentage of circulating effector T cells and memory B cells significantly declined. Conversion from CNI to belatacept, in this setting, was feasible and safe, provided it was performed over a 2-month time-period. Monitoring urinary CXCL9 may further increase safety through earlier identification of patients at risk for acute rejection. The procedure associates with improved blood pressure, metabolic profile, and reduced circulating effector T and B cells.

Renal Pre-Competitive Consortium (RPC2): discovering therapeutic targets together

Despite significant effort, patients with kidney disease have not seen their outcomes improved significantly over the past two decades. This has motivated clinicians and researchers to consider alternative methods to identifying risk factors, disease progression markers, and effective therapies. Genome-scale data sets from patients with renal disease can be used to establish a platform to improve understanding of the molecular basis of disease; however, such studies require expertise and resources. To overcome these challenges, we formed an academic-industry consortium to share molecular target identification efforts and expertise across academia and the pharmaceutical industry. The Renal Pre-Competitive Consortium (RPC²) aims to accelerate novel drug development for kidney diseases through a systems biology approach. Here, we describe the rationale, philosophy, establishment, and initial results of this strategy.

Precision medicine comes of age in nephrology: identification of novel biomarkers and therapeutic targets for chronic kidney disease

The goal of "precision medicine" is to characterize diseases based on the underlying molecular biology, in order to identify specific biomarkers and therapeutic targets that will ultimately improve clinical outcomes. The nephrology research community has developed a strong foundation for precision medicine, and recent publications demonstrate the feasibility of this approach to identify potential biomarkers and therapeutic targets in chronic kidney disease.

Arecoline-induced pro-fibrotic proteins in LLC-PK1 cells are dependent on c-Jun N-terminal kinase

Areca nut (AN) chewing is associated with chronic kidney disease (CKD). However, the molecular mechanisms of AN-induced CKD are not known. Thus, we studied the effects of arecoline, a major alkaloid of AN, on proximal tubule (LLC-PK1) cells in terms of cytotoxicity, fibrosis, transforming growth factor-β (TGF-β) and c-Jun N-terminal kinase (JNK). We found that arecoline dose (0.1-0.5mM) and time (24-72h)-dependently induced cytotoxicity without causing cell death. Arecoline (0.25 mM) also time-dependently (24-72h) increased fibronectin and plasminogen activator inhibitor-1 (PAI1) protein expressions. Arecoline (0.25 mM) time-dependently (24-72h) increased TGF-β gene transcriptional activity and supernatant levels of active TGF-β1. Moreover, arecoline (0.25 mM) activated JNK while SP600125 (a JNK inhibitor) attenuated arecoline-induced TGF-β gene transcriptional activity. SP600125, but not SB431542 (a TGF-β receptor type I kinase inhibitor), attenuated arecoline-induced fibronectin and PAI1 protein expressions. Finally, tubulointerstitial fibrosis occurred and renal cortical expressions of fibronectin and PAI1 proteins increased in arecoline-fed mice at 24 weeks. We concluded that arecoline induced tubulointerstitial fibrosis in mice while arecoline-induced TGF-β and pro-fibrotic proteins (fibronectin, PAI1) are dependent on JNK in LLC-PK1 cells.

Analysis of relative expression level of VEGF ( vascular endothelial growth factor ), HIF-1α ( hypoxia inducible factor 1α ) and CTGF ( connective tissue growth factor ) genes in chronic glomerulonephritis (CGN) patients

BACKGROUND/AIMS

Analysis of gene expression in renal tissue is considered to be a diagnostic tool predicting the clinical course of glomerulonephritis. The present study quantified the relative transcript levels of VEGF, CTGF and HIF-1α in renal tissue to establish their relationship with some clinical variables in patients suffering from chronic glomerulonephritis (CGN).

METHODS

28 patients (6F and 22M, mean age 51.2±15.0) with CGN were enrolled. Type of CNG recognized by kidney biopsy (histopatological evaluation) was as follows: minimal change disease (MCD)-3pts, IgA nephropathy-5pts, FSGS-3pts, membranous nephropathy-4pts, mesangio-proliferative glomerulonephritis-3pts; MPGN-1pts, lupus nephritis-6pts, granulomatosis with polyangitis-2 pts; hypertensive nephropathy- 3pts. Renal tissue from 3 individuals with normal eGFR and histology was taken as control. Mean clinical follow-up of patients was 12 months after biopsy eGFR and daily urinary protein excretion (DPE) was assessed at the time of biopsy and then in 6 months intervals. Real-time PCR was used to determine relative gene expression. The housekeeping gene GAPDH was used as normalization control.

RESULTS

At the time of the biopsy relative expression of 3 analyzed genes was diminished in comparison to control. There were statistically significant differences in VEGF gene relative expression level in patients which varied according to eGFR and tendency in patients which varied according to DPE. HIF-alfa and CTGF gene showed only a tendency.

CONCLUSIONS

Overexpression of the VEGF gene in subjects with DPE>3,5 g may point to insufficient oxygen supply in renal tissue which may result in tubulointerstitial fibrosis with further functional renal impairment and decline of eGFR.

Perspectives on systems biology applications in diabetic kidney disease

Diabetic kidney disease (DKD) is a microvascular complication of type 1 and 2 diabetes with a devastating impact on individuals with the disease, their families, and society as a whole. DKD is the single most frequent cause of incident chronic kidney disease cases and accounts for over 40% of the population with end-stage renal disease. Contributing factors for the high prevalence are the increase in obesity and subsequent diabetes combined with an improved long-term survival with diabetes. Environment and genetic variations contribute to DKD susceptibility and progressive loss of kidney function. How the molecular mechanisms of genetic and environmental exposures interact during DKD initiation and progression is the focus of ongoing research efforts. The development of standardized, unbiased high-throughput profiling technologies of human DKD samples opens new avenues in capturing the multiple layers of DKD pathobiology. These techniques routinely interrogate analytes on a genome-wide scale generating comprehensive DKD-associated fingerprints. Linking the molecular fingerprints to deep clinical phenotypes may ultimately elucidate the intricate molecular interplay in a disease stage and subtype-specific manner. This insight will form the basis for accurate prognosis and facilitate targeted therapeutic interventions. In this review, we present ongoing efforts from large-scale data integration translating "-omics" research efforts into improved and individualized health care in DKD.

Molecular evaluation of renal biopsies: a search for predictive and prognostic markers in lupus nephritis

The therapeutic management of patients with lupus nephritis (LN) remains a major challenge. The availability of biomarkers that accurately predict renal flares, response to immunosuppressive treatment and risk of progression to end-stage renal disease would allow the more effective use of currently available immunosuppression, with less toxicity. The molecular analysis of renal biopsy samples provides direct insights into pathologic processes in LN, and constitutes a valuable approach to discover biomarkers that may be used to improve the outcome of LN patients. Reich et al. recently described a method for simultaneously detecting multiple mRNA transcripts in archived formalin-fixed renal biopsy samples. The authors identify three transcripts (EGF, MMP7 and COL1A1) that relate to pathological indices of kidney injury and function.

Molecular markers of injury in kidney biopsy specimens of patients with lupus nephritis

Prediction of prognosis in patients who have lupus nephritis is inadequate, limiting individualization of potentially toxic therapy. Advances in tissue molecular techniques offer new approaches to study mechanisms underlying kidney injury, and add to prognostic information gleaned from biopsy specimens. Analysis of mRNA expression in formalin-fixed, paraffin-embedded renal biopsy specimens is limited by both quantity and quality of RNA, requiring RNA pre-amplification, which can introduce bias. Accordingly, we developed a new technique for RNA extraction from human kidney formalin fixed paraffin embedded biopsy specimens, and used Taqman low-density arrays Applied Biosystems, Carlsbad, CA to simultaneously measure 48 mRNAs in duplicate, in a single biopsy. We extracted mRNA from more than 150 blocks to determine the quantity and vintage of biopsy tissue suitable for analysis using this protocol. We then used Taqman low-density arrays to identify suitable housekeeping genes in lupus nephritis. Finally, we measured expression of 48 mRNA transcripts in archived lupus biopsy specimens (n = 54). We identified that the mRNA levels of three transcripts (MMP7, EGF, COL1A1) relate to pathological indices of kidney injury and kidney function at the time of biopsy; these were associated with parallel changes in expression of these proteins. This new method for measurement of kidney biopsy mRNA expression has enabled us to identify tissue biomarkers of kidney damage and function, and potentially can increase the information yielded from diagnostic kidney biopsy specimens to improve tailoring of therapy.

The story of Notch and chronic kidney disease

PURPOSE OF REVIEW

The Notch pathway is an evolutionary conserved cell-cell communication mechanism that plays a key role in kidney development. Here, we will discuss a number of recently published papers describing the role of Notch signaling in kidney development, homeostasis, injury and repair.

RECENT FINDINGS

Recent gene expression studies identified regulation of the Notch pathway in patients with chronic kidney disease (CKD). Mechanistic experiments performed using transgenic and knock-out mouse models indicate that Notch plays an important functional role in the development of proteinuria and renal fibrosis. Inhibition of the Notch pathway ameliorated diabetic kidney disease, nephrotic syndrome and fibrosis in different rodent models.

SUMMARY

An increasing amount of evidence suggests that Notch plays a role in CKD development. Understanding the role of Notch signaling in the kidney can aid in the development of new therapeutics for CKD.

A molecular signature of proteinuria in glomerulonephritis

Proteinuria is the most important predictor of outcome in glomerulonephritis and experimental data suggest that the tubular cell response to proteinuria is an important determinant of progressive fibrosis in the kidney. However, it is unclear whether proteinuria is a marker of disease severity or has a direct effect on tubular cells in the kidneys of patients with glomerulonephritis. Accordingly we studied an in vitro model of proteinuria, and identified 231 “albumin-regulated genes” differentially expressed by primary human kidney tubular epithelial cells exposed to albumin. We translated these findings to human disease by studying mRNA levels of these genes in the tubulo-interstitial compartment of kidney biopsies from patients with IgA nephropathy using microarrays. Biopsies from patients with IgAN (n = 25) could be distinguished from those of control subjects (n = 6) based solely upon the expression of these 231 “albumin-regulated genes.” The expression of an 11-transcript subset related to the degree of proteinuria, and this 11-mRNA subset was also sufficient to distinguish biopsies of subjects with IgAN from control biopsies. We tested if these findings could be extrapolated to other proteinuric diseases beyond IgAN and found that all forms of primary glomerulonephritis (n = 33) can be distinguished from controls (n = 21) based solely on the expression levels of these 11 genes derived from our in vitro proteinuria model. Pathway analysis suggests common regulatory elements shared by these 11 transcripts. In conclusion, we have identified an albumin-regulated 11-gene signature shared between all forms of primary glomerulonephritis. Our findings support the hypothesis that albuminuria may directly promote injury in the tubulo-interstitial compartment of the kidney in patients with glomerulonephritis.

Fine tuning gene expression: the epigenome

An epigenetic trait is a stably inherited phenotype resulting from changes in a chromosome without alterations in the DNA sequence. Epigenetic modifications such as DNA methylation, together with covalent modification of histones, are thought to alter chromatin density and accessibility of the DNA to cellular machinery, thereby modulating the transcriptional potential of the underlying DNA sequence. As environmental changes influence epigenetic marks, epigenetics provides an added layer of variation that might mediate the relationship between genotype and internal and external environmental factors. Integration of our knowledge in genetics, epigenomics, and genomics with the use of systems biology tools may present investigators with new, powerful tools to study many complex human diseases such as kidney disease.

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.

Urinary expression of kidney injury markers in renal transplant recipients

BACKGROUND AND OBJECTIVES

The outcome of renal transplantation after an episode of acute rejection is difficult to predict, even with an allograft biopsy. We examined whether urinary expression of specific biomarker mRNA could be used as a noninvasive prognostic marker in kidney transplant recipients.

DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS

We studied 63 kidney transplant recipients who require graft biopsy because of progressive worsening of kidney function. The mRNA of neutrophil gelatinase-associated lipocalin, kidney injury molecule-1 (KIM-1), IL-18, surfactant protein-C, and S100 calcium-binding proteins A8 and A9 in urinary sediment were quantified.

RESULTS

Urinary expressions of neutrophil gelatinase-associated lipocalin, KIM-1, and IL-18, but not other target genes, were significantly different between histologic groups (P < 0.0001 for all). After followed for an average of 39.7 ± 21.1 months, the rate of renal function decline significantly correlated with urinary KIM-1 expression (r = -0.434, P = 0.0004) but not other target genes. At 48 months, the graft survival rate for the high and low KIM-1 groups were 46.2 and 78.6%, respectively. After adjusting for confounding variables, each log of higher urinary KIM-1 expression conferred an ~2.9-fold higher risk of developing graft failure (95% confidence interval, 1.3- to 6.2-fold; P = 0.006). The result remained similar when only patients with no acute cellular rejection were analyzed.

CONCLUSIONS

In kidney allograft recipients, urinary KIM-1 expression provides prognostic information in relation to the rate of renal function decline, irrespective of the kidney pathology.

Tissue proteomics: a new investigative tool for renal biopsy analysis

Renal biopsy is viewed as the gold standard for diagnosis and management of many kidney diseases, especially glomerulopathies. However, the histopathological descriptions currently used in clinical practice often are neither diagnostic nor prognostic. The paper by Sethi et al. highlights the availability of a newer investigative tool that can be used to better define pathogenesis and, perhaps more important, to discover robust biomarkers of kidney disease cause and outcome.

Enhanced expression of Janus kinase-signal transducer and activator of transcription pathway members in human diabetic nephropathy

OBJECTIVE

Glomerular mesangial expansion and podocyte loss are important early features of diabetic nephropathy, whereas tubulointerstitial injury and fibrosis are critical for progression of diabetic nephropathy to kidney failure. Therefore, we analyzed the expression of genes in glomeruli and tubulointerstitium in kidney biopsies from diabetic nephropathy patients to identify pathways that may be activated in humans but not in murine models of diabetic nephropathy that fail to progress to glomerulosclerosis, tubulointerstitial fibrosis, and kidney failure.

RESEARCH DESIGN AND METHODS

Kidney biopsies were obtained from 74 patients (control subjects, early and progressive type 2 diabetic nephropathy). Glomerular and tubulointerstitial mRNAs were microarrayed, followed by bioinformatics analyses. Gene expression changes were confirmed by real-time RT-PCR and immunohistological staining. Samples from db/db C57BLKS and streptozotocin-induced DBA/2J mice, commonly studied murine models of diabetic nephropathy, were analyzed.

RESULTS

In human glomeruli and tubulointerstitial samples, the Janus kinase (Jak)-signal transducer and activator of transcription (Stat) pathway was highly and significantly regulated. Jak-1, -2, and -3 as well as Stat-1 and -3 were expressed at higher levels in patients with diabetic nephropathy than in control subjects. The estimated glomerular filtration rate significantly correlated with tubulointerstitial Jak-1, -2, and -3 and Stat-1 expression (R(2) = 0.30-0.44). Immunohistochemistry found strong Jak-2 staining in glomerular and tubulointerstitial compartments in diabetic nephropathy compared with control subjects. In contrast, there was little or no increase in expression of Jak/Stat genes in the db/db C57BLKS or diabetic DBA/2J mice.

CONCLUSIONS

These data suggest a direct relationship between tubulointerstitial Jak/Stat expression and progression of kidney failure in patients with type 2 diabetic nephropathy and distinguish progressive human diabetic nephropathy from nonprogressive murine diabetic nephropathy.

Laser capture microdissection of kidney tissue

Kidney tissue laser capture microdissection (LCM) is of great clinical relevance since genome wide studies on total kidney messenger RNA (mRNA) potentially miss important factors involved in the pathogenesis of the disease in glomeruli and tubules. This technique is readily applicable to study mRNA from isolated glomeruli and tubules of human kidney biopsy material. In this chapter we present a "cook-book" practical approach of utilizing LCM in combination with RNA isolation technique in downstream applications in nephrology.

Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge

Diabetic nephropathy (DN) is the most common cause for end stage renal disease (ESRD). Next to environmental factors, genetic predispositions determine the susceptibility for DN and its rate of progression to ESRD. With the availability of genome wide expression profiling we have the opportunity to define relevant pathways activated in the individual diabetic patient, integrating both environmental exposure and genetic background. In this review we summarize current understanding of how to link comprehensive gene expression data sets with biomedical knowledge and present strategies to build a transcriptional network of DN. Information about the individual disease processes of DN might allow the implementation of a personalized molecular medicine approach with mechanism-based patient management. Web based search engines like Nephromine are essential tools to facilitate access to molecular data of genomics, proteomics and metabolomics of DN.

Genetic predictors of renal failure

BACKGROUND

Both environmental and genetic factors contribute to the development and progression of chronic kidney disease. The completion of the human genome sequence and advances in genomic technology make possible identification of gene variants associated with renal failure.

OBJECTIVE

This review discusses the relevant genetic studies in chronic kidney disease, with particular emphasis on the most common causes of end stage renal failure, diabetic nephropathy and glomerulonephritis.

METHODS

Most of the studies presented were performed in recent years and employed association studies, both population-based and with candidate genes, as well as the genome-wide association and genome-wide scan approaches.

RESULTS/CONCLUSION

Increasing evidence supports an important role of genetic susceptibility in the development and progression of renal failure. Identification of disease genes will allow the identification of patients at high risk and the development of new strategies to prevent or delay the renal disease process.

Quantification of gene expression in urinary sediment for the study of renal diseases

Urinalysis has been used extensively in clinical practice to aid in the diagnosis of various renal diseases. With the advances in technology of molecular biology, gene expression and proteomic studies are now possible for urinary sediment. In this review article, we focus on the quantification of messenger RNA expression in urinary sediment by reverse-transcription and real-time quantitative polymerase chain reaction. Recently, this technique has been explored for three potential applications: (i) distinguishing the different causes of kidney disease; (ii) assessment of kidney disease activity, progression and response to therapy; and (iii) as a tool to study the pathogenesis. Although the method is simple and non-invasive, it requires further research to define the role in routine clinical practice. At this moment, the technique should only be considered experimental albeit promising.

Gene expression profiling analysis in nephrology: towards molecular definition of renal disease

The increase in progressive kidney disease, resulting in a constantly rising prevalence of endstage renal disease (ESRD), urgently warrants the development of more effective strategies to diagnose, prevent, and intervene in renal disease. Histological information obtained by renal biopsies (RBx) is a cornerstone of the current management of kidney disease. Renal tissue can provide critical information on the disease process not available by nontissue-based approaches. However, insight gained by conventional histopathology remains limited and additional strategies to define renal disease on a molecular level are required. The sequencing of the human genome, together with recent advances in genome-wide profiling techniques, has provided the framework for a comprehensive analysis of renal disease-associated transcriptional programs. In this review, strategies to apply these technological advances towards the analysis of RBx will be described, with special emphasis on their potential impact on clinical management, but also on their inherent limitations. Finally, an outlook towards the emerging proteomic studies of renal disease will be given.

Diabetic Nephropathy: A Frontier for Personalized Medicine: Figure 1

Diabetic nephropathy (DNP) develops after latency periods that may vary by several years in approximately one third of patients with diabetes. This diabetic complication is a complex disorder whereby various genetic and environmental factors determine susceptibility and progression to ESRD. Despite rapid research progress, robust predictors to assess prospectively with high precision the risk for DNP in individuals with diabetes are still lacking. Thus, currently available therapies are usually initiated at more advanced stages of DNP characterized by clinically overt manifestations, including increased urinary albumin excretion and decreased glomerular filtration. In addition, although these interventions have proven efficacy in slowing the progression of DNP, they typically cannot prevent ESRD. New insights into the molecular mechanisms that underlie the origin and progression of DNP are emerging rapidly from advanced large-scale genetic and molecular studies in experimental models and humans. Thus, genetic loci that confer risk for albuminuria and/or progression of kidney disease associated with diabetes are being refined to identify the relevant genetic variants in specific genes. Molecular mRNA profiles that are obtained through microarray screens are being validated to elucidate further their potential as molecular markers and to identify new targets for novel preventive or therapeutic approaches aiming at curing DNP. The challenge before the field is to translate the large amount of new genetic and molecular data to empower clinicians and investigators with reliable predictors of DNP for improved design of preventive clinical trials and for individualized clinical management for millions of individuals affected by diabetes worldwide.

Glomerular disease workshop

Recent observations regarding intrinsic glomerular cell biology, particularly in the podocyte, have provided exciting new insights into potential pathogenic mechanisms of human glomerular disease. Although both immune and nonimmune mechanisms of glomerular injury have been studied previously, experimental models of disease and recent techniques that provide tools for molecular profiling show great promise for identifying glomerular disease biomarkers. Despite these recent advances, additional work in both basic and clinical studies of glomerular disease is needed to advance the field. Standardization of animal models of distinct forms of glomerular disease would likely facilitate the search for biomarkers. Several factors limit current efforts to implement clinical trials of glomerular disease. Identification of disease biomarkers, development of disease-specific end points, and organization of collaborative clinical groups are critical for ultimately designing and implementing appropriately powered trials of glomerular disease.

Expression of surfactant protein-C, S100A8, S100A9, and B cell markers in renal allografts: investigation of the prognostic value

The intent of this study was to identify genes of which expression during acute rejection is associated with progression to chronic allograft nephropathy using gene expression profiling. Ten patients who had graft loss through chronic allograft nephropathy (progression [PR] group) and 18 patients who had stable graft function over time (nonprogression [NP] group) were studied. Rejection severity and extent of infiltrating leukocytes in acute rejection biopsies were similar for both groups. Microarray analysis and real-time PCR validation showed that surfactant protein-C (SP-C), S100 calcium-binding protein A8 (S100A8), S100A9, and beta-globin levels distinguished the two groups. Relationship between expression of B cell markers and prognosis was also examined. Location in the graft of the protein and mRNA expression of candidate genes was investigated. The prognostic value of mRNA transcripts was tested in an independent cohort of 43 rejection biopsies. mRNA and protein expression of S100A8 and S100A9 in infiltrating cells was significantly higher in the NP group compared with the PR group. Expression of SP-C was four-fold higher in the PR group and was detected in glomeruli. No association between B cell clusters and outcome was found. In the second group of acute rejection biopsies, SP-C mRNA levels predicted renal function course beyond 6 mo in multivariate analysis. Relatively high expression of S100A8 and S100A9 during acute rejection is associated with a favorable prognosis, and high SP-C expression is associated with an unfavorable prognosis. Messenger RNA transcripts complement the biopsy in the prediction of graft function deterioration.

The use of extracellular matrix probes and extracellular matrix-related probes for assessing diagnosis and prognosis in renal diseases

PURPOSE OF REVIEW

Scarring in the kidney results from excessive local synthesis and exogenous accumulation of extracellular matrix components. Once chronic damage is present in the biopsy, therapeutic intervention for the renal patient encounters severe limitations. It is therefore essential to determine clinical outcome preferably at a time point before the development of overt scarring. Clinical parameters and morphologic alterations in the biopsy are currently used as tools for the diagnosis of the renal disease entity and for assessment of the patient's prognosis. Expression levels of extracellular matrix and matrix-related components may serve as additive and even superior prognostic indicators to conventional parameters. We will elaborate on studies supporting this concept.

RECENT FINDINGS

Several investigators have shown in experimental models for renal disease that extracellular matrix probes and related probes reflect disease progression and predict outcome. In this review, we will provide an update on the most recent studies of human renal biopsies showing that expression of extracellular matrix components, regulators of matrix degradation, and cytokines affecting matrix deposition may be employed for discrimination of diagnostic groups and predicting prognosis.

SUMMARY

Molecular techniques are expected to be used more and more for diagnostic and prognostic purposes in nephrological practice to supplement the histopathological analysis of the renal biopsy. Assessment of expression of matrix molecules, matrix-regulating cytokines, and metalloproteinases in renal kidney biopsies is helpful to distinguish patients who are at risk of developing progressive renal failure from patients who are likely to recover from renal tissue injury by natural remodeling mechanisms.

Gene expression analysis of human renal biopsies: recent developments towards molecular diagnosis of kidney disease

PURPOSE OF REVIEW

The analysis of renal tissue from kidney biopsies by histology, electron microscopy and immunohistology represents the current standards used to establish a specific diagnosis in nephrology. Recent progress in gene expression-based tissue analysis may provide fundamentally novel information in renal biopsy interpretation. In this review, progress towards the routine application of this approach is summarized.

RECENT FINDINGS

Renal disease is characterized by closely interrelated mechanisms of inflammation, repair, scarring and atrophy affecting over 20 different intrinsic renal cell types. The renal biopsy sample represents a 'snapshot' of these dynamic processes. A central question for molecular diagnosis is whether specific gene expression patterns can adequately define segments of these disease processes. Can molecular markers be extracted as effectively as has been shown in oncology? Several studies have been able to correlate renal gene expression patterns with clinical parameters, renal histological findings and patient follow-up data. In small populations, molecular markers have been able to provide novel diagnostic, prognostic and differential therapeutic information beyond conventional histology.

SUMMARY

A growing number of renal gene expression projects are generating targets for the integration of molecular approaches into kidney biopsy evaluation. If these molecular makers can pass rigorous testing for their diagnostic value, they should become an indispensable part of the management of the renal patient.

Practice guidelines for the renal biopsy

Biopsy of the kidney should never be undertaken without careful consideration of the risks vs benefits. Given the importance of a correct diagnosis in the treatment and prognosis of renal disease, the pathological evaluation should use all available modalities. Native kidney biopsies require examination by light microscopy, immunohistochemistry and electron microscopy. The processing of the renal biopsy is complex and requires the support of a fully equipped anatomic pathology laboratory. Technical expertise is required to process the small fragments of tissue and to produce sections of highest quality. The correct diagnosis requires a well-trained renal pathologist with thorough knowledge of not only renal pathology but also renal medicine in order to correlate intricate tissue-derived information with detailed clinical data. In view of the importance and consequences of the pathologic diagnosis, the Renal Pathology Society appointed an Ad Hoc Committee on Practice Guidelines, to define the essential ingredients necessary to provide quality renal pathology diagnoses. This document incorporates the consensus opinions of the committee and the RPS membership at large.

Differentiation between chronic rejection and chronic cyclosporine toxicity by analysis of renal cortical mRNA

BACKGROUND

In kidney transplantation, chronic allograft nephropathy (CAN) is the major cause of graft loss. Causes of CAN include chronic rejection and chronic cyclosporine A (CsA) nephrotoxicity. It is necessary to differentiate between these two entities in order to apply the appropriate therapeutic regimen for the individual patient, but this is hampered by the lack of discriminating functional and morphologic parameters. We investigated whether renal cortical mRNA levels for several matrix proteins can serve as discriminating parameters.

METHODS

Patients with chronic rejection (N= 19) and chronic CsA toxicity (N= 17) were selected by clinical and histologic criteria. Protocol biopsies without histologic abnormalities, taken at 6 months after transplantation from patients receiving CsA, were used as controls (N= 6). Total RNA was extracted from the renal biopsy tissue, and mRNA levels of transforming growth factor-beta (TGF-beta) and the extracellular matrix (ECM) molecules collagen Ialpha1, IIIalpha1, IValpha3, decorin, fibronectin, and laminin beta2 were measured by real-time polymerase chain reaction (PCR).

RESULTS

In both patient groups, the mean collagen IValpha3 and fibronectin mRNA levels were significantly elevated compared to those in controls, whereas only in CsA toxicity were the laminin beta2 and TGF-beta mRNA levels significantly increased. The increase of laminin beta2 and TGF-beta mRNA levels was significantly higher in the CsA toxicity group than in the chronic rejection group (P < 0.001 and P= 0.004, respectively). Receiver-operating characteristic (ROC) curve analysis showed that with a 15.6-fold increase in laminin beta2 mRNA expression as cut-off point, the presence of CsA toxicity could be predicted with an 87% sensitivity and an 88% specificity.

CONCLUSION

Renal laminin beta2 and TGF-beta mRNA levels can be used to differentiate between chronic rejection and chronic CsA toxicity in renal transplants. The method of mRNA quantification might be applicable as an additional diagnostic tool in clinical practice.

Gene expression fingerprints in human tubulointerstitial inflammation and fibrosis as prognostic markers of disease progression

BACKGROUND

Gene expression profiling of nephropathies may facilitate development of diagnostic strategies for complex renal diseases as well as provide insight into the molecular pathogenesis of kidney diseases. To test molecular based renal disease categorization, differential gene expression profiles were compared between control and hydronephrotic kidneys showing varying degrees of inflammation and fibrosis.

METHODS

RNA expression profiles from 9 hydronephrotic and 3 control kidneys were analyzed using small macroarrays dedicated to genes involved in cell-cell contact, matrix turnover, and inflammation. In parallel, the degree of tubulointerstitial inflammation, fibrosis, and tubular atrophy using light microscopy and quantitative immunohistochemical parameters was determined.

RESULTS

Hierarchic clustering and self-organizing maps led to a gene expression dendrogram with three distinct nodes representing the control group, four kidneys with high inflammation, and five kidneys giving high fibrosis scores. To evaluate the clinical applicability of the marker set, the expression of nine genes (6Ckine, IL-8, MMP-9, MMP-3, MMP-7, urokinase R, CXCR5, integrin-beta4, and pleiotrophin) was tested in tubulointerstitial samples from routine renal biopsies. Seven mRNA markers showed differential regulation in inflammation and fibrosis in the biopsy population. Clinical follow-up revealed stringent correlation between gene expression data and progression of renal disease, and allowed segregation of the biopsies into progressive or stable disease course based on gene expression profiles.

CONCLUSION

This study suggests the feasibility of gene expression-based disease categorization in human nephropathies based on the extraction of marker gene sets.

Splicing alterations in human renal allografts: detection of a new splice variant of protein kinase Par1/Emk1 whose expression is associated with an increase of inflammation in protocol biopsies of transplanted patients

Protein kinase Emk1/Par1 (GenBank accession no. X97630) has been identified as a regulator of the immune system homeostasis. Since immunological factors are critical for the development of chronic allograft nephropathy (CAN), we reasoned that expression of Par1/Emk1 could be altered in kidney allografts undergoing CAN. In this paper, we have analysed the association among renal allograft lesions and expression of Par1/Emk1, studied by RT-PCR on total RNA from 51 protocol biopsies of transplanted kidneys, five normal kidneys, and five dysfunctional allografts. The most significant result obtained has been the detection of alterations in the normal pattern of alternative splicing of the Par1/Emk1 transcript, alterations that included loss of expression of constitutively expressed isoforms, and the inclusion of a cryptic exon to generate a new Emk1 isoform (Emk1C). Expression of Emk1C was associated with an increase in the extension of the interstitial infiltrate (0.88+/-0.33 in Emk1C([+]) vs. 0.41+/-0.50 in Emk1C([-]); P<0.011), and with a trend to display higher interstitial scarring (0.66+/-0.70 vs. 0.29+/-0.52; P=0.09) in protocol biopsies when evaluated according to the Banff schema. Moreover, a higher mean arterial pressure (MAP) was also observed (110+/-11 vs. 99+/-11 mm Hg; P=0.012). From these results we propose that Par1/Emk1 could have a role in the development of CAN in kidney allografts.

Genomic strategies for diabetic nephropathy

Insight into the molecular mechanisms that underlie the origin and progression of diabetic nephropathy remains limited in part because conventional research tools have restricted investigators to focus on single genes or isolated pathways. Microarray technologies provide opportunities for evaluating genetic factors and environmental effects at a genomic scale during the pathogenesis of diabetic nephropathy. Despite the enormous power of the microarray technology, there are several pitfalls that need to be considered. This article discusses conceptual, practical, statistical, and logistical considerations for the use of microarrays in studies of experimental and human diabetic renal disease. New knowledge in this field will facilitate new approaches for molecular diagnosis and drug discovery.

ECM homeostasis in renal diseases: a genomic approach

Chronic renal disease is in general histologically accompanied by a vast amount of scar tissue, ie glomerulosclerosis and interstitial fibrosis. Scarring results from excessive accumulation of extracellular matrix (ECM) components, a process driven by a plethora of cytokines and growth factors. Studies in experimental renal disease which target these regulators using gene therapy limit or prevent the development of scarring. This review focuses specifically on the role of transforming growth factor-beta, platelet-derived growth factor, connective tissue growth factor, hepatocyte growth factor, and epidermal growth factor. The results obtained in animal models hold promise for molecular intervention strategies in human renal disease. Microarray technology allows large-scale gene expression profiling in kidney tissue to identify common molecular pathways in a step towards discovery of new drug targets. Molecular techniques are expected to be used for diagnostic and prognostic purposes in nephrological practice to supplement renal biopsy. Several studies already show that molecular techniques might be of use in routine diagnostic practice. Improvement of diagnosis and prediction of outcome in renal patients might lead to more efficient and earlier therapeutic intervention.

Validation of endogenous controls for gene expression analysis in microdissected human renal biopsies

BACKGROUND

The appropriate choice of an internal reference is critical for quantitative RNA analysis. However, no comparison of frequently used "housekeeping" genes is available for renal biopsy studies.

METHODS

Microdissected biopsies from 165 patients, including a wide range of histopathologic diagnoses, were analyzed [immunoglobulin A (IgA) nephritis, membranous glomerulopathy, rapid progressive glomerulonephritis, minimal change disease, focal segmental glomerulosclerosis (FSGS), nephrosclerosis, diabetic nephropathy, interstitial nephritis, and controls]. Expression of three frequently used housekeeping genes [glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S rRNA, and cyclophilin A] was examined by real-time reverse transcription-polymerase chain reaction (RT-PCR).

RESULTS

Absolute expression values of reference genes obtained from the renal biopsies were related to each other. In tubulointerstitial compartment, a positive correlation coefficient (r) of 0.96 was observed between 18S rRNA and cyclophilin A. However, a subset of samples showed lower expression levels for GAPDH in relation to 18S rRNA or cyclophilin A, resulting in a decrease to r = 0.77 and r = 0.73, respectively, consistent with considerable mRNA regulation of GAPDH. In glomerular samples, a comparable low correlation between GAPDH versus 18S rRNA (r = 0.75) was obtained.

CONCLUSION

Using a single housekeeper gene as reference for renal biopsy studies, differences in gene expression ratios may reflect regulation of the internal control rather than the mRNA under investigation. Relating the gene expression to several housekeepers in parallel (i.e., 18S rRNA and cyclophilin A) should result in robust expression data.

Renal mRNA levels as prognostic tools in kidney diseases

Molecular biologic techniques are currently considered as new diagnostic and prognostic parameters with a sensitivity and specificity exceeding those of histologic and functional data currently used in clinical practice. The results in various clinical settings have been of limited value up to now. This study is an investigation of the use of tissue levels of RNA determined in routine clinical kidney biopsies as prognostic tools. The focus was on RNA encoding for molecules known to be involved in the pathogenesis of renal disorders. Fresh kidney biopsy tissue was obtained from 52 patients with various renal diseases. The GFR was followed for 12 mo. The extent of glomerulosclerosis and interstitial fibrosis in the biopsies was determined with quantitative digital image analysis. Glomerular and tubulointerstitial compartments from each biopsy specimen were separated, and mRNA levels of TGF-beta, collagen I, collagen IV, and fibronectin were quantitated by real-time PCR. Correlations, along with 95% confidence intervals (CI), between all variables tested at time biopsy were determined. To assess their prognostic value, these variables were correlated with the slope of GFR within several time intervals after biopsy. In addition, to evaluate the predictive value of the variables for outcome in individual patients, differences for each variable were tested between patients showing progressive decline in renal function (slope GFR < 0) and patients showing stable or improving renal function over time (slope GFR >or= 0). In chronic renal diseases, the extent of histologic damage correlated with the GFR at the time of biopsy (r = -0.44; CI -0.68 to -0.11), but it did not correlate with the slope expressing a change in GFR after the biopsy. Tubulointerstitial TGF-beta mRNA levels correlated with the rate of change in GFR between time of biopsy and 1 mo later (r = 0.41; CI, 0.07 to 0.67). The GFR at the time of biopsy correlated with the slope of change in GFR between time of biopsy and 12 mo later (r = -0.50; CI, -0.73 to -0.18). In chronic renal diseases, glomerular fibronectin mRNA levels, in comparison with the GFR at time of biopsy, correlated relatively strongly with the slope of change in GFR between 3 and 12 mo (r = 0.50; CI, 0.16 to 0.74). Patients with favorable renal outcome after 12 mo showed significantly higher TGF-beta mRNA levels and lower proteinuria levels at time of biopsy (P < 0.05) than patients with a progressive decline in renal function. This study shows that mRNA levels measured in kidney biopsies can function as prognostic tools in human renal diseases. In particular, relatively high levels of tubulointerstitial TGF-beta mRNA and glomerular fibronectin mRNA are associated with less deterioration in renal function.