Proteome Analysis of Glomerular Formalin-Fixed Paraffin Embedded Kidney Samples Distinguishes Diabetic Nephropathy from Controls

Journal of the American Society of Nephrology, vol. 32, pp. 258–259

Abstract

Background: Liquid chromatography tandem-mass spectrometry (LC-MS/MS) is a sensitive technique for in depth proteome analysis but its usage as a diagnostic tool for kidney diseases is still in development. We investigated the potential use of LC-MS/MS in diagnosing diabetic nephropathy (DN) in renal biopsies. Methods: Biopsies from 10 DN patients without renal comorbidity were compared to 10 pretransplantation biopsies. Glomerular cross-sections were collected using laser capture microdissection and tryptic peptides were analysed using LC-MS/MS. Resulting spectra were used for protein identification and further analysis. Results: Based on all identified proteins, DN patients and controls clustered separately (Figure 1). Moreover, we identified 47 significant differentially expressed proteins after adjusting for multiple testing. In DN proteins with increased expression included collagens IV, VI and XVIII, fibronectin, vitronectin, fibulin, complement component C3, C4 and C9, complement factor H, clusterin, fibrinogen and apolipoprotein E. Proteins with decreased expression in DN included nephrin, chloride intracellular channel protein 5, Rab GDP dissociation inhibitor alpha and complement receptor 1.Figure 1.: Principal component analysis and clustering on glomerular samples of diabetic nephropathy patients and controls. Principal component analysis and hierarchical clustering on Euclidean distances and complete linkage using the rlog transformed unique peptide counts from microdissected glomerular tissue samples. A major part of the variance between groups can be attributed to differences between diabetic nephropathy and controls. Clustering of the samples within groups and separation of samples between groups can be observed. DN = diabetic nephropathy.Conclusions: Proteins identified by LC-MS/MS from glomerular cross-sections successfully distinguished kidney biopsies with DN from normal kidneys. Moreover, a set of differentially expressed proteins were identified, most of which were previously suggested to play a role in the development of DN, which further emphasizes the applicability of LC-MS/MS as a diagnostic tool. Funding: Private Foundation Support, Government Support - Non-U.S.

Authors 9

1. Sophie I. Nagelkerken Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leids Universitair Medisch Centrum Afdeling Pathologie, Leiden, Netherlands;

2. George M. C. Janssen Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leids Universitair Medisch Centrum Center for Proteomics and Metabolomics, Leiden, Netherlands;

3. Kimberley Veraar Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leids Universitair Medisch Centrum Afdeling Pathologie, Leiden, Netherlands;

4. Peter A. van Veelen Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leids Universitair Medisch Centrum Center for Proteomics and Metabolomics, Leiden, Netherlands;

5. Hans J. Baelde Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leids Universitair Medisch Centrum Afdeling Pathologie, Leiden, Netherlands;

6. Roy Lardenoije

   Harvard University · McLean Hospital · Universitätsmedizin Göttingen · University of Göttingen

   Affiliation as printed

   Harvard Medical School Department of Psychiatry McLean Hospital, Belmont, MA;

   University Medical Center Göttingen Department of Psychiatry and Psychotherapy, Göttingen, Germany;

7. Joris I. Rotmans Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leids Universitair Medisch Centrum Niercentrum, Leiden, Netherlands

8. Jan A. Bruijn Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leids Universitair Medisch Centrum Afdeling Pathologie, Leiden, Netherlands;

9. Ingeborg M. Bajema Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leids Universitair Medisch Centrum Afdeling Pathologie, Leiden, Netherlands;