Background/Purpose:

NZM2328 mice spontaneously develop glomerulonephritis (GN) and females commonly progress to renal failure. Our previous study showed that acute GN (aGN) and chronic GN (cGN) are two pathological stages, controlled by different genetic loci, and aGN need not progress to cGN. In this study, glomerular and tubular transcriptional profiles were obtained from kidneys of NZM2328 female mice at 8-9, 26, and 36 weeks of age. Transcriptome analysis was employed to characterize the pathologic processes in the separate regions of the affected kidneys to develop better insight into the check points operative in the control of tissue pathology.

Methods:

Glomerular and tubular cells were collected separately using Laser Microdissection (LMD) from the same kidneys of NZM2328 female mice at 8-9, 26, and 38 weeks of age. Total RNA from LMD-derived cells were labeled and hybridized on Affymetrix Mouse Genome 430 v2.0 microarrays. LIMMA statistical analyses in R software was used to generate lists of genes with significant differential expression (DE) compared with young mice using a FDR < 0.2 threshold. Weighted gene co-expression network analysis (WGCNA) and module preservation analyses in R were used to find the modules specific for different disease stages. Gene set variation analysis (GSVA) was used to identify the enriched gene clusters in the various GN stages. Upstream regulators(UR) were identified using Ingenuity Pathway Analysis (IPA) combined with LIMMA DE results.

Results:

Hierarchical analyses using LIMMA and GSVA showed that glomerular transcriptional profiles from kidney samples can be classified into four distinct groups, normal, aGN, tGN and cGN, which correlated with tissue histology. In contrast, tubular transcriptional profiles from the same kidneys could only be separated into normal and GN, indicating common tubular gene expression profiles across GN stages. Gene clusters generated by WGCNA not only could identify specific modules for tGN and cGN stages in the glomeruli, but also were able to identify gene modules specific for aGN, tGN and cGN stages in tubular cells. Upstream regulators, such as IL1β, and Tgfβ1, were found in tGN glomerular modules, indicating that these genes might play an important role in the disease progression from aGN to cGN. However, UR failed to be identified in tubular gene clusters at the aGN or the tGN stage, suggesting that tubular changes at these stages might be related to changes resulting from glomerular insult.

Conclusion:

Both hierarchical analysis and GSVA showed that glomeruli expression changes correlated with disease progression. However, tubules exhibited diversity in their gene expression profiles. WGCNA-generated gene clusters and their upstream regulators were identified in glomeruli at the tGN and cGN stages, as well as in tubular cells at the cGN stage. These novel co-expression gene network clusters could provide a basis to identify specific pathways and biomarkers governing the progression through different disease stages in both the glomeruli and tubules of lupus nephritis.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/glomerular-and-tubular-transcriptional-profiles-reveal-gene-clusters-specific-for-different-stages-of-glomerulonephritis-in-nzm2328-mice/