RNA Sequencing Identifies Novel Translational Biomarkers of Kidney Fibrosis

Abstract

CKD is the gradual, asymptomatic loss of kidney function, but current tests only identify CKD when significant loss has already happened. Several potential biomarkers of CKD have been reported, but none have been approved for preclinical or clinical use. Using RNA sequencing in a mouse model of folic acidinduced nephropathy, we identified ten genes that track kidney fibrosis development, the common pathologic finding in patients with CKD. The gene expression of all ten candidates was confirmed to be significantly higher (approximately ten-to 150-fold) in three well established, mechanistically distinct mouse models of kidney fibrosis than in models of nonfibrotic AKI. Protein expression of these genes was also high in the folic acid model and in patients with biopsy-proven kidney fibrosis. mRNA expression of the ten genes increased with increasing severity of kidney fibrosis, decreased in response to therapeutic intervention, and increased only modestly (approximately two-to five-fold) with liver fibrosis in mice and humans, demonstrating specificity for kidney fibrosis. Using targeted selected reaction monitoring mass spectrometry, we detected three of the ten candidates in human urine: cadherin 11 (CDH11), macrophage mannose receptor C1 (MRC1), and phospholipid transfer protein (PLTP). Furthermore, urinary levels of each of these three proteins distinguished patients with CKD (n=53) from healthy individuals (n=53; P,0.05). In summary, we report the identification of urinary CDH11, MRC1, and PLTP as novel noninvasive biomarkers of CKD.

RNA-binding Protein Musashi Homologue 1 Regulates Kidney Fibrosis by Translational Inhibition of p21 and Numb mRNA

“…of pentobarbital sodium) by ligation of the left ureter with two separate silk ties as previously described (12,13). Mice were euthanized 3, 7, and 14 days after UUO.…”

“…and UUO (12,13). The extent of fibrosis in these two models was determined by Masson's trichrome staining as shown in Fig.…”

“…In our quest to understand the molecular pathogenesis of kidney fibrosis, a major underlying process leading to chronic kidney disease, we identified Msi1 to be significantly up-regulated (ϳ18-fold, p ϭ 0.003) in mouse kidneys subjected to folic acid-induced chronic progressive fibrosis (12). The objective of this study was to investigate the role of Msi1 in the progression of kidney fibrosis.…”

Genetic-Variation-Driven Gene-Expression Changes Highlight Genes with Important Functions for Kidney Disease

“…Many of these transcription factors have been shown to be important in kidney development or kidney disease. 42,49,50 An example of a kidney-specific eQTL is shown in Figure 2D, where the rs946213 variant influences the expression of RRP15 (MIM: 611193). The SNP is located at a promoter and the variant interrupted the GATA5 binding motif.…”

Kidneys

“…Overall these observations indicate that certain apolipoproteins and enzymes on HDL particles pass through the glomerulus and can be reabsorbed, metabolized, or excreted in the urine. Interestingly, mass spectrometry of urine from patients with fibrotic kidney disease revealed that an HDL component, PLTP, along with cadherin and macrophage mannose receptor C1, is significantly increased [10]. Complimentary experimental studies showed that urinary exertion of PLTP paralleled increased gene and protein expression in tubules of kidneys from several animal models and biopsy specimens, suggesting PLTP may be a novel biomarker of kidney fibrosis.…”