Mapping of the amniotic fluid proteome of fetuses with congenital anomalies of the kidney and urinary tract identifies plastin 3 as a protein involved in glomerular integrity

Abstract

Congenital anomalies of the kidney and the urinary tract (CAKUT) are the first cause of chronic kidney disease in childhood. Several genetic and environmental origins are associated with CAKUT, but most pathogenic pathways remain elusive. Considering the amniotic fluid (AF) composition as a proxy for fetal kidney development, we analyzed the AF proteome from non-severe CAKUT (n = 19), severe CAKUT (n = 14), and healthy control (n = 22) fetuses using LC-MS/MS. We identified 471 significant proteins that discriminated the three AF groups with 81% precision. Among them, eight proteins independent of gestational age (CSPG4, LMAN2, ENDOD1, ANGPTL2, PRSS8, NGFR, ROBO4, PLS3) were associated with both the presence and the severity of CAKUT. Among those, five were part of a protein-protein interaction network involving proteins previously identified as being potentially associated with CAKUT. The actin-bundling protein PLS3 (plastin 3) was the only protein displaying a gradually increased AF abundance from control, via non-severe, to severe CAKUT. Immunohistochemistry experiments showed that PLS3 was expressed in the human fetal as well as in both the fetal and the postnatal mouse kidney. In zebrafish embryos, depletion of PLS3 led to a general disruption of embryonic growth including reduced pronephros development. In postnatal Pls3-knockout mice, kidneys were macroscopically normal, but the glomerular ultrastructure showed thickening of the basement membrane and fusion of podocyte foot processes. These structural changes were associated with albuminuria and decreased expression of podocyte markers including Wilms' tumor-1 protein, nephrin, and podocalyxin. In conclusion, we provide the first map of the CAKUT AF proteome that will serve as a reference for future studies. Among the proteins strongly associated with CAKUT, PLS3 did surprisingly not specifically affect nephrogenesis but was found as a new contributor in the maintenance of normal kidney function, at least in part through the control of glomerular integrity.

Proteomic profiling and correlations with clinical features reveal biomarkers indicative of diabetic retinopathy with diabetic kidney disease

“…The proteins with the lowest FC values included LMAN2, ACTC1, C1QA, MYOC and VCAM1. LMAN2 encodes a type 1 transmembrane lectin that shuttles between the endoplasmic reticulum, Golgi apparatus and plasma membrane ( 21 ) and is associated with the risk of kidney function decline ( 22 ). ACTC1 encodes actin, which is involved in various types of cell motility, especially cardiac diseases.…”

Integrative analysis of CAKUT multi-omics data

“…The CAKUT multi-omics data set was obtained from a previously published study and reinvestigated in collaboration with the authors of the original study 6,22 . The initial study contains amniotic fluid samples from proteome and peptidome.…”

“…The peptidome and the proteome data sets were quantile normalised and log2 transformed as previously described 36,37 . Before transformation, peptide IDs were mapped to protein IDs, and were summarised into single protein-level values using geometric mean 22 . The miRNome data set was already normalised and transformed, thus the information of their target genes could be added to each miRNA ID without additional data manipulation, using the information provided by miTaRBase.…”

“…The CAKUT multi-omics data sets for the proteomics and peptidomics data sets are available with the original studies 6,22 and the repositories mentioned there. The miRNome data is available at https://zenodo.org/record/7866785#.ZE9wZXZBwuV.…”

Association between aberrant amino acid metabolism and nonchromosomal modifications fetal structural anomalies: A cohort study

“…Liquid chromatography-tandem mass spectrometry (LC-MS/ MS) is a current, routine, highly accurate application in newborn screening (14,15). Similarly, metabolomics can be applied to fetal malformations by exploring the AF metabolome, and several studies have reported promising results (16,17), revealing the possibility of using this technology in clinical practice. Since AF can reflect both maternal and fetal health, linking AF metabolic profiles with structural anomalies is conducive to biomarker discovery, and will better guide clinical practice.…”