Glomerular Disease with Nephrotic Syndrome
The common types of glomerular diseases that often present with nephrotic syndrome in adults are focal segmental glomerulosclerosis (FSGS) - a progressive scarring in the glomerulus, or capillary system in the renal corpuscle, and membranous nephropathy (MN), which is the deposition of immune complexes in the glomerular basement membrane of the kidney. Minimal change disease (MCD), a kidney disease in which large amounts of protein are lost in the urine, is also common and usually leads to nephrotic syndrome.
Most glomerular diseases have autoimmune causes and are usually associated with nephritic syndrome - a condition in which excessive amounts of protein are excreted in the urine. The term nephritic syndrome refers to a number of different signs and symptoms that occur as a result of inflammation of the kidneys. The common types of glomerular diseases that often present with nephrotic syndrome in adults are focal segmental glomerulosclerosis (FSGS) - a progressive scarring in the glomerulus, or capillary system in the renal corpuscle, and membranous nephropathy (MN), which is the deposition of immune complexes in the glomerular basement membrane of the kidney. Minimal change disease (MCD), a kidney disease in which large amounts of protein are lost in the urine, is also common and usually leads to nephrotic syndrome.
The cause of these diseases is often unknown, but they are thought to be multifactorial. Recent research has suggested that the apolipoprotein L1 gene (APOL1) contributes to the development of FSGS in populations of African descent. Immune system dysregulation is thought to play a role in the development of all three diseases. Using machine learning methods, researchers have identified characteristic glomerular gene expression profiles in patients with MN. The identification of common molecular pathways in patients with FSGS, MN, and MCD could lead to the development of new therapeutic targets for the treatment of nephrotic syndrome.
Identyfing Dysregulated Molecular Pathways in Glomerular Disease Using Machine Learning and Gene Expression Analysis
Now, researchers have set out to investigate the presence of molecular signaling pathways that are dysregulated in these glomerular diseases. In this study, gene expression data from the Gene Expression Omnibus (GEO) were used to identify common signaling pathways in the three forms of nephrotic syndrome (FSGS, MN, and MCD) mentioned before. Differentially expressed genes (DEGs) were analyzed and merged using GEO2R to identify common up- or down-regulated transcripts. Enriched metabolic pathways were identified using R packages and mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic database. Machine learning technology was used to determine the meaning of each transcript. Bioinformatics tools Cytoscape and DAVID were used to uncover enriched transcripts that reference key gene ontology (GO) terms.
The top 200 upregulated transcripts for each form of nephrotic syndrome were selected and merged into an overlapping transcript list. This list was narrowed down by gene-entity ID and internally merged with enriched transcripts for the major GO term. The resulting gene list was imported into a protein-protein interaction prediction web tool to visualize the physical interactions of the major gene-encoded proteins. The study also used the results of single-cell RNA sequencing analysis and protein distribution patterns to identify the distribution patterns of the encoded hub genes on kidney sections. Additional gene expression data sets were obtained from kidney biopsies to validate the differential gene expression of key transcripts. The study was based on publicly available data and without direct patient involvement.
Common Molecular Pathways and Key Genes Contributing to Glomerular Disease
Results showed 1087 significant DEGs common to all three diseases, with focal adhesion and Rap1 pathway showing the highest levels of support. Machine learning algorithms identified ZYX as the major contributor to FSGS, MN, and MCD. GO analysis using Cytoscape and DAVID tools revealed that upregulated transcripts were enriched in terms related to plasma membrane and cytoskeletal protein binding, whereas downregulated transcripts did not yield significant hits.
Further, the researchers identified a list of 72 genes that were upregulated in all three forms of the disease and then narrowed this down to a list of 28 genes that were relevant to the plasma membrane. They then examined the physical interactions of the proteins encoded by these genes using the STRING bioinformatics tool. The authors also used scRNA-seq data to determine the renal cell types expressing these core genes and found that ZYX was highly expressed in most renal cells, whereas ENG was mainly expressed in glomerular endothelial cells and mesangial cells, and CRK was expressed in most renal cells, with lower levels in glomerular endothelial cells. The authors also validated the differential expression of ZYX in human glomerulopathies compared with normal controls and found that it was upregulated in several data sets.
10 Key Findings on The Molecular Basis of Common Forms of Nephrotic Syndrome
FSGS, MN, and MCD are diseases with different etiologies, but they all display heavy proteinuria.
Dysregulation of adherens junction, focal adhesion, and also actin cytoskeleton pathways is observed across all three diseases.
Actinin (ACTN4), filamin (FLNA), talin (TLN1), myosin II (MYH9), Arp2/3 (ARPC2/ARPC3), CRK, ZYX, integrin (ITGA), and extracellular matrix (ECM1) are upregulated in the glomerular compartment of patients with FSGS, MN, and MCD.
Focal adhesions are sites where cells connect to the extracellular matrix (ECM).
Focal adhesion molecules and the actin cytoskeleton play a crucial role in maintaining proper podocyte functional structure with foot processes attached to the glomerular basement membrane (GBM).
ZYX is the most important molecule within the focal adhesion pathway contributing to these common forms of nephrotic syndrome.
ZYX plays a key role in force-induced actin polymerization at focal adhesions through recruitment of Ena/VASP.
It interacts with α-actinin (ACTN4) to impact all three forms of nephrotic syndrome.
ZYX-associated focal adhesion malfunction might implicate multiple kidney cell types in development of nephrotic syndrome.
CRK is a family of adaptors required for the formation of focal adhesions and is upregulated in FSGS, MN, and MCD glomeruli.