Using stem cells derived from Alport syndrome (AS) patients to examine their genetic and protein profile, scientists identified three factors — microRNA-4775, ELV-like protein 1-A (ELAVL1), and epidermal growth factor receptor (EGFR) — as likely candidates in this genetic disease’s underlying mechanisms, and possible targets for treatments.
The study “Establishment of microRNA, transcript and protein regulatory networks in Alport syndrome induced pluripotent stem cells” was published in the journal Molecular Medicine Reports.
AS, an hereditary disease, causes injury to the kidneys known as glomerulonephritis, and it can also give rise to hearing loss and vision problems.
The disease’s origin has been linked to a genetic error or mutation in the genes COL4A3, COL4A4, and COL4A5, which lead to defects in the collagen IV protein, the major constituent of the mature mammalian glomerular basement membrane (GBM), a part of the kidney.
Although progress has been made in understanding the genetic basis of AS, the exact mechanisms that lead to clinical symptoms are not well understood.
A research team in China used kidney cells, called renal tubular cells, taken from and healthy controls (all members of a family with three generations of AS patients) to generate pluripotent stem cells (iPSCs) — stems cells that are able to become almost any type of cell in the body.
A total of six family members were selected: two sisters and a mother for the AS group; and another sister, a brother and a father for the control group. From the generated iPSCs, researchers extracted genetic material, RNA, and protein for further analysis.
They first focused on microRNAs (miRNAs). Unlike other RNA molecules, microRNAs do not give rise to a protein but regulate gene expression (protein production).
By comparing patient iPSCs with control iPSCs, they found a total of 155 miRNAs whose activity was significantly changed between these two groups.
Moreover, the activity of over one thousand genes (1,168) were significantly changed — in iPSCs from AS patients, 786 genes had their activity increased (or upregulated) and 382 decreased (downregulated). The levels of 383 proteins were also significantly different, with 227 at higher levels among patients and 156 at lower levels.
With these miRNA, RNA, and protein profiles, a computational analysis was conducted to build a regulatory network that connected the expression of miRNAs to RNAs to proteins.
This is the first attempt for “investigating miRNA‐target transcript, miRNA-target protein and transcript-protein networks in the context of an iPSC AS disease model,” the researchers wrote.
The computer analysis identified cellular pathways as especially altered in patients’ iPSCs, namely “carbon metabolism” and “cell adhesion molecules.”
miRNAs and their targets were linked with changes in the cell’s membrane — researchers highlighted how alterations in the glomerular basement membrane, a key part of the kidney’s filtration system, marks Alport syndrome.
Changes in cell adhesion, fibrosis, and abnormal metabolism have also been described in AS patients.
The analysis identified the microRNA hsa-miR-4755, ELALV1, and the protein EGFR as most potentially relevant targets in treating AS.
“Numerous diseases have been linked to the misregulation or malfunction of proteins that interact with RNA. Thus, deciphering RNA-protein interactions at the molecular and cellular level is essential for understanding human physiology and disease
Hsa‐miR‐4775 and ELALV1 have both been linked with cancer invasion and progression; ELAV1 in the case human renal cell carcinoma. , while EGFR is known to have a key role in chronic renal failure.
“Therefore,” the researchers wrote, “it may be hypothesized that [the] upregulated EGFR [gene] was involved in chronic renal failure of AS. “
Their study concluded: “Integration of multiple profiling datasets provides a novel way of examining gene regulation by miRNAs in conjunction with proteins and transcripts. This approach may enhance the understanding of the pathogenesis [disease development] of AS and provide novel diagnostic and treatment strategies for AS.”
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