Blocking the inhibition of PKD1 and PKD2 gene expression by deleting a binding site for microRNAs hindered the formation and growth of kidney cysts in autosomal dominant polycystic kidney disease (ADPKD) models, UT Southwestern researchers reported. The findings, published in Nature Communications, suggest a strategy for gene therapy with the potential to arrest or cure ADPKD.
“For more than 25 years, we have known that ADPKD is caused by mutations of PKD1 or PKD2 genes. Yet, no therapeutic strategy exists to go after these root causes,” said Vishal Patel, M.D., Associate Professor of Internal Medicine in the Division of Nephrology at UTSW and corresponding author of the paper.
ADPKD is among the most common human genetic conditions and the most frequent genetic cause of kidney failure, affecting an estimated 12.5 million people worldwide. ADPKD is an inherited disease in which patients typically inherit one mutated copy of PKD1 (or PKD2) and one normal copy.
The disease is characterized by the frequent formation of many small fluid-filled sacs called kidney cysts, which are believed to form when the levels of PKD1 or PKD2 fall below a critical threshold. This can occur when the normal copy of the gene does not produce enough of the proteins Polycystin-1/Polycystin-2.
Proteins are produced (or translated) from a gene’s messenger ribonucleic acid (mRNA). At one end of the mRNA strand is a region of code that helps protect it from degradation but can also control how much of the protein is made. The binding of microRNAs to this region of the mRNA code can block translation, leading to production of less protein.
PKD1 contains a binding site for miR-17, a microRNA that is highly expressed and active in models of ADPKD. So, Dr. Patel and his colleagues asked if blocking the binding of miR-17 to PKD1 could prevent kidney cyst formation.
The researchers deleted the miR-17 binding site from PKD1 mRNA in cell cultures and an ADPKD mouse model. Their results indicated that deletion of the binding site increased stability of the mRNA strand, raised Polycystin-1 levels, and decreased kidney cyst growth. Moreover, the group found that blocking miR-17 binding to PKD1 mRNA with an anti-miR-17 drug after cyst formation also decreased cyst growth, indicating that this interaction could be a promising target for polycystic kidney disease (PKD) treatment.
“There are numerous genetic conditions where one copy of the causative gene is mutated, but the other copy is still normal. Our approach to harnessing the remaining normal copy is likely applicable to many other diseases besides PKD,” said Dr. Patel.
PKD1 loss-of-function as the genetic cause of ADPKD was discovered over 25 years ago29–31, but approaches to restore PKD1 expression remain elusive. We provide a feasible framework for increasing endogenous PKD1 and show for the first time that monoallelic Pkd1 derepression is sufficient to alleviate preclinical PKD. As an attractive safety feature, Pkd1 cis-inhibition appears to be an ADPKD-specific phenomenon since we observed that the Pkd1 miR-17 motif has minimal impact in wild-type adult mouse kidneys.
Furthermore, our work suggests that restoring even hypomorphic Pkd1 mutants may be beneficial. On a cautionary note, particularly for modalities employing exogenous PKD1 supplementation, raising Pkd1 above wild-type levels produces cystic disease in mice32,33. However, the uniqueness of our approach is that, rather than transactivation, it relies on preventing inhibition, making it unlikely that PKD1 will rise to the supratherapeutic range.
Our studies clarify the role of PKD1 in cyst initiation and its continual expansion. A unifying and parsimonious explanation for ADPKD onset is that cystogenesis ensues when the PKD1 dosage falls by 70-80%, dipping below a critical threshold3. Thus, heterozygous germline PKD1 inactivation alone cannot account for this magnitude of dose reduction. Additional stochastic events that repress the remaining allele are required and critical in determining disease onset. However, the somatic inhibitory mechanism(s) in addition to the ‘second-hit’ mutations are unknown. Our discovery of cis-interference resulting in inefficient translation of mRNAs transcribed by the non-inactivated PKD1 allele represents a novel and targetable ADPKD onset mechanism.
Along with cyst initiation, PKD1 inhibition unleashes large-scale transcriptomic and metabolic dysregulation and activates numerous oncogenic pathways, such as cAMP and c-Myc/Yap4,34–42. In turn, this downstream cyst-pathogenic signaling fuels cyst expansion. Remarkably, even in the face of such widespread dysregulation, a recent elegant study reported that transgenic Pkd1 or Pkd2 reconstitution rapidly reverts established cystic disease in mice43. Consistently, we found that acute Pkd1/2 derepression reigns in established cystic disease and makes Pkd1-mutant cells resistant to pro-cystogenic stimuli such as cAMP and SAM. Collectively, these observations point to PKD1 as the primary, if not the sole, factor governing both cyst onset and growth.
We report an unexpected finding that Pkd2 influences the cystic phenotype of Pkd1-mutant models. PC1 and PC2 physically interact and are coexpressed at multiple subcellular locations, indicating that the two proteins function in the same physiological pathway44–47. We add a new dimension by extending this relationship into the pathological context. Perhaps, enhancing Pkd2 expression in Pkd1-mutant cells may lead to improved PC1 trafficking and more heteromeric PC1-PC2 protein complexes.
Our work highlights an underappreciated aspect of gene regulation. Canonical thinking is that miRNAs simultaneously but subtly repress large mRNA networks. In contrast, we made the surprising finding that, under certain circumstances, miRNAs transform into potent single-target inhibitors. In fact, we show that an individual 3’-UTR MBE has a marked disease-modifying impact. Most miRNAs are dispensable for homeostatic tissue functions, and they are pharmaceutically inhibited with relative ease.
Despite these favorable characteristics, miRNA-based drug development has languished in comparison to other forms of RNA therapeutics48. This is partly because the pleiotropic molecular mechanism of numerous downstream mRNA targets makes it difficult to validate the miRNA biological effect or develop pharmacodynamic readouts of anti-miRNA drugs. We argue that prioritizing miRNAs that function as tonic inhibitors of a handful of disease-central mRNAs is likely to be a fruitful drug development strategy. Importantly, our insights are transferable, and we speculate that similar modes of therapeutically targetable cis-inhibitory regulation exist in other disorders, especially haploinsufficient monogenetic conditions.
reference link: https://www.biorxiv.org/content/10.1101/2022.02.23.479396v1.full
More information: Ronak Lakhia et al, PKD1 and PKD2 mRNA cis-inhibition drives polycystic kidney disease progression, Nature Communications (2022). DOI: 10.1038/s41467-022-32543-2