Managing the Spatial Covariance of Genetic Diversity in Niemann-Pick C1 Through Modulation of the Hsp70 Chaperone System

Abstract

Genetic diversity provides a rich repository for understanding the role of proteostasis in the management of the protein fold to allow biology to evolve through variation in the population and in response to the environment. Failure in proteostasis can trigger multiple disease states affecting both human health and lifespan. Niemann-Pick C (NPC) disease is a genetic disorder mainly caused by mutations in NPC1, a multi-spanning transmembrane protein that is trafficked through the exocytic pathway to late endosomes and lysosomes (LE/Ly) to manage cholesterol homeostasis. Proteostatic defects triggered by >600 NPC1 variants found in the human population inhibit export of NPC1 protein from ER or function in downstream LE/Ly, leading to accumulation of cholesterol and rapid onset neurodegeneration in childhood for most patients. We now show that chemical allosteric inhibitors, such as JG98, targeting the cytosolic Hsp70 chaperone/co-chaperone complex improves the trafficking and stability of NPC1 variants with diverse NPC1 genotypes. By exploiting the knowledge-base of NPC1 variants found in the world-wide patient population using Variation Spatial Profiling (VSP), a Gaussianprocess based machine learning (ML) approach, we show how the Hsp70 chaperone system alters the spatial covariance (SCV) tolerance of the ER and the SCV set-points for each residue of the NPC1 polypeptide chain differentially to improve trafficking efficiency and post-ER stability for variants distributed across the entire NPC1 polypeptide. The impact of JG98 is supported by the observation that silencing of Hsp70 specific nucleotide exchange factors (NEF) (BCL-anthogene (BAG) family) cochaperones significantly improve the folding status of NPC1 variants. Together, these studies suggest that targeting the cytosolic Hsp70 system to adjust the SCV tolerance of the proteostasis network can improve recognition of the plasticity of the NPC1 fold found in the disease population for trafficking to the LE/Ly compartments.

Correction of Niemann-Pick type C1 disease with the histone deacetylase inhibitor valproic acid

“…We posit that a combination of VPA-mediated correction of NPC1 trafficking and CQmediated alteration of lysosomal pH, that affects rescued NPC1 variant function, may provide a more favorable LE/Ly environment that could have clinical value in improving HPCD based therapies. Because HPCD based therapies only impact the toxic build-up of cholesterol in cells, they fail to address the fundamental problem in disease which will require restoration of a functional NPC1 fold in the context of the genetic diversity found in the patient population (17,18). We posit that in response to the reduced cholesterol load generated by HPCD, pharmaceuticals that boost NPC1 variant function will be necessary to restore cholesterol recycling and downstream neuropsychological activity impacting patients.…”

“…Patient fibroblasts homozygous for the I1061T variant exhibit reduced protein expression and defective folding of NPC1, leading to its retention in the ER where it is subsequently degraded by the ubiquitin-proteasome system (UPS) (33). In contrast, other variants show efficient trafficking to the LE/Ly compartments but lack activity (17,18). Given the critical role played by NPC1 in cholesterol homeostasis, uncovering small molecules or biological pathways that restore the trafficking of a functional form of the I1061T variant to LE/Ly compartments will be critical for the treatment of NPC disease.Current therapeutic opportunities for NPC disease include a clinical trial for the intrathecal administration of the cholesterol homeostasis modulator, 2-hydroxypropyl--cyclodextrin (HPCD) (https://clinicaltrials.gov/ct2/show/NCT03879655), marketed as VTS-270, and arimoclomol , a heat shock protein (Hsp) activator (34-37).…”