Overexpression of Nfe2l1 increases proteasome activity and delays vision loss in a preclinical model of human blindness

Proteasomes are the central proteolytic machines that are critical for breaking down most of the damaged and abnormal proteins in human cells. Although universally applicable drugs are not yet available, the stimulation of proteasomal activity is being analyzed as a proof-of-principle strategy to increase cellular resistance to a broad range of proteotoxic stressors. These approaches have included the stimulation of proteasomes through the overexpression of individual proteasome subunits, phosphorylation, or conformational changes induced by small molecules or peptides. In contrast to these approaches, we evaluated a transcription-driven increase in the total proteasome pool to enhance the proteolytic capacity of degenerating retinal neurons. We show that overexpression of nuclear factor erythroid-2-like 1 (Nfe2l1) transcription factor stimulated proteasome biogenesis and activity, improved the clearance of the ubiquitin-proteasomal reporter, and delayed photoreceptor neuron loss in a preclinical mouse model of human blindness caused by misfolded proteins. The findings highlight Nfe2l1 as an emerging therapeutic target to treat neurodegenerative diseases linked to protein misfolding.

Methods for In Vivo Characterization of Proteostasis in the Mouse Retina

An increasing number of studies connect inherited and age-related retinal degenerations with changes in the regulation of proteostasis. Here, we describe technical aspects of existing assays allowing to assess the status of the ubiquitin-proteasome system (UPS), changes in autophagy, and protein translation in mouse retina in vivo. These methods are helpful for the development and testing approaches to modulate proteostasis and delay vision loss.

Very long chain fatty acid-containing lipids: a decade of novel insights from the study of ELOVL4

Lipids play essential roles in maintaining cell structure and function by modulating membrane fluidity and cell signaling. The fatty acid elongase-4 (ELOVL4) protein, expressed in retina, brain, Meibomian glands, skin, testes and sperm, is an essential enzyme that mediates tissue-specific biosynthesis of both VLC-PUFA and VLC-saturated fatty acids (VLC-SFA). These fatty acids play critical roles in maintaining retina and brain function, neuroprotection, skin permeability barrier maintenance, and sperm function, among other important cellular processes. Mutations in ELOVL4 that affect biosynthesis of these fatty acids cause several distinct tissue-specific human disorders that include blindness, age-related cerebellar atrophy and ataxia, skin disorders, early-childhood seizures, mental retardation, and mortality, which underscores the essential roles of ELOVL4 products for life. However, the mechanisms by which one tissue makes VLC-PUFA and another makes VLC-SFA, and how these fatty acids exert their important functional roles in each tissue, remain unknown. This review summarizes research over that last decade that has contributed to our current understanding of the role of ELOVL4 and its products in cellular function. In the retina, VLC-PUFA and their bioactive "Elovanoids" are essential for retinal function. In the brain, VLC-SFA are enriched in synaptic vesicles and mediate neuronal signaling by determining the rate of neurotransmitter release essential for normal neuronal function. These findings point to ELOVL4 and its products as being essential for life. Therefore, mutations and/or age-related epigenetic modifications of fatty acid biosynthetic gene activity that affect VLC-SFA and VLC-PUFA biosynthesis contribute to age-related dysfunction of ELOVL4-expressing tissues.

Phosphoinositide Profile of the Mouse Retina

Phosphoinositides are known to play multiple roles in eukaryotic cells. Although dysregulation of phosphoinositide metabolism in the retina has been reported to cause visual dysfunction in animal models and human patients, our understanding of the phosphoinositide composition of the retina is limited. Here, we report a characterization of the phosphoinositide profile of the mouse retina and an analysis of the subcellular localization of major phosphorylated phosphoinositide forms in light-sensitive photoreceptor neurons. Using chromatography of deacylated phosphatidylinositol headgroups, we established PI(4,5)P₂ and PI(4)P as two major phosphorylated phosphoinositides in the retina. Using high-resolution mass spectrometry, we revealed 18:0/20:4 and 16:0/20:4 as major fatty-acyl chains of retinal phosphoinositides. Finally, analysis of fluorescent phosphoinositide sensors in rod photoreceptors demonstrated distinct subcellular distribution patterns of major phosphoinositides. The PI(4,5)P₂ reporter was enriched in the inner segments and synapses, but was barely detected in the light-sensitive outer segments. The PI(4)P reporter was mostly found in the outer and inner segments and the areas around nuclei, but to a lesser degree in the synaptic region. These findings provide support for future mechanistic studies defining the biological significance of major mono- (PI(4)P) and bisphosphate (PI(4,5)P₂) phosphatidylinositols in photoreceptor biology and retinal health.

Clarin-1 expression in adult mouse and human retina highlights a role of Müller glia in Usher syndrome

Usher syndrome type 3 (USH3) is an autosomal recessively inherited disorder caused by mutations in the gene clarin‐1 (CLRN1), leading to combined progressive hearing loss and retinal degeneration. The cellular distribution of CLRN1 in the retina remains uncertain, either because its expression levels are low or because its epitopes are masked. Indeed, in the adult mouse retina, Clrn1 mRNA is developmentally downregulated, detectable only by RT‐PCR. In this study we used the highly sensitive RNAscope in situ hybridization assay and single‐cell RNA‐sequencing techniques to investigate the distribution of Clrn1 and CLRN1 in mouse and human retina, respectively. We found that Clrn1 transcripts in mouse tissue are localized to the inner retina during postnatal development and in adult stages. The pattern of Clrn1 mRNA cellular expression is similar in both mouse and human adult retina, with CLRN1 transcripts being localized in Müller glia, and not photoreceptors. We generated a novel knock‐in mouse with a hemagglutinin (HA) epitope‐tagged CLRN1 and showed that CLRN1 is expressed continuously at the protein level in the retina. Following enzymatic deglycosylation and immunoblotting analysis, we detected a single CLRN1‐specific protein band in homogenates of mouse and human retina, consistent in size with the main CLRN1 isoform. Taken together, our results implicate Müller glia in USH3 pathology, placing this cell type to the center of future mechanistic and therapeutic studies to prevent vision loss in this disease. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Systemic Delivery of Genes to Retina Using Adeno-Associated Viruses

Mutations in more than 80 genes lead to photoreceptor degeneration. Although subretinal delivery of genes to photoreceptor neurons using AAV vectors has proven itself as an efficient therapeutic and investigative tool in various mouse models, the surgical procedure itself could lead to loss of retinal function even in healthy animals, complicating the interpretation of experimental studies and requiring thoroughly designed controls. A noninvasive approach, such as a systemic delivery of genes with AAV through the bloodstream, may serve as a promising direction in tool development. Previous studies have established that AAV9 is capable of crossing the blood-brain and blood-retina barrier and even has a limited capacity to transduce photoreceptors. AAV-PHP.eB is a novel AAV9-based mutant capsid that crosses the blood-brain barrier and efficiently transduces central nervous system in the adult mice. Here, we investigated its ability to cross the blood-retina barrier and transduce retinal neurons. Control experiments demonstrated virtually nonexisting ability of this capsid to transduce retinal cells via intravitreal administration but high efficiency to transduce photoreceptors via subretinal route. Systemic delivery of AAV-PHP.eB in adult mice robustly transduced horizontal cells throughout the entire retina, but not photoreceptors. Our study suggests that AAV-PHP.eB crosses the intra-retinal blood-retinal barrier (IR-BRB), efficiently transduces horizontal cells located adjacent to IR-BRB, but has very limited ability to further penetrate retina and reach photoreceptors.

Loss of Arf4 causes severe degeneration of the exocrine pancreas but not cystic kidney disease or retinal degeneration

Arf4 is proposed to be a critical regulator of membrane protein trafficking in early secretory pathway. More recently, Arf4 was also implicated in regulating ciliary trafficking, however, this has not been comprehensively tested in vivo. To directly address Arf4’s role in ciliary transport, we deleted Arf4 specifically in either rod photoreceptor cells, kidney, or globally during the early postnatal period. Arf4 deletion in photoreceptors did not cause protein mislocalization or retinal degeneration, as expected if Arf4 played a role in protein transport to the ciliary outer segment. Likewise, Arf4 deletion in kidney did not cause cystic disease, as expected if Arf4 were involved in general ciliary trafficking. In contrast, global Arf4 deletion in the early postnatal period resulted in growth restriction, severe pancreatic degeneration and early death. These findings are consistent with Arf4 playing a critical role in endomembrane trafficking, particularly in the pancreas, but not in ciliary function.

Primary cilia are sensory organelles found on most cells and contain specific receptors that detect extracellular stimuli. Defects in trafficking receptors to cilia cause a diverse set of diseases called ciliopathies, which include polycystic kidney disease, obesity, cerebral anomalies and retinal degeneration. Based mostly on in vitro studies, the small GTPase Arf4 was thought to be critically important for localizing rhodopsin to the outer segment of photoreceptor cells and cystoproteins to kidney cilia. Here we genetically remove Arf4 from mice in either a tissue specific or time dependent manner. To our surprise, the loss of Arf4 does not cause retinal degeneration or cystic kidney disease. Since ciliary dysfunction causes retinal degeneration and cystic disease, our findings indicate that Arf4 does not play a role in ciliary function. Instead, mice have zymogen granule defects and degeneration of the exocrine pancreas supporting roles for Arf4 in regulating endomembrane trafficking in specific cells.

Blood flow controls coagulation onset via the positive feedback of factor VII activation by factor Xa

Background

Blood coagulation is a complex network of biochemical reactions, which is peculiar in that it is time- and space-dependent, and has to function in the presence of rapid flow. Recent experimental reports suggest that flow plays a significant role in its regulation. The objective of this study was to use systems biology techniques to investigate this regulation and to identify mechanisms creating a flow-dependent switch in the coagulation onset.

Results

Using a detailed mechanism-driven model of tissue factor (TF)-initiated thrombus formation in a two-dimensional channel we demonstrate that blood flow can regulate clotting onset in the model in a threshold-like manner, in agreement with existing experimental evidence. Sensitivity analysis reveals that this is achieved due to a combination of the positive feedback of TF-bound factor VII activation by activated factor X (Xa) and effective removal of factor Xa by flow from the activating patch depriving the feedback of "ignition". The level of this trigger (i.e. coagulation sensitivity to flow) is controlled by the activity of tissue factor pathway inhibitor.

Conclusions

This mechanism explains the difference between red and white thrombi observed in vivo at different shear rates. It can be speculated that this is a special switch protecting vascular system from uncontrolled formation and spreading of active coagulation factors in vessels with rapidly flowing blood.

Growth factor receptor-bound protein 14 undergoes light-dependent intracellular translocation in rod photoreceptors: functional role in retinal insulin receptor activation

Growth factor receptor-bound protein 14 (Grb14) is involved in growth factor receptor tyrosine kinase signaling. Here we report that light causes a major redistribution of Grb14 among the individual subcellular compartments of the retinal rod photoreceptor. Grb14 is localized predominantly to the inner segment, nuclear layer, and synapse in dark-adapted rods, whereas in the light-adapted rods, Grb14 redistributed throughout the entire cell, including the outer segment. The translocation of Grb14 requires photoactivation of rhodopsin, but not signaling through the phototransduction cascade, and is not based on direct Grb14-rhodopsin interactions. We previously hypothesized that Grb14 protects light-dependent insulin receptor (IR) activation in rod photoreceptors against dephosphorylation by protein tyrosine phosphatase 1B. Consistent with this hypothesis, we failed to observe light-dependent IR activation in Grb14(-/-) mouse retinas. Our studies suggest that Grb14 translocates to photoreceptor outer segments after photobleaching of rhodopsin and protects IR phosphorylation in rod photoreceptor cells. These results demonstrate that Grb14 can undergo subcellular redistribution upon illumination and suggest that rhodopsin photoexcitation may trigger signaling events alternative to the classical transducin activation.

Transducin translocation in rods is triggered by saturation of the GTPase-activating complex

Light causes massive translocation of G-protein transducin from the light-sensitive outer segment compartment of the rod photoreceptor cell. Remarkably, significant translocation is observed only when the light intensity exceeds a critical threshold level. We addressed the nature of this threshold using a series of mutant mice and found that the threshold can be shifted to either a lower or higher light intensity, dependent on whether the ability of the GTPase-activating complex to inactivate GTP-bound transducin is decreased or increased. We also demonstrated that the threshold is not dependent on cellular signaling downstream from transducin. Finally, we showed that the extent of transducin alpha subunit translocation is affected by the hydrophobicity of its acyl modification. This implies that interactions with membranes impose a limitation on transducin translocation. Our data suggest that transducin translocation is triggered when the cell exhausts its capacity to activate transducin GTPase, and a portion of transducin remains active for a sufficient time to dissociate from membranes and to escape from the outer segment. Overall, the threshold marks the switch of the rod from the highly light-sensitive mode of operation required under limited lighting conditions to the less-sensitive energy-saving mode beneficial in bright light, when vision is dominated by cones.

Minimal determinants for binding activated G alpha from the structure of a G alpha(i1)-peptide dimer

G-proteins cycle between an inactive GDP-bound state and an active GTP-bound state, serving as molecular switches that coordinate cellular signaling. We recently used phage display to identify a series of peptides that bind G alpha subunits in a nucleotide-dependent manner [Johnston, C. A., Willard, F. S., Jezyk, M. R., Fredericks, Z., Bodor, E. T., Jones, M. B., Blaesius, R., Watts, V. J., Harden, T. K., Sondek, J., Ramer, J. K., and Siderovski, D. P. (2005) Structure 13, 1069-1080]. Here we describe the structural features and functions of KB-1753, a peptide that binds selectively to GDP x AlF4(-)- and GTPgammaS-bound states of G alpha(i) subunits. KB-1753 blocks interaction of G alpha(transducin) with its effector, cGMP phosphodiesterase, and inhibits transducin-mediated activation of cGMP degradation. Additionally, KB-1753 interferes with RGS protein binding and resultant GAP activity. A fluorescent KB-1753 variant was found to act as a sensor for activated G alpha in vitro. The crystal structure of KB-1753 bound to G alpha(i1) x GDP x AlF4(-) reveals binding to a conserved hydrophobic groove between switch II and alpha3 helices and, along with supporting biochemical data and previous structural analyses, supports the notion that this is the site of effector interactions for G alpha(i) subunits.

Complex dynamics of the formation of spatially localized standing structures in the vicinity of saddle-node bifurcations of waves in the reaction-diffusion model of blood clotting

Local activation in a one-dimensional three-component reaction-diffusion model of blood clotting may lead to a formation of spatially localized standing structures (peaks) via several complex scenarios. In the first scenario, two concentration pulses first propagate from the site of activation, then stop and transform into peaks [Zarnitsina et al., Chaos 11, 57 (2001)]. Here, we examine this scenario, and also describe a different scenario of peak formation. In this scenario, two trigger waves propagate initially in opposite directions away from the site of activation. Then they stop and change direction of propagation toward each other to the activation site, where they interact and form a peak. Both of these scenarios of stable peak formation are observed in the vicinity of saddle-node bifurcation and may be viewed as a memory of the extinct wave modes.

Running pulses of complex shape in a reaction-diffusion model

In a one-dimensional reaction-diffusion model of an active medium, stable steady-state wave pulses of a new type are described. They are called multihumped because their waveforms contain several maxima of similar size. Presumably, the multihumped pulses arise via a bifurcation at which an unstable trigger wave disappears. The parameter governing this bifurcation is the diffusion coefficient for the model inhibitor. The model is analyzed by varying this parameter to determine the conditions for the emergence of multihumped pulses. The results of this analysis show how their waveform and dynamics of excitation depend on the inhibitor diffusion coefficient.

[From nonequilibrium thermodynamics to nonlinear dynamics]

Differences between the thermodynamic and kinetic approaches were discussed by using a system with two or more different steady states as an example. It was shown that the behavior of such systems can be described adequately by the kinetic approach only.

Unstable trigger waves induce various intricate dynamic regimes in a reaction-diffusion system of blood clotting

In this work we demonstrate that the unstable trigger waves, connecting stable and unstable spatially uniform steady states, can create intricate dynamic regimes in one-dimensional three-component reaction-diffusion model describing blood clotting. Among the most interesting regimes are the composite and replicating waves running at a constant velocity. The front part of the running composite wave remains constant, while its rear part oscillates in a complex manner. The rear part of the running replicating wave periodically gives rise to new daughter waves, which propagate in the direction opposite the parent wave. The domain of these intricate regimes in parameter space lies in the region of monostability near the region of bistability.