Biology subjects

Koning, R. I.

Publications and source records attributed to Koning, R. I..

12 recordsLinked to original sources

bioRxiv2026

Retinal Phd2 ablation partially rescues Crb1Crb2-associated Leber congenital amaurosis and alters metabolic signaling

Leber congenital amaurosis (LCA) is a severe early-onset retinal dystrophy caused by pathogenic variants in several genes, including CRB1. CRB1-associated LCA is characterized by disrupted retinal polarity, lamination, and photoreceptor organization, with no restorative treatment. We investigated whether retinal deletion of Phd2 (Egln1), encoding prolyl hydroxylase domain protein 2 (PHD2), could provide mutation-independent neuroprotection in a severe developmental model of CRB1-associated LCA. Using conditional Crb1/Crb2-deficient mice, we additionally deleted Phd2 throughout the neural retina and assessed retinal function, structure, visually guided behavior, and glycolysis-associated gene and protein expression at one and two months. Compared with Crb1/Crb2-deficient mice, additional Phd2 deletion partially improved scotopic responses and significantly increased the optomotor spatial-frequency threshold, whereas b-wave and cone-mediated responses remained impaired. Phd2Crb1Crb2-deficient retinas displayed more organized photoreceptor rosettes containing rod- and cone-marker-positive cells, in contrast to the diffuse outer-retinal disorganization and nuclear-layer amalgamation observed in Crb1/Crb2-deficient retinas. Polarity- and synapse-associated proteins showed improved local compartmentalization within these structures. Metabolic responses were temporally selective: Glut1 and Vegfa transcript levels increased at one month, whereas GLUT1 and LDHA protein levels increased at two months; Pdk1 transcript levels decreased at 2M, whereas PDK1 protein abundance remained unchanged. Although Phd2 deletion did not correct the underlying Crumbs-complex defect or normalize retinal lamination, and elevated Vegfa coincided with persistent vascular abnormalities, these findings demonstrate that retinal Phd2 deletion partially modifies the structural and functional consequences of severe Crb1/Crb2 deficiency and supports further investigation of PHD2-associated metabolic signaling as a potential disease-modifying target for severe CRB1-associated retinal degeneration.

neuroscience↗

bioRxiv2026

USH2A High-Capacity Adenoviral Vector Restores usherin, whirlin, and ADGRV1 in Photoreceptor Cells of Retinal Organoids

Development of gene therapies for USH2A-associated diseases has been limited by the large size of the USH2A coding sequence, which exceeds the packaging capacity of adeno-associated viral vectors. Here, we evaluated high-capacity adenoviral vectors (HC-AdVs) as vehicles for a mutation-independent USH2A gene supplementation strategy in USH2A human retinal organoids. First, we generated human induced pluripotent stem cell (hiPSC) lines carrying a nonsense mutation in USH2A exon-61 (61KO). Similarly to our previously established exon-13 knockout model (13KO), 61KO hiPSC-derived retinal organoids showed reduced levels of usherin and its interacting proteins, adhesion G protein-coupled receptor V1 (ADGRV1), and whirlin, at the photoreceptor connecting cilium. Delivery of a HC-AdV5 encoding full-length USH2A under the control of the photoreceptor-specific human rhodopsin kinase (hGRK1) promoter restored usherin expression and promoted re-localization of ADGRV1 and whirlin to their physiological sites at the connecting cilium in 13KO and 61KO photoreceptors. Unexpectedly, usherin expression was also observed within mutant Muller glial cells. These findings provide proof-of-concept that HC-AdV5-mediated delivery of full-length USH2A can successfully promote the rescue of usherin and relocate its interacting partners in USH2A-defective retinal organoids, demonstrating its potential as a variant-independent therapeutic approach for inherited retinal disorders caused by USH2A mutations.

neuroscience↗

bioRxiv2026

Selectivity and dynamics of VAP family tether exchange across membrane contact sites

To integrate diverse cellular function and coordinate homeostasis, the endoplasmic reticulum (ER) communicates with all other intracellular compartments through physical interfaces termed membrane contact sites (MCSs). Given the sheer diversity of possible MCS pairings, how the ER discriminates between simultaneously available binding partners remains unclear. To explore this, we performed comparative endogenous contact site mapping for three closely related VAP family tethers and uncovered a unique set of FFAT motif selectivity and MCS footprints for each: VAPA at mitochondria and TGN, VAPB at mitochondria and peroxisomes, and MOSPD2 at mature endosomes, lysosomes and lipid droplets. In line with their MCS selectivity profiles, co-depletion of VAPA and VAPB, but not MOSPD2, caused systemic breakdown in mitochondrial integrity, while silencing of MOSPD2 alone was sufficient to disrupt the organization and transport of (endo)lysosomes. Unexpectedly, coincident loss of VAPA and VAPB instigated ER contact site rewiring by redirecting endogenous MOSPD2 to the collapsing mitochondrial network. Our findings define hierarchies of ER contact site formation and reveal compensation mechanisms exploited by cells to safeguard organelle homeostasis and crosstalk.

cell biology↗

bioRxiv2026

Loss of ABCA4 from photoreceptor discs triggers changes in glial cell homeostasis

Loss-of-function mutations in the ABCA4 gene cause Stargardt disease (STGD1), the most common inherited macular dystrophy leading to progressive central vision loss. Here, we generated hiPSC-derived retinal organoids harboring a premature stop codon in exon-24 of ABCA4 to evaluate the impact of this mutation on mRNA and protein levels in a human model. Immunofluorescence analysis revealed the absence of ABCA4 protein in the mutant photoreceptor outer segment discs, while single-cell RNA sequencing detected no major transcriptional alterations in rods and cones. Unexpectedly, differential gene expression and pathway enrichment analyses of Muller glial cells (MGCs) and astrocytes highlighted disruption of neuronal development, microenvironment of glial cells, intercellular communication, and programmed cell death pathways. These findings suggest that ABCA4 might play a role in maintaining the retinal microenvironment homeostasis, and that the early transcriptomic response of MGCs and astrocytes preceding photoreceptor degeneration could contribute to Stargardt disease development. Significance StatementHuman induced pluripotent stem cell (hiPSC)-derived retinal organoids provide a powerful platform to investigate inherited retinal diseases. In this study, we generated ABCA4-mutant hiPSC lines and differentiated them into retinal organoids to model Stargardt disease. Despite complete loss of ABCA4 protein from the photoreceptor outer segment discs, rods and cones exhibited minimal transcriptional alterations. In contrast, the ABCA4 variant triggered changes in the glial cell homeostasis, suggesting that Muller glial cells and astrocytes might exhibit an early response to photoreceptor dysfunction in the absence of ABCA4. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/718110v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1d8dbf6org.highwire.dtl.DTLVardef@51239corg.highwire.dtl.DTLVardef@f8fbdborg.highwire.dtl.DTLVardef@5f0b44_HPS_FORMAT_FIGEXP M_FIG Human induced pluripotent stem cells (hiPSCs) were engineered to generate ABCA4-mutant cell lines, later differentiated into retinal organoids as a model of Stargardt disease. The organoids showed loss of ABCA4 from the outer segment discs of rod and cone photoreceptors, while the mutant Muller glial cells and astrocytes exhibited transcriptional changes in pathways involved in neuronal development, microenvironment, and programmed cell death. C_FIG

neuroscience↗

bioRxiv2026

VAPB and its binding partner AKAP11 promote lipid droplet degradation

The endoplasmic reticulum (ER) is the master regulator of various cellular processes. To achieve its diverse functions, the ER interacts with other organelles at membrane contact sites, regions where organelles are brought into proximity. Most ER membrane contact sites are facilitated by the ER-resident VAP proteins. To address the role of VAP proteins in regulating cellular lipid homeostasis, we performed a targeted lipidomic screen after silencing individual VAPs. The loss of VAPB increases cellular levels of neutral lipids stored in lipid droplets (LDs). The increase in neutral lipids is reflected in the size, number and motility of LDs, and is due to the impaired degradation of these organelles. VAPB requires its contact site forming ability to regulate LDs, prompting the identification of protein kinase A (PKA) anchor AKAP11 as a VAPB interaction partner in regulating LD degradation and dynamics. Collectively, our findings identify a role for the ER-resident VAPB-AKAP11 interaction and PKA activity in regulating LD homeostasis. SummaryThe ER-resident membrane contact site protein VAPB and its interaction partner AKAP11 regulate lipid droplet size and motility by mediating neutral lipid degradation. VAPB requires its ability to form membrane contact sites and interact with AKAP11, protein kinase A anchor protein, for mediating lipid droplet homeostasis. This paper uncovers a role for VAPB-AKAP11-PKA axis in regulating the homeostasis of lipid droplets.

cell biology↗

bioRxiv2026

Supervised machine learning versus expert assessment of ultrastructural changes in wild-type and OGT knockout macrophages

Automated transmission electron microscopy (TEM) generates large datasets that challenge traditional qualitative analysis of cellular ultrastructure. Quantitative assessment of structural differences between different samples remains difficult due to structural variability in thin sections of organelles. Here we applied supervised machine learning (sML) to segment, quantify and compare cellular structures -including nuclei, chromatin, mitochondria, rough endoplasmic reticulum, and endocytic vesicles- in large TEM images of wild-type macrophages versus those with altered cellular physiology due to deficiency in O-GlcNAc Transferase (OGT). sML revealed that OGT knockout macrophages are larger and more oval, with increased euchromatin, nucleoli size, and relative mitochondrial and rER surface areas. Comparison with six TEM experts showed sML provides more objective and sensitive quantification of subtle differences, while expert consensus is only achieved for larger structural variations. These findings demonstrate that sML enhances quantitative TEM analysis and complements human expertise in ultrastructural studies.

cell biology↗

bioRxiv2026

O-GlcNAcylation drives macrophage IL-4 responsiveness and tissue residency through metabolic and cell cycle calibration

The metabolic requirements for macrophage IL-4 polarization remain contentious, while immunometabolic studies of tissue resident macrophages are still sparse. Hexosamine biosynthesis has gained attention regarding its immune regulatory potential via downstream O-GlcNAcylation. Here we identify protein O-GlcNAcylation as a requirement for IL-4 polarization in vitro and proliferative expansion in vivo during cytokine challenge or infection. We further show that O-GlcNAcylation is critical for controlling tissue residency. By enforcing metabolic and cell cycle quiescence during differentiation, O-GlcNAcylation is needed for adult monocytes to establish a long-live residency program. In this context, its absence leads to perpetual DNA vulnerability and damage via reactive oxygen species, resulting in a senescent-like state poised for cell death. Conversely, long-lived populations instead require O-GlcNAcylation for self-renewal and inflammatory expansion. Our findings altogether suggest O-GlcNAcylation, fueled by hexosamine biosynthesis, serves as a central metabolic rheostat for resident macrophage formation and maintenance during homeostasis and disease.

immunology↗

bioRxiv2025

A human sensory neuron model for varicella-zoster virus latency and reactivation in vitro.

Varicella-zoster virus (VZV) is a ubiquitous human neurotropic alphaherpesvirus that establishes lifelong latency in sensory ganglionic neurons. Subsequent viral reactivation causes herpes zoster, a morbid disease often complicated by neuropathic pain. Mechanisms underlying VZV latency and reactivation are not understood, mostly due to the lack of permissive animal models and challenges of current in vitro latency modelling. Here, we evaluated HD10.6 cells, a simplified and easily expandable human sensory neuron line to model VZV latency and reactivation. Mature HD10.6 (mHD10.6) differentiated neurons supported productive VZV infection, viral DNA replication, production of infectious progeny, and viral spread in cultures. VZV infection was associated with limited cytopathic effects and ultrastructural changes. Infecting mHD10.6 neurons with cell-free VZV in the presence of antivirals resulted in a quiescent-persistent state, characterized by persistent VZV genomes with restricted VZV gene expression and absence of infectious virus. Importantly, VZV could be reactivated by treatment with capsaicin, as evidenced by increased lytic viral transcription and virus spread. In conclusion, this study establishes human HD10.6 neurons as a novel and scalable in vitro model for studying VZV latency and reactivation to identify virus and host factors governing latency that may serve as therapeutic targets to restrict VZV reactivation. ImportanceMost individuals carry latent varicella-zoster virus (VZV) in their dorsal root ganglia (DRG), which can reactivate to cause shingles and chronic pain. The mechanisms by which VZV establishes latency and triggers of reactivation are incompletely understood. Current platforms for the study of VZV latency do not easily support functional experiments (ganglia) or are difficult to expand and complicated by mixed neuronal populations (stem cell-derived neurons). Here, we demonstrate that matured HD10.6 (mHD10.6) cells derived from immortalized human DRG-derived neurons provide a clonal, scalable, and easy-to-expand platform for studying lytic, latent, and reactivated VZV infection in sensory neurons. We propose that the HD10.6 platform could provide the basis to conduct studies on the viral latent state that have hitherto not been possible.

microbiology↗

bioRxiv2023

A lipid transfer protein knockout library reveals ORP9-ORP11 dimer mediating PS/PI(4)P exchange at the ER-trans Golgi contact site to promote sphingomyelin synthesis

Numerous lipids are heterogeneously distributed among organelles. Most lipid trafficking between organelles is achieved by a group of lipid transfer proteins (LTPs) that carry lipids using their hydrophobic cavities. The human genome encodes many intracellular LTPs responsible for lipid trafficking and the function of many LTPs in defining cellular lipid levels and distributions is unclear. Here, we created a gene knockout library targeting 90 intracellular LTPs and performed whole-cell lipidomics analysis. This analysis confirmed known lipid disturbances and identified new ones caused by loss of LTPs. Among these, we found major sphingolipid imbalances in ORP9 and ORP11 knockout cells, two proteins of previously unknown function in sphingolipid metabolism. ORP9 and ORP11 form a heterodimer to localize at the ER-trans Golgi membrane contact sites, where the dimer exchanges phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between the two organelles. Consequently, loss of either protein causes phospholipid imbalances in the Golgi apparatus that result in lowered sphingomyelin synthesis at this organelle. Overall, our LTP knockout library toolbox identifies various proteins in control of cellular lipid levels, including the ORP9-ORP11 heterodimer, which exchanges PS and PI(4)P at the ER-Golgi membrane contact site as a critical step in sphingomyelin synthesis in the Golgi apparatus.

cell biology↗

bioRxiv2022

A high-impact COL6A3 mutation alters the response of chondrocytes in neo-cartilage organoids to hyper-physiologic mechanical loading

ObjectivesThe etiology of osteoarthritis revolves around the interplay between genetic predisposition and perturbing environmental cues, such as mechanical stress. The pericellular matrix, with its hallmark proteins collagen type VI and fibronectin, surrounds chondrocytes and is critical in transducing the biomechanical cues. The objective is to study the functional effects of an OA disease-risk mutation in COL6A3 in interaction with hyper-physiological mechanical cues in a tailored human induced pluripotent stem cells (hiPSCs) derived cartilage organoid model. MethodTo identify pathogenic OA mutations exome sequencing in symptomatic OA patients was performed. To study functional effects, CRISPR-Cas9 genome engineering was used to introduce the mutation in our established human induced pluripotent stem cell-derived in-vitro neo-cartilage organoid model in interaction with hyper-physiological mechanical loading conditions. ResultsA high-impact mutation in COL6A3 was identified that resulted in significantly lower binding between the PCM proteins COLVI and fibronectin (FN) and provoked an osteoarthritic chondrocyte state. Moreover, aberrant function of the PCM, secondary to the COL6A3 mutation, abolished the initial stress responses marked particularly by upregulation of PTGS2 encoding cyclooxygenase-2 (COX-2), after hyper-physiological mechanical loading conditions. ConclusionThese findings demonstrate that ablating the characteristic transient COX-2 response after injurious mechanical cues may have a direct negative impact on chondrocyte health. What is already knownO_LIThe etiology of osteoarthritis revolves around the interplay between genetic predisposition and perturbing environmental cues, such as mechanical stress. C_LIO_LIThe pericellular matrix, with its hallmark proteins collagen type VI and fibronectin, surrounds the chondrocytes and is critical in transducing biomechanical cues from the extracellular matrix to chondrocytes henceforth it determines the chondrocyte mechanical environment. C_LIO_LIThe mechanical environment of the chondrocytes is a critical factor that influences chondrocyte health as it determines the balance between synthesis and degradation of the articular cartilage extracellular matrix. C_LI What this study addsO_LIA sustainable human induced pluripotent stem cell-derived in-vitro neo-cartilage organoid model that is tailored to study detailed biologic effects of mechanical cues to chondrocytes. C_LIO_LIAn OA disease-risk mutation in COL6A3 reduces the binding between collagen type VI to fibronectin and provoked an osteoarthritic chondrocyte state. C_LIO_LIUpon hyper-physiological mechanical loading, aberrant function of the pericellular matrix, secondary to the COL6A3 mutation, ablates the initial transient inflammatory response, characterized particularly by PTGS2 encoding cyclooxygenase-2 (COX-2). C_LI How this study might affect research practice or policyO_LIInhibiting COX-2, as an important transient inflammatory response after hyper-physiological mechanical cues, could worsen the loss of structural integrity of the cartilage in osteoarthritis patients. Henceforth, prescription of COX-2 inhibitors as pain treatment for OA patients should be reconsidered. C_LI

molecular biology↗

bioRxiv2022

Vimentin intermediate filaments organize organellar architecture in response to ER stress

Compartmentalization of organelles in space and time affects their functional state and enables higher order regulation of essential cellular processes. How organellar residence is maintained in a defined area of the cell remains poorly understood. In this study, we uncover a new role for intermediate filaments in the maintenance of organellar architecture and dynamics, which is executed through a functional connection between Vimentin and the ER-embedded ubiquitin ligase ring finger protein 26 (RNF26). While the ubiquitin ligase function of RNF26 promotes perinuclear positioning of endolysosomes, its catalytically inactive mutant I382R preferentially binds Vimentin through the RNF26 C-terminal tail. Loss of either RNF26 or Vimentin redistributes endolysosomes throughout the cytosol and mobilizes ER membranes from the perinuclear ER towards the periphery. Furthermore, RNF26 and Vimentin control changes in ER morphology and organelle compartmentalization during ER stress. Collectively, we define a new function for Vimentin-containing intermediate filaments as anchors of a dynamic interplay between the ER and endosomes, critical to the integrity of the perinuclear ER and corresponding perinuclear endosomal cloud during homeostatic and stress conditions. SynopsisThe perinuclear area hosts a wide variety of cellular organelles, and their interaction with the ER governs essential cellular processes. To spatiotemporally organize endosomes and ER in the perinuclear region, the ER-embedded E3 ubiquitin ligase RNF26 interacts with Vimentin to physically link the perinuclear ER membrane with the intermediate filament cytoskeleton. As a result, Vimentin ensures perinuclear RNF26 retention, which in turn controls the perinuclear location of ER membranes and endosomes, which can be affected during stressed conditions. O_LIVimentin interacts with inactive RNF26 in the ER membrane C_LIO_LIRNF26 by virtue of the Vimentin interaction controls perinuclear organization of ER membranes and the endosomal system C_LIO_LIVimentin immobilizes ER membranes in the perinuclear area C_LIO_LIVimentin and RNF26 compartmentalize organelles in the perinuclear region during ER stress C_LIO_LIWe define a new function of Vimentin intermediate filaments in the control of the perinuclear endosomal and ER organization C_LI

cell biology↗

bioRxiv2020

A molecular pore spans the double membrane of the coronavirus replication organelle

Coronavirus genome replication is associated with virus-induced cytosolic double-membrane vesicles, which may provide a tailored micro-environment for viral RNA synthesis in the infected cell. However, it is unclear how newly synthesized genomes and mRNAs can travel from these sealed replication compartments to the cytosol to ensure their translation and the assembly of progeny virions. Here, using cellular electron cryo-microscopy, we unveiled a molecular pore complex that spans both membranes of the double-membrane vesicle and would allow export of RNA to the cytosol. A hexameric assembly of a large viral transmembrane protein was found to form the core of the crown-shaped complex. This coronavirus-specific structure likely plays a critical role in coronavirus replication and thus constitutes a novel drug target

microbiology↗