Introduction:Primary cilia are critical sensory organelles whose structure and composition are tightly regulated. The Scribble polarity complex protein DLG1 has recently been implicated in controlling both ciliary protein composition and length in mouse kidney epithelial cells. In addition, the palmitoyl transferase ZDHHC5 localizes to primary cilia and negatively regulates their length. However, the molecular mechanisms underlying DLG1-mediated ciliary regulation and its interaction network remain poorly defined. Methods:To identify cilium-associated DLG1 interactors, mouse inner medullary collecting duct (IMCD3) cells stably expressing DLG1-BioID2 were generated and subjected to proximity-dependent biotinylation proteomics in ciliated conditions. Candidate interactions were validated using immunoprecipitation, AlphaFold structural modeling, and quantitative immunofluorescence microscopy. Functional relevance was further assessed in vivo using zebrafish models with depletion of zdhhc5 paralogs. Results:Proximity labeling identified 46 high-confidence DLG1 interactors, of which 35 were previously associated with ciliary or centrosomal protein networks. Among these, ZDHHC5 was confirmed as a DLG1 interactor by immunoprecipitation, and structural modeling supported a potential direct interaction. Quantitative imaging demonstrated that ZDHHC5 localizes to primary cilia independently of DLG1. Additional analyses revealed that DLG1 also interacts with SCAMP3 and STXBP1 and is required for proper localization of STXBP1 at the ciliary base. In zebrafish, depletion of zdhhc5a and zdhhc5b resulted in ciliopathy-like phenotypes, including brain edema, curved body axis, and enlarged glomerular structures, accompanied by significantly elongated cilia in both the brain and pronephros. Discussion:These findings expand the DLG1 interactome and identify key cilia-associated partners, including ZDHHC5 and STXBP1, that may contribute to the regulation of ciliary structure and function. The data support a model in which DLG1 modulates ciliary length and signaling through specific protein-protein interactions, with disruption of this network leading to ciliopathy-related phenotypes. Together, this study provides new mechanistic insight into polarity complex-mediated control of primary cilia in kidney epithelial cells.

Inositol polyphosphate-5-phosphatase E (INPP5E) encodes the ciliary protein INPP5E, which plays an important role in regulating the phospholipid membrane makeup of the primary cilium. Here, we utilize proximity labeled proteomics of INPP5E to broaden the number of known functional modules that work in close proximity to the protein. In doing so, we identified the EH-binding protein EHBP1 as a ciliary protein that localizes to the basal body and ciliary compartment of the primary cilium in human-derived fibroblasts and RPE cells. Additionally, we show that EHBP1 localizes to the rudimentary outer segment membrane of developing photoreceptors in retinal organoids. Dysfunction of INPP5E - either due to pathogenic variants in human fibroblasts or CRISPR/Cas9-generated loss-of-function variants in human retinal organoids - causes the localization of EHBP1 to be altered. Our data suggest that EHBP1 functions at the primary cilium and photoreceptors, where it is regulated by INPP5E. This provides further insights into the disease pathogenesis of retinal ciliopathies caused by pathogenic variants in INPP5E, and suggests that EHBP1 might be a candidate gene for retinal ciliopathies.

The deposition of circulating complement factor H-related (FHR) proteins in tissues around the body has been implicated in a series of complement-mediated diseases. However, the array of blood-borne binding partners with which they interact remains unclear. Here, we identify novel blood-borne binding partners of FHR proteins, firstly through preliminary untargeted immunoprecipitation and mass spectrometry, and subsequently validating direct interactions through solid-phase binding assays. We uncover direct interactions between FHRs and soluble immune mediators including complement C4 (C4), cathepsin G (CTSG), mannose-binding lectin 2 (MBL2), and platelet basic protein (PPBP). Functional assays show that FHR-1 and FHR-2 attenuate CTSG-mediated C3b degradation, while FHR-5 and FHL-1 appear to affect lectin pathway activation via MBL2 binding. These interactions suggest that FHRs perhaps confer activity not only through surface competition with factor H, but also via selective engagement with circulating ligands. Our findings expand the known FHR interactome and reveal potential new avenues for understanding FHR biology and targeting complement dysregulation in disease.

Mutations in the ciliary gene INPP5E, encoding inositol polyphosphate-5-phosphatase E (INPP5E), can cause retinal degeneration as part of the ciliopathy Joubert syndrome or non-syndromic retinitis pigmentosa (RP). INPP5E regulates the membrane makeup of the primary cilium; however, its function in the specialized sensory photoreceptor cells of the human retina remain unclear. Here, we utilize control and CRISPR/Cas9-generated INPP5E knockout (INPP5ED477N/D477N) human induced pluripotent stem cells (iPSCs) to generate retinal organoids (ROs). Through proteomic and immunofluorescence analysis, we show that INPP5E plays an important role in early retinal development and photoreceptor progenitor cell differentiation. In mature ROs, INPP5E localizes to the connecting cilium of photoreceptors, and the loss of INPP5E leads to altered localization of ARL13B and rhodopsin in mature photoreceptors. Furthermore, photoreceptor outer segment structure is affected, leading to elongated outer segment membranes in both cone and rod photoreceptors, suggesting an important role for INPP5E in photoreceptor outer segment membrane biogenesis. Together, these data underline the importance of INPP5E in retina development and photoreceptor structure and highlight the usability of ROs to study protein function in a human context.

The classical approach of using adjacent pieces of fresh-frozen tissue for various omics analysis from the same sample possesses a risk of biological mismatch between arising from intrinsic tissue heterogeneity. We propose an alternative approach of tissue cryogenic pulverization and lyophilization before distribution for omics studies for a more reliable analysis. Here, we compare individual omics layer readouts from fresh-frozen adjacent tissue pieces and homogenized powder in mouse brain, kidney, and liver. Genomics, transcriptomics, proteomics, and metabolomics analyses showed comparable RNA integrity, DNA methylation, and coverage of transcripts, proteins, and metabolites across both methods. Moreover, the homogenized-lyophilized powder usage led to reduced heterogeneity between biological replicates. We conclude that the cryogenically pulverized-lyophilized tissue approach not only maintains a critical molecular feature coverage and quality but also provides a homogenous basis for various omics analysis enhancing reproducibility, sample transport, storage and enabling multi omics base on one and the same tissue aliquot.

Introduction: Nephronophthisis (NPHP) is an autosomal recessive kidney disease resulting mainly from primary cilium defects, with unspecific and variable symptoms that can progress to kidney failure needing replacement therapy at a young age. Currently, up to 64% of likely NPHP cases can be diagnosed by assessing known genes. Therefore, there is a need to gain more insight in what genes can cause this disease. METHODS:In a diagnostic setting, we performed broad genetic testing in patients with advanced kidney disease. We carried out in silico and in vitro analyses for TMEM72, including immunohistochemistry and affinity proteomics, and in vivo experiments to further interpret our findings. RESULTS:We identified biallelic TMEM72 variants in 9 patients from six families with a phenotype suggestive for NPHP. Five families presented with kidney failure at a (young) adult age. One family had a different phenotype with prenatal onset of kidney failure and neurological symptoms. The phenotypes of the patients correspond to TMEM72 expression mainly in the kidney. In silico analyses indicate that homozygous loss-of-function variants are likely not tolerated in TMEM72. Immunohistochemistry staining of kidney biopsies revealed altered localization and expression of TMEM72 in cases compared to controls. In human-derived tubuloids, we showed that TMEM72 localizes to the cilium. Furthermore, using an affinity proteomics approach, we found an association of TMEM72 and ciliary function, more specifically in selective ciliary cholesterol transport. CONCLUSION:We present the first genetic evidence, underlined by immunohistochemistry and protein binding assays, linking TMEM72 variants to kidney disease and ciliary function. We conclude that TMEM72 is a candidate gene for NPHP. Future work is needed to further characterize TMEM72 variants and unravel its disease mechanism. .

Genotype-phenotype correlations of rare diseases are complicated by low patient number, high phenotype variability, and compound heterozygosity. Mutations may cause instability of single proteins, and affect protein complex formation or overall robustness of a specific process in a given cell. Ciliopathies offer an interesting case for studying genotype-phenotype correlations as they have a spectrum of severity and include diverse phenotypes depending on different mutations in the same protein. For instance, mutations in the intraflagellar transport protein IFT140 cause a vast spectrum of ciliopathies ranging from isolated retinal dystrophy to severe skeletal abnormalities and multi-organ diseases such as Mainzer-Saldino and Jeune syndrome. Here, the quantitative effects of 23 missense mutations in IFT140, which forms part of the crucial IFT-A complex of the ciliary machinery, were analyzed using affinity purification coupled with mass spectrometry (AP-MS). A subset of 10 mutations led to a significant and domain-specific reduction in IFT140-IFT-A complex interaction indicating complex formation issues and potentially hampering its molecular function. Knockout of IFT140 led to loss of cilia, as shown before. However, phenotypically only mild effects concerning cilia assembly were observed for two out of four tested IFT140 missense mutations. Therefore, our results demonstrate the utility of AP-MS in discerning pathogenic MMs from polymorphisms, and we postulate that reduced function is tolerated by the evolutionarily highly conserved IFT-A system.

A major proportion of retinal disease-causing genes are related to the primary cilium, a microtubule-based signalling organelle essential for multiple developmental pathways. Previous work has shown that the primary cilium plays a crucial role in the development of the retinal pigment epithelium (RPE) affecting homeostasis and function, in particular phagocytosis. We used a cell biology approach to analyse the influence of ciliary genes on RPE phagocytosis and dissect the underlying molecular mechanisms. We found that loss of ciliary trafficking via depletion of Ift20 and Ift88 in RPE-J cells resulted in impaired phagocytosis, specifically by reducing photoreceptor outer segments binding, changes in apical membrane morphology and altered mitochondrial metabolism, whereas loss of Bbs6 showed no functionality phenotype. In addition, proteomics revealed mis-regulated pathways and targets, through which new phagocytosis-related proteins were identified. Our data highlight the role of primary cilia proteins in RPE function and metabolism, essential for visual health. ### Competing Interest Statement The authors have declared no competing interest. Johannes Gutenberg University Mainz, https://ror.org/023b0x485 Deutsche Forschungsgemeinschaft, FOR5547 – Project-ID MA 6139/6-1 503306912 Bardet-Biedl France Fondation Maladies Rares, Pigmentary retinopathy 2024 IHU FOReSIGHT, ANR-18-IAHU-0001 Centre National de la Recherche Scientifique, https://ror.org/02feahw73 Institut National de la Santé et de la Recherche Médicale DIM C-BRAINS Sorbonne Université Studienstiftung des deutschen Volkes Studienstiftung des deutschen Volkes

Bialleleic pathogenic variants in LCA5 cause one of the most severe forms of Leber congenital amaurosis, an early-onset retinal disease that results in severe visual impairment. Here, we report the use of gene editing to generate isogenic LCA5 knock-out (LCA5 KO) induced pluripotent stem cells (iPSC) and their differentiation to retinal organoids. The molecular and cellular phenotype of the LCA5 KO retinal organoids was studied in detail and compared to isogenic controls as well as patient-derived retinal organoids. The absence of LCA5 was confirmed in retinal organoids by immunohistochemistry and western blotting. There were no major changes in retinal organoid differentiation or ciliation, however, the localisation of CEP290 and IFT88 was significantly altered in LCA5 KO and patient photoreceptor cilia with extension along the axoneme. The LCA5-deficient organoids also had shorter outer segments and rhodopsin was mislocalised to the outer nuclear layer. We also identified transcriptomic and proteomic changes associated with the loss of LCA5. Importantly, treatment with the small molecules eupatilin, fasudil or a combination of both drugs reduced CEP290 and IFT88 accumulation along the cilia. The treatments also improved rhodopsin traffic to the outer segment and reduced mislocalisation of rhodopsin in the outer nuclear layer (ONL). The improvements in cilia-associated protein localisation and traffic were accompanied by significant changes in the transcriptome towards control gene expression levels in many of the differentially expressed genes. In summary, iPSC-derived retinal organoids are a powerful model for investigating the molecular and cellular changes associated with loss of LCA5 function and highlight the therapeutic potential of small molecules to treat retinal ciliopathies.

Dynamic control of ciliary membrane protein content is crucial for the organelle's homeostasis and signaling function and involves removal of ciliary components by intraflagellar transport (IFT) and BBSome-mediated export, endocytic retrieval, and/or extracellular vesicle (EV) shedding. We report that the kinesin-3 motor KIF13B regulates ciliary protein composition and EV shedding in cultured kidney epithelial cells, with effects that vary over time. In early stages of ciliation, Kif13b-/- cells aberrantly accumulate polycystin-2 (PC2) within cilia and release large EVs enriched with CCDC198 and the centriole distal appendage protein CCDC92, which also localizes to the ciliary tip. These cells also produce fewer small EVs through the neutral sphingomyelinase 2 pathway. Upon cilia maturation, Kif13b-/- cells accelerate large EV release of numerous ciliary proteins, including PC2, BBSome, and IFT components, which correlates with gradual depletion of CCDC92 and PC2 from the ciliary tip and shaft, respectively. Furthermore, over time, Kif13b-/- cells show an upregulation in the release of small EVs, which differ in composition from wild-type small EVs. Specifically, mutant small EVs lack several proteins that are enriched in small EVs from BBSome-deficient cells, including palmitoyl transferase ZDHHC5, which localizes to cilia where it accumulates upon BBSome dysfunction and regulates ciliary length and PC2 levels. Our results suggest that KIF13B acts at the level of centriole distal appendages to limit ciliary protein entry and promote endocytic retrieval downstream of the BBSome, thereby suppressing EV release from cilia. Furthermore, the ciliary localization of CCDC198 and ZDHHC5 indicates they are potential novel ciliopathy candidates.

The polycystic kidney disease gene product polycystin-2 (PC2) localizes to and is released from primary cilia in extracellular vesicles (EVs). We report that KIF13B regulates ciliary EV release and PC2 levels in kidney epithelial cells in a time-dependent manner and show that KIF13B itself is released from the ciliary tip. In early stages of ciliation, Kif13b -/- cells displayed excessive ciliary accumulation of PC2 and initially released fewer small EVs than control cells. Over time, ciliated Kif13b -/- cells increased their small EV release rate to control levels, however proteomic analysis identified >50 proteins depleted from mutant EV samples. These included the ubiquitin E3 ligase ITCH and palmitoyl transferase ZDHHC5, which localized to primary cilia. Mature Kif13b -/- cilia exhibited aberrant membrane bulges and decreased PC2 and ALIX, an ITCH substrate that negatively regulated ciliary PC2 levels. Our work provides new insight into the mechanisms of ciliary EV release, which is important for regulating ciliary membrane homeostasis and signalling function. ### Competing Interest Statement The authors have declared no competing interest.

Biological complexity is achieved through elaborate interactions between relatively few individual components. Affinity purification (AP) has allowed these networks of protein-protein interactions that regulate key biological processes to be interrogated systematically. In order to perform these studies at the required scale, easily transfectable immortalized cell lines have typically been used. Gene-editing now affords the systematic creation of isogenic mouse models carrying endogenous tags for affinity proteomics. This may allow protein-protein interactions to be characterized in the appropriate tissue for a particular biological process or disease phenotype under physiological conditions, and for interaction landscapes to be compared across tissues. Here we demonstrate application to intraflagellar transport (IFT) proteins, which are WD40-domain-containing proteins that are essential for the formation and function of all types of cilia. We describe a method to generate mice with an endogenous C-terminal streptavidin/FLAG tag, using Ift80 as an example, and demonstrate the successful implementation of AP in this model. This method can easily be adapted for N- and C-terminal tagging of many other proteins in vivo.

Rationale: Bronchiectasis is a pathological dilatation of the bronchi in the respiratory airways associated with environmental or genetic causes (e.g., cystic fibrosis, primary ciliary dyskinesia, and primary immunodeficiency disorders), but most cases remain idiopathic. Objectives: To identify novel genetic defects in unsolved cases of bronchiectasis presenting with severe rhinosinusitis, nasal polyposis, and pulmonary Pseudomonas aeruginosa infection. Methods: DNA was analyzed by next-generation or targeted Sanger sequencing. RNA was analyzed by quantitative PCR and single-cell RNA sequencing. Patient-derived cells, cell cultures, and secretions (mucus, saliva, seminal fluid) were analyzed by Western blotting and immunofluorescence microscopy, and mucociliary activity was measured. Blood serum was analyzed by electrochemiluminescence immunoassay. Protein structure and proteomic analyses were used to assess the impact of a disease-causing founder variant. Measurements and Main Results: We identified biallelic pathogenic variants in WAP four-disulfide core domain 2 (WFDC2) in 11 individuals from 10 unrelated families originating from the United States, Europe, Asia, and Africa. Expression of WFDC2 was detected predominantly in secretory cells of control airway epithelium and also in submucosal glands. We demonstrate that WFDC2 is below the limit of detection in blood serum and hardly detectable in samples of saliva, seminal fluid, and airway surface liquid from WFDC2-deficient individuals. Computer simulations and deglycosylation assays indicate that the disease-causing founder variant p.Cys49Arg structurally hampers glycosylation and, thus, secretion of mature WFDC2. Conclusions: WFDC2 dysfunction defines a novel molecular etiology of bronchiectasis characterized by the deficiency of a secreted component of the airways. A commercially available blood test combined with genetic testing allows its diagnosis.

Polarized vesicular trafficking directs specific receptors and ion channels to cilia, but the underlying mechanisms are poorly understood. Here we describe a role for DLG1, a core component of the Scribble polarity complex, in regulating ciliary protein trafficking in kidney epithelial cells. Conditional knockout of Dlg1 in mouse kidney caused ciliary elongation and cystogenesis, and cell-based proximity labelling proteomics and fluorescence microscopy showed alterations in the ciliary proteome upon loss of DLG1. Specifically, the retromer-associated protein SDCCAG3, IFT20 and polycystin-2 (PC2) were reduced in cilia of DLG1 deficient cells compared to control cells. This phenotype was recapitulated in vivo and rescuable by re-expression of wildtype DLG1, but not a Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)-associated DLG1 variant, p.T489R. Finally, biochemical approaches and Alpha Fold modelling suggested that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Our work identifies a key role for DLG1 in regulating ciliary protein composition and suggests that ciliary dysfunction of the p.T489R DLG1 variant may contribute to CAKUT.