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1.
RNA ; 2022 Oct 31.
Article En | MEDLINE | ID: mdl-36316088

Neurons critically depend on regulated RNA localization and tight control of spatio-temporal gene expression to maintain their morphological and functional integrity. Mutations in the kinesin motor protein gene KIF1C cause Hereditary Spastic Paraplegia, an autosomal recessive disease leading to predominant degeneration of the long axons of central motoneurons. In this study we aimed to gain insight into the molecular function of KIF1C and understand how KIF1C dysfunction contributes to motoneuron degeneration. We used affinity proteomics in neuronally differentiated neuroblastoma cells (SH-SY5Y) to identify the protein complex associated with KIF1C in neuronal cells; candidate interactions were then validated by immunoprecipitation and mislocalization of putative KIF1C cargoes was studied by immunostainings. We found KIF1C to interact with all core components of the exon junction complex (EJC); expression of mutant KIF1C in neuronal cells leads to loss of the typical localization distally in neurites. Instead, EJC core components accumulate in the pericentrosomal region, here co-localizing with mutant KIF1C. These findings suggest KIF1C as a neuronal transporter of the EJC. Interestingly, the binding of KIF1C to the EJC is RNA-mediated, as treatment with RNAse prior to immunoprecipitation almost completely abolishes the interaction. Silica-based solid-phase extraction of UV-crosslinked RNA-protein complexes furthermore supports direct interaction of KIF1C with RNA, as recently also demonstrated for kinesin heavy chain. Taken together, our findings are consistent with a model where KIF1C transports mRNA in an EJC-bound and therefore transcriptionally silenced state along neurites, thus providing the missing link between the EJC and mRNA localization in neurons.

2.
Nat Commun ; 13(1): 4540, 2022 08 04.
Article En | MEDLINE | ID: mdl-35927244

During pancreas development endocrine cells leave the ductal epithelium to form the islets of Langerhans, but the morphogenetic mechanisms are incompletely understood. Here, we identify the Ca2+-independent atypical Synaptotagmin-13 (Syt13) as a key regulator of endocrine cell egression and islet formation. We detect specific upregulation of the Syt13 gene and encoded protein in endocrine precursors and the respective lineage during islet formation. The Syt13 protein is localized to the apical membrane of endocrine precursors and to the front domain of egressing endocrine cells, marking a previously unidentified apical-basal to front-rear repolarization during endocrine precursor cell egression. Knockout of Syt13 impairs endocrine cell egression and skews the α-to-ß-cell ratio. Mechanistically, Syt13 is a vesicle trafficking protein, transported via the microtubule cytoskeleton, and interacts with phosphatidylinositol phospholipids for polarized localization. By internalizing a subset of plasma membrane proteins at the front domain, including α6ß4 integrins, Syt13 modulates cell-matrix adhesion and allows efficient endocrine cell egression. Altogether, these findings uncover an unexpected role for Syt13 as a morphogenetic driver of endocrinogenesis and islet formation.


Endocrine Cells , Islets of Langerhans , Integrins , Morphogenesis , Pancreas , Synaptotagmins/genetics
3.
Molecules ; 27(10)2022 May 12.
Article En | MEDLINE | ID: mdl-35630584

The very large G-protein-coupled receptor 1 (VLGR1/ADGRV1) is the largest member of the adhesion G-protein-coupled receptor (ADGR) family. Mutations in VLGR1/ADGRV1 cause human Usher syndrome (USH), a form of hereditary deaf-blindness, and have been additionally linked to epilepsy. In the absence of tangible knowledge of the molecular function and signaling of VLGR1, the pathomechanisms underlying the development of these diseases are still unknown. Our study aimed to identify novel, previously unknown protein networks associated with VLGR1 in order to describe new functional cellular modules of this receptor. Using affinity proteomics, we have identified numerous new potential binding partners and ligands of VLGR1. Tandem affinity purification hits were functionally grouped based on their Gene Ontology terms and associated with functional cellular modules indicative of functions of VLGR1 in transcriptional regulation, splicing, cell cycle regulation, ciliogenesis, cell adhesion, neuronal development, and retinal maintenance. In addition, we validated the identified protein interactions and pathways in vitro and in situ. Our data provided new insights into possible functions of VLGR1, related to the development of USH and epilepsy, and also suggest a possible role in the development of other neuronal diseases such as Alzheimer's disease.


Proteomics , Receptors, G-Protein-Coupled , Humans , Receptors, G-Protein-Coupled/metabolism , Retina/metabolism , Signal Transduction
4.
Internet Interv ; 28: 100517, 2022 Apr.
Article En | MEDLINE | ID: mdl-35251940

BACKGROUND: Alcohol use disorder, a prevalent and disabling mental health problem, is often characterized by a chronic disease course. While effective inpatient and aftercare treatment options exist, the transferal of treatment success into everyday life is challenging and many patients remain without further assistance. App-based interventions with human guidance have great potential to support individuals after inpatient treatment, yet evidence on their efficacy remains scarce. OBJECTIVES: To develop an app-based intervention with human guidance and evaluate its usability, efficacy, and cost-effectiveness. METHODS: Individuals with alcohol use disorder (DSM-5), aged 18 or higher, without history of schizophrenia, undergoing inpatient alcohol use disorder treatment (N = 356) were recruited in eight medical centres in Bavaria, Germany, between December 2019 and August 2021. Participants were randomized in a 1:1 ratio to either receive access to treatment as usual plus an app-based intervention with human guidance (intervention group) or access to treatment as usual plus app-based intervention after the active study phase (waitlist control/TAU group). Telephone-based assessments are conducted by diagnostic interviewers three and six weeks as well as three and six months after randomization. The primary outcome is the relapse risk during the six months after randomization assessed via the Timeline Follow-Back Interview. Secondary outcomes include intervention usage, uptake of aftercare treatments, AUD-related psychopathology, general psychopathology, and quality of life. DISCUSSION: This study will provide further insights into the use of app-based interventions with human guidance as maintenance treatment in individuals with AUD. If shown to be efficacious, the intervention may improve AUD treatment by assisting individuals in maintaining inpatient treatment success after returning into their home setting. Due to the ubiquitous use of smartphones, the intervention has the potential to become part of routine AUD care in Germany and countries with similar healthcare systems.

5.
iScience ; 24(4): 102283, 2021 Apr 23.
Article En | MEDLINE | ID: mdl-33851099

VLGR1 (very large G protein-coupled receptor-1) is by far the largest adhesion G protein-coupled receptor in humans. Homozygous pathologic variants of VLGR1 cause hereditary deaf blindness in Usher syndrome 2C and haploinsufficiency of VLGR1 is associated with epilepsy. However, its molecular function remains elusive. Herein, we used affinity proteomics to identify many components of focal adhesions (FAs) in the VLGR1 interactome. VLGR1 is localized in FAs and assembles in FA protein complexes in situ. Depletion or loss of VLGR1 decreases the number and length of FAs in hTERT-RPE1 cells and in astrocytes of Vlgr1 mutant mice. VLGR1 depletion reduces cell spread and migration kinetics as well as the response to mechanical stretch characterizing VLGR1 as a metabotropic mechanosensor in FAs. Our data reveal a critical role of VLGR1 in the FA function and enlighten potential pathomechanisms in diseases related to VLGR1.

6.
Nat Commun ; 11(1): 5520, 2020 11 02.
Article En | MEDLINE | ID: mdl-33139725

Axonemal dynein ATPases direct ciliary and flagellar beating via adenosine triphosphate (ATP) hydrolysis. The modulatory effect of adenosine monophosphate (AMP) and adenosine diphosphate (ADP) on flagellar beating is not fully understood. Here, we describe a deficiency of cilia and flagella associated protein 45 (CFAP45) in humans and mice that presents a motile ciliopathy featuring situs inversus totalis and asthenospermia. CFAP45-deficient cilia and flagella show normal morphology and axonemal ultrastructure. Proteomic profiling links CFAP45 to an axonemal module including dynein ATPases and adenylate kinase as well as CFAP52, whose mutations cause a similar ciliopathy. CFAP45 binds AMP in vitro, consistent with structural modelling that identifies an AMP-binding interface between CFAP45 and AK8. Microtubule sliding of dyskinetic sperm from Cfap45-/- mice is rescued with the addition of either AMP or ADP with ATP, compared to ATP alone. We propose that CFAP45 supports mammalian ciliary and flagellar beating via an adenine nucleotide homeostasis module.


Adenine Nucleotides/metabolism , Asthenozoospermia/genetics , Cytoskeletal Proteins/deficiency , Situs Inversus/genetics , Adolescent , Adult , Animals , Asthenozoospermia/pathology , Axoneme/ultrastructure , CRISPR-Cas Systems/genetics , Cilia/metabolism , Cilia/ultrastructure , Cytoskeletal Proteins/genetics , DNA Mutational Analysis , Disease Models, Animal , Epididymis/pathology , Female , Flagella/metabolism , Flagella/ultrastructure , Humans , Loss of Function Mutation , Male , Mice , Mice, Knockout , Middle Aged , Planarians/cytology , Planarians/genetics , Planarians/metabolism , Respiratory Mucosa/cytology , Respiratory Mucosa/pathology , Situs Inversus/diagnostic imaging , Situs Inversus/pathology , Sperm Motility/genetics , Tomography, X-Ray Computed , Exome Sequencing
7.
Nat Commun ; 11(1): 499, 2020 01 24.
Article En | MEDLINE | ID: mdl-31980649

Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.


Cell Transformation, Neoplastic/pathology , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , ErbB Receptors/metabolism , Mutation/genetics , Protein Interaction Maps , Proto-Oncogene Proteins p21(ras)/genetics , Cell Line, Tumor , Humans , Phosphorylation , Prognosis , Survival Analysis , bcl-Associated Death Protein/metabolism
8.
Ann N Y Acad Sci ; 1456(1): 144-167, 2019 11.
Article En | MEDLINE | ID: mdl-31441075

Adhesion G protein-coupled receptors (ADGRs) have recently become a target of intense research. Their unique protein structure, which consists of a G protein-coupled receptor combined with long adhesive extracellular domains, suggests a dual role in cell signaling and adhesion. Despite considerable progress in the understanding of ADGR signaling over the past years, the knowledge about ADGR protein networks is still limited. For most receptors, only a few interaction partners are known thus far. We aimed to identify novel ADGR-interacting partners to shed light on cellular protein networks that rely on ADGR function. For this, we applied affinity proteomics, utilizing tandem affinity purifications combined with mass spectrometry. Analysis of the acquired proteomics data provides evidence that ADGRs not only have functional roles at synapses but also at intracellular membranes, namely at the endoplasmic reticulum, the Golgi apparatus, mitochondria, and mitochondria-associated membranes (MAMs). Specifically, we found an association of ADGRs with several scaffold proteins of the membrane-associated guanylate kinases family, elementary units of the γ-secretase complex, the outer/inner mitochondrial membrane, MAMs, and regulators of the Wnt signaling pathways. Furthermore, the nuclear localization of ADGR domains together with their physical interaction with nuclear proteins and several transcription factors suggests a role of ADGRs in gene regulation.


Proteomics , Receptors, G-Protein-Coupled/metabolism , HEK293 Cells , HeLa Cells , Humans , Signal Transduction , Subcellular Fractions/metabolism
9.
PLoS One ; 14(5): e0216705, 2019.
Article En | MEDLINE | ID: mdl-31095607

The cilium is an essential organelle at the surface of mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse, zebrafish and nematode) and techniques. For example, we show that OSCP1, which has previously been implicated in two distinct non-ciliary processes, causes ciliogenic and ciliopathy-associated tissue phenotypes when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 956 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/.


Cilia/genetics , Genomics , Animals , Bayes Theorem , Caenorhabditis elegans/cytology , Caenorhabditis elegans/genetics , Molecular Sequence Annotation , Phenotype , Reproducibility of Results , Sensory Receptor Cells/metabolism , Zebrafish/genetics
10.
Mol Cell Proteomics ; 17(7): 1285-1294, 2018 07.
Article En | MEDLINE | ID: mdl-29615496

CRISPR/Cas9-mediated gene editing allows manipulation of a gene of interest in its own chromosomal context. When applied to the analysis of protein interactions and in contrast to exogenous expression of a protein, this can be studied maintaining physiological stoichiometry, topology, and context. We have used CRISPR/Cas9-mediated genomic editing to investigate Cluap1/IFT38, a component of the intraflagellar transport complex B (IFT-B). Cluap1 has been implicated in human development as well as in cancer progression. Cluap1 loss of function results in early developmental defects with neural tube closure, sonic hedgehog signaling and left-right defects. Herein, we generated an endogenously tagged Cluap1 for protein complex analysis, which was then correlated to the corresponding interactome determined by ectopic expression. Besides IFT-B complex components, new interacting proteins like Ephrin-B1 and TRIP6, which are known to be involved in cytoskeletal arrangement and protein transport, were identified. With the identification of platelet-derived growth factor A (PDGFA) and coiled-coil domain-containing protein 6 (CCDC6) two new interactions were discovered, which link Cluap1 to ciliogenesis and cancer development. The CRISPR/Cas9-mediated knockout of Cluap1 revealed a new phenotype affecting the actin cytoskeleton. Together, these data provide first evidence for a role of Cluap1 not only for cilia assembly and maintenance but also for cytoskeletal rearrangement and intracellular transport processes.


Actins/metabolism , Antigens, Neoplasm/metabolism , CRISPR-Associated Protein 9/metabolism , CRISPR-Cas Systems/genetics , Gene Editing , Actin Cytoskeleton/metabolism , Cell Movement , Cilia/metabolism , HEK293 Cells , Humans , Protein Isoforms/metabolism , Telomerase/metabolism
11.
Hum Mol Genet ; 26(21): 4190-4202, 2017 11 01.
Article En | MEDLINE | ID: mdl-28973524

Mutations in the PRKCSH, SEC63 and LRP5 genes cause autosomal dominant polycystic liver disease (ADPLD). The proteins products of PRKCSH (alias GIIB) and SEC63 function in protein quality control and processing in the endoplasmic reticulum (ER), while LRP5 is implicated in Wnt/ß-catenin signaling. To identify common denominators in the PLD pathogenesis, we mapped the PLD interactome by affinity proteomics, employing both HEK293T cells and H69 cholangiocytes. Identification of known complex members, such as glucosidase IIA (GIIA) for PRKCSH, and SEC61A1 and SEC61B for SEC63, confirmed the specificity of the analysis. GANAB, encoding GIIA, was very recently identified as an ADPLD gene. The presence of GIIA in the LRP5 complex pinpoints a potential functional connection with PRKCSH. Interestingly, all three PLD-associated protein complexes included filamin A (FLNA), a multifunctional protein described to play a role in ciliogenesis as well as canonical Wnt signalling. As ciliary dysfunction may also contribute to hereditary liver cyst formation, we evaluated the requirement of PRKCSH and SEC63 for ciliogenesis and Wnt signaling. By CRISPR/Cas9 induced knockdown of both ADPLD genes in HEK293T cells and H69 cholangiocytes, we identified that their depletion results in defective ciliogenesis. However, only H69 knockouts displayed reduced Wnt3a activation. Our results suggest that loss of PRKCSH and SEC63 leads to general defects in ciliogenesis, while quenching of the Wnt signaling cascade is cholangiocyte-restricted. Interactions of all three PLD-associated protein complexes with FLNA may mark a common link between the ADPLD proteins and the cystogenic processes driving this disease.


Cilia/pathology , Cysts/metabolism , Cysts/pathology , Glucosidases/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Liver Diseases/metabolism , Liver Diseases/pathology , Membrane Proteins/metabolism , Calcium-Binding Proteins , Cilia/genetics , Cilia/metabolism , Cysts/genetics , Endoplasmic Reticulum/pathology , Gene Knockout Techniques , Glucosidases/genetics , HEK293 Cells , Humans , Intracellular Signaling Peptides and Proteins/genetics , Liver/metabolism , Liver/pathology , Liver Diseases/genetics , Low Density Lipoprotein Receptor-Related Protein-5/genetics , Low Density Lipoprotein Receptor-Related Protein-5/metabolism , Membrane Proteins/genetics , Molecular Chaperones , RNA-Binding Proteins , Wnt Signaling Pathway , Wnt1 Protein/genetics , Wnt1 Protein/metabolism , alpha-Glucosidases/metabolism , beta Catenin/genetics , beta Catenin/metabolism
12.
Cell Signal ; 28(9): 1432-1439, 2016 09.
Article En | MEDLINE | ID: mdl-27345148

The BRAF proto-oncogene serine/threonine-protein kinase, known as BRAF, belongs to the RAF kinase family. It regulates the MAPK/ERK signalling pathway affecting several cellular processes such as growth, survival, differentiation, and cellular transformation. BRAF is mutated in ~8% of all human cancers with the V600E mutation constituting ~90% of mutations. Here, we have used quantitative mass spectrometry to map and compare phosphorylation site patterns between BRAF and BRAF V600E. We identified sites that are shared as well as several quantitative differences in phosphorylation abundance. The highest difference is phosphorylation of S614 in the activation loop which is ~5fold enhanced in BRAF V600E. Mutation of S614 increases the kinase activity of both BRAF and BRAF V600E and the transforming ability of BRAF V600E. The phosphorylation of S614 is mitogen inducible and the result of autophosphorylation. These data suggest that phosphorylation at this site is inhibitory, and part of the physiological shut-down mechanism of BRAF signalling.


Cell Transformation, Neoplastic/metabolism , Cell Transformation, Neoplastic/pathology , Phosphoserine/metabolism , Proto-Oncogene Proteins B-raf/metabolism , Amino Acid Sequence , Animals , Cell Line , Humans , Mice , Mitogen-Activated Protein Kinase Kinases/metabolism , Mutation/genetics , Phosphorylation , Protein Binding , Proto-Oncogene Mas , Proto-Oncogene Proteins B-raf/chemistry , Rats
13.
Nat Commun ; 7: 11491, 2016 05 13.
Article En | MEDLINE | ID: mdl-27173435

Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine.


Cilia/metabolism , Ciliopathies/genetics , Dwarfism/genetics , Muscle Hypotonia/genetics , Protein Interaction Maps , Proteins/metabolism , Spine/abnormalities , Biological Transport/physiology , Chromatography, Affinity/methods , Ciliopathies/pathology , Ciliopathies/therapy , DNA Mutational Analysis , Datasets as Topic , Dwarfism/pathology , Dwarfism/therapy , Fibroblasts , HEK293 Cells , Humans , Mass Spectrometry , Molecular Targeted Therapy/methods , Muscle Hypotonia/pathology , Muscle Hypotonia/therapy , Protein Interaction Mapping/methods , Proteins/genetics , Proteins/isolation & purification , Proteomics/methods , Spine/pathology , Systems Analysis
14.
PLoS Genet ; 11(10): e1005574, 2015 Oct.
Article En | MEDLINE | ID: mdl-26485514

Ciliopathies are Mendelian disorders caused by dysfunction of cilia, ubiquitous organelles involved in fluid propulsion (motile cilia) or signal transduction (primary cilia). Retinal dystrophy is a common phenotypic characteristic of ciliopathies since photoreceptor outer segments are specialized primary cilia. These ciliary structures heavily rely on intracellular minus-end directed transport of cargo, mediated at least in part by the cytoplasmic dynein 1 motor complex, for their formation, maintenance and function. Ninein-like protein (NINL) is known to associate with this motor complex and is an important interaction partner of the ciliopathy-associated proteins lebercilin, USH2A and CC2D2A. Here, we scrutinize the function of NINL with combined proteomic and zebrafish in vivo approaches. We identify Double Zinc Ribbon and Ankyrin Repeat domains 1 (DZANK1) as a novel interaction partner of NINL and show that loss of Ninl, Dzank1 or both synergistically leads to dysmorphic photoreceptor outer segments, accumulation of trans-Golgi-derived vesicles and mislocalization of Rhodopsin and Ush2a in zebrafish. In addition, retrograde melanosome transport is severely impaired in zebrafish lacking Ninl or Dzank1. We further demonstrate that NINL and DZANK1 are essential for intracellular dynein-based transport by associating with complementary subunits of the cytoplasmic dynein 1 motor complex, thus shedding light on the structure and stoichiometry of this important motor complex. Altogether, our results support a model in which the NINL-DZANK1 protein module is involved in the proper assembly and folding of the cytoplasmic dynein 1 motor complex in photoreceptor cells, a process essential for outer segment formation and function.


Carrier Proteins/genetics , Dyneins/genetics , Larva/genetics , Microtubule-Associated Proteins/genetics , Nuclear Proteins/genetics , Photoreceptor Cells, Vertebrate , Retina/growth & development , Zebrafish Proteins/genetics , Animals , Biological Transport/genetics , Cilia/genetics , HEK293 Cells , Humans , Larva/growth & development , Neurogenesis/genetics , Proteomics , Signal Transduction , Zebrafish/genetics , Zebrafish/growth & development
15.
Structure ; 23(11): 2122-32, 2015 Nov 03.
Article En | MEDLINE | ID: mdl-26455799

Cilia are small antenna-like cellular protrusions critical for many developmental signaling pathways. The ciliary protein Arl3 has been shown to act as a specific release factor for myristoylated and farnesylated ciliary cargo molecules by binding to the effectors Unc119 and PDE6δ. Here we describe a newly identified Arl3 binding partner, CCDC104/CFAP36. Biochemical and structural analyses reveal that the protein contains a BART-like domain and is called BARTL1. It recognizes an LLxILxxL motif at the N-terminal amphipathic helix of Arl3, which is crucial for the interaction with the BART-like domain but also for the ciliary localization of Arl3 itself. These results seem to suggest a ciliary role of BARTL1, and possibly link it to the Arl3 transport network. We thus speculate on a regulatory mechanism whereby BARTL1 aids the presentation of active Arl3 to its GTPase-activating protein RP2 or hinders Arl3 membrane binding in the area of the transition zone.


ADP-Ribosylation Factors/metabolism , Amino Acid Motifs , Amino Acid Sequence , Animals , Binding Sites , Cell Line , Cilia/metabolism , Mice , Molecular Sequence Data , Protein Binding , Protein Transport , Proteins
16.
Nat Cell Biol ; 17(8): 1074-1087, 2015 Aug.
Article En | MEDLINE | ID: mdl-26167768

Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease.


Cilia/genetics , Ciliary Motility Disorders/genetics , Genetic Markers , Genetic Testing/methods , Genomics/methods , Photoreceptor Cells , RNA Interference , Abnormalities, Multiple , Animals , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Caenorhabditis elegans/ultrastructure , Cerebellar Diseases/genetics , Cerebellum/abnormalities , Cilia/metabolism , Cilia/pathology , Ciliary Motility Disorders/metabolism , Ciliary Motility Disorders/pathology , Cytoskeletal Proteins , Databases, Genetic , Ellis-Van Creveld Syndrome/genetics , Eye Abnormalities/genetics , Genetic Predisposition to Disease , Genome-Wide Association Study , HEK293 Cells , High-Throughput Nucleotide Sequencing , Humans , Kidney Diseases, Cystic/genetics , Membrane Proteins/deficiency , Membrane Proteins/genetics , Mice, Inbred C57BL , Mice, Knockout , Mutation , Phenotype , Photoreceptor Cells/metabolism , Photoreceptor Cells/ultrastructure , Pregnancy Proteins/genetics , Pregnancy Proteins/metabolism , Proteins/genetics , Proteins/metabolism , Reproducibility of Results , Retina/abnormalities , Suppressor Factors, Immunologic/genetics , Suppressor Factors, Immunologic/metabolism , Transfection , Zebrafish/genetics , Zebrafish/metabolism
17.
Mol Cell Proteomics ; 13(5): 1382-91, 2014 May.
Article En | MEDLINE | ID: mdl-24563533

Analyzing the molecular architecture of native multiprotein complexes via biochemical methods has so far been difficult and error prone. Protein complex isolation by affinity purification can define the protein repertoire of a given complex, yet, it remains difficult to gain knowledge of its substructure or modular composition. Here, we introduce SDS concentration gradient induced decomposition of protein complexes coupled to quantitative mass spectrometry and in silico elution profile distance analysis. By applying this new method to a cellular transport module, the IFT/lebercilin complex, we demonstrate its ability to determine modular composition as well as sensitively detect known and novel complex components. We show that the IFT/lebercilin complex can be separated into at least five submodules, the IFT complex A, the IFT complex B, the 14-3-3 protein complex and the CTLH complex, as well as the dynein light chain complex. Furthermore, we identify the protein TULP3 as a potential new member of the IFT complex A and showed that several proteins, classified as IFT complex B-associated, are integral parts of this complex. To further demonstrate EPASIS general applicability, we analyzed the modular substructure of two additional complexes, that of B-RAF and of 14-3-3-ε. The results show, that EPASIS provides a robust as well as sensitive strategy to dissect the substructure of large multiprotein complexes in a highly time- as well as cost-effective manner.


Mass Spectrometry/methods , Multiprotein Complexes/chemistry , Multiprotein Complexes/isolation & purification , Protein Subunits/metabolism , 14-3-3 Proteins/chemistry , 14-3-3 Proteins/isolation & purification , HEK293 Cells , Humans , Intracellular Signaling Peptides and Proteins , Mass Spectrometry/economics , Proteins/metabolism , Proteomics , Proto-Oncogene Proteins B-raf/chemistry , Proto-Oncogene Proteins B-raf/isolation & purification , Sodium Dodecyl Sulfate
18.
PLoS Genet ; 9(12): e1003977, 2013.
Article En | MEDLINE | ID: mdl-24339792

Cilia are microtubule-based cell appendages, serving motility, chemo-/mechano-/photo- sensation, and developmental signaling functions. Cilia are comprised of distinct structural and functional subregions including the basal body, transition zone (TZ) and inversin (Inv) compartments, and defects in this organelle are associated with an expanding spectrum of inherited disorders including Bardet-Biedl syndrome (BBS), Meckel-Gruber Syndrome (MKS), Joubert Syndrome (JS) and Nephronophthisis (NPHP). Despite major advances in understanding ciliary trafficking pathways such as intraflagellar transport (IFT), how proteins are transported to subciliary membranes remains poorly understood. Using Caenorhabditis elegans and mammalian cells, we investigated the transport mechanisms underlying compartmentalization of JS-associated ARL13B/ARL-13, which we previously found is restricted at proximal ciliary membranes. We now show evolutionary conservation of ARL13B/ARL-13 localisation to an Inv-like subciliary membrane compartment, excluding the TZ, in many C. elegans ciliated neurons and in a subset of mammalian ciliary subtypes. Compartmentalisation of C. elegans ARL-13 requires a C-terminal RVVP motif and membrane anchoring to prevent distal cilium and nuclear targeting, respectively. Quantitative imaging in more than 20 mutants revealed differential contributions for IFT and ciliopathy modules in defining the ARL-13 compartment; IFT-A/B, IFT-dynein and BBS genes prevent ARL-13 accumulation at periciliary membranes, whereas MKS/NPHP modules additionally inhibit ARL-13 association with TZ membranes. Furthermore, in vivo FRAP analyses revealed distinct roles for IFT and MKS/NPHP genes in regulating a TZ barrier to ARL-13 diffusion, and intraciliary ARL-13 diffusion. Finally, C. elegans ARL-13 undergoes IFT-like motility and quantitative protein complex analysis of human ARL13B identified functional associations with IFT-B complexes, mapped to IFT46 and IFT74 interactions. Together, these findings reveal distinct requirements for sequence motifs, IFT and ciliopathy modules in defining an ARL-13 subciliary membrane compartment. We conclude that MKS/NPHP modules comprise a TZ barrier to ARL-13 diffusion, whereas IFT genes predominantly facilitate ARL-13 ciliary entry and/or retention via active transport mechanisms.


ADP-Ribosylation Factors/genetics , Caenorhabditis elegans/genetics , Cerebellar Diseases/genetics , Cilia/genetics , Eye Abnormalities/genetics , Kidney Diseases, Cystic/genetics , Retina/abnormalities , ADP-Ribosylation Factors/metabolism , Abnormalities, Multiple , Animals , Bardet-Biedl Syndrome/genetics , Bardet-Biedl Syndrome/pathology , Biological Transport, Active/genetics , Caenorhabditis elegans/metabolism , Cerebellar Diseases/pathology , Cerebellum/abnormalities , Cilia/metabolism , Ciliary Motility Disorders/genetics , Ciliary Motility Disorders/pathology , Cytoskeletal Proteins/genetics , Cytoskeletal Proteins/metabolism , Encephalocele/genetics , Encephalocele/pathology , Eye Abnormalities/pathology , Humans , Kidney Diseases, Cystic/pathology , Membranes/metabolism , Polycystic Kidney Diseases/genetics , Polycystic Kidney Diseases/pathology , Retina/pathology , Retinitis Pigmentosa , Transcription Factors/genetics , Transcription Factors/metabolism
19.
Nat Genet ; 45(8): 951-6, 2013 Aug.
Article En | MEDLINE | ID: mdl-23793029

Nephronophthisis is an autosomal recessive cystic kidney disease that leads to renal failure in childhood or adolescence. Most NPHP gene products form molecular networks. Here we identify ANKS6 as a new NPHP family member that connects NEK8 (NPHP9) to INVS (NPHP2) and NPHP3. We show that ANKS6 localizes to the proximal cilium and confirm its role in renal development through knockdown experiments in zebrafish and Xenopus laevis. We also identify six families with ANKS6 mutations affected by nephronophthisis, including severe cardiovascular abnormalities, liver fibrosis and situs inversus. The oxygen sensor HIF1AN hydroxylates ANKS6 and INVS and alters the composition of the ANKS6-INVS-NPHP3 module. Knockdown of Hif1an in Xenopus results in a phenotype that resembles loss of other NPHP proteins. Network analyses uncovered additional putative NPHP proteins and placed ANKS6 at the center of this NPHP module, explaining the overlapping disease manifestation caused by mutation in ANKS6, NEK8, INVS or NPHP3.


Kidney Diseases, Cystic/genetics , Kinesins/genetics , Nuclear Proteins/genetics , Protein Kinases/genetics , Transcription Factors/genetics , Animals , Cilia/metabolism , Consanguinity , Exons , Gene Knockdown Techniques , Humans , Introns , Kidney Diseases, Cystic/metabolism , Kinesins/metabolism , Mice , Mutation , NIMA-Related Kinases , Nuclear Proteins/metabolism , Phenotype , Polycystic Kidney Diseases/genetics , Protein Binding , Protein Interaction Maps , Protein Kinases/metabolism , Protein Transport , Transcription Factors/metabolism , Xenopus/embryology , Xenopus/metabolism , Zebrafish/genetics , Zebrafish/metabolism , Zebrafish Proteins/genetics , Zebrafish Proteins/metabolism
20.
J Cardiothorac Vasc Anesth ; 20(2): 162-6, 2006 Apr.
Article En | MEDLINE | ID: mdl-16616654

OBJECTIVE: The purpose of this study was to investigate the effect of the phosphodiesterase (PDE) type 3 inhibitor milrinone on the adhesion of platelets to monocytes in vitro. DESIGN: Prospective study. SETTING: University experimental laboratory. PARTICIPANTS: Ten healthy volunteers. INTERVENTIONS: Whole blood was incubated with 1, 10, or 100 micromol/L of milrinone. After stimulation with N-formyl-methionyl-leucyl-phenylalanine (FMLP) or adenosine-5-diphosphate (ADP), platelet-monocyte adhesion and CD11b, PSGL-1, GPIIb/IIIa, and P-selectin expression were measured by flow cytometry. MEASUREMENTS AND RESULTS: The formation of platelet-monocyte conjugates after PDE3 inhibition depended on the type of stimulation. In unstimulated and FMLP-stimulated blood platelet monocytes, aggregation was enhanced by increasing concentrations of milrinone. This augmentation was accompanied by a rise in P-selectin expression in platelets. In ADP-stimulated blood the number of platelet-monocyte aggregates decreased with increasing concentrations of milrinone. Concurrent with the reported antiinflammatory properties of PDE-inhibition, an inhibition of CD11b expression was found in monocytes after stimulation with FMLP. In contrast, in unstimulated samples lower concentrations of milrinone caused an increase in CD11b. CONCLUSIONS: These findings suggest that the effects of PDE3 inhibition on platelets and monocytes are modified by the type of stimulation and only partially suppress the inflammatory response of platelets and monocytes. The increase in platelet-monocyte conjugates in unstimulated and FMLP-stimulated blood suggested that PDE3 inhibition may also trigger proinflammatory reactions.


3',5'-Cyclic-AMP Phosphodiesterases/antagonists & inhibitors , Milrinone/pharmacology , Monocytes/physiology , Phosphodiesterase Inhibitors/pharmacology , Platelet Adhesiveness/drug effects , CD11b Antigen/biosynthesis , Cell Adhesion/drug effects , Cyclic Nucleotide Phosphodiesterases, Type 3 , Humans , In Vitro Techniques , Membrane Glycoproteins/biosynthesis , P-Selectin/biosynthesis , Platelet Glycoprotein GPIIb-IIIa Complex/biosynthesis , Prospective Studies
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