Biology subjects

Firat-Karalar, E. N.

Publications and source records attributed to Firat-Karalar, E. N..

14 recordsLinked to original sources

bioRxiv2026

SatelliteQ: an open-source workflow for multidimensional, object-based quantification of centriolar satellites

Centriolar satellites are membrane-less organelles that store, modify and traffic proteins, in particular those of the centrosome and the primary cilium, and their deregulation is linked to ciliopathies, neurodevelopmental and neurodegenerative disorders. Satellite number, size, intensity and spatial distribution vary with cell type and cell state, yet satellites are usually quantified by a single readout, the pericentrosomal fluorescence intensity in maximum-projected images, which cannot distinguish changes in satellite number, size and position. Here we present SatelliteQ, an open-source Fiji and Python workflow for object-based quantification of satellites in 2D, 3D and time-lapse images. SatelliteQ segments satellites, detects centrosomes or primary cilia in the same cells, and reports satellite number, size, intensity, distance to the centrosome, shape and spatial distribution per satellite and per cell, with interactive graph and spatial viewers. Its measurements correlate closely with Imaris-based quantification; absolute values depend on segmentation settings and analysis mode, whereas the biological differences tested here were preserved across matched settings. Using SatelliteQ, we resolved distinct spatial signatures of satellite dispersal induced by microtubule depolymerization and by disruption of weak hydrophobic interactions, quantified differences between cell types and the scaling of satellite number with cell size, captured PCM1 granule dynamics in living cells, and compared satellite organization between ciliated and unciliated cells. Depletion of the ciliopathy-associated satellite protein CEP290 altered satellite abundance and pericentrosomal organization, while patient-derived cells carrying CEP290 mutations displayed divergent satellite phenotypes that were not explained by ciliation alone. SatelliteQ thus establishes satellite properties as a multidimensional cellular phenotype and provides an accessible framework for exploring satellites as an organelle-level readout in disease.

cell biology↗

bioRxiv2026

CCDC66 couples actin-microtubule crosslinking to KANK1-associated microtubule targeting and focal adhesion turnover

Cell migration requires actin-based protrusion to be coordinated with microtubule (MT)-dependent focal adhesion (FA) remodeling. Although KANK proteins link talin-containing FAs to cortical MT-capture machinery, how this machinery couples to force-bearing actin networks remains unclear. Here, we identify the ciliopathy-associated protein CCDC66 as an actin-MT crosslinker required for FA turnover and migration. CCDC66 depletion impaired collective, Transwell, and random migration, whereas CCDC66 overexpression enhanced wound closure and Matrigel invasion. Mechanistically, CCDC66 loss reduced MT targeting to peripheral FAs and shifted cells into a ROCK-dependent contractile state marked by impaired lamellipodial protrusion, stress fiber accumulation, enlarged long-lived adhesions, and increased RhoA-ROCK signaling. ROCK or formin inhibition suppressed this state, whereas Rac1 activation failed to restore productive protrusion, indicating that CCDC66 maintains the balance between protrusive and contractile actin organization. In vitro TIRF reconstitution demonstrated that purified CCDC66 directly crosslinks actin filaments and MTs. In cells, CCDC66 associated with KANK1, supported its peri-adhesion organization, and functioned with KANK1 in an overlapping migration pathway. TCGA analyses further revealed that a coordinated CCDC66/KANK/ROCK-associated module, but not CCDC66 expression alone, stratified outcome in chromophobe renal cell carcinoma. These findings reveal a non-ciliary role for CCDC66 in coupling actin-MT integration to FA turnover and contractile-state control, with relevance to developmental disease and cancer-associated motility.

cell biology↗

bioRxiv2026

The Joubert syndrome protein CSPP1 is a conserved regulator of vertebrate multiciliogenesis and motile cilia function

Cilia are conserved microtubule-based organelles required for signaling and fluid transport, and their dysfunction causes ciliopathies. Clinical overlap between sensory and motile ciliopathies suggests that primary and motile ciliogenesis depend on shared regulatory modules. Here, we identify Centrosome and Spindle Pole-associated Protein 1 (CSPP1), a microtubule-associated protein mutated in the neurodevelopmental ciliopathy Joubert syndrome, as a conserved regulator of vertebrate multiciliogenesis. Using mouse tracheal epithelial cultures and Xenopus embryonic epidermis, we show that CSPP1 localizes to fibrous granules and deuterosomes during centriole amplification, and to basal bodies and ciliary axonemes in differentiated multiciliated cells. Loss of CSPP1 impairs centriole amplification, basal body apical migration, spacing, and rotational polarity, and is accompanied by disorganization of the apical microtubule network. CSPP1 depletion also disrupts axoneme assembly, resulting in fewer and shorter cilia with ultrastructural defects, reduced ciliary beating, and impaired cilia driven fluid flow in vivo. Together, our findings identify CSPP1 as a conserved regulator of multiciliogenesis and motile cilia function and establish a basis for future work on how shared cytoskeletal pathways may underlie overlapping features of sensory and motile ciliopathies.

cell biology↗

bioRxiv2025

Centriolar satellites are dynamic membrane-less organelles that assemble via a hierarchical pathway

Centriolar satellites (CS) are ubiquitous, membrane-less organelles recognized for organelle crosstalk, plasticity, diverse functions and links to developmental and neuronal diseases. However, the molecular principles governing their assembly and regulation remain poorly understood. To address this, we developed cellular and in vitro biogenesis assays that allow spatiotemporal quantification of CS granule properties during assembly, remodeling and maintenance. Using these tools, we show that CS assemble via a hierarchical pathway initiated by PCM1 scaffold formation followed by regulated client recruitment. PCM1 intrinsically assembles into granules through multimerization, a process modulated by cytoskeleton. High-resolution imaging revealed that PCM1 and its clients occupy distinct subdomains with different compositions and dynamics, adding an additional layer of regulation. Perturbing PCM1 multimerization impaired ciliary signaling, underscoring its functional importance. Collectively, these findings define the molecular basis of CS biogenesis, establish new tools to probe their context-dependent functions, and provide a framework for understanding how CS deregulation contributes to disease. More broadly, the principles uncovered here may extend to other membrane-less organelles, explaining their specificity and plasticity.

cell biology↗

bioRxiv2024

ALS driven by mutant NEK1 aggregation is accelerated by Pml loss, but clinically reversed through pharmacologic induction of Pml-mediated degradation

Germinal mono-allelic loss-of-function mutations of NEK1 drive Amyotrophic Lateral Sclerosis (ALS) at variable penetrance, presumably through haploinsufficiency. Modeling the ALS-associated Arg812Ter mutation in mice revealed that the resulting truncated Nek1 (Nek1t) is aggregation-prone, particularly in alpha-motoneurons (MNs), and drives canonical ALS symptoms when bi-allelically expressed (Nek1t/t). Promyelocytic leukemia (Pml) ablation allows for ALS symptoms to occur even in heterozygote Nek1wt/t animals, mimicking the human situation. Pml precludes disease occurrence by promoting SUMO-facilitated degradation of Nek1t proteins through PML nuclear bodies (NBs). Conversely, Pml induction, achieved by activating the interferon pathway via poly(I:C) treatment, clears Nek1t aggregates in MNs, dramatically reducing ALS-associated symptoms and extending survival by 5 months. Our studies highlight the role of NEK1 aggregates in ALS pathogenesis and identifies activation of interferon pathways as a candidate therapeutic strategy that not only promotes Pml-triggered SUMOylation/degradation of toxic misfolded proteins in vivo, but also facilitates the clearance of protein aggregates, yielding dramatic clinical improvement. These observations validate PML as a relevant therapeutic target in neurodegenerative conditions associated with protein aggregation.

pathology↗

bioRxiv2024

Ccdc66 regulates primary cilium stability, disassembly and signaling important for epithelial organization

The primary cilium is a conserved, microtubule-based organelle that transduces signaling pathways essential for development and homeostasis. It is a dynamic structure that assembles and disassembles in response to intrinsic and extrinsic stimuli while maintaining remarkable stability and tightly controlled length. Although cilium assembly is well-understood, less is known about the molecular players and pathways governing their stability, length and disassembly. Here, we elucidated the function of Ccdc66, a microtubule-associated protein linked to ciliopathies, in cilium maintenance and disassembly in mouse epithelial cells. We found that Ccdc66 depletion disrupts cilium disassembly, length and stability, but does not affect assembly in these cells. Live imaging of these processes revealed that cilia in Ccdc66-depleted cells frequently fluctuate in length and exhibit increased ectocytosis from the cilium tip. Phenotypic rescue experiments and in vitro microtubule stabilization assays showed that Ccdc66 mediates these functions via regulating the stability of microtubules. Temporal proximity mapping of CCDC66 identified potential new regulators and molecular pathways involved in cilium disassembly. Additionally, depletion of CCDC66 compromised Hedgehog and Wnt pathway activation and disrupted epithelial cell organization and polarity in two-dimensional and three-dimensional cultures. Collectively, our results define Ccdc66 as a new microtubule-stabilizing factor that regulates cilium stability and disassembly, providing insights into the mechanisms of cilium homeostasis and the pathologies associated with Ccdc66.

cell biology↗

bioRxiv2023

CilioGenics: an integrated method and database for predicting novel ciliary genes

Discovering the entire list of human ciliary genes would help in the diagnosis of cilia-related human disorders known as ciliopathy, but at present the genetic diagnosis of many ciliopathies (over 30%) is far from complete (Bachmann-Gagescu et al., 2015; Knopp et al., 2015; Paff et al., 2018). In a theory, many independent approaches may uncover the whole list of ciliary genes, but 30% of the genes on the ciliary gene list are still ciliary candidate genes (van Dam et al., 2019; Vasquez et al., 2021). All of these cutting-edge techniques, however, have relied on a different single strategy to discover ciliary candidate genes. Because different methodologies demonstrated distinct capabilities with varying quality, categorizing the ciliary candidate genes in the ciliary gene list without further evidence has been difficult. Here, we present a method for predicting ciliary capacity of each human gene that incorporates diverse methodologies (single-cell RNA sequencing, protein-protein interactions (PPIs), comparative genomics, transcription factor (TF)-network analysis, and text mining). By integrating multiple approaches, we reveal previously undiscovered ciliary genes. Our method, CilioGenics, outperforms other approaches that are dependent on a single method. Our top 500 gene list contains 256 new candidate ciliary genes, with 31 experimentally validated. Our work suggests that combining several techniques can give useful evidence for predicting the ciliary capability of all human genes.

bioinformatics↗

bioRxiv2023

CCDC15 localizes to the centriole inner scaffold and regulates centriole integrity and ciliogenesis

Centrioles are evolutionarily conserved microtubule-based organelles critical to form centrosomes and cilia, which act as microtubule-organizing, signaling and motility centers. Biogenesis and maintenance of centrioles with proper number, size and architecture are crucial for their functions during development and physiology. Consequently, their deregulation causes developmental disorders and cancer. Although centriole number control has been extensively studied, less is known about how centrioles are maintained as stable structures with conserved size and architecture over successive cell divisions and upon ciliary and flagellar motility. Here, we addressed this question by identifying and characterizing new components of the centriole inner scaffold, a recently discovered centriolar sub-compartment critical for centriole size control and integrity. To this end, we generated proximity interactomes of Centrin-2 and POC5 and used them to define CCDC15 as a new centriolar protein that co-localizes and interacts with known inner scaffold proteins. Ultrastructure expansion microscopy analysis of CCDC15-depleted cells revealed its functions in centriole length control and integrity, resulting in defective ciliogenesis and Hedgehog signaling. Loss-of-function experiments also defined CCDC15 as a dual regulator for the recruitment of the inner scaffold protein POC1B and the distal SFI1/Centrin complex to the centrioles. Together, our findings uncovered new players and mechanisms of centriole architectural integrity and thereby, provide insights into diseases linked to centriolar defects.

cell biology↗

bioRxiv2022

The ciliopathy protein CCDC66 controls mitotic progression and cytokinesis by promoting microtubule nucleation and organization

Precise spatiotemporal control of microtubule nucleation and organization is critical for faithful segregation of cytoplasmic and genetic material during cell division and signaling via the primary cilium in quiescent cells. Microtubule-associated proteins (MAPs) govern assembly, maintenance, and remodeling of diverse microtubule arrays. While a set of conserved MAPs are only active during cell division, an emerging group of MAPs acts as dual regulators in dividing and non-dividing cells. Here, we elucidated the nonciliary functions and molecular mechanism of action of the ciliopathy-linked protein CCDC66, which we previously characterized as a regulator of ciliogenesis in quiescent cells. We showed that CCDC66 dynamically localizes to the spindle poles, the bipolar spindle, the spindle midzone, the central spindle and the midbody in dividing cells and interacts with the core machinery of centrosome maturation and MAPs involved in cell division. Loss-of-function experiments revealed its functions during mitotic progression and cytokinesis. Specifically, CCDC66 depletion resulted in defective spindle assembly and positioning, kinetochore fiber stability, chromosome alignment in metaphase as well as central spindle and midbody assembly and organization in anaphase and cytokinesis. Notably, CCDC66 regulates mitotic microtubule nucleation via noncentrosomal and centrosomal pathways via recruitment of gamma-tubulin to the spindle poles and the spindle. Additionally, CCDC66 bundles microtubules in vitro and in cells by its C-terminal microtubule-binding domain. Phenotypic rescue experiments showed that the microtubule and centrosome-associated pools of CCDC66 individually or cooperatively mediate its mitotic and cytokinetic functions. Collectively, our findings identify CCDC66 as a multifaceted regulator of the nucleation and organization of the diverse mitotic and cytokinetic microtubule arrays and provides new insight into nonciliary defects that underlie ciliopathies.

cell biology↗

bioRxiv2022

CCDC66 regulates primary cilium length and signaling competence via multi-site interactions with transition zone and axonemal proteins

The primary cilium is a conserved microtubule-based organelle that serves as a hub for many signaling pathways. It functions as part of the centrosome/cilium complex, which also contains the basal body and the centriolar satellites. Little is known about the mechanisms by which the microtubule-based axoneme of the cilium is assembled with proper length and structure, particularly in terms of the activity of microtubule-associated proteins (MAPs) and the crosstalk between the different compartments of the centrosome/cilium complex. Here, we analyzed CCDC66, a MAP implicated in cilium biogenesis and ciliopathies affecting eye and brain. Live-cell imaging revealed that CCDC66 compartmentalizes between centrosomes, centriolar satellites, and the ciliary axoneme and tip during cilium assembly and disassembly. CCDC66 loss-of-function in human cells causes defects in cilium assembly, length and morphology. Notably, CCDC66 interacts with the MAPs and ciliopathy proteins CEP104 and CSPP1 and cooperates with them during axonemal length regulation. Moreover, CCDC66 interacts with the transition zone protein CEP290 selectively at the centriolar satellites. Its loss disrupts basal body recruitment of transition zone proteins and IFT-B machinery and causes defective Hedgehog signaling. Overall, our results establish CCDC66 as a multifaceted regulator of the primary cilium, and propose a mechanistic insight into how the cooperation of ciliary MAPs as well as subcompartments ensures assembly of a functional cilium.

cell biology↗

bioRxiv2021

ENKD1 is a centrosomal and ciliary microtubule-associated protein important for primary cilium assembly and Hedgehog signaling

Centrioles and cilia are conserved, microtubule-based structures critical for cell function and development. Their structural and functional defects cause cancer and developmental disorders. How microtubules are organized into ordered structures by microtubule-associated proteins (MAPs) and tubulin modifications is best understood during mitosis but is largely unexplored for the centrioles and the ciliary axoneme, which are composed of remarkably stable microtubules that maintain their length at steady state. In particular, we know little about the identity of the centriolar and ciliary MAPs and how they work together during the assembly and maintenance of the cilium and centriole. Here, we identified Enkurin domain containing 1 (ENKD1) as a component of the centriole wall and the axoneme in mammalian cells, and showed that it has extensive proximity interactions with these compartments and MAPs. Using in vitro and cellular assays, we found that ENKD1 is a new MAP that promotes microtubule polymerization and regulates microtubule organization and stability. Consistently, overexpression of ENKD1 increased tubulin polymerization and acetylation and disrupted microtubule organization. Cells depleted for ENKD1 were defective in ciliary length and content regulation and failed to respond to Hedgehog pathway activation. Together, our results establish ENKD1 as a new centriolar and ciliary MAP that regulate primary cilium structure and function, and advances our understanding of the functional and regulatory relationship between MAPs and the primary cilium.

cell biology↗

bioRxiv2020

Aurora Kinase A proximity interactome reveals centriolar satellites as regulators of its function during primary cilium biogenesis

Aurora kinase A (AURKA) is a conserved kinase that plays crucial roles in numerous cellular processes. Although AURKA overexpression is frequent in human cancers, its pleiotropic functions and complex spatiotemporal regulation have presented challenges in its therapeutic targeting. An essential step to overcome these challenges is the identification of the full range of AURKA regulators and substrates, which are often weak and transient. Previous proteomic studies were limited in monitoring dynamic and non-mitotic AURKA interactions. Here, we generated the first in vivo proximity interactome of AURKA, which consisted of over 100 proteins involving multiple biological processes and cellular compartments. Importantly, AURKA had extensive proximity interactions to centriolar satellites, key regulators of the primary cilium. Affinity pulldown and phosphoproteomics experiments confirmed this proximity relationship at the physical level. Loss-of-function experiments defined satellites as negative regulators of AURKA activity, abundance and localization in quiescent cells. Notably, loss of satellites increased AURKA activation at the basal body and resulted in defective cilium assembly and enhanced cilium disassembly. Collectively, our results provide a powerful resource for dissecting AURKA function and regulation and uncover proteostatic regulation of AURKA by centriolar satellites as a new regulatory mechanism for its non-mitotic functions.

cell biology↗

bioRxiv2020

Acute inhibition of centriolar satellite function and positioning reveals their functions at the primary cilium

Centriolar satellites are dynamic, membrane-less granules composed of over 200 proteins. They store, modify, and traffic centrosome and primary cilium proteins, and help to regulate both the biogenesis and some functions of centrosomes and cilium. In most cell types, satellites cluster around the perinuclear centrosome, but their integrity and cellular distribution are dynamically remodeled in response to different stimuli, such as cell cycle cues. Dissecting the specific and temporal functions and mechanisms of satellites and how these are influenced by their cellular positioning and dynamics has been challenging using genetic approaches, particularly in ciliated and proliferating cells. To address this, we developed a chemical-based trafficking assay to rapidly and efficiently redistribute satellites to either the cell periphery or center, and fuse them into stable clusters in a temporally-controlled way. Induced satellite clustering at either the periphery or center resulted in antagonistic changes in the pericentrosomal levels of a subset of proteins, revealing a direct role for their positioning in protein targeting and sequestration. Systematic analysis of the interactome of peripheral satellite clusters revealed enrichment of proteins implicated in cilium biogenesis and mitosis. Importantly, inducible peripheral satellite targeting in ciliated cells revealed a function for satellites not just for efficient cilium assembly, but also in the maintenance of steady-state cilia and in cilia disassembly by regulating the structural integrity of the ciliary axoneme. Finally, although perturbing satellite distribution and dynamics inhibited their mitotic dissolution, it did not cause mitotic defects. Collectively, our results for the first time showed a direct link between satellite functions and their pericentrosomal clustering, and provided a new tool for probing temporal satellite functions in different contexts.

cell biology↗

bioRxiv2018

Differential requirement for centriolar satellites in cilium formation among different vertebrate cells

Centriolar satellites are ubiquitous in vertebrate cells. They have recently emerged as key regulators of centrosome/cilium biogenesis, and their mutations are linked to ciliopathies. However, their precise functions and mechanisms of action, which potentially differ between cell types, remain poorly understood. Here, we generated retinal pigmental and kidney epithelial cells lacking satellites by genetically ablating PCM1 to investigate their functions. While satellites were essential for cilium assembly in retinal epithelial cells, kidney epithelial cells lacking satellites still formed full-length cilia but at significantly lower levels, with reduced centrosomal levels of key ciliogenesis factors. Using these cells, we identified the first satellite-specific functions at cilia, specifically in regulating ciliary content, Hedgehog signalling, and epithelial cell organization. However, other satellite-linked functions, namely proliferation, cell cycle progression and centriole duplication, were unaffected in these cells. Quantitative transcriptomic and proteomic profiling revealed that loss of satellites scarcely affects transcription, but significantly alters the proteome, particularly actin cytoskeleton pathways and neuronal functions. Together, our findings identify cell type-specific roles for satellites and provide insight into the phenotypic heterogeneity of ciliopathies.

cell biology↗