Meningomyelocele (also known as spina bifida) is considered to be a genetically complex disease resulting from a failure of the neural tube to close. Individuals with meningomyelocele display neuromotor disability and frequent hydrocephalus, requiring ventricular shunting. A few genes have been proposed to contribute to disease susceptibility, but beyond that it remains unexplained1. We postulated that de novo mutations under purifying selection contribute to the risk of developing meningomyelocele2. Here we recruited a cohort of 851 meningomyelocele trios who required shunting at birth and 732 control trios, and found that de novo likely gene disruption or damaging missense mutations occurred in approximately 22.3% of subjects, with 28% of such variants estimated to contribute to disease risk. The 187 genes with damaging de novo mutations collectively define networks including actin cytoskeleton and microtubule-based processes, Netrin-1 signalling and chromatin-modifying enzymes. Gene validation demonstrated partial or complete loss of function, impaired signalling and defective closure of the neural tube in Xenopus embryos. Our results indicate that de novo mutations make key contributions to meningomyelocele risk, and highlight critical pathways required for neural tube closure in human embryogenesis.

Meningomyelocele (MM) is considered a genetically complex disease resulting from failure of neural tube closure (NTD). Patients display neuromotor disability and frequent hydrocephalus requiring ventricular shunting. A few proposed genes contribute to disease susceptibility, but most risk remains unexplained[1][1]. We postulated that de novo mutations (DNMs) under purifying selection contribute to MM risk[2][2]. Here we recruited a cohort of 851 MM trios requiring shunting at birth, compared with 732 control trios, and found that de novo likely gene disrupting or damaging missense mutations occur in approximately 22.3% of subjects, 28% of which are estimated to contribute to disease risk. The 187 genes with damaging DNMs collectively define networks including actin cytoskeleton and microtubule-based processes, axon guidance, and histone modification. Gene validation demonstrates partial or complete loss of function, impaired signaling and defective neural tube closure in Xenopus embryos. Our results suggest DNMs make key contributions to MM risk, and highlight critical pathways required for neural tube closure in human embryogenesis. ### Competing Interest Statement AA and ARS are full time employees of Regeneron Genetics Center. SK is cofounder of AIMA Inc., which seeks to develop techniques for early cancer diagnosis based on circulating tumor DNA. ### Clinical Protocols ### Funding Statement This work was funded by the NIH. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All subjects or their guardians provided written informed consent approved by the UCSD Institutional Review Board S99075 protocol 140028, expiration date Aug 1, 2024. Recruitment processes were conducted in accordance with the approval by review boards of the University of California San Diego, operating under Federal-wide Assurance number, FWA00004495. The above rulings cover all aspects of our study, not just recruitment and consent. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Exome and genome sequencing data are available in publicly accessible databases for the 1,576 subjects enrolled after inclusion of dbGaP language into the consenting process/ became standard. These data are at dbGaP (accession #phs002591.v1.p1, phs000744.v5.p2 (Yale Mendelian Sequencing Center), Kids First: Whole Genome Sequencing in Structural Defects of the Neural Tube Accession (phs002591.v1.p1). Sequencing data on the remaining 743 subjects is available upon request. [1]: #ref-1 [2]: #ref-2

The cytoskeleton comprises three polymerizing structures that have been studied for a long time, actin microfilaments, microtubules and intermediate filaments, plus more recently investigated dynamic assemblies like septins or the endocytic-sorting complex required for transport (ESCRT) complex. These filament-forming proteins control several cell functions through crosstalks with each other and with membranes. In this review, we report recent works that address how septins bind to membranes, and influence their shaping, organization, properties and functions, either by binding to them directly or indirectly through other cytoskeleton elements.

Cell resistance to taxanes involves several complementary mechanisms, among which septin relocalization from actin stress fibers to microtubules plays an early role. By investigating the molecular mechanism underlying this relocalization, we found that acute paclitaxel treatment triggers the release from stress fibers and subsequent proteasome-mediated degradation of binder of Rho GTPases 2 (BORG2)/Cdc42 effector protein 3 (Cdc42EP3) and to a lesser extent of BORG3/Cdc42EP5, two Cdc42 effectors that link septins to actin in interphase cells. BORG2 or BORG3 silencing not only caused septin detachment from stress fibers but also mimicked the effects of paclitaxel by triggering both septin relocalization to microtubules and significant drug resistance. Conversely, BORG2 or BORG3 overexpression retained septins on actin fibers even after paclitaxel treatment, without affecting paclitaxel sensitivity. We found that drug-induced inhibition of Cdc42 resulted in a drop in BORG2 level and in the relocalization of septins to microtubules. Accordingly, although septins relocalized when overexpressing an inactive mutant of Cdc42, the expression of a constitutively active mutant acted locally at actin stress fibers to prevent septin release, even after paclitaxel treatment. These findings reveal the role of Cdc42 upstream of BORG2 and BORG3 in controlling the interplay between septins, actin fibers, and microtubules in basal condition and in response to taxanes.

This review extensively reports data from the literature concerning the complex relationships between the stress-induced c-Jun N-terminal kinases (JNKs) and the four main cytoskeleton elements, which are actin filaments, microtubules, intermediate filaments, and septins. To a lesser extent, we also focused on the two membrane-associated cytoskeletons spectrin and ESCRT-III. We gather the mechanisms controlling cytoskeleton-associated JNK activation and the known cytoskeleton-related substrates directly phosphorylated by JNK. We also point out specific locations of the JNK upstream regulators at cytoskeletal components. We finally compile available techniques and tools that could allow a better characterization of the interplay between the different types of cytoskeleton filaments upon JNK-mediated stress and during development. This overview may bring new important information for applied medical research.

The stress-induced c-Jun N-terminal kinase (JNK) controls microtubule dynamics by enhancing both microtubule growth and rescues. Here, we show that upon cell stress, JNK directly phosphorylates the microtubule rescue factor CLIP-170 in its microtubule-binding domain to increase its rescue-promoting activity. Phosphomimetic versions of CLIP-170 enhance its ability to promote rescue events in vitro and in cells. Furthermore, while phosphomimetic mutations do not alter CLIP-170's capability to form comets at growing microtubule ends, both phosphomimetic mutations and JNK activation increase the occurrence of CLIP-170 remnants on the microtubule lattice at the rear of comets. As the CLIP-170 remnants, which are potential sites of microtubule rescue, display a shorter lifetime when CLIP-170 is phosphorylated, we propose that instead of acting at the time of rescue occurrence, CLIP-170 would rather contribute in preparing the microtubule lattice for future rescues at these predetermined sites.

Cancer cell resistance to taxanes is a complex, multifactorial process, which results from the combination of several molecular and cellular changes. In breast cancer cells adapted to long-term paclitaxel treatment, we previously identified a new adaptive mechanism that contributes to resistance and involves high levels of tubulin tyrosination and long-chain polyglutamylation coupled with high levels of septin expression, especially that of SEPT9_i1. This in turn led to higher CLIP-170 and MCAK recruitment to microtubules to enhance microtubule dynamics and therefore counteract the stabilizing effects of taxanes. Here, we explored to which extent this new mechanism alone could trigger taxane resistance. We show that coupling septins (including SEPT9_i1) overexpression together with long-chain tubulin polyglutamylation induce significant paclitaxel resistance in several naive (taxane-sensitive) cell lines and accordingly stimulate the binding of CLIP-170 and MCAK to microtubules. Strikingly, such resistance was paralleled by a systematic relocalization of septin filaments from actin fibers to microtubules. We further show that this relocalization resulted from the overexpression of septins in a context of enhanced tubulin polyglutamylation and reveal that it could also be promoted by an acute treatment with paclitaxel of sensitve cell displaying a high basal level of SEPT9_i1. These findings point out the functional importance and the complex cellular dynamics of septins in the onset of cell resistance to death caused by microtubule-targeting antimitotic drugs of the taxane family.

Microtubule reorientation into a longitudinal network during the phototropic response in Arabidopsis thaliana depends on their severing by katanin at crossovers. Lindeboom et al. (2019. J. Cell Biol. https://doi.org/10.1083/jcb.201805047) show that at newly generated plus ends, the anti-catastrophe activity of CLASP is essential for further growth.

Early recurrence is a frequent cause of poor survival after hepatocellular carcinoma (HCC) resection. At the cell level, efforts to link HCC with the dysfunction of signalling pathways identified several alterations, especially in the Wnt/β-catenin pathway.1 Wnt signalling controls the balance between cell proliferation and differentiation and its regulation relies partly on subcellular compartmentalisation at the plasma membrane in late endosomes and/or on the cytoskeleton (see refs. 2 ,3 for reviews) (figure 1A). Figure 1 The Wnt/β-catenin pathway: regulation by subcellular compartmentalisation and links with the cell cycle through the involvement of Protein Regulator of Cytokinesis 1 (PRC1). (A) (1) The β-catenin destruction complex, which comprises adenomatous polyposis coli (APC), Axin, glycogen synthase kinase 3β (GSK3β) and casein kinase 1 (CK1), functions to phosphorylate free β-catenin, allowing its recognition by the E3 enzyme β-Transducin repeats-Containing Protein (β-TrCP) and its consecutive degradation by the proteasome. (2) The lipoprotein receptor-related protein (LRP)5/6 signalosome: Wnt agonist binding to its receptor complex (Frizzled+LRP5/6) allows LRP5/6 phosphorylation, Axin and Microtubule-Actin Crosslinking Factor 1 (MACF1) recruitment to the signalosome and then inactivation of GSK3β. (3) APC motorisation towards the microtubule plus ends allows its interaction with end-binding 1 (EB1) and mDia to stabilise microtubules at the migrating cell front. (4) Cytoplasmic PRC1 binds to microtubule bundles and interacts with the destruction complex to inactivate it. (5) Inactivation of the destruction complex leads to β-catenin nuclear entry and association with the T-cell factor/lymphoid enhancer factor (TCF/LEF) transcription factor to promote gene expression. (6) Nuclear localisation of Axin, APC, Dishevelled (Dvl) and PRC1 modulates the Wnt/β-catenin signalling pathway. Nuclear APC competes with TCF/LEF for binding to β-catenin and favours its nuclear export. Nuclear Axin binds to the promoter region and competes with the binding of the β-catenin transcription complex on the promoter of target genes …

Background: The control of apical-basal polarity in epithelial layers is a fundamental event in many processes, ranging from embryonic development to tumor formation. A key feature of polarized epithelial cells is their ability to maintain an asymmetric distribution of specific molecular complexes, including the phosphoinositides PI(4,5)P2 and PI(3,4,5)P3. The spatiotemporal regulation of these phosphoinositides is controlled by the concerted action of phosphoinositide kinases and phosphatases.Results: Using the Drosophila follicular epithelium as a model system in vivo, we show here that PI(4,5)P2 is crucial to maintain apical-basal polarity. PI(4,5)P2 is essentially regulated by the PI4P5 kinase Skittles (SKTL), whereas neither the phosphatase PTEN nor the PI(4,5)P3 kinase DP110 lead to loss of apical-basal polarity. By inactivating SKTL and thereby strongly reducing PI(4,5)P2 levels in a single cell of the epithelium, we observe the disassembly of adherens junctions, actin cytoskeleton reorganization, and apical constriction leading to delamination, a process similar to that observed during epithelial-nnesenchymal transition. We provide evidence that PI(4,5) P2 controls the apical targeting of PAR-3/Bazooka to the plasma membrane and that the loss of this polarized distribution is sufficient to induce a similar cell shape change. Finally, we show that PI(4,5)P2 is excluded from the cell apex and that PAR-3 diffuses laterally just prior to the apical constriction in a context of endogenous invagination.Conclusions: All together, these results indicate that the PIP5 kinase SKTL, by controlling PI(4,5)P2 polarity, regulates PAR-3 localization and thus the size of the apical domain.

Microtubules (MTs) are essential for cell division, shape, intracellular transport, and polarity. MT stability is regulated by many factors, including MT-associated proteins and proteins controlling the amount of free tubulin heterodimers available for polymerization. Tubulin-binding cofactors are potential key regulators of free tubulin concentration, since they are required for α-β–tubulin dimerization in vitro. In this paper, we show that mutation of the Drosophila tubulin-binding cofactor B (dTBCB) affects the levels of both α- and β-tubulins and dramatically destabilizes the MT network in different fly tissues. However, we find that dTBCB is dispensable for the early MT-dependent steps of oogenesis, including cell division, and that dTBCB is not required for mitosis in several tissues. In striking contrast, the absence of dTBCB during later stages of oogenesis causes major defects in cell polarity. We show that dTBCB is required for the polarized localization of the axis-determining mRNAs within the oocyte and for the apico-basal polarity of the surrounding follicle cells. These results establish a developmental function for the dTBCB gene that is essential for viability and MT-dependent cell polarity, but not cell division.

In Drosophila, the polarity cues controlling the axis formation of the adult fly are asymmetrically distributed in the oocyte, a process depending on the microtubule (MT) network. In order to identify new genes controlling the oocyte polarity, a genetic screen after mutagenesis has been done in the laboratory. In one of the mutants identified, that we named mercury, the posterior determinant oskar mRNA and the nucleus were strongly mislocalised. In the Drosophila germline, the germ cells are surrounded by a monolayer of somatic epithelial cells called the follicle cells. In mercury mutant follicle cells, the apical localisation of Par3 and aPKC and the lateral localization of α-spectrin were strongly disrupted indicating a loss of polarity. The follicle cells also formed multilayers, a characteristic of mispolarised cells. We next mapped the mutation and identified the mutated gene as the homologous of mammalian Tubulin Binding Cofactor B (TBCB). Tubulin binding cofactors have been demonstrated to be necessary for the formation of the αβ-tubulin heterodimers and are therefore potential regulators of the αβ-tubulin pool and of the microtubule stability. In agreement with this, we found that, in mercury mutant oocytes and follicle cells, the microtubule network was strongly destabilised. As the establishment of polarity is a MT dependant process, the loss of polarity observed in mercury mutant cells is probably a consequence of the destabilization of the MT network. Finally, we found that total α- and β-tubulin protein decreased strongly in the mutant cells.

Genetic control of embryogenesis switches from the maternal to the zygotic genome during the maternal-to-zygotic transition (MZT), when maternal mRNAs are destroyed, high-level zygotic transcription is initiated, the replication checkpoint is activated and the cell cycle slows. The midblastula transition(MBT) is the first morphological event that requires zygotic gene expression. The Drosophila MBT is marked by blastoderm cellularization and follows 13 cleavage-stage divisions. The RNA-binding protein Smaug is required for cleavage-independent maternal transcript destruction during the Drosophila MZT. Here, we show that smaug mutants also disrupt syncytial blastoderm stage cell-cycle delays, DNA replication checkpoint activation, cellularization, and high-level zygotic expression of protein coding and micro RNA genes. We also show that Smaug protein levels increase through the cleavage divisions and peak when the checkpoint is activated and zygotic transcription initiates, and that transgenic expression of Smaug in an anterior-to-posterior gradient produces a concomitant gradient in the timing of maternal transcript destruction, cleavage cell cycle delays,zygotic gene transcription, cellularization and gastrulation. Smaug accumulation thus coordinates progression through the MZT.

Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset syndrome characterized by progressive degeneration of particular muscles. OPMD is caused by short GCG repeat expansions within the gene encoding the nuclear poly(A)-binding protein 1 (PABPN1) that extend an N-terminal polyalanine tract in the protein. Mutant PABPN1 aggregates as nuclear inclusions in OMPD patient muscles. We have created a Drosophila model of OPMD that recapitulates the features of the human disorder: progressive muscle degeneration, with muscle defects proportional to the number of alanines in the tract, and formation of PABPN1 nuclear inclusions. Strikingly, the polyalanine tract is not absolutely required for muscle degeneration, whereas another domain of PABPN1, the RNA-binding domain and its function in RNA binding are required. This demonstrates that OPMD does not result from polyalanine toxicity, but from an intrinsic property of PABPN1. We also identify several suppressors of the OPMD phenotype. This establishes our OPMD Drosophila model as a powerful in vivo test to understand the disease process and develop novel therapeutic strategies.

Translational control of maternal mRNA through regulation of poly(A) tail length is crucial during early development. The nuclear poly(A) binding protein, PABP2, was identified biochemically from its role in nuclear polyadenylation. Here, we analyze the in vivo function of PABP2 in Drosophila. PABP2 is required in vivo for polyadenylation, and Pabp2 function, including poly(A) polymerase stimulation, is essential for viability. We also demonstrate an unanticipated cytoplasmic function for PABP2 during early development. In contrast to its role in nuclear polyadenylation, cytoplasmic PABP2 acts to shorten the poly(A) tails of specific mRNAs. PABP2, together with the deadenylase CCR4, regulates the poly(A) tails of oskar and cyclin B mRNAs, both of which are also controlled by cytoplasmic polyadenylation. Both Cyclin B protein levels and embryonic development depend upon this regulation. These results identify a regulator of maternal mRNA poly(A) tail length and highlight the importance of this mode of translational control.

The Suppressor of forked [Su(f)] protein is the Drosophila homologue of CstF-77, a subunit of human cleavage stimulation factor (CstF) that is required for the first step of the mRNA 3' end processing reaction in vitro. We have addressed directly the role of su(f) in the mRNA 3' end processing reaction in vivo. We show that su(f) is required for the cleavage of pre-mRNA during mRNA 3' end formation. Analysis of the functional complementation between Su(f) and CstF-77 shows that most of the Drosophila protein (85%) can be exchanged for the human protein to produce chimeric CstF-77/Su(f) proteins that rescue lethality and cleavage defect during mRNA 3' end formation in su(f) mutants. Interestingly, we show that a domain in human CstF-77 is limiting for the rescue and that this domain is not able to reproduce protein interactions with the CstF subunits of Drosophila. We also show that chimeric CstF-77/Su(f) proteins that rescue lethality of su(f) mutants cannot restore utilization of a regulated poly(A) site in Drosophila. Taken together, these results demonstrate that CstF-77 and Su(f) have the same function in mRNA 3' end formation in vivo, but that these two proteins are not interchangeable for regulation of poly(A) site utilization.

La formation de l'extremite 3' des ARNm est un processus general de maturation des ARNm qui peut etre regule et permettre le controle de l'expression genique. Chez la drosophile, les facteurs de polyadenylation sont conserves par rapport aux mammiferes et nous avons montre que les proteines Suppressor of forked (Su(f)) et poly(A) binding protein II (PABP2), les homologues respectifs de CstF-77 et PABP2 de mammiferes, sont impliquees in vivo dans la reaction de clivage et polyadenylation. En effet, differentes proteines chimeres CstF-77/Su(f) sauvent le clivage 3' des ARNm dans les mutants su(f), demontrant que 85 % de la proteine CstF-77 est interchangeable avec Su(f). L'analyse des interactions proteiques in vitro, suggere que seul un domaine de 90 acides amines est limitant pour le sauvetage et ne reproduit pas les interactions proteiques avec les autres partenaires du complexe CstF. Nous avons montre que la proteine PABP2 de drosophile remplace son homologue mammifere in vitro. En accord avec un role in vivo de PABP2 dans la formation des queues poly(A), un mutant nul du gene Pabp2 presente des queues poly(A) de taille reduite. Enfin, nous avons mis en evidence un nouveau role de la proteine PABP2 dans le controle de la taille des queues poly(A) dans le cytoplasme au cours du developpement precoce. Cette regulation semble specifique des ARN qui subissent la polyadenylation cytoplasmique, un processus qui permet l'activation traductionnelle de ces genes a un moment precis du developpement.

The Suppressor of forked protein is the Drosophila homolog of the 77K subunit of human cleavage stimulation factor, a complex required for the first step of the mRNA 3'-end-processing reaction. We have shown previously that wild-type su(f) function is required for the accumulation of a truncated su(f) transcript polyadenylated in intron 4 of the gene. This led us to propose a model in which the Su(f) protein would negatively regulate its own accumulation by stimulating 3'-end formation of this truncated su(f) RNA. In this article, we demonstrate this model and show that su(f) autoregulation is tissue specific. The Su(f) protein accumulates at a high level in dividing tissues, but not in nondividing tissues. We show that this distribution of the Su(f) protein results from stimulation by Su(f) of the tissue-specific utilization of the su(f) intronic poly(A) site, leading to the accumulation of the truncated su(f) transcript in nondividing tissues. Utilization of this intronic poly(A) site is affected in a su(f) mutant and restored in the mutant with a transgene encoding wild-type Su(f) protein. These data provide an in vivo example of cell-type-specific regulation of a protein level by poly(A) site choice, and confirm the role of Su(f) in regulation of poly(A) site utilization.

The poly(A)-binding protein II (PABP2) is one of the polyadenylation factors required for proper 3'-end formation of mammalian mRNAs. We have cloned Pabp2, the gene encoding the Drosophila homolog of mammalian PABP2, by using a molecular screen to identify new Drosophila proteins with RNP-type RNA-binding domains. Sequence comparison of PABP2 from Drosophila and mammals indicates that the most conserved domains are the RNA-binding domain and a coiled-coil like domain which could be involved in protein-protein interactions. Pabp2 produces four mRNAs which result from utilization of alternative poly(A) sites and encode the same protein. Using an antibody raised against Drosophila PABP2, we show that the protein accumulates in nuclei of all transcriptionally active cells throughout Drosophila development. This is consistent with a general role of PABP2 in mRNA polyadenylation. Analysis of Drosophila PABP2 function in a reconstituted mammalian polyadenylation system shows that the protein has the same functions as its bovine homolog in vitro : it stimulates poly(A) polymerase and is able to control poly(A) tail length.