EMBO Reports

Cell proliferation and fate specification are fundamental processes that ensure the generation of organs with proper size and patterning. Oxidative stress caused by accumulation of reactive oxygen species (ROS) can lead to cell cycle arrest, senescence, cell death and cell fate misspecification, thereby impairing normal development and contributing to many pathological processes. In this study, we identify Drosophila Ciz1 as a critical factor that safeguards epithelial homeostasis and development by preventing oxidative stress. Knockdown of Ciz1 in the Drosophila wing imaginal disc, an epithelial tissue that serves as the larval precursor of the adult wing, results in a small wing phenotype accompanied by thickened and ectopic veins. We further demonstrate that reduced Ciz1 expression leads to accumulation of donut-shaped mitochondria and elevated ROS levels. The increased oxidative stress subsequently suppresses proliferation via activation of JNK and promotes excessive vein formation by upregulating Rhomboid, a positive regulator of EGFR signaling. Interestingly, although Ciz1 is a zinc finger protein that predominantly localizes to the nucleus, neither its zinc finger motifs nor its nuclear localization is required for suppression of oxidative stress. Instead, the prion-like domain in its N-terminal part is essential for this activity. Our work identifies Ciz1 as an important factor in preventing oxidative stress and maintaining epithelial homeostasis.

Intrinsic apoptosis, or programmed cell death, is a vital response to stress and DNA damage in cells, and dysregulation of this pathway is common in cancers. The release of pro-apoptotic factors from mitochondria by the pro-apoptotic protein Bax is preceded by changes in the membrane properties of the outer mitochondrial membrane. We find that the membrane remodeling protein endophilin B1 primes membranes rich in the mitochondria-specific lipid cardiolipin for Bax-mediated membrane permeabilization, via a dual regulatory mechanism. We also show evidence that endophilin B1 translocates to the surface of mitochondria to co-localize with Bax during apoptosis in situ, where it forms biomolecular condensates.

Immune effects of membrane attack complexes (MAC) have been widely attributed to their abilities to cause cell death. Here, we show that the MAC component, C9, forms non-cytolytic aggregates with pro-inflammatory effects. Intracellular aggregates of C9 are detected within inflamed tissues of patients in association with endothelial cell (EC) activation but not increased cell death. We identify NUMBL as a Rab35 effector that directly binds surface-bound C9 to promote C9 internalization and entry into the endolysosomal pathway. Within acidified endolysosomes, C9 forms insoluble aggregates that are targeted for degradative aggrephagy in a process that activates NF-{kappa}B. For C9 aggrephagy to occur, ZFYVE21, a Rab5 effector, complexes with RNF34 to bridge C9 aggregates to LC3B+ aggresome membranes. We detect C9 aggregates in vivo, and we show that a ZFYVE21-RNF34 signaling axis is required for C9 aggrephagy and NF-{kappa}B -dependent EC activation in three separate mouse models. Mice with conditional loss of ZFYVE21 in ECs show reduced aggregraphy, resulting in attenuated systemic inflammation and reduced tissue injury following skin transplantation. Our data show that the C9 component of MACs forms intracellular aggregates with alarmin-like properties.

In metazoans, mitochondria optimally distribute to sites of need through long-range transport events on microtubules. The prevailing model for this trafficking mechanism is that the tail-anchored calcium-binding GTPase, Miro, recruits cytosolic TRAK and associated molecular motors to the outer mitochondrial membrane. Therefore, Miro is proposed to be an obligate adaptor for TRAK required for bulk mitochondrial transport, a process that is considered particularly important for long-range trafficking in neurons, and thus, for viability. Here, we impaired Miro-TRAK interaction in vivo by introducing a point mutation into the Drosophila TRAK orthologue Milton, that impairs its interaction with Miro, based on recent structural evidence. Flies harbouring this point mutation are viable to adulthood. Moreover, neurons carrying this mutation exhibit little to no observable reduction in axonal mitochondria. Mutant flies, however, display progressive loss of motor function with age and reduced lifespan. We therefore call into question the long-standing view that Miro plays an obligatory role in mitochondrial trafficking and challenge the canonical model for mitochondrial transport.

p53-binding protein 1 (53BP1) is a key mediator of the DNA damage response and genome stability. While its interphase function is well-characterized, its mitotic role remains less understood. Here we show that aberrant activation of 53BP1 through the loss of its negative regulator, TIRR, leads to mitotic abnormalities including altered spindle geometry, kinetochore-microtubule (k-MT) attachment errors and whole chromosome missegregation. We demonstrate that loss of TIRR results in excess interaction between 53BP1 and the key mitotic kinase Polo-like kinase 1 (PLK1), altering PLK1s activation, spatial distribution, and its interaction with known PLK1 substrates at multiple mitotic stages. Moreover, due to PLK1s established role in CENP-A loading, hyperactivation of 53BP1 compromises CENP-A loading, triggers gradual loss of CENP-A from centromeres and generates severe kinetochore assembly defects. These findings uncover a non-canonical mitotic function of 53BP1 as a key regulator of PLK1 activity and chromosome segregation fidelity.

The spatiotemporal regulation of an actin mesh during Drosophila oogenesis is essential for proper localization of cell polarity determinants that establish the future patterning of the embryo. Here, we reveal an unexpected role for Semaphorin-2a (Sema2a) in actin mesh regulation and oogenesis. Sema2a classically functions as a secreted guidance cue that binds its cognate Plexin-B (PlexB) receptor to establish neural circuits. In contrast, we find that Sema2a is expressed inside the germarium, germline, and follicle cells of the developing ovary. Sema2a mutants possess small ovaries that fail to develop past mid-oogenesis. We demonstrate that Sema2a interacts with Cappuccino (Capu), a key actin nucleator crucial for building the actin mesh in Drosophila oocytes. Sema2a inhibits the actin assembly activity of Capu in vitro. Furthermore, genetic interaction between Sema2a and Capu influences mesh density and disrupts oskar mRNA localization. PlexB mutants, however, exhibit wild-type size ovaries with oskar mRNA localization distinct from Sema2a mutants, confirming the non-canonical role of Sema2a in oogenesis. SummaryThis study reveals a novel interaction between the actin nucleator Cappuccino and the typically secreted neural guidance factor Semaphorin-2a. It is shown that Semaphorin-2a inhibits the actin polymerization activity of Cappuccino in vitro and play an intracellular role in oogenesis.

Susceptibility to viral infection varies widely but is not fully explained by genetics, immune status, or exposure level. We show that time of day strongly influences infection outcome, with up to 100-fold differences in enteric viral burden depending on infection timing. This temporal gating is abolished in mice lacking a functional circadian clock. We identify the antiviral transcription factor IRF1 as a direct target of the circadian transcription factor BMAL1, resulting in rhythmic expression of a basal antiviral gene program prior to infection. Loss of IRF1 eliminates this program and abrogates time-of-day-dependent differences in viral replication. This circuit operates within intestinal myeloid cells, establishing a preexisting antiviral state. These findings indicate that the circadian clock programs host susceptibility in the intestine, before infection occurs.

The vertebrate neural retina is composed of several neuronal types that precisely organize into layers, with photoreceptors facing the outer surface and the projection neurons, retinal ganglion cells, at the innermost layer. This organization, essential for its function, is established during early development through a complex process involving cell-cell interactions such as adhesion. In the case of photoreceptors, two adhesion complexes, based on the adhesive proteins Cadherin2 and Crumbs, appear essential for their correct localization at the outer nuclear layer (ONL). We here aimed at better characterizing the role of the scaffolding protein PALS1, a central component of the Crumbs complex. Through a validated pals1a/nok morpholino knockdown strategy in zebrafish embryos, we demonstrate that its reduced expression causes photoreceptor progenitors to initially disperse as actively migrating cells, to then coalesce into cell groups around the central retina. They eventually start polarizing, forming rosette-like structures with the apical border towards the inside. Conversely, in organoids derived from uncommitted neuroepithelial retinal progenitors, PALS1 deficiency causes an inversion of their localization from internal rosette-like structures to an organized superficial layer. In both conditions, photoreceptors show signs of polarization, with apical borders towards the inside of rosettes in wild-type organoids, to surface-directed apical borders in morphants. Altogether, our results support previous observations of the pivotal function of the Crumbs complex in ONL formation, but also indicate that either the Crumbs complex, or PALS1 itself, are central for the delicate balance in differential cell adhesion partly responsible for retinal lamination.

Activation of innate inflammatory signaling and tumor-specific antigen presentation in cancer cells provides a foundation for anti-cancer immunotherapies. Here, we show that Insulin-like Growth Factor 2 mRNA-Binding Proteins (IGF2BP1, IGF2BP2, and IGF2BP3), which are upregulated across various human malignancies, including acute myeloid leukemia (AML), suppress the activity of RNA-sensing pattern recognition receptors and downstream ISRE- and NF-{kappa}B-driven transcription. IGF2BPs exert a strong inhibitory effect on RIG-I signaling. This suppression is most pronounced when all three paralogs are co-expressed, particularly in embryonic-like hematoendothelial and leukemia stem cells. IGF2BPs suppress innate immune signaling via direct binding with TNFAIP3 mRNA and support of its RNA and protein expression. Genetic and pharmacological inhibition of IGF2BPs activates innate immune signaling and induces MHC class I gene expression in AML, highlighting a promising strategy for RIG-I- and TLR-based cancer immunotherapies.

Mitochondria are subcellular organelles responsible for energy production, and a hub for several cellular signaling pathways that ultimately control cellular processes ranging from cell death to innate immunity. Genotoxic stress, including cellular irradiation, has been shown to cause the mitochondrial-dependent activation of innate immunity via release of mitochondrial nucleic acids in the cytosol. Yet, how the other cellular events triggered by genotoxic stress affects mitochondria and mitochondrial immunity is largely unexplored. Nuclear DNA damage responses (DDR) are a set of well-described responses to genotoxic stressors that allow the cells to, through characterized mechanisms including transcriptional responses and checkpoint activation, survive or die. Whether canonical DDR directly influence mitochondrial structure and activation of downstream pathways of immunity remains unclear. Here, we identify mito-blobs: enlarged TOMM20-positive mitochondrial structures induced by genotoxic stress that are enriched for TFAM-marked mitochondrial DNA nucleoids, FASTKD2-positive mitochondrial RNA granules, and immunogenic double-stranded RNA. While structurally resembling other mitochondria stress responsive rearrangements, mito-blobs carry the distinctive feature of being induced by nuclear DNA double-stranded breaks alone. Strikingly, mitochondrial double-stranded breaks failed to induce mito-blobs, indicating nuclear-to-mitochondrial signaling rather than an autonomous response to mitochondrial genome damage. Mechanistically, we show that mito-blobs formation strictly requires MFN1/2- and OPA1-dependent fusion machinery, while nuclear DNA damage invokes a classical ATM-p53 response, which lead to cell cycle block in the G1 phase that reduce DRP1 S616 phosphorylation and shifting mitochondrial morphology toward a low-fission pro-fusion state. Strikingly, the use of the standard of care CDK4/6 inhibitor palbociclib, was sufficient to trigger mito-blobs without nuclear DNA damage. Considering the mito-blobs high content in nucleic acids, we additionally investigated if affecting their life cycle could perturb inflammatory and interferon-associated gene expression downstream of genotoxic stress. We describe how autophagic-lysosomal clearance triggered upon cell cycle block limited mito-blob persistence, and blocking autophagy disposal unmasked a strong inflammatory response. Taken together, these findings suggest mito-blobs are the product of an active mitochondrial remodeling process elicited in response to nuclear genotoxic stress and that concentrate immunogenic mitochondrial nucleic acids in defined structures for their correct disposal via autophagy and avoid aberrant activation of innate immunity. HighlightsO_LIGenotoxic stress induces enlarged mitochondrial structures called mito-blobs. C_LIO_LIMito-blobs concentrate mitochondrial DNA, RNA granules, and double-stranded RNA. C_LIO_LINuclear DNA damage, but not mitochondrial, is sufficient to induce mito-blobs. C_LIO_LICDK4 Inhibitors Trigger Mito-blob Formation. C_LIO_LIMito-blob formation and clearance alter inflammatory gene expression. C_LI eTOC blurbYu et al. identify mito-blobs as enlarged mitochondrial structures that form after genotoxic stress. They show that nuclear DNA breaks - as opposed to mitochondrial DNA breaks - trigger mito-blob formation through nuclear-to-mitochondrial signaling involving altered DRP1 phosphorylation and mitochondrial fusion machinery. Mito-blob persistence is limited by autophagic clearance and is associated with inflammatory and interferon-associated gene expression after stress.

Oxygen is indispensable for survival in aerobic organisms, necessitating mechanisms to sense and respond to fluctuations in oxygen availability. Physiological processes such as early development, proceeds in an oxygen-sensitive environment and this appears conserved across vertebrate evolution. Owing to their avascular nature epithelial tissues routinely experience hypoxia but the epithelial responses to hypoxia and the underlying adaptive molecular regulation remains to be fully understood. We used the bilayered epidermis of Zebrafish embryos to ask how a developing epithelium responds to and copes with hypoxia. We show that under hypoxic conditions, despite the changes in cell morphologies, disruption in E-cadherin polarisation and the presence of intercellular gaps in the outer epidermal layer, the tight junctions are maintained. Our data indicate that ROCK (Rho-associated kinase) mediates the change in cell morphology and the maintenance of barrier function via non-muscle Myosin-II (NM-II). Furthermore, a high level of NM-II activity is essential to suppress Crb3-dependent cell delamination and apoptosis under hypoxia. Genetic perturbations reveal that neither increasing levels of active NMII nor augmenting tight junctions alone improves barrier function defects, indicating both these ROCK-dependent processes are necessary to maintain the barrier function under hypoxia. Our study uncovers the hitherto unappreciated importance of ROCK signaling in the maintenance of epithelial architecture and barrier function in a developing epithelium, ensuring organism survival.

Mitochondrial quality control (MQC) is essential for retinal homeostasis, yet how distinct mitophagy pathways are coordinated within specialized retinal cell types remains poorly understood. Here, we show that Muller glia engage distinct mitophagy programmes that are differentially activated across physiological, metabolic stress, and differentiation contexts. Using pathway-resolved analyses supported by mouse and human single-cell transcriptomic datasets, we demonstrate that PINK1-dependent and receptor-mediated mitophagy pathways coexist within Muller glia and exhibit distinct functional and spatial regulation. To enable precise, time-resolved interrogation of these processes, we developed MQ-MG2, a spontaneously immortalised Muller glial model stably expressing the Mito-QC reporter while preserving endogenous mitophagy adaptors and metabolic features of primary Muller cells. Using this system, we identify context-dependent activation of mitophagy pathways with spatial relevance in vivo and reveal transient coordination of PINK1-dependent and receptor-associated mitophagy during Muller glial neurogenic differentiation. Suppression of fission-dependent mitophagy impaired the acquisition of complex neurite features in MQ-MG2, with a comparable phenotype observed following targeted PINK1 deletion in human neurogenic cells. Together, these findings position Muller glia as active integrators of mitochondrial quality control, capable of engaging distinct mitophagy programmes according to cellular context.

Msc1 is a yeast nuclear envelope (NE) protein that facilitates DNA double-strand break repair. In its absence, cells exhibit abnormal nuclear morphologies and maldistribution of nuclear pore complexes (NPCs). Msc1 is not uniformly distributed across the NE but concentrates onto dynamic patches that often coincide with blebs or herniations. Here, we report that Msc1 abundance and the number of patches dramatically increase after the diauxic shift. Msc1 patches are devoid of NPCs and fully colocalize with nucleus-vacuole junctions (NVJs), which are involved in piecemeal micronucleophagy. In the absence of Msc1, abnormal NPC aggregates accumulate adjacent to vacuoles, both at and outside the NE. We conclude that Msc1 is the key factor that maintains NPC homeostasis as cells prepare to enter quiescence.

Centrosome amplification is frequently associated with chromosomal instability and tumor progression, but how cells coordinate centriole assembly with the control of centrosome numbers and quality remains poorly understood. TIAM1 is a RAC1 guanine nucleotide exchange factor previously implicated in centrosome-associated signaling and {beta}TrCP-dependent control of PLK4 abundance. Here, we examined how Tiam1 regulates autophagy-lysosome homeostasis in mouse embryonic fibroblasts induced to overexpress PLK4. In contrast to a previous model in which Tiam1 loss promotes productive centriole overduplication, we found, by super-resolution imaging and expansion microscopy, an abnormal distribution of PLK4 on the centrioles centriole-associated structures following TIAM1 depletion, suggesting that TIAM1 may support the organization or maturation of centrioles. TIAM1 depletion also resulted in increased LC3B-positive puncta and enlarged LAMP1-positive compartments, but this was not accompanied by increased LC3B-II accumulation after bafilomycin A1 treatment. These findings suggest that TIAM1 may act at the interface between centriole assembly and endolysosomal/autolysosomal organization, linking TIAM1 to lysosome-associated centrosome quality-control pathways.

Mitochondrial homeostasis is maintained by multiple quality control pathways, including mitophagy, which targets dysfunctional mitochondria for degradation. During receptor-mediated mitophagy, the outer membrane proteins BNIP3 and NIX directly recruit autophagy machinery to the mitochondrial surface, though their precise regulation is still unclear. In recent years, new BNIP3- and NIX-interacting proteins have been identified that influence mitophagic flux. PPTC7 and FBXL4 target BNIP3 and NIX for proteasomal turnover to keep levels of the receptors low, whereas TMEM11 is proposed to spatially control mitophagy by interacting with receptors at active mitophagy sites. However, it is unclear how each of these interactions is controlled and how they interplay with each other. Here, we identify a repressor of mitophagy, ARMC1, which forms a complex with TMEM11, BNIP3, and NIX. During mitophagy activation, ARMC1 dissociates from the complex, freeing the receptors to initiate mitophagy. We find that TMEM11 then acts in an antagonistic relationship with PPTC7, protecting the receptors from proteasomal degradation. Our data are consistent with a two-stage model. At steady state, a population of sentinel receptors is repressed and primed to respond to mitochondrial dysfunction. Once mitophagy is activated, TMEM11 protects BNIP3 and NIX, ensuring a sustained mitophagic response. Our findings provide a framework for understanding how two key regulatory pathways intersect to modulate receptor-mediated mitophagy.

TMEM127 is an adaptor protein that bridges substrates to E3 ubiquitin ligases of the HECT family. Among its interacting partners is the major histocompatibility class I (MHC-I), a critical component of the antigen presentation pathway and the adaptive immune response. MHC-I is ubiquitinated and fated for lysosome-mediated degradation by the WWP2 E3 ligase in a complex that involves TMEM127 and a second adaptor protein, SUSD6. However, the interacting dynamics among complex components remains to be determined, a key knowledge gap towards the development of pharmacological modulators. Here, using in vitro and in vivo models, we report that TMEM127-WWP2 interaction stabilizes the MHC-I degradation complex and reveals an asymmetric role of the two adaptor proteins. Specifically, we find that TMEM127 regulates WWP2 catalytic activity, abundance and localization through its canonical PY motif interaction with the WW domain of WWP2 with contribution of a TMEM127 endocytic motif, providing a mechanism to restrain complex activity. Further, we validate the impact of TMEM127 dosage in the endogenous complex assembly and regulation. Our results nominate TMEM127 as a critical member of the MHC-I degradation complex and highlight the TMEM127-WWP2 interaction as a target for augmenting MHC-I-mediated antigen presentation, a long sought goal in cancer immunology.

Kinesins are microtubule-dependent motors, yet the functions of the kinesin-4 family member KIF27 remain poorly understood. Here, we demonstrate a dynamic and cell-cycle-dependent localization of KIF27, consistent with its functional roles in mitotic progression. Upon mitotic entry, KIF27 relocates to condensed chromosomes. During anaphase, a fraction of KIF27 accumulates at the spindle midzone, and in telophase and late stages of cytokinesis it localizes at the midbody, colocalizing with key cytokinetic regulators at both structures. Recruitment of KIF27 to the midbody depends on KIF23 and CEP55. KIF27 depletion results in profound cell division defects, altered midbody and microtubule morphology, delayed cytokinesis and cytokinesis failure. Beyond cell division, KIF27 depletion directly compromises nuclear morphology, and pan-cancer transcriptomic analyses correlate low KIF27 expression with aneuploidy and poor patient survival in several cancer types. Together, our results identify KIF27 as a novel regulator of mitotic fidelity and genome stability.

Recent evidence indicates that mitochondria, through the activity of the E3 Ub ligase MARCH5, are critical for de novo peroxisome biogenesis. Here we report that peroxisome biogenesis factor Pex26 is a MARCH5 client protein. In peroxisome-containing cells, MARCH5 interacts with Pex26 and facilitates the transfer of newly synthesized Pex26 from the OMM to peroxisomes. MARCH5 also controls peroxisomal delivery of other candidate peroxins in peroxisome-containing cells. On the other hand, in peroxisome-deficient cells, the turnover rate of Pex26 is dramatically increased, and MARCH5 targets this protein for p97-dependent proteasomal degradation. Both activities are mediated by MARCH5-dependent Pex26 ubiquitination. Knockout of Pex26 induces the accumulation of cells containing Tom20-positive, Catalase-deficient pre-peroxisomes. Further supporting the critical role of MARCH5 in peroxisome biogenesis, these structures are absent in Pex26/MARCH5 double knockout cells. The data support the model, where in peroxisome-containing cells, MARCH5 acts as a peroxisome biogenesis factor, while with defective peroxisome biogenesis, as in Zellweger syndrome cells, it protects mitochondria from potentially toxic accumulation of peroxins on the OMM.

Membrane contact sites (MCSs) enable communication between organelles and play central roles in lipid metabolism. In budding yeast, the nucleus-vacuole junction (NVJ) functions as a dynamic platform that integrates lipid metabolism and stress responses. However, it remains unclear whether NVJ structure and function are broadly conserved across eukaryotes, particularly because Nvj1, the key membrane tethering factor that mediates NVJ formation in budding yeast, is absent in higher eukaryotes. Here, we investigated whether an MCS analogous to the NVJ in budding yeast exists in fission yeast (Schizosaccharomyces pombe), which lacks Nvj1. We show that an NVJ is present in fission yeast and serves as a platform for the accumulation of sterol synthesis factors, including the HMG-CoA reductase Hmg1 and the INSIG homolog Ins1. We further demonstrate that the localization of these factors depends on the membrane protein insertase Snd302 and is dynamically regulated by nutrient conditions. Our findings reveal that, despite the absence of Nvj1, the NVJ is functionally conserved as a site for sterol synthesis in fission yeast, suggesting a conserved role of spatial organization in lipid metabolism.

Repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) counteracts genome instability and carcinogenesis. Cancer cells frequently show defects in HR which can be therapeutically exploited by hypersensitivity to poly(ADP-ribose) polymerase inhibitor (PARPi) treatment. Here we identify an unforeseen function of HIPK2 in HR repair and PARPi sensitivity. HIPK2 accumulates at DSBs and associates with DSB repair factors at DNA damage foci. DSB recruitment of HIPK2 requires checkpoint kinase ATM activity. DNA repair pathway analysis revealed that HIPK2 depletion specifically impairs HR. Mechanistically, we found that HIPK2 binds BRCA1 and phosphorylates BRCA1 at Ser1191, a site that regulates damage-induced BRCA1 protein stability. Consistently, HIPK2 depletion or pharmacological inhibition of HIPK2 results in reduced BRCA1 protein levels, and sensitizes BRCA1-proficient cancer cells to IR damage and PARPi treatment. In sum, our results identify a role for HIPK2 in HR through regulating BRCA1 protein levels, and propose HIPK2 inhibition as a novel strategy to sensitize BRCA1-proficient cancer cells to PARPi treatment.